[galaxy-commits] commit/galaxy-central: 26 new changesets

26 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/705149e31b10/ Changeset: 705149e31b10 User: martenson Date: 2014-07-17 23:02:13 Summary: work on permission API and UI, mostly for library datasets, some bugfixes too Affected #: 5 files diff -r 8a608db6cf83b653a433f43b501f4047f63d248b -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -208,74 +208,95 @@ roles.add( role ) return self.sort_by_attr( [ role for role in roles ], 'name' ) + def get_roles_for_action( self, item, action ): + """ + Return a list containing the roles associated with given action on given item + where item is one of Library, LibraryFolder, LibraryDatasetDatasetAssociation, + LibraryDataset, Dataset. + """ + roles = [] + for item_permission in item.actions: + permission_action = self.get_action( item_permission.action ) + if permission_action == action: + roles.append( item_permission.role ) + return roles + def get_valid_dataset_roles( self, trans, dataset, query, page, page_limit ): """ This method retrieves the list of possible roles that user can select in the dataset permissions form. Admins can select any role so the results are paginated in order to save the bandwidth and to speed things up. - Standard users can select their own private role, any fo their + Standard users can select their own private role, any of their sharing roles and any public role (not private and not sharing). """ roles = [] if query is not None: query = query.replace( '_', '/_' ).replace( '%', '/%' ).replace( '/', '//' ) search_query = query + '%' + log.debug('search_query: ' + str(search_query)) + # Limit the query only to get the page needed limit = page * page_limit + total_count = None - # Admins see it all - if trans.user_is_admin(): - # Add all roles that fit the query + # For public datasets admins can choose from all roles + if trans.user_is_admin() and self.dataset_is_public( dataset ): + # Add all non-deleted roles that fit the query db_query = trans.sa_session.query( trans.app.model.Role ).filter( self.model.Role.table.c.deleted == False ) if query is not None: db_query = db_query.filter( self.model.Role.table.c.name.like( search_query, escape='/' ) ) - for role in ( db_query.order_by( self.model.Role.table.c.name ).limit( limit ) ): + total_count = db_query.count() + # Takes the least number of results from beginning that includes the requested page + roles = db_query.order_by( self.model.Role.table.c.name ).limit( limit ).all() + + page_start = ( page * page_limit ) - page_limit + page_end = page_start + page_limit + if total_count < page_start: + # Return empty list if there are less results than the requested position + roles = [] + else: + roles = roles[ page_start:page_end ] + # Non-admin and public dataset + elif self.dataset_is_public( dataset ): + # Add the current user's private role + roles.append( self.get_private_user_role( trans.user ) ) + # Add the current user's sharing roles + for role in self.get_sharing_roles( trans.user ): roles.append( role ) - # Take last page of the selection - roles = roles[ ( -page_limit ): ] - - # Non-admins see the list of relevant roles + # Add all remaining non-private, non-sharing roles + for role in trans.sa_session.query( trans.app.model.Role ) \ + .filter( and_( self.model.Role.table.c.deleted == False, + self.model.Role.table.c.type != self.model.Role.types.PRIVATE, + self.model.Role.table.c.type != self.model.Role.types.SHARING ) ) \ + .order_by( self.model.Role.table.c.name ): + roles.append( role ) + # User is not admin and dataset is not public else: - if self.dataset_is_public( dataset ): - # Add the current user's private role - roles.append( self.get_private_user_role( trans.user ) ) - # Add the current user's sharing roles - for role in self.get_sharing_roles( trans.user ): + # If item has roles associated with the access permission, we need to start with them. + access_roles = dataset.get_access_roles( trans ) + for role in access_roles: + if trans.user_is_admin() or self.ok_to_display( trans.user, role ): roles.append( role ) - # Add all remaining non-private, non-sharing roles - for role in trans.sa_session.query( trans.app.model.Role ) \ - .filter( and_( self.model.Role.table.c.deleted == False, - self.model.Role.table.c.type != self.model.Role.types.PRIVATE, - self.model.Role.table.c.type != self.model.Role.types.SHARING ) ) \ - .order_by( self.model.Role.table.c.name ): - roles.append( role ) - - else: - # If item has roles associated with the access permission, we need to start with them. - access_roles = dataset.get_access_roles( trans ) - for role in access_roles: - if trans.user_is_admin() or self.ok_to_display( trans.user, role ): - roles.append( role ) - # Each role potentially has users. We need to find all roles that each of those users have. - for ura in role.users: - user = ura.user - for ura2 in user.roles: - if trans.user_is_admin() or self.ok_to_display( trans.user, ura2.role ): - roles.append( ura2.role ) - # Each role also potentially has groups which, in turn, have members ( users ). We need to - # find all roles that each group's members have. - for gra in role.groups: - group = gra.group - for uga in group.users: - user = uga.user - for ura in user.roles: - if trans.user_is_admin() or self.ok_to_display( trans.user, ura.role ): - roles.append( ura.role ) + # Each role potentially has users. We need to find all roles that each of those users have. + for ura in role.users: + user = ura.user + for ura2 in user.roles: + if trans.user_is_admin() or self.ok_to_display( trans.user, ura2.role ): + roles.append( ura2.role ) + # Each role also potentially has groups which, in turn, have members ( users ). We need to + # find all roles that each group's members have. + for gra in role.groups: + group = gra.group + for uga in group.users: + user = uga.user + for ura in user.roles: + if trans.user_is_admin() or self.ok_to_display( trans.user, ura.role ): + roles.append( ura.role ) # Omit duplicated roles by converting to set return_roles = set( roles ) - return self.sort_by_attr( [ role for role in return_roles ], 'name' ) + return self.sort_by_attr( [ role for role in return_roles ], 'name' ), total_count def get_legitimate_roles( self, trans, item, cntrller ): """ diff -r 8a608db6cf83b653a433f43b501f4047f63d248b -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -44,26 +44,30 @@ .. seealso:: :attr:`galaxy.web.base.controller.UsesLibraryMixinItems.get_library_dataset` """ try: - dataset = self.get_library_dataset( trans, id=id, check_ownership=False, check_accessible=True ) + library_dataset = self.get_library_dataset( trans, id=id, check_ownership=False, check_accessible=True ) except Exception: - raise exceptions.ObjectNotFound( 'Requested dataset was not found.' ) + raise exceptions.ObjectNotFound( 'Requested library_dataset was not found.' ) + + current_user_roles = trans.get_current_user_roles() # Build the full path for breadcrumb purposes. - full_path = self._build_path( trans, dataset.folder ) - dataset_item = ( trans.security.encode_id( dataset.id ), dataset.name ) + full_path = self._build_path( trans, library_dataset.folder ) + dataset_item = ( trans.security.encode_id( library_dataset.id ), library_dataset.name ) full_path.insert(0, dataset_item) full_path = full_path[ ::-1 ] - nice_size = util.nice_size( int( dataset.library_dataset_dataset_association.get_size() ) ) + nice_size = util.nice_size( int( library_dataset.library_dataset_dataset_association.get_size() ) ) - date_uploaded = dataset.library_dataset_dataset_association.create_time.strftime( "%Y-%m-%d %I:%M %p" ) + date_uploaded = library_dataset.library_dataset_dataset_association.create_time.strftime( "%Y-%m-%d %I:%M %p" ) - rval = trans.security.encode_all_ids( dataset.to_dict() ) - rval[ 'deleted' ] = dataset.deleted + rval = trans.security.encode_all_ids( library_dataset.to_dict() ) + rval[ 'deleted' ] = library_dataset.deleted rval[ 'folder_id' ] = 'F' + rval[ 'folder_id' ] rval[ 'full_path' ] = full_path rval[ 'file_size' ] = nice_size rval[ 'date_uploaded' ] = date_uploaded + rval[ 'can_user_modify' ] = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset) or trans.user_is_admin() + rval[ 'can_user_manage' ] = trans.app.security_agent.can_manage_dataset( current_user_roles, library_dataset.library_dataset_dataset_association.dataset) or trans.user_is_admin() return rval @expose_api @@ -71,63 +75,93 @@ """ show_roles( self, trans, id, **kwd ): GET /api/libraries/datasets/{encoded_dataset_id}/permissions: - Displays information about current and available roles + Displays information about current or available roles for a given dataset permission. """ + current_user_roles = trans.get_current_user_roles() - - page = kwd.get( 'page', None ) - if page is not None: - page = int( page ) - - page_limit = kwd.get( 'page_limit', None ) - if page_limit is not None: - page_limit = int( page_limit ) - - query = kwd.get( 'q', None ) - - if page is None: - page = 1 - - if page_limit is None: - page_limit = 10 - - try: - library_dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) - except Exception, e: - raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) - library = library_dataset.folder.parent_library - dataset = library_dataset.library_dataset_dataset_association.dataset - - can_manage = trans.app.security_agent.can_manage_dataset( current_user_roles, dataset ) or trans.user_is_admin() - if not can_manage: - raise exceptions.InsufficientPermissionsException( 'You do not have proper permissions to access permissions.' ) - - roles = trans.app.security_agent.get_valid_dataset_roles( trans, dataset, query, page, page_limit ) - - total_roles = len( roles ) - return_roles = [] - for role in roles: - return_roles.append( dict( id=role.name, name=role.name, type=role.type ) ) - - return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) - - @expose_api - def get_roles( self, trans, encoded_dataset_id, **kwd ): try: library_dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) except Exception, e: raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) dataset = library_dataset.library_dataset_dataset_association.dataset - roles = dataset.get_access_roles( trans ) + # User has to have manage permissions in order to see the roles. + can_manage = trans.app.security_agent.can_manage_dataset( current_user_roles, dataset ) or trans.user_is_admin() + if not can_manage: + raise exceptions.InsufficientPermissionsException( 'You do not have proper permissions to access permissions.' ) - # roles = dataset.get_manage_permissions_roles( trans ) + scope = kwd.get( 'scope', None ) - # roles = trans.app.security_agent.get_current_dataset_roles( trans, dataset, trans.app.security_agent.permitted_actions.DATASET_ACCESS ) - # Omit duplicated roles by converting to set - roles = set( roles ) - return [ role.name for role in roles ] + # Return all roles currently set for relevant permissions. + if scope == 'current' or scope is None: + # Omit duplicated roles by converting to set + access_roles = set( dataset.get_access_roles( trans ) ) + modify_roles = set( trans.app.security_agent.get_roles_for_action( library_dataset, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) + manage_roles = set( dataset.get_manage_permissions_roles( trans ) ) + + # legit_roles = trans.app.security_agent.get_legitimate_roles( trans, dataset, 'library_admin' ) + # log.debug( 'CXXXXXCXCXCXCXCXCC legit roles: ' + str( [ legit_role.name for legit_role in legit_roles ] ) ) + + # all_permissions = trans.app.security_agent.get_permissions( library_dataset ) + # for k,v in all_permissions.items(): + # log.debug( '*******************************************' ) + # log.debug( 'permission action: ' + str( k.action ) ) + # log.debug( 'permission roles: ' + str( [ role.name for role in v ] ) ) + + access_dataset_role_list = [ access_role.name for access_role in access_roles ] + manage_dataset_role_list = [ manage_role.name for manage_role in manage_roles ] + modify_item_role_list = [ modify_role.name for modify_role in modify_roles ] + + return dict( access_dataset_roles=access_dataset_role_list, modify_item_roles=modify_item_role_list, manage_dataset_roles=manage_dataset_role_list ) + + # Return roles that are available to select. + if scope == 'available': + page = kwd.get( 'page', None ) + if page is not None: + page = int( page ) + else: + page = 1 + + page_limit = kwd.get( 'page_limit', None ) + if page_limit is not None: + page_limit = int( page_limit ) + else: + page_limit = 10 + + query = kwd.get( 'q', None ) + + # try: + # library_dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) + # except Exception, e: + # raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) + # dataset = library_dataset.library_dataset_dataset_association.dataset + # library = library_dataset.folder.parent_library + + roles, total_roles = trans.app.security_agent.get_valid_dataset_roles( trans, dataset, query, page, page_limit ) + + return_roles = [] + for role in roles: + return_roles.append( dict( id=role.name, name=role.name, type=role.type ) ) + + return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) + + # @expose_api + # def get_roles( self, trans, encoded_dataset_id, **kwd ): + # try: + # library_dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) + # except Exception, e: + # raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) + # dataset = library_dataset.library_dataset_dataset_association.dataset + + # roles = dataset.get_access_roles( trans ) + + # # roles = dataset.get_manage_permissions_roles( trans ) + + # # roles = trans.app.security_agent.get_current_dataset_roles( trans, dataset, trans.app.security_agent.permitted_actions.DATASET_ACCESS ) + # # Omit duplicated roles by converting to set + # roles = set( roles ) + # return [ role.name for role in roles ] @expose_api def delete( self, trans, encoded_dataset_id, **kwd ): diff -r 8a608db6cf83b653a433f43b501f4047f63d248b -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 lib/galaxy/webapps/galaxy/api/permissions.py --- a/lib/galaxy/webapps/galaxy/api/permissions.py +++ b/lib/galaxy/webapps/galaxy/api/permissions.py @@ -11,6 +11,7 @@ log = logging.getLogger( __name__ ) + class PermissionsController( BaseAPIController ): # Method not ideally named @@ -49,4 +50,3 @@ item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) return item - diff -r 8a608db6cf83b653a433f43b501f4047f63d248b -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -253,11 +253,11 @@ action='show_roles', conditions=dict( method=[ "GET" ] ) ) - webapp.mapper.connect( 'show_legitimate_lda_roles', - '/api/libraries/datasets/:encoded_dataset_id/permissions/current', - controller='lda_datasets', - action='get_roles', - conditions=dict( method=[ "GET" ] ) ) + # webapp.mapper.connect( 'show_legitimate_lda_roles', + # '/api/libraries/datasets/:encoded_dataset_id/permissions/current', + # controller='lda_datasets', + # action='get_roles', + # conditions=dict( method=[ "GET" ] ) ) webapp.mapper.connect( 'delete_lda_item', '/api/libraries/datasets/:encoded_dataset_id', diff -r 8a608db6cf83b653a433f43b501f4047f63d248b -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -3,10 +3,11 @@ "mvc/library/library-model", 'mvc/ui/ui-select' ], -function(mod_toastr, - mod_library_model, - mod_select - ) { +function( + mod_toastr, + mod_library_model, + mod_select + ) { var LibraryDatasetView = Backbone.View.extend({ el: '#center', @@ -188,65 +189,170 @@ var self = this; // load all current permissions - $.get( "/api/libraries/datasets/" + self.id + "/permissions/current").done(function(fetched_permissions) { - var selected_roles = []; - for (var i = 0; i < fetched_permissions.length; i++) { - selected_roles.push(fetched_permissions[i] + ':' + fetched_permissions[i]); + $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + var selected_access_dataset_roles = []; + for (var i = 0; i < fetched_permissions.access_dataset_roles.length; i++) { + selected_access_dataset_roles.push(fetched_permissions.access_dataset_roles[i] + ':' + fetched_permissions.access_dataset_roles[i]); } + var selected_modify_item_roles = []; + for (var i = 0; i < fetched_permissions.modify_item_roles.length; i++) { + selected_modify_item_roles.push(fetched_permissions.modify_item_roles[i] + ':' + fetched_permissions.modify_item_roles[i]); + } + var selected_manage_dataset_roles = []; + for (var i = 0; i < fetched_permissions.manage_dataset_roles.length; i++) { + selected_manage_dataset_roles.push(fetched_permissions.manage_dataset_roles[i] + ':' + fetched_permissions.manage_dataset_roles[i]); + } + // ACCESS PERMISSIONS - if (is_admin){ // Admin has a special select that allows remote searching + if (is_admin){ // Admin has a special select that allows AJAX searching var access_select_options = { - minimumInputLength: 1, - css: 'access_perm', - multiple:true, - placeholder: 'Click to select a role', - container: self.$el.find('#access_perm'), - ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions", - dataType: 'json', - quietMillis: 100, - data: function (term, page) { // page is the one-based page number tracked by Select2 - return { - q: term, //search term - page_limit: 10, // page size - page: page // page number - }; - }, - results: function (data, page) { - var more = (page * 10) < data.total; // whether or not there are more results available - // notice we return the value of more so Select2 knows if more results can be loaded - return {results: data.roles, more: more}; - } - }, - formatResult : function roleFormatResult(role) { - return role.name + ' type: ' + role.type; - }, + minimumInputLength: 0, + css: 'access_perm', + multiple:true, + placeholder: 'Click to select a role', + container: self.$el.find('#access_perm'), + ajax: { + url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + dataType: 'json', + quietMillis: 100, + data: function (term, page) { // page is the one-based page number tracked by Select2 + return { + q: term, //search term + page_limit: 10, // page size + page: page // page number + }; + }, + results: function (data, page) { + var more = (page * 10) < data.total; // whether or not there are more results available + // notice we return the value of more so Select2 knows if more results can be loaded + return {results: data.roles, more: more}; + } + }, + formatResult : function roleFormatResult(role) { + return role.name + ' type: ' + role.type; + }, - formatSelection: function roleFormatSelection(role) { - return role.name; - }, - initSelection: function(element, callback) { - // the input tag has a value attribute preloaded that points to a preselected role's id - // this function resolves that id attribute to an object that select2 can render - // using its formatResult renderer - that way the role name is shown preselected - var data = []; - $(element.val().split(",")).each(function() { - var item = this.split(':'); - data.push({ - id: item[1], - name: item[1] - }); - }); - callback(data); - }, - initialData: selected_roles.join(','), - dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller + formatSelection: function roleFormatSelection(role) { + return role.name; + }, + initSelection: function(element, callback) { + // the input tag has a value attribute preloaded that points to a preselected role's id + // this function resolves that id attribute to an object that select2 can render + // using its formatResult renderer - that way the role name is shown preselected + var data = []; + $(element.val().split(",")).each(function() { + var item = this.split(':'); + data.push({ + id: item[1], + name: item[1] + }); + }); + callback(data); + }, + initialData: selected_access_dataset_roles.join(','), + dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller + }; + var modify_select_options = { + minimumInputLength: 0, + css: 'modify_perm', + multiple:true, + placeholder: 'Click to select a role', + container: self.$el.find('#modify_perm'), + ajax: { + url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + dataType: 'json', + quietMillis: 100, + data: function (term, page) { // page is the one-based page number tracked by Select2 + return { + q: term, //search term + page_limit: 10, // page size + page: page // page number + }; + }, + results: function (data, page) { + var more = (page * 10) < data.total; // whether or not there are more results available + // notice we return the value of more so Select2 knows if more results can be loaded + return {results: data.roles, more: more}; + } + }, + formatResult : function roleFormatResult(role) { + return role.name + ' type: ' + role.type; + }, + + formatSelection: function roleFormatSelection(role) { + return role.name; + }, + initSelection: function(element, callback) { + // the input tag has a value attribute preloaded that points to a preselected role's id + // this function resolves that id attribute to an object that select2 can render + // using its formatResult renderer - that way the role name is shown preselected + var data = []; + $(element.val().split(",")).each(function() { + var item = this.split(':'); + data.push({ + id: item[1], + name: item[1] + }); + }); + callback(data); + }, + initialData: selected_modify_item_roles.join(','), + dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller + }; + var manage_select_options = { + minimumInputLength: 0, + css: 'manage_perm', + multiple:true, + placeholder: 'Click to select a role', + container: self.$el.find('#manage_perm'), + ajax: { + url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + dataType: 'json', + quietMillis: 100, + data: function (term, page) { // page is the one-based page number tracked by Select2 + return { + q: term, //search term + page_limit: 10, // page size + page: page // page number + }; + }, + results: function (data, page) { + var more = (page * 10) < data.total; // whether or not there are more results available + // notice we return the value of more so Select2 knows if more results can be loaded + return {results: data.roles, more: more}; + } + }, + formatResult : function roleFormatResult(role) { + return role.name + ' type: ' + role.type; + }, + + formatSelection: function roleFormatSelection(role) { + return role.name; + }, + initSelection: function(element, callback) { + // the input tag has a value attribute preloaded that points to a preselected role's id + // this function resolves that id attribute to an object that select2 can render + // using its formatResult renderer - that way the role name is shown preselected + var data = []; + $(element.val().split(",")).each(function() { + var item = this.split(':'); + data.push({ + id: item[1], + name: item[1] + }); + }); + callback(data); + }, + initialData: selected_manage_dataset_roles.join(','), + dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller }; this.accessSelectObject = new mod_select.View(access_select_options); + this.modifySelectObject = new mod_select.View(modify_select_options); + this.manageSelectObject = new mod_select.View(manage_select_options); } else { // Non-admins have select with pre-loaded options - var template = this.templateAccessSelect(); - $.get( "/api/libraries/datasets/" + self.id + "/permissions", function( data ) { + var template = self.templateAccessSelect(); + $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) { $('.access_perm').html(template({options:data.roles})); this.accessSelectObject = $('#access_select').select2(); }).fail(function() { @@ -277,9 +383,16 @@ tmpl_array.push(' <div id="library_toolbar">'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify dataset" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>'); - tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Change permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>'); + + tmpl_array.push(' <% if (item.get("can_user_modify")) { %>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("can_user_manage")) { %>'); + tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </div>'); @@ -500,8 +613,8 @@ tmpl_array.push('<div class="library_style_container">'); tmpl_array.push(' <div id="library_toolbar">'); - tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> go to Folder</span></button></a>'); - tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> see the Dataset</span></button><a>'); + tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>'); + tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>'); tmpl_array.push(' </div>'); @@ -517,35 +630,48 @@ tmpl_array.push(' <% }); %>'); tmpl_array.push('</ol>'); - tmpl_array.push('<h1><%= _.escape(item.get("name")) %></h1>'); - tmpl_array.push('<div class="alert alert-success">You have rights to change permissions on this dataset. That means you can control who can access it, who can modify it and also appoint others that can manage permissions on it.</div>'); + tmpl_array.push('<h1>Permissions: <%= _.escape(item.get("name")) %></h1>'); + + tmpl_array.push('<div class="dataset_table">'); - tmpl_array.push('<h2>Basic permissions</h2>'); + // tmpl_array.push('<h2>Basic</h2>'); tmpl_array.push('<p>You can remove all access restrictions on this dataset. '); - tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to see the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button"><span class="fa fa-globe"></span> Remove restrictions</span></button>'); + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button"><span class="fa fa-globe"></span> Remove restrictions</span></button>'); tmpl_array.push('</p>'); tmpl_array.push('<p>You can make this dataset private to you. '); - tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Only you will be able to see the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"></span> Make private</span></button>'); + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"></span> Make private</span></button>'); tmpl_array.push('</p>'); tmpl_array.push('<p>You can share this dataset with another Galaxy user. '); - tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Only you and the other user will be able to see the dataset." class="btn btn-default btn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Only you and the other user will be able to access the dataset." class="btn btn-default btn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); tmpl_array.push('</p>'); - tmpl_array.push('<h2>Advanced permissions</h2>'); - tmpl_array.push('<p>You can assign any number of roles to any of the following three dataset permission types. However please read carefully the implications of such actions.</p>'); - tmpl_array.push('<h3>Access Roles</h3>'); - tmpl_array.push('<div class="alert alert-info">User has to have <strong>all these roles</strong> in order to see this dataset.</div>'); + // tmpl_array.push('<h2>Advanced</h2>'); + tmpl_array.push('<p>You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.</p>'); + tmpl_array.push('<hr/>'); + + tmpl_array.push('<h2>Library-related permissions</h2>'); + tmpl_array.push('<div class="alert alert-success">You have the permission to modify this Library item. This includes changing its metadata and other information. It does not include modifying the underlying dataset.</div>'); + tmpl_array.push('<h4>Roles that can modify the library item</h4>'); + tmpl_array.push('<div id="modify_perm" class="modify_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify the information about this library item.</div>'); + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); + tmpl_array.push('<hr/>'); + + tmpl_array.push('<h2>Dataset-related permissions</h2>'); + tmpl_array.push('<div class="alert alert-success">You have the permission to manage permissions on this dataset. That means you can control who can access it and also appoint others that can manage permissions on it. Changes made here will affect <strong>every</strong> library item and every history this dataset is part of.</div>'); + tmpl_array.push('<h4>Roles that can access dataset</h4>'); tmpl_array.push('<div id="access_perm" class="access_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>'); tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); - tmpl_array.push('<h3>Modify Roles</h3>'); - tmpl_array.push('<div class="alert alert-info">Users with <strong>any</strong> of these roles can modify the information about this dataset.</div>'); - tmpl_array.push('<div id="modify_perm" class="modify_perm"></div>'); - tmpl_array.push('<h3>Manage Roles</h3>'); - tmpl_array.push('<div class="alert alert-info">Users with <strong>any</strong> of these roles can change permissions of this dataset.</div>'); - tmpl_array.push('<div id="manage_perm" class="manage_perm"></div>'); + tmpl_array.push('<h4>Roles that can manage permissions on the dataset</h4>'); + tmpl_array.push('<div id="manage_perm" class="manage_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>'); + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); + + tmpl_array.push('</div>'); @@ -585,6 +711,7 @@ return _.template(tmpl_array.join('')); } + }); return { https://bitbucket.org/galaxy/galaxy-central/commits/37ae922a5820/ Changeset: 37ae922a5820 User: martenson Date: 2014-07-17 23:04:21 Summary: Merge Affected #: 347 files diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 .hgignore --- a/.hgignore +++ b/.hgignore @@ -11,6 +11,9 @@ scripts/scramble/lib scripts/scramble/archives +# Python virtualenv +.venv + # Database stuff database/beaker_sessions database/community_files @@ -62,6 +65,7 @@ data_manager_conf.xml shed_data_manager_conf.xml object_store_conf.xml +job_metrics_conf.xml config/* static/welcome.html.* static/welcome.html diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 .hgtags --- a/.hgtags +++ b/.hgtags @@ -9,4 +9,4 @@ 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -f7dd0060c2966f2b9c66c5ac739d0e5a9a31faa0 latest_2014.06.02 +8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02 diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/app.css --- a/config/plugins/visualizations/charts/static/app.css +++ b/config/plugins/visualizations/charts/static/app.css @@ -1,3 +1,19 @@ +.charts-tooltip { + position: absolute; + text-align: center; + padding: 3px 5px 3px 5px; + font: 12px sans-serif; + background: white; + border: 1px solid gray; + border-radius: 4px; + pointer-events: none; +} + +.charts-tooltip-first { + font-weight: bold; + text-align: left; + padding-right: 5px; +} .charts-grid .item { padding: 5px; @@ -18,6 +34,7 @@ .charts-grid .image { padding: 10px; width: 100px; + height: 86px; } .charts-grid .title { @@ -48,7 +65,7 @@ margin-left: 5px; top: -1px; font-size: 1.0em; - display: inline-block; + display: inline; } .charts-viewport .icon { diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -1,26 +1,26 @@ // dependencies define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils', - 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage', + 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage', 'plugin/library/deferred', 'plugin/views/viewer', 'plugin/views/editor', 'plugin/models/config', 'plugin/models/chart', 'plugin/charts/types'], - function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage, + function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage, Deferred, ViewerView, EditorView, Config, Chart, Types ) { -// widget -return Backbone.View.extend( -{ +/** + * Main application class. + */ +return Backbone.View.extend({ // initialize - initialize: function(options) - { + initialize: function(options){ // deactivate all debugs outputs //window.console.debug = function() {}; // link options this.options = options; - + // link galaxy modal or create one if (Galaxy && Galaxy.modal) { this.modal = Galaxy.modal; @@ -41,6 +41,7 @@ this.jobs = new Jobs(this); this.datasets = new Datasets(this); this.storage = new Storage(this); + this.deferred = new Deferred(); // // views @@ -62,7 +63,7 @@ // draw chart var self = this; - this.chart.deferred.execute(function() { + this.deferred.execute(function() { self.chart.trigger('redraw'); }); } @@ -100,19 +101,6 @@ console.debug('FAILED App:chartPath() - Invalid format: ' + chart_type); } return undefined; - }, - - // execute command - execute: function(options) { - }, - - // unload - onunload: function() { - }, - - // log - log: function(location, message) { - console.log(location + ' ' + message); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var 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i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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r=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),a=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="ui-button-menu '+e.cls+'">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:i,Button:s,Icon:o,ButtonIcon:u,Input:h,Anchor:a,Message:f,Searchbox:l,Select:t,ButtonMenu:c,Modal:n,Textarea:p,Image:r,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas_list:t.canvas_list});t.chart_definition.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error(r)}}function r(e){var t=e.$el,n=e.url,r=e.name,o=new XMLSerializer,u="",a=this,f=0,l=0;return t.find("svg").each(function(){var e=$(this);i(e),f=parseInt(e.css("height")),l=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:l,height:f}),e.find(".highcharts-button").hide(),u+=o.serializeToString(this),e.find(".highcharts-button").show()}),s(t,n,{filename:r||"chart",type:"application/pdf",height:f,width:l,scale:2,svg:u}),u}function i(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function s(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button:new t.ButtonIcon({icon:"fa-camera",tooltip:"SVGs are converted to PDF via "+o.app.config.get("screenshot_url")+" and CANVAS-based charts to PNG-files.",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create({$el:o.viewport_view.$el,url:o.app.config.get("screenshot_url"),title:o.chart.get("title"),error:function(e){o.message.update({message:"Please reduce your chart to a single panel and try again.",status:"danger"})}})})}})}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register(),l={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)}};this.app.datasets.request(l)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=[],l=n[e];o&&f.push({label:"Column: Row Number",value:"auto"});var c=t.metadata_column_types;for(var h in c){var p=!1;c[h]=="int"||c[h]=="float"?p=u:p=s,p&&f.push({label:"Column: "+(parseInt(h)+1)+" ["+c[h]+"]",value:h})}l.update(f);if(!l.exists(this.group.get(e))){var d=l.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+d+'".'),this.group.set(e,d)}a?l.value(this.chart.groups.first().get(e)):l.value(this.group.get(e)),this.group.on("change:"+e,function(){l.value(i.group.get(e))}),l.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),l.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r];o.append(e.wrap(this._template_item({id:r,title:i.title+" ("+i.library+")",url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new 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e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the 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h=D.yScale().invert(i.mouseY),p=Math.abs(D.yScale().domain()[0]-D.yScale().domain()[1]),d=.03*p,m=e.nearestValueIndex(c.map(function(e){return e.value}),h,d);m!==null&&(c[m].highlight=!0)}var g=n.tickFormat()(D.x()(s,f),f);o.tooltip.position({left:l+u.left,top:i.mouseY+u.top}).chartContainer(A.parentNode).enabled(v).valueFormatter(function(e,t){return r.tickFormat()(e)}).data({value:g,series:c})(),o.renderGuideLine(l)}),o.dispatch.on("elementMouseout",function(e){k.tooltipHide(),t.clearHighlights()}),k.on("tooltipShow",function(e){v&&_(e,A.parentNode)}),k.on("changeState",function(e){typeof e.disabled!="undefined"&&(b.forEach(function(t,n){t.disabled=e.disabled[n]}),x.disabled=e.disabled),typeof e.index!="undefined"&&(M.i=e.index,M.x=O(M.i),x.index=e.index,tt.data([M])),typeof e.rescaleY!="undefined"&&(y=e.rescaleY),D.update()})}),D}function P(e,n){return n.map(function(n,r){if(!n.values)return n;var i=n.values[e];if(i==null)return n;var s=t.y()(i,e);return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],k.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){k.tooltipHide(e)}),k.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),D.dispatch=k,D.lines=t,D.legend=i,D.xAxis=n,D.yAxis=r,D.interactiveLayer=o,d3.rebind(D,t,"defined","isArea","x","y","xScale","yScale","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id"),D.options=e.utils.optionsFunc.bind(D),D.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,D):u},D.width=function(e){return arguments.length?(f=e,D):f},D.height=function(e){return arguments.length?(l=e,D):l},D.color=function(t){return 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e.y},f=[0],l=e.utils.defaultColor(),c=!1,h=d3.format(",.2f"),p,d,v,m,g=d3.dispatch("chartClick","elementClick","elementDblClick","elementMouseover","elementMouseout"),y="discreteBar",b,w;return E.dispatch=g,E.options=e.utils.optionsFunc.bind(E),E.x=function(e){return arguments.length?(u=e,E):u},E.y=function(e){return arguments.length?(a=e,E):a},E.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,E):t},E.width=function(e){return arguments.length?(n=e,E):n},E.height=function(e){return arguments.length?(r=e,E):r},E.xScale=function(e){return arguments.length?(s=e,E):s},E.yScale=function(e){return arguments.length?(o=e,E):o},E.xDomain=function(e){return arguments.length?(p=e,E):p},E.yDomain=function(e){return arguments.length?(d=e,E):d},E.xRange=function(e){return arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"","float":"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","plugin/library/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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S=e.filter(function(e){return!e.disabled});e=d3.layout.stack().order(l).offset(f).values(function(e){return e.values}).x(o).y(u).out(function(e,t,n){var r=u(e)===0?0:n;e.display={y:r,y0:t}})(S);var T=w.selectAll("g.nv-wrap.nv-stackedarea").data([e]),N=T.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedarea"),C=N.append("defs"),k=N.append("g"),L=T.select("g");k.append("g").attr("class","nv-areaWrap"),k.append("g").attr("class","nv-scatterWrap"),T.attr("transform","translate("+t.left+","+t.top+")"),v.width(a).height(b).x(o).y(function(e){return e.display.y+e.display.y0}).forceY([0]).color(e.map(function(e,t){return e.color||i(e,e.seriesIndex)}));var A=L.select(".nv-scatterWrap").datum(e);A.call(v),C.append("clipPath").attr("id","nv-edge-clip-"+s).append("rect"),T.select("#nv-edge-clip-"+s+" rect").attr("width",a).attr("height",b),L.attr("clip-path",h?"url(#nv-edge-clip-"+s+")":"");var O=d3.svg.area().x(function(e,t){return p(o(e,t))}).y0(function(e){return 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/library/deferred","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})}); \ No newline at end of file diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/forms/default.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/forms/default.js @@ -0,0 +1,252 @@ +define([], function() { + +return { + title : '', + category : '', + library : '', + tag : '', + keywords : '', + query_limit : 0, + settings : { + separator_x : { + title : 'X axis', + type : 'separator' + }, + x_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'X-axis', + placeholder : 'Axis label' + }, + x_axis_type : { + title : 'Axis value type', + info : 'Select the value type of the axis.', + type : 'select', + init : 'auto', + data : [ + { + label : '-- Do not show values --', + value : 'hide', + operations : { + hide : ['x_axis_precision'] + } + }, + { + label : 'Auto', + value : 'auto', + operations : { + hide : ['x_axis_precision'] + } + }, + { + label : 'Float', + value : 'f', + operations : { + show : ['x_axis_precision'] + } + }, + { + label : 'Exponent', + value : 'e', + operations : { + show : ['x_axis_precision'] + } + }, + { + label : 'Integer', + value : 'd', + operations : { + hide : ['x_axis_precision'] + } + }, + { + label : 'Percentage', + value : 'p', + operations : { + show : ['x_axis_precision'] + } + }, + { + label : 'SI-prefix', + value : 's', + operations : { + hide : ['x_axis_precision'] + } + } + ] + }, + x_axis_precision : { + title : 'Axis tick format', + info : 'Select the tick format for the axis.', + type : 'select', + init : '1', + data : [ + { + label : '0.00001', + value : '5' + }, + { + label : '0.0001', + value : '4' + }, + { + label : '0.001', + value : '3' + }, + { + label : '0.01', + value : '2' + }, + { + label : '0.1', + value : '1' + }, + { + label : '1', + value : '0' + } + ] + + }, + separator_y : { + title : 'Y axis', + type : 'separator' + }, + y_axis_label : { + title : 'Axis label', + info : 'Provide a label for the axis.', + type : 'text', + init : 'Y-axis', + placeholder : 'Axis label' + }, + y_axis_type : { + title : 'Axis value type', + info : 'Select the value type of the axis.', + type : 'select', + init : 'auto', + data : [ + { + label : '-- Do not show values --', + value : 'hide', + operations : { + hide : ['y_axis_precision'] + } + }, + { + label : 'Auto', + value : 'auto', + operations : { + hide : ['y_axis_precision'] + } + }, + { + label : 'Float', + value : 'f', + operations : { + show : ['y_axis_precision'] + } + }, + { + label : 'Exponent', + value : 'e', + operations : { + show : ['y_axis_precision'] + } + }, + { + label : 'Integer', + value : 'd', + operations : { + hide : ['y_axis_precision'] + } + }, + { + label : 'Percentage', + value : 'p', + operations : { + show : ['y_axis_precision'] + } + }, + { + label : 'SI-prefix', + value : 's', + operations : { + hide : ['y_axis_precision'] + } + } + ] + }, + y_axis_precision : { + title : 'Axis tick format', + info : 'Select the tick format for the axis.', + type : 'select', + init : '1', + data : [ + { + label : '0.00001', + value : '5' + }, + { + label : '0.0001', + value : '4' + }, + { + label : '0.001', + value : '3' + }, + { + label : '0.01', + value : '2' + }, + { + label : '0.1', + value : '1' + }, + { + label : '1', + value : '0' + } + ] + + }, + separator_legend : { + title : 'Others', + type : 'separator' + }, + show_legend : { + title : 'Show legend', + info : 'Would you like to add a legend?', + type : 'radiobutton', + init : 'true', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + }, + use_panels : { + title : 'Use multi-panels', + info : 'Would you like to separate your data into individual panels?', + type : 'radiobutton', + init : 'false', + data : [ + { + label : 'Yes', + value : 'true' + }, + { + label : 'No', + value : 'false' + } + ] + } + } +}; + +}); \ No newline at end of file diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js @@ -2,38 +2,24 @@ define(['plugin/charts/jqplot/common/wrapper'], function(Plot) { // widget -return Backbone.View.extend( -{ - // initialize +return Backbone.Model.extend({ initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var plot = new Plot(this.app, this.options); - plot.draw({ - process_id : process_id, - chart : chart, - request_dictionary : request_dictionary, - makeConfig : function(groups, plot_config){ - $.extend(true, plot_config, { - seriesDefaults: { - renderer : $.jqplot.BarRenderer + options.makeConfig = function(groups, plot_config){ + $.extend(true, plot_config, { + seriesDefaults: { + renderer : $.jqplot.BarRenderer + }, + axes: { + xaxis: { + min : -1 }, - axes: { - xaxis: { - pad : 1.2 - }, - - yaxis: { - pad : 1.2 - } + yaxis: { + pad : 1.2 } - }); - } - }); + } + }); + }; + new Plot(app, options); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png Binary file config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png has changed diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js @@ -6,13 +6,11 @@ { // initialize initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - // configure request + // get request dictionary + var request_dictionary = options.request_dictionary; + var chart = options.chart; + + // modify request var index = 0; for (var i in request_dictionary.groups) { var group = request_dictionary.groups[i]; @@ -23,11 +21,13 @@ } } } - var plot = new Plot(this.app, this.options); - plot.draw({ - process_id : process_id, - chart : chart, - request_dictionary : request_dictionary, + + // create plot + var plot = new Plot(app, { + process_id : options.process_id, + chart : options.chart, + request_dictionary : options.request_dictionary, + canvas_list : options.canvas_list, makeConfig : function(groups, plot_config){ var boundary = Tools.getDomains(groups, 'x'); $.extend(true, plot_config, { @@ -74,15 +74,14 @@ }]; }, makeSeries: function (groups) { - /* example data + /*/ example data var catOHLC = [ [0, 138.7, 139.68, 135.18, 135.4], [1, 143.46, 144.66, 139.79, 140.02], [2, 140.67, 143.56, 132.88, 142.44], [3, 136.01, 139.5, 134.53, 139.48] ]; - return [catOHLC]; - */ + return [catOHLC];*/ // plot data var plot_data = []; diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/common/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js @@ -1,108 +1,21 @@ -define([], function() { +define(['plugin/charts/forms/default'], function(config_default) { -return { +return $.extend(true, {}, config_default, { title : '', category : '', - library : 'JqPlot', + library : 'jqPlot', tag : 'div', - keywords : 'default medium', + zoomable : true, + keywords : 'medium', query_limit : 10000, settings : { - separator_label : { - title : 'X axis', + separator_grid : { + title : 'Grids', type : 'separator' }, - x_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'X-axis', - placeholder : 'Axis label' - }, - x_axis_type : { - title : 'Axis value type', - info : 'Select the value type of the axis.', - type : 'select', - init : 'auto', - data : [ - { - label : '-- Do not show values --', - value : 'hide', - hide : ['x_axis_tick'] - }, - { - label : 'Auto', - value : 'auto', - hide : ['x_axis_tick'] - }, - { - label : 'Float', - value : 'f', - show : ['x_axis_tick'] - }, - { - label : 'Exponent', - value : 'e', - show : ['x_axis_tick'] - }, - { - label : 'Integer', - value : 'd', - hide : ['x_axis_tick'] - }, - { - label : 'Percentage', - value : 'p', - show : ['x_axis_tick'] - }, - { - label : 'Rounded', - value : 'r', - show : ['x_axis_tick'] - }, - { - label : 'SI-prefix', - value : 's', - show : ['x_axis_tick'] - } - ] - }, - x_axis_tick : { - title : 'Axis tick format', - info : 'Select the tick format for the axis.', - type : 'select', - init : '.1', - data : [ - { - label : '0.00001', - value : '.5' - }, - { - label : '0.0001', - value : '.4' - }, - { - label : '0.001', - value : '.3' - }, - { - label : '0.01', - value : '.2' - }, - { - label : '0.1', - value : '.1' - }, - { - label : '1', - value : '1' - } - ] - - }, x_axis_grid : { title : 'Axis grid', - info : 'Would you like to show grid lines for this axis?', + info : 'Would you like to show grid lines for the X axis?', type : 'radiobutton', init : 'false', data : [ @@ -116,101 +29,9 @@ } ] }, - separator_tick : { - title : 'Y axis', - type : 'separator' - }, - y_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'Y-axis', - placeholder : 'Axis label' - }, - y_axis_type : { - title : 'Axis value type', - info : 'Select the value type of the axis.', - type : 'select', - init : 'auto', - data : [ - { - label : '-- Do not show values --', - value : 'hide', - hide : ['y_axis_tick'] - }, - { - label : 'Auto', - value : 'auto', - hide : ['y_axis_tick'] - }, - { - label : 'Float', - value : 'f', - show : ['y_axis_tick'] - }, - { - label : 'Exponent', - value : 'e', - show : ['y_axis_tick'] - }, - { - label : 'Integer', - value : 'd', - hide : ['y_axis_tick'] - }, - { - label : 'Percentage', - value : 'p', - show : ['y_axis_tick'] - }, - { - label : 'Rounded', - value : 'r', - show : ['y_axis_tick'] - }, - { - label : 'SI-prefix', - value : 's', - show : ['y_axis_tick'] - } - ] - }, - y_axis_tick : { - title : 'Axis tick format', - info : 'Select the tick format for the axis.', - type : 'select', - init : '.1', - data : [ - { - label : '0.00001', - value : '.5' - }, - { - label : '0.0001', - value : '.4' - }, - { - label : '0.001', - value : '.3' - }, - { - label : '0.01', - value : '.2' - }, - { - label : '0.1', - value : '.1' - }, - { - label : '1', - value : '1' - } - ] - - }, y_axis_grid : { title : 'Axis grid', - info : 'Would you like to show grid lines for this axis?', + info : 'Would you like to show grid lines for the Y axis?', type : 'radiobutton', init : 'true', data : [ @@ -223,44 +44,8 @@ value : 'false' } ] - }, - separator_legend : { - title : 'Others', - type : 'separator' - }, - show_legend : { - title : 'Show legend', - info : 'Would you like to add a legend?', - type : 'radiobutton', - init : 'true', - data : [ - { - label : 'Yes', - value : 'true' - }, - { - label : 'No', - value : 'false' - } - ] - }, - use_panels : { - title : 'Use multi-panels', - info : 'Would you like to separate your data into individual panels?', - type : 'radiobutton', - init : 'false', - data : [ - { - label : 'Yes', - value : 'true' - }, - { - label : 'No', - value : 'false' - } - ] } } -}; +}); }); \ No newline at end of file diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js @@ -8,38 +8,16 @@ var settings = chart.settings; var plot_config = { enablePlugins: true, - seriesColors: function() { - var colors = []; - var colorScale = d3.scale.category20(); - for (var i = 0; i < chart.groups.length; i++) { - colors.push(colorScale(i)); - } - return colors; - }(), - + seriesColors: d3.scale.category20().range(), seriesDefaults: { renderer : $.jqplot.LineRenderer, - //lineWidth : 1, // Width of the line in pixels. + //lineWidth : 1, // width of the line in pixels. shadow : false, // show shadow or not. showLine : true, // whether to render the line segments or not. - - // Show point labels to the right ('e'ast) of each bar. - // edgeTolerance of -15 allows labels flow outside the grid - // up to 15 pixels. If they flow out more than that, they - // will be hidden. - //pointLabels : { show: true, location: 'e', edgeTolerance: -15 }, - // Rotate the bar shadow as if bar is lit from top right. - //shadowAngle : 135, - // Here's where we tell the chart it is oriented horizontally. rendererOptions: { shadowDepth : 0, - //barDirection : 'horizontal', - //barPadding : 5, - //barMargin : 2, - //barWidth : Math.max(0.5 / chart.groups.length, 2), - barWidth : 10, - //fillToZero : true, - //stackedValue : true + barWidth : 3, + barPadding : 3 }, markerRenderer : $.jqplot.MarkerRenderer, markerOptions: { @@ -51,9 +29,9 @@ shadow : false, // wether to draw shadow on marker or not. shadowAngle : 45, // angle of the shadow. Clockwise from x axis. shadowOffset : 1, // offset from the line of the shadow, - shadowDepth : 3, // Number of strokes to make when drawing shadow. Each stroke + shadowDepth : 3, // number of strokes to make when drawing shadow. Each stroke // offset by shadowOffset from the last. - shadowAlpha : 0.07 // Opacity of the shadow + shadowAlpha : 0.07 // opacity of the shadow } }, @@ -78,7 +56,6 @@ angle : chart.settings.get('use_panels') === 'true' ? 0 : -30, showGridline : chart.settings.get('x_axis_grid') === 'true' }, - tickInterval : 1, pad : 0 }, yaxis: { @@ -112,7 +89,7 @@ series: [] }; - // Show the legend and put it outside the grid + // show the legend and put it outside the grid if (chart.settings.get('show_legend') == 'true') { plot_config.legend = { renderer : $.jqplot.EnhancedLegendRenderer, diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js @@ -1,38 +1,23 @@ // dependencies define(['plugin/charts/jqplot/common/plot-config', 'plugin/charts/tools'], function(configmaker, Tools) { -// widget -return Backbone.View.extend( -{ - // plot series - plot_series: { - name : '', - data : [], - tooltip: { - headerFormat : '<em>{point.key}</em><br/>' - } - }, - +/** + * This is the common wrapper for jqplot based visualizations. + */ +return Backbone.View.extend({ // initialize initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(options) { - _.extend(this.options, options); + // get parameters + this.options = options; + + // define render function var self = this; - var plot = new Tools.panelHelper({ - app : this.app, - process_id : this.options.process_id, - canvas_list : this.options.canvas_list, - chart : this.options.chart, - request_dictionary : this.options.request_dictionary, - render : function(canvas_id, groups) { - return self.render(canvas_id, groups) - } - }); + options.render = function(canvas_id, groups) { + return self.render(canvas_id, groups) + }; + + // call panel helper + Tools.panelHelper(app, options); }, // draw all data into a single canvas @@ -54,7 +39,7 @@ this._makeAxes(groups, plot_config, chart.settings); // make custom series call - if (makeSeries) { + if (makeSeriesLabels) { plot_config.series = makeSeriesLabels(groups, plot_config); } else { plot_config.series = this._makeSeriesLabels(groups); @@ -92,7 +77,6 @@ var plot = drawGraph(); // catch window resize event - var self = this; $(window).on('resize', function () { drawGraph(); }); @@ -126,41 +110,21 @@ categories = Tools.makeCategories(groups); } - // make axis + // make axes function makeAxis (id) { - var axis = plot_config.axes[id + 'axis'].tickOptions; - var type = settings.get(id + '_axis_type'); - var tick = settings.get(id + '_axis_tick'); - var is_category = categories.array[id]; - - // hide axis - if (type == 'hide') { - axis.formatter = function(format, value) { return '' }; - return; - } - - // format values/labels - if (type == 'auto') { - if (is_category) { - axis.formatter = function(format, value) { - return categories.array[id][value] || ''; - }; - } - } else { - var formatter = d3.format(tick + type); - if (is_category) { - axis.formatter = function(format, value) { - return formatter(categories.array[id][value]); - }; - } else { - axis.formatter = function(format, value) { - return formatter(value); + Tools.makeTickFormat({ + categories : categories.array[id], + type : settings.get(id + '_axis_type'), + precision : settings.get(id + '_axis_precision'), + formatter : function(formatter) { + if (formatter) { + plot_config.axes[id + 'axis'].tickOptions.formatter = function(format, value) { + return formatter(value); + }; } } - } + }); }; - - // make axes makeAxis('x'); makeAxis('y'); }, diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js @@ -0,0 +1,24 @@ +define(['plugin/charts/jqplot/common/config'], function(default_config) { + +return $.extend(true, {}, default_config, { + title : 'Discrete Histogram', + category : 'Data processing (requires \'charts\' tool from Toolshed)', + execute : 'histogramdiscrete', + keywords : 'small medium large', + columns : { + x : { + title : 'Observations', + is_label : true + } + }, + settings : { + x_axis_label : { + init : 'Breaks' + }, + y_axis_label : { + init : 'Density' + } + } +}); + +}); \ No newline at end of file diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png Binary file config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png has changed diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js @@ -0,0 +1,57 @@ +// dependencies +define(['plugin/charts/jqplot/common/wrapper'], function(Plot) { + +// widget +return Backbone.Model.extend({ + initialize: function(app, options) { + // link request + var request_dictionary = options.request_dictionary; + + // configure request + var index = 1; + var tmp_dict = { + id : request_dictionary.id, + groups : [] + }; + + // configure groups + for (var group_index in request_dictionary.groups) { + var group = request_dictionary.groups[group_index]; + tmp_dict.groups.push({ + key : group.key, + columns : { + x: { + index : 0, + is_label : true + }, + y: { + index : index++ + } + } + }); + } + + // add new request dictionary + options.request_dictionary = tmp_dict; + + // add config maker + options.makeConfig = function(groups, plot_config){ + $.extend(true, plot_config, { + seriesDefaults: { + renderer : $.jqplot.BarRenderer + }, + axes: { + xaxis: { + min : -1 + }, + yaxis: { + pad : 1.2 + } + } + }); + }; + new Plot(app, options); + } +}); + +}); \ No newline at end of file diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js @@ -2,22 +2,9 @@ define(['plugin/charts/jqplot/common/wrapper'], function(Plot) { // widget -return Backbone.View.extend( -{ - // initialize +return Backbone.Model.extend({ initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var plot = new Plot(this.app, this.options); - plot.draw({ - process_id : process_id, - chart : chart, - request_dictionary : request_dictionary - }); + new Plot(app, options); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js @@ -2,33 +2,20 @@ define(['plugin/charts/jqplot/common/wrapper'], function(Plot) { // widget -return Backbone.View.extend( -{ - // initialize +return Backbone.Model.extend({ initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var plot = new Plot(this.app, this.options); - plot.draw({ - process_id : process_id, - chart : chart, - request_dictionary : request_dictionary, - makeConfig : function(groups, plot_config){ - $.extend(true, plot_config, { - seriesDefaults: { - renderer: $.jqplot.LineRenderer, - showLine: false, - markerOptions : { - show : true - } + options.makeConfig = function(groups, plot_config){ + $.extend(true, plot_config, { + seriesDefaults: { + renderer: $.jqplot.LineRenderer, + showLine: false, + markerOptions : { + show : true } - }); - } - }); + } + }); + }; + new Plot(app, options); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js @@ -2,22 +2,10 @@ define(['plugin/charts/nvd3/common/wrapper'], function(NVD3) { // widget -return Backbone.View.extend({ - // initialize +return Backbone.Model.extend({ initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw({ - type : 'multiBarChart', - process_id : process_id, - chart : chart, - request_dictionary : request_dictionary - }); + options.type = 'multiBarChart'; + new NVD3(app, options); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js @@ -3,7 +3,6 @@ return $.extend(true, {}, nvd3_config, { title : 'Horizontal', category : 'Bar diagrams', - keywords : 'default small', settings : { x_axis_type : { init : 'hide' diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js @@ -2,22 +2,10 @@ define(['plugin/charts/nvd3/common/wrapper'], function(NVD3) { // widget -return Backbone.View.extend({ - // initialize +return Backbone.Model.extend({ initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw({ - type : 'multiBarHorizontalChart', - process_id : process_id, - chart : chart, - request_dictionary : request_dictionary - }); + options.type = 'multiBarHorizontalChart'; + new NVD3(app, options); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js @@ -3,7 +3,6 @@ return $.extend(true, {}, nvd3_config, { title : 'Stacked horizontal', category : 'Bar diagrams', - keywords : 'default small', settings : { x_axis_type : { init : 'hide' diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js @@ -2,25 +2,13 @@ define(['plugin/charts/nvd3/common/wrapper'], function(NVD3) { // widget -return Backbone.View.extend({ - // initialize +return Backbone.Model.extend({ initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw({ - type : 'multiBarHorizontalChart', - process_id : process_id, - chart : chart, - request_dictionary : request_dictionary, - makeConfig : function(nvd3_model) { - nvd3_model.stacked(true); - } - }); + options.type = 'multiBarHorizontalChart'; + options.makeConfig = function(nvd3_model) { + nvd3_model.stacked(true); + }; + new NVD3(app, options); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js @@ -3,7 +3,6 @@ return $.extend(true, {}, nvd3_config, { title : 'Stacked', category : 'Bar diagrams', - keywords : 'default small', columns : { x : { title : 'Values for x-axis', diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js @@ -2,25 +2,13 @@ define(['plugin/charts/nvd3/common/wrapper'], function(NVD3) { // widget -return Backbone.View.extend({ - // initialize +return Backbone.Model.extend({ initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw({ - type : 'multiBarChart', - process_id : process_id, - chart : chart, - request_dictionary : request_dictionary, - makeConfig : function(nvd3_model) { - nvd3_model.stacked(true); - } - }); + options.type = 'multiBarChart'; + options.makeConfig = function(nvd3_model) { + nvd3_model.stacked(true); + }; + new NVD3(app, options); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/common/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/config.js @@ -1,234 +1,11 @@ -define(['plugin/plugins/nvd3/nv.d3'], function() { - -return { +define(['plugin/charts/forms/default', 'plugin/plugins/nvd3/nv.d3'], function(config_default) { +return $.extend(true, {}, config_default, { title : '', category : '', library : 'NVD3', tag : 'svg', keywords : 'small', - query_limit : 500, - settings : { - separator_label : { - title : 'X axis', - type : 'separator' - }, - x_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'X-axis', - placeholder : 'Axis label' - }, - x_axis_type : { - title : 'Axis value type', - info : 'Select the value type of the axis.', - type : 'select', - init : 'auto', - data : [ - { - label : '-- Do not show values --', - value : 'hide', - hide : ['x_axis_tick'] - }, - { - label : 'Auto', - value : 'auto', - hide : ['x_axis_tick'] - }, - { - label : 'Float', - value : 'f', - show : ['x_axis_tick'] - }, - { - label : 'Exponent', - value : 'e', - show : ['x_axis_tick'] - }, - { - label : 'Integer', - value : 'd', - hide : ['x_axis_tick'] - }, - { - label : 'Percentage', - value : 'p', - show : ['x_axis_tick'] - }, - { - label : 'Rounded', - value : 'r', - show : ['x_axis_tick'] - }, - { - label : 'SI-prefix', - value : 's', - show : ['x_axis_tick'] - } - ] - }, - x_axis_tick : { - title : 'Axis tick format', - info : 'Select the tick format for the axis.', - type : 'select', - init : '.1', - data : [ - { - label : '0.00001', - value : '.5' - }, - { - label : '0.0001', - value : '.4' - }, - { - label : '0.001', - value : '.3' - }, - { - label : '0.01', - value : '.2' - }, - { - label : '0.1', - value : '.1' - }, - { - label : '1', - value : '1' - } - ] - - }, - separator_tick : { - title : 'Y axis', - type : 'separator' - }, - y_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'Y-axis', - placeholder : 'Axis label' - }, - y_axis_type : { - title : 'Axis value type', - info : 'Select the value type of the axis.', - type : 'select', - init : 'auto', - data : [ - { - label : '-- Do not show values --', - value : 'hide', - hide : ['y_axis_tick'] - }, - { - label : 'Auto', - value : 'auto', - hide : ['y_axis_tick'] - }, - { - label : 'Float', - value : 'f', - show : ['y_axis_tick'] - }, - { - label : 'Exponent', - value : 'e', - show : ['y_axis_tick'] - }, - { - label : 'Integer', - value : 'd', - hide : ['y_axis_tick'] - }, - { - label : 'Percentage', - value : 'p', - show : ['y_axis_tick'] - }, - { - label : 'Rounded', - value : 'r', - show : ['y_axis_tick'] - }, - { - label : 'SI-prefix', - value : 's', - show : ['y_axis_tick'] - } - ] - }, - y_axis_tick : { - title : 'Axis tick format', - info : 'Select the tick format for the axis.', - type : 'select', - init : '.1', - data : [ - { - label : '0.00001', - value : '.5' - }, - { - label : '0.0001', - value : '.4' - }, - { - label : '0.001', - value : '.3' - }, - { - label : '0.01', - value : '.2' - }, - { - label : '0.1', - value : '.1' - }, - { - label : '1', - value : '1' - } - ] - - }, - separator_legend : { - title : 'Others', - type : 'separator' - }, - show_legend : { - title : 'Show legend', - info : 'Would you like to add a legend?', - type : 'radiobutton', - init : 'true', - data : [ - { - label : 'Yes', - value : 'true' - }, - { - label : 'No', - value : 'false' - } - ] - }, - use_panels : { - title : 'Use multi-panels', - info : 'Would you like to separate your data into individual panels?', - type : 'radiobutton', - init : 'false', - data : [ - { - label : 'Yes', - value : 'true' - }, - { - label : 'No', - value : 'false' - } - ] - } - } -}; + query_limit : 500 +}); }); \ No newline at end of file diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js @@ -1,29 +1,23 @@ // dependencies define(['plugin/charts/tools'], function(Tools) { -// widget -return Backbone.View.extend( -{ +/** + * This is the common wrapper for nvd3 based visualizations. + */ +return Backbone.View.extend({ // initialize initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(options) { - _.extend(this.options, options); + // get parameters + this.options = options; + + // define render function var self = this; - var plot = Tools.panelHelper({ - app : this.app, - process_id : this.options.process_id, - canvas_list : this.options.canvas_list, - chart : this.options.chart, - request_dictionary : this.options.request_dictionary, - render : function(canvas_id, groups) { - return self.render(canvas_id, groups) - } - }); + options.render = function(canvas_id, groups) { + return self.render(canvas_id, groups) + }; + + // call panel helper + Tools.panelHelper(app, options); }, // render @@ -80,9 +74,21 @@ .call(d3chart); // add zoom/pan handler - var zoom_mode = chart.definition.zoomable; - if (zoom_mode == 'axis' || zoom_mode == 'svg') { - self._addZoom(d3chart, canvas, zoom_mode); + if (chart.definition.zoomable && chart.definition.zoomable != 'native') { + // clip edges + if (d3chart.clipEdge) { + d3chart.clipEdge(true); + } + + // add zoom + Tools.addZoom({ + xAxis : d3chart.xAxis, + yAxis : d3chart.yAxis, + yDomain: d3chart.yDomain, + xDomain: d3chart.xDomain, + redraw : function() { d3chart.update() }, + svg : canvas + }); } // refresh on window resize @@ -92,122 +98,32 @@ } }); + // return return true; }, - // add zoom handler - _addZoom: function(nvd3_model, svg, zoom_mode) { - // clip edges - if (nvd3_model.clipEdge) { - nvd3_model.clipEdge(true); - } - - // get canvas dimensions - var width = parseInt(svg.style('width')); - var height = parseInt(svg.style('height')); - - // create x scales - var x_domain = nvd3_model.xAxis.scale().domain(); - var x = d3.scale.linear() - .domain(x_domain) - .range([0, width]); - - // create y scale - var y_domain = nvd3_model.yAxis.scale().domain(); - var y = d3.scale.linear() - .domain(y_domain) - .range([height, 0]); - - // min/max boundaries - var x_boundary = nvd3_model.xScale().domain().slice(); - var y_boundary = nvd3_model.yScale().domain().slice(); - - // create d3 zoom handler - var d3zoom = d3.behavior.zoom(); - - // fix domain - function fixDomain(domain, boundary) { - domain[0] = Math.max(domain[0], boundary[0]); - domain[1] = Math.min(domain[1], boundary[1]); - return domain; - }; - - // zoom event handler - function zoomed() { - if (zoom_mode == 'axis') { - nvd3_model.xDomain(fixDomain(x.domain(), x_boundary)); - nvd3_model.yDomain(fixDomain(y.domain(), y_boundary)); - nvd3_model.update(); - } else { - var translate = d3.event.translate; - svg.select('.nvd3').attr("transform", "translate(" + translate + ") scale(" + d3.event.scale + ")"); - } - }; - - // zoom event handler - function unzoomed() { - if (zoom_mode == 'axis') { - nvd3_model.xDomain(x_boundary); - nvd3_model.yDomain(y_boundary); - nvd3_model.update(); - d3zoom.scale(1); - d3zoom.translate([0,0]); - } else { - var translate = d3.event.translate; - svg.select('.nvd3').attr("transform", "translate([0,0]) scale(1)"); - } - }; - - // initialize wrapper - d3zoom.x(x) - .y(y) - .scaleExtent([1, 10]) - .on("zoom", zoomed); - - // add handler - svg.call(d3zoom).on("dblclick.zoom", unzoomed); - }, - // create axes formatting _makeAxes: function(d3chart, groups, settings) { // result var categories = Tools.makeCategories(groups); - - // make axis - function makeAxis (id) { - var axis = d3chart[id + 'Axis']; - var type = settings.get(id + '_axis_type'); - var tick = settings.get(id + '_axis_tick'); - var is_category = categories.array[id]; - - // hide axis - if (type == 'hide') { - axis.tickFormat(function() { return '' }); - return; - } - - // format values/labels - if (type == 'auto') { - if (is_category) { - axis.tickFormat(function(value) { - return categories.array[id][value] - }); + + // make axes + function makeTickFormat (id) { + Tools.makeTickFormat({ + categories : categories.array[id], + type : settings.get(id + '_axis_type'), + precision : settings.get(id + '_axis_precision'), + formatter : function(formatter) { + if (formatter) { + d3chart[id + 'Axis'].tickFormat(function(value) { + return formatter(value); + }); + } } - } else { - var formatter = d3.format(tick + type); - if (is_category) { - axis.tickFormat(function(value) { - return formatter(categories.array[id][value]); - }); - } else { - axis.tickFormat(formatter); - } - } + }); }; - - // make axes - makeAxis('x'); - makeAxis('y'); + makeTickFormat('x'); + makeTickFormat('y'); }, // handle error diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js @@ -21,7 +21,7 @@ y_axis_type : { init : 'f' }, - y_axis_tick : { + y_axis_precision : { init : '.2' } } diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png has changed diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js @@ -2,15 +2,11 @@ define(['plugin/charts/nvd3/common/wrapper'], function(NVD3) { // widget -return Backbone.View.extend({ - // initialize +return Backbone.Model.extend({ initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary){ + // link request + var request_dictionary = options.request_dictionary; + // configure request var index = 1; for (var i in request_dictionary.groups) { @@ -26,20 +22,12 @@ } } - // link this - var self = this; - - // load nvd3 - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw({ - type : 'multiBarChart', - process_id : process_id, - chart : chart, - request_dictionary : request_dictionary, - makeConfig : function(nvd3_model) { - nvd3_model.options({showControls: true}); - } - }); + // setup chart wrapper + options.type = 'multiBarChart'; + options.makeConfig = function(nvd3_model) { + nvd3_model.options({showControls: true}); + }; + new NVD3(app, options); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js @@ -5,6 +5,7 @@ category : 'Data processing (requires \'charts\' tool from Toolshed)', execute : 'histogramdiscrete', keywords : 'small medium large', + query_limit : 10000, columns : { x : { title : 'Observations', @@ -21,8 +22,8 @@ y_axis_type : { init : 'f' }, - y_axis_tick : { - init : '.2' + y_axis_precision : { + init : '2' } } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png Binary file config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png has changed diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js @@ -2,17 +2,11 @@ define(['plugin/charts/nvd3/common/wrapper'], function(NVD3) { // widget -return Backbone.View.extend( -{ - // initialize +return Backbone.Model.extend({ initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) - { + // link request + var request_dictionary = options.request_dictionary; + // configure request var index = 1; var tmp_dict = { @@ -37,17 +31,13 @@ }); } - // draw - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw({ - type : 'multiBarChart', - process_id : process_id, - chart : chart, - request_dictionary : tmp_dict, - makeConfig : function(nvd3_model) { - nvd3_model.options({showControls: true}); - } - }); + // setup chart wrapper + options.type = 'multiBarChart'; + options.request_dictionary = tmp_dict; + options.makeConfig = function(nvd3_model) { + nvd3_model.options({showControls: true}); + }; + new NVD3(app, options); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/line/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/line/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/line/config.js @@ -3,7 +3,7 @@ return $.extend(true, {}, nvd3_config, { title : 'Line chart', category : 'Others', - zoomable : 'axis', + zoomable : true, columns : { x : { title : 'Values for x-axis', diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js @@ -2,22 +2,10 @@ define(['plugin/charts/nvd3/common/wrapper'], function(NVD3) { // widget -return Backbone.View.extend({ - // initialize +return Backbone.Model.extend({ initialize: function(app, options) { - this.app = app; - this.options = options; - }, - - // render - draw : function(process_id, chart, request_dictionary) { - var nvd3 = new NVD3(this.app, this.options); - nvd3.draw({ - type : 'lineChart', - process_id : process_id, - chart : chart, - request_dictionary : request_dictionary - }); + options.type = 'lineChart'; + new NVD3(app, options); } }); diff -r 705149e31b10b1e6862be7ea8682fa1d02b9e4c3 -r 37ae922a58203cb34c5d5246dfe5331c89848552 config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js @@ -3,7 +3,7 @@ return $.extend(true, {}, nvd3_config, { title : 'Line with focus', category : 'Others', - keywords : 'default small', + zoomable : 'native', columns : { x : { title : 'Values for x-axis', This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/9a63eaf328c6/ Changeset: 9a63eaf328c6 User: martenson Date: 2014-07-21 22:00:46 Summary: some more work on permissions API, docs Affected #: 5 files diff -r 37ae922a58203cb34c5d5246dfe5331c89848552 -r 9a63eaf328c6058bf046d48cbc947c76f390193c lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -296,6 +296,8 @@ # Omit duplicated roles by converting to set return_roles = set( roles ) + if total_count is None: + total_count = len( return_roles ) return self.sort_by_attr( [ role for role in return_roles ], 'name' ), total_count def get_legitimate_roles( self, trans, item, cntrller ): diff -r 37ae922a58203cb34c5d5246dfe5331c89848552 -r 9a63eaf328c6058bf046d48cbc947c76f390193c lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -127,6 +127,7 @@ # When both are False the dataset is 'restricted' is_private = False is_unrestricted = False + # Access rights are checked on the dataset level, not on the ld or ldda level to maintain consistency if trans.app.security_agent.dataset_is_public( content_item.library_dataset_dataset_association.dataset ): is_unrestricted = True else: diff -r 37ae922a58203cb34c5d5246dfe5331c89848552 -r 9a63eaf328c6058bf046d48cbc947c76f390193c lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -41,6 +41,7 @@ :rtype: dictionary :returns: detailed dataset information from base controller + .. seealso:: :attr:`galaxy.web.base.controller.UsesLibraryMixinItems.get_library_dataset` """ try: @@ -67,6 +68,8 @@ rval[ 'file_size' ] = nice_size rval[ 'date_uploaded' ] = date_uploaded rval[ 'can_user_modify' ] = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset) or trans.user_is_admin() + + # Manage dataset permission is always attached to the dataset itself, not the the ld or ldda to maintain consistency rval[ 'can_user_manage' ] = trans.app.security_agent.can_manage_dataset( current_user_roles, library_dataset.library_dataset_dataset_association.dataset) or trans.user_is_admin() return rval @@ -74,9 +77,20 @@ def show_roles( self, trans, encoded_dataset_id, **kwd ): """ show_roles( self, trans, id, **kwd ): - GET /api/libraries/datasets/{encoded_dataset_id}/permissions: + * GET /api/libraries/datasets/{encoded_dataset_id}/permissions Displays information about current or available roles for a given dataset permission. + + :param encoded_dataset_id: the encoded id of the dataset to query + :type encoded_dataset_id: an encoded id string + + :param scope: either 'current' or 'available' + :type scope: string + + :rtype: dictionary + :returns: either dict of current roles for all permission types or + dict of available roles to choose from (is the same for any permission type) + """ current_user_roles = trans.get_current_user_roles() @@ -146,30 +160,66 @@ return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) - # @expose_api - # def get_roles( self, trans, encoded_dataset_id, **kwd ): - # try: - # library_dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) - # except Exception, e: - # raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) - # dataset = library_dataset.library_dataset_dataset_association.dataset + @expose_api + def update( self, trans, encoded_dataset_id, **kwd ): + """ + def update( self, trans, encoded_dataset_id, **kwd ): + *POST /api/libraries/datasets/{encoded_dataset_id}/permissions - # roles = dataset.get_access_roles( trans ) + :param encoded_dataset_id: the encoded id of the dataset to make private + :type encoded_dataset_id: an encoded id string - # # roles = dataset.get_manage_permissions_roles( trans ) + :param action: (required) describes what action should be performed + available actions: make_private, remove_restrictions + :type action: string - # # roles = trans.app.security_agent.get_current_dataset_roles( trans, dataset, trans.app.security_agent.permitted_actions.DATASET_ACCESS ) - # # Omit duplicated roles by converting to set - # roles = set( roles ) - # return [ role.name for role in roles ] + :rtype: dictionary + :returns: dict containing information about the dataset + """ + try: + dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) + except Exception, e: + raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) + + # User has to have manage permissions on dataset in order to remove access restrictions. + current_user_roles = trans.get_current_user_roles() + can_manage = trans.app.security_agent.can_manage_dataset( current_user_roles, dataset ) or trans.user_is_admin() + if not can_manage: + raise exceptions.InsufficientPermissionsException( 'You do not have proper permissions to manage permissions on this dataset.' ) + + action = kwd.get( 'action', None ) + if action is None: + raise exceptions.RequestParameterMissingException( 'The mandatory parameter "action" is missing.' ) + elif action == 'remove_restrictions': + trans.app.security_agent.make_dataset_public( dataset ) + elif action == 'make_private': + trans.app.security_agent.make_dataset_public( dataset ) + private_role = self.model.security_agent.get_private_user_role( trans.user ) + dp = trans.model.DatasetPermissions( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, dataset, private_role ) + trans.sa_session.add( dp ) + trans.sa_session.flush() + + rval = trans.security.encode_all_ids( dataset.to_dict() ) + rval[ 'update_time' ] = dataset.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + rval[ 'deleted' ] = dataset.deleted + rval[ 'folder_id' ] = 'F' + rval[ 'folder_id' ] + return rval @expose_api def delete( self, trans, encoded_dataset_id, **kwd ): """ delete( self, trans, encoded_dataset_id, **kwd ): * DELETE /api/libraries/datasets/{encoded_dataset_id} - Marks the dataset deleted or undeletes it based on the value - of the undelete flag (if present). + Marks the dataset deleted or undeleted based on the value + of the undelete flag. + If the flag is not present it is considered False and the + item is marked deleted. + + :param encoded_dataset_id: the encoded id of the dataset to change + :type encoded_dataset_id: an encoded id string + + :rtype: dictionary + :returns: dict containing information about the dataset """ undelete = util.string_as_bool( kwd.get( 'undelete', False ) ) try: diff -r 37ae922a58203cb34c5d5246dfe5331c89848552 -r 9a63eaf328c6058bf046d48cbc947c76f390193c lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -253,6 +253,12 @@ action='show_roles', conditions=dict( method=[ "GET" ] ) ) + webapp.mapper.connect( 'modify_permissions', + '/api/libraries/datasets/:encoded_dataset_id/permissions', + controller='lda_datasets', + action='update', + conditions=dict( method=[ "POST" ] ) ) + # webapp.mapper.connect( 'show_legitimate_lda_roles', # '/api/libraries/datasets/:encoded_dataset_id/permissions/current', # controller='lda_datasets', diff -r 37ae922a58203cb34c5d5246dfe5331c89848552 -r 9a63eaf328c6058bf046d48cbc947c76f390193c static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -635,7 +635,6 @@ tmpl_array.push('<div class="dataset_table">'); - // tmpl_array.push('<h2>Basic</h2>'); tmpl_array.push('<p>You can remove all access restrictions on this dataset. '); tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button"><span class="fa fa-globe"></span> Remove restrictions</span></button>'); tmpl_array.push('</p>'); @@ -648,7 +647,6 @@ tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Only you and the other user will be able to access the dataset." class="btn btn-default btn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); tmpl_array.push('</p>'); - // tmpl_array.push('<h2>Advanced</h2>'); tmpl_array.push('<p>You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.</p>'); tmpl_array.push('<hr/>'); @@ -661,7 +659,8 @@ tmpl_array.push('<hr/>'); tmpl_array.push('<h2>Dataset-related permissions</h2>'); - tmpl_array.push('<div class="alert alert-success">You have the permission to manage permissions on this dataset. That means you can control who can access it and also appoint others that can manage permissions on it. Changes made here will affect <strong>every</strong> library item and every history this dataset is part of.</div>'); + tmpl_array.push('<div class="alert alert-success">You have the permission to manage permissions on this dataset. That means you can control who can access it and also appoint others that can manage permissions on it.</div>'); + tmpl_array.push('<div class="alert alert-danger">Changes made here will affect <strong>every</strong> library item and every history this dataset is part of.</div>'); tmpl_array.push('<h4>Roles that can access dataset</h4>'); tmpl_array.push('<div id="access_perm" class="access_perm roles-selection"></div>'); tmpl_array.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>'); https://bitbucket.org/galaxy/galaxy-central/commits/d0a550fd70bb/ Changeset: d0a550fd70bb User: martenson Date: 2014-07-21 22:01:35 Summary: Merge Affected #: 26 files diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -413,12 +413,12 @@ # Make sure the current user's API key proves he is an admin user in this Galaxy instance. if not trans.user_is_admin(): raise HTTPForbidden( detail='You are not authorized to reset metadata on repositories installed into this Galaxy instance.' ) - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=False, order=False ) + irmm = InstalledRepositoryMetadataManager( trans.app ) + query = irmm.get_query_for_setting_metadata_on_repositories( order=False ) # Now reset metadata on all remaining repositories. for repository in query: repository_id = trans.security.encode_id( repository.id ) try: - irmm = InstalledRepositoryMetadataManager( trans.app ) invalid_file_tups, metadata_dict = irmm.reset_all_metadata_on_installed_repository( repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -30,6 +30,7 @@ from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import tool_panel_manager log = logging.getLogger( __name__ ) @@ -244,7 +245,10 @@ if kwd.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools_for_display_in_tool_panel: # Handle tool panel alterations. - tool_util.remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, uninstall=remove_from_disk_checked ) + tpm = tool_panel_manager.ToolPanelManager( trans.app ) + tpm.remove_from_tool_panel( tool_shed_repository, + shed_tool_conf, + uninstall=remove_from_disk_checked ) if tool_shed_repository.includes_data_managers: data_manager_util.remove_from_data_manager( trans.app, tool_shed_repository ) if tool_shed_repository.includes_datatypes: @@ -1116,9 +1120,9 @@ return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repositories', **kwd ) ) - shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans ) + shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans.app ) tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans.app, shed_tool_conf ) - tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans ) + tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans.app ) if len( repo_info_dicts ) == 1: # If we're installing or updating a single repository, see if it contains a readme or # dependencies that we can display. @@ -1333,13 +1337,14 @@ # its repository dependencies. includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies if tool_shed_repository.includes_tools_for_display_in_tool_panel: + tpm = tool_panel_manager.ToolPanelManager( trans.app ) # Handle the selected tool panel location for loading tools included in the tool shed repository. tool_section, tool_panel_section_key = \ - tool_util.handle_tool_panel_selection( toolbox=trans.app.toolbox, - metadata=metadata, - no_changes_checked=no_changes_checked, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_selection( toolbox=trans.app.toolbox, + metadata=metadata, + no_changes_checked=no_changes_checked, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) if tool_section is not None: # Just in case the tool_section.id differs from tool_panel_section_id, which it shouldn't... tool_panel_section_id = str( tool_section.id ) @@ -1636,7 +1641,7 @@ original_section_name = '' else: original_section_name = '' - tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans ) + tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans.app ) no_changes_check_box = CheckboxField( 'no_changes', checked=True ) if original_section_name: message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ @@ -1652,7 +1657,7 @@ no_changes_check_box = None original_section_name = '' tool_panel_section_select_field = None - shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans ) + shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans.app ) dd = dependency_display.DependencyDisplayer( trans.app ) containers_dict = \ dd.populate_containers_dict_for_new_install( tool_shed_url=tool_shed_url, @@ -1703,13 +1708,13 @@ @web.expose @web.require_admin def reset_metadata_on_selected_installed_repositories( self, trans, **kwd ): + irmm = InstalledRepositoryMetadataManager( trans.app ) if 'reset_metadata_on_selected_repositories_button' in kwd: - irmm = InstalledRepositoryMetadataManager( trans.app ) message, status = irmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repositories_select_field = suc.build_repository_ids_select_field( trans ) + repositories_select_field = irmm.build_repository_ids_select_field( trans ) return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, @@ -1939,19 +1944,19 @@ updating_installed_repository=True, persist=True ) if 'tools' in metadata_dict: + tpm = tool_panel_manager.ToolPanelManager( trans.app ) tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository ) repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) - tool_util.add_to_tool_panel( app=trans.app, - repository_name=str( repository.name ), - repository_clone_url=repository_clone_url, - changeset_revision=str( repository.installed_changeset_revision ), - repository_tools_tups=repository_tools_tups, - owner=str( repository.owner ), - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=False ) + tpm.add_to_tool_panel( repository_name=str( repository.name ), + repository_clone_url=repository_clone_url, + changeset_revision=str( repository.installed_changeset_revision ), + repository_tools_tups=repository_tools_tups, + owner=str( repository.owner ), + shed_tool_conf=shed_tool_conf, + tool_panel_dict=tool_panel_dict, + new_install=False ) # Add new Data Manager entries if 'data_manager' in metadata_dict: new_data_managers = data_manager_util.install_data_managers( trans.app, diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -392,7 +392,8 @@ my_writable = True handled_repository_ids = [] repository_ids = [] - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=False ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + query = rmm.get_query_for_setting_metadata_on_repositories( my_writable=my_writable, order=False ) # Make sure repositories of type tool_dependency_definition are first in the list. for repository in query: if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: @@ -426,13 +427,12 @@ This param can be used as an alternative to the above encoded_ids_to_skip. """ - def handle_repository( trans, repository, results ): + def handle_repository( trans, rmm, repository, results ): log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) repository_id = trans.security.encode_id( repository.id ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, repository_id ) + rmm.reset_all_metadata_on_repository_in_tool_shed( repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, @@ -451,7 +451,7 @@ status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) results = dict( start_time=start_time, repository_status=[], @@ -473,7 +473,7 @@ my_writable = util.asbool( payload.get( 'my_writable', False ) ) else: my_writable = True - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=False ) + query = rmm.get_query_for_setting_metadata_on_repositories( my_writable=my_writable, order=False ) # First reset metadata on all repositories of type repository_dependency_definition. for repository in query: encoded_id = trans.security.encode_id( repository.id ) @@ -481,7 +481,7 @@ log.debug( "Skipping repository with id %s because it is in encoded_ids_to_skip %s" % \ ( str( repository.id ), str( encoded_ids_to_skip ) ) ) elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: - results = handle_repository( trans, repository, results ) + results = handle_repository( trans, rmm, repository, results ) # Now reset metadata on all remaining repositories. for repository in query: encoded_id = trans.security.encode_id( repository.id ) @@ -489,7 +489,7 @@ log.debug( "Skipping repository with id %s because it is in encoded_ids_to_skip %s" % \ ( str( repository.id ), str( encoded_ids_to_skip ) ) ) elif repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: - results = handle_repository( trans, repository, results ) + results = handle_repository( trans, rmm, repository, results ) stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) results[ 'stop_time' ] = stop_time return json.dumps( results, sort_keys=True, indent=4 ) @@ -511,10 +511,9 @@ results = dict( start_time=start_time, repository_status=[] ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, - trans.security.encode_id( repository.id ) ) + rmm.reset_all_metadata_on_repository_in_tool_shed( trans.security.encode_id( repository.id ) ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -348,13 +348,16 @@ @web.expose @web.require_admin def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ): + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) if 'reset_metadata_on_selected_repositories_button' in kwd: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) - message, status = rmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) + message, status = rmm.reset_metadata_on_selected_repositories( **kwd ) else: message = util.restore_text( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) - repositories_select_field = suc.build_repository_ids_select_field( trans ) + repositories_select_field = rmm.build_repository_ids_select_field( name='repository_ids', + multiple=True, + display='checkboxes', + my_writable=False ) return trans.fill_template( '/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -48,8 +48,8 @@ repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) update_repository( repo, ctx_rev=None ) # Set metadata using the repository files on disk. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) - error_message, status = rmm.set_repository_metadata( trans.request.host, trans.user, repository ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + error_message, status = rmm.set_repository_metadata( trans.request.host, repository ) if status == 'ok' and error_message: log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ ( str( repository.name ), str( repository.user.username ), error_message ) ) diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -20,6 +20,7 @@ from tool_shed.galaxy_install import dependency_display from tool_shed.metadata import repository_metadata_manager +from tool_shed.tools import tool_validator from tool_shed.util import basic_util from tool_shed.util import common_util @@ -1164,7 +1165,10 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) - repository, tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) + tv = tool_validator.ToolValidator( trans.app ) + repository, tool, message = tv.load_tool_from_changeset_revision( repository_id, + changeset_revision, + tool_config ) if message: status = 'error' tool_state = tool_util.new_state( trans, tool, invalid=False ) @@ -2144,15 +2148,17 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'error' ) render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) - repository, tool, error_message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) + tv = tool_validator.ToolValidator( trans.app ) + repository, tool, error_message = tv.load_tool_from_changeset_revision( repository_id, + changeset_revision, + tool_config ) tool_state = tool_util.new_state( trans, tool, invalid=True ) invalid_file_tups = [] if tool: - invalid_file_tups = tool_util.check_tool_input_params( trans.app, - repository.repo_path( trans.app ), - tool_config, - tool, - [] ) + invalid_file_tups = tv.check_tool_input_params( repository.repo_path( trans.app ), + tool_config, + tool, + [] ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, @@ -2747,9 +2753,9 @@ def reset_all_metadata( self, trans, id, **kwd ): """Reset all metadata on the complete changelog for a single repository in the tool shed.""" # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, id, **kwd ) + rmm.reset_all_metadata_on_repository_in_tool_shed( id, **kwd ) if invalid_file_tups: repository = suc.get_repository_in_tool_shed( trans.app, id ) message = tool_util.generate_message_for_invalid_tools( trans.app, @@ -2768,13 +2774,16 @@ @web.expose def reset_metadata_on_my_writable_repositories_in_tool_shed( self, trans, **kwd ): + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) if 'reset_metadata_on_selected_repositories_button' in kwd: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) - message, status = rmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) + message, status = rmm.reset_metadata_on_selected_repositories( **kwd ) else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repositories_select_field = suc.build_repository_ids_select_field( trans, my_writable=True ) + repositories_select_field = rmm.build_repository_ids_select_field( name='repository_ids', + multiple=True, + display='checkboxes', + my_writable=True ) return trans.fill_template( '/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, @@ -2834,9 +2843,8 @@ if tip == repository.tip( trans.app ): message += 'No changes to repository. ' else: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - trans.user, repository, **kwd ) if error_message: @@ -3391,6 +3399,7 @@ metadata = repository_metadata.metadata if metadata: if 'tools' in metadata: + tv = tool_validator.ToolValidator( trans.app ) for tool_metadata_dict in metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: work_dir = tempfile.mkdtemp() @@ -3398,29 +3407,26 @@ guid = tool_metadata_dict[ 'guid' ] full_path_to_tool_config = os.path.abspath( relative_path_to_tool_config ) full_path_to_dir, tool_config_filename = os.path.split( full_path_to_tool_config ) - can_use_disk_file = tool_util.can_use_tool_config_disk_file( trans, - repository, - repo, - full_path_to_tool_config, - changeset_revision ) + can_use_disk_file = tv.can_use_tool_config_disk_file( repository, + repo, + full_path_to_tool_config, + changeset_revision ) if can_use_disk_file: trans.app.config.tool_data_path = work_dir tool, valid, message, sample_files = \ - tool_util.handle_sample_files_and_load_tool_from_disk( trans, - repo_files_dir, - repository_id, - full_path_to_tool_config, - work_dir ) + tv.handle_sample_files_and_load_tool_from_disk( repo_files_dir, + repository_id, + full_path_to_tool_config, + work_dir ) if message: status = 'error' else: tool, message, sample_files = \ - tool_util.handle_sample_files_and_load_tool_from_tmp_config( trans, - repo, - repository_id, - changeset_revision, - tool_config_filename, - work_dir ) + tv.handle_sample_files_and_load_tool_from_tmp_config( repo, + repository_id, + changeset_revision, + tool_config_filename, + work_dir ) if message: status = 'error' basic_util.remove_dir( work_dir ) diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -262,10 +262,9 @@ ( len( files_to_remove ), upload_point ) else: message += " %d files were removed from the repository root. " % len( files_to_remove ) - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) status, error_message = \ rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - trans.user, repository, content_alert_str=content_alert_str, **kwd ) diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -727,9 +727,8 @@ results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message try: - rmm = repository_metadata_manager.RepositoryMetadataManager( self.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( self.app, self.user ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( self.host, - self.user, repository, content_alert_str=content_alert_str ) if error_message: diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -33,6 +33,7 @@ from tool_shed.galaxy_install.tool_dependencies.recipe.install_environment import InstallEnvironment from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager +from tool_shed.galaxy_install.tools import tool_panel_manager log = logging.getLogger( __name__ ) @@ -535,7 +536,8 @@ self.app.config.shed_tool_data_table_config, persist=True ) if 'tools' in metadata_dict: - tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) + tpm = tool_panel_manager.ToolPanelManager( self.app ) + tool_panel_dict = tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) sample_files = metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) @@ -555,16 +557,18 @@ sample_files_copied ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the # local Galaxy instance. - tool_util.copy_sample_files( self.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) - tool_util.add_to_tool_panel( app=self.app, - repository_name=tool_shed_repository.name, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, - repository_tools_tups=repository_tools_tups, - owner=tool_shed_repository.owner, - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=True ) + tool_util.copy_sample_files( self.app, + sample_files, + tool_path=tool_path, + sample_files_copied=sample_files_copied ) + tpm.add_to_tool_panel( repository_name=tool_shed_repository.name, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.installed_changeset_revision, + repository_tools_tups=repository_tools_tups, + owner=tool_shed_repository.owner, + shed_tool_conf=shed_tool_conf, + tool_panel_dict=tool_panel_dict, + new_install=True ) if 'data_manager' in metadata_dict: new_data_managers = data_manager_util.install_data_managers( self.app, self.app.config.shed_data_manager_config_file, @@ -644,10 +648,11 @@ tool_shed_url = installation_dict[ 'tool_shed_url' ] # Handle contained tools. if includes_tools_for_display_in_tool_panel and ( new_tool_panel_section_label or tool_panel_section_id ): + tpm = tool_panel_manager.ToolPanelManager( self.app ) tool_panel_section_key, tool_section = \ - tool_util.handle_tool_panel_section( self.app.toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) else: tool_panel_section_key = None tool_section = None diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -11,11 +11,11 @@ from tool_shed.util import datatype_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util -from tool_shed.util import tool_util from tool_shed.util import xml_util from galaxy.model.orm import and_ from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import tool_panel_manager log = logging.getLogger( __name__ ) @@ -80,19 +80,19 @@ repository.deleted = False repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools_for_display_in_tool_panel: + tpm = tool_panel_manager.ToolPanelManager( self.app ) metadata = repository.metadata repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata ) # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] - tool_util.add_to_tool_panel( self.app, - repository.name, - repository_clone_url, - repository.installed_changeset_revision, - repository_tools_tups, - repository.owner, - shed_tool_conf, - tool_panel_dict, - new_install=False ) + tpm.add_to_tool_panel( repository.name, + repository_clone_url, + repository.installed_changeset_revision, + repository_tools_tups, + repository.owner, + shed_tool_conf, + tool_panel_dict, + new_install=False ) if repository.includes_data_managers: tp, data_manager_relative_install_dir = repository.get_tool_relative_path( self.app ) # Hack to add repository.name here, which is actually the root of the installed repository diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -3,6 +3,7 @@ from galaxy import util from galaxy.util import inflector +from galaxy.web.form_builder import SelectField from tool_shed.metadata import metadata_generator @@ -19,6 +20,32 @@ super( InstalledRepositoryMetadataManager, self ).__init__( app ) self.app = app + def build_repository_ids_select_field( self, name='repository_ids', multiple=True, display='checkboxes' ): + """Generate the current list of repositories for resetting metadata.""" + repositories_select_field = SelectField( name=name, multiple=multiple, display=display ) + query = self.get_query_for_setting_metadata_on_repositories( order=True ) + for repository in query: + owner = str( repository.owner ) + option_label = '%s (%s)' % ( str( repository.name ), owner ) + option_value = '%s' % self.app.security.encode_id( repository.id ) + repositories_select_field.add_option( option_label, option_value ) + return repositories_select_field + + def get_query_for_setting_metadata_on_repositories( self, order=True ): + """ + Return a query containing repositories for resetting metadata. The order parameter + is used for displaying the list of repositories ordered alphabetically for display on + a page. When called from the Galaxy API, order is False. + """ + if order: + return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ + .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) \ + .order_by( self.app.install_model.ToolShedRepository.table.c.name, + self.app.install_model.ToolShedRepository.table.c.owner ) + else: + return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ + .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) + def reset_all_metadata_on_installed_repository( self, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" invalid_file_tups = [] diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/galaxy_install/repair_repository_manager.py --- a/lib/tool_shed/galaxy_install/repair_repository_manager.py +++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py @@ -5,13 +5,14 @@ from tool_shed.galaxy_install import install_manager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import tool_panel_manager from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import shed_util_common as suc from tool_shed.util import repository_maintenance_util from tool_shed.util import tool_dependency_util -from tool_shed.util import tool_util + class RepairRepositoryManager(): @@ -119,10 +120,11 @@ tool_panel_section_id = section_dict[ 'id' ] tool_panel_section_name = section_dict[ 'name' ] if tool_panel_section_id: + tpm = tool_panel_manager.ToolPanelManager( self.app ) tool_panel_section_key, tool_panel_section = \ - tool_util.get_or_create_tool_section( self.app.toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=tool_panel_section_name ) + tpm.get_or_create_tool_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=tool_panel_section_name ) else: tool_dependencies = None repo_info_dict = repository_maintenance_util.create_repo_info_dict( app=self.app, @@ -156,15 +158,17 @@ log.debug( error_message ) repair_dict [ repository.name ] = error_message elif repository.status not in [ self.app.install_model.ToolShedRepository.installation_status.INSTALLED ]: - shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( self.app, repository ) + shed_tool_conf, tool_path, relative_install_dir = \ + suc.get_tool_panel_config_tool_path_install_dir( self.app, repository ) # Reset the repository attributes to the New state for installation. if metadata: + tpm = tool_panel_manager.ToolPanelManager( self.app ) tool_section, tool_panel_section_key = \ - tool_util.handle_tool_panel_selection( self.app.toolbox, - metadata, - no_changes_checked=True, - tool_panel_section_id=None, - new_tool_panel_section_label=None ) + tpm.handle_tool_panel_selection( self.app.toolbox, + metadata, + no_changes_checked=True, + tool_panel_section_id=None, + new_tool_panel_section_label=None ) else: # The tools will be loaded outside of any sections in the tool panel. tool_panel_section_key = None diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py --- a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py +++ b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py @@ -10,11 +10,12 @@ from galaxy.util import asbool +from tool_shed.galaxy_install.tools import tool_panel_manager + from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import encoding_util from tool_shed.util import shed_util_common as suc -from tool_shed.util import tool_util log = logging.getLogger( __name__ ) @@ -216,19 +217,20 @@ if can_update_db_record: # The database record for the tool shed repository currently being processed can be updated. # Get the repository metadata to see where it was previously located in the tool panel. + tpm = tool_panel_manager.ToolPanelManager( self.app ) if repository_db_record and repository_db_record.metadata: tool_section, tool_panel_section_key = \ - tool_util.handle_tool_panel_selection( toolbox=self.app.toolbox, - metadata=repository_db_record.metadata, - no_changes_checked=no_changes_checked, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_selection( toolbox=self.app.toolbox, + metadata=repository_db_record.metadata, + no_changes_checked=no_changes_checked, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) else: # We're installing a new tool shed repository that does not yet have a database record. tool_panel_section_key, tool_section = \ - tool_util.handle_tool_panel_section( self.app.toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) tool_shed_repository = \ suc.create_or_update_tool_shed_repository( app=self.app, name=name, diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -14,6 +14,7 @@ from tool_shed.galaxy_install import install_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager +from tool_shed.galaxy_install.tools import tool_panel_manager from tool_shed.util import basic_util from tool_shed.util import common_util @@ -30,23 +31,31 @@ class ToolMigrationManager( object ): - def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies ): + def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, + install_dependencies ): """ - Check tool settings in tool_shed_install_config and install all repositories that are not already installed. The tool - panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. + Check tool settings in tool_shed_install_config and install all repositories + that are not already installed. The tool panel configuration file is the received + migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. """ self.app = app self.toolbox = self.app.toolbox self.migrated_tools_config = migrated_tools_config - # If install_dependencies is True but tool_dependency_dir is not set, do not attempt to install but print informative error message. + self.tpm = tool_panel_manager.ToolPanelManager( self.app ) + # If install_dependencies is True but tool_dependency_dir is not set, do not attempt + # to install but print informative error message. if install_dependencies and app.config.tool_dependency_dir is None: - message = 'You are attempting to install tool dependencies but do not have a value for "tool_dependency_dir" set in your universe_wsgi.ini ' - message += 'file. Set this location value to the path where you want tool dependencies installed and rerun the migration script.' + message = 'You are attempting to install tool dependencies but do not have a value ' + message += 'for "tool_dependency_dir" set in your universe_wsgi.ini file. Set this ' + message += 'location value to the path where you want tool dependencies installed and ' + message += 'rerun the migration script.' raise Exception( message ) - # Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml). + # Get the local non-shed related tool panel configs (there can be more than one, and the + # default name is tool_conf.xml). self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) - # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config. + # Set the location where the repositories will be installed by retrieving the tool_path + # setting from migrated_tools_config. tree, error_message = xml_util.parse_xml( migrated_tools_config ) if tree is None: print error_message @@ -66,21 +75,24 @@ self.tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url( self.tool_shed_url ) self.repository_owner = common_util.REPOSITORY_OWNER index, self.shed_config_dict = suc.get_shed_tool_conf_dict( app, self.migrated_tools_config ) - # Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in - # tool_conf.xml. If no tools associated with the migration stage are defined, no repositories will be installed on disk. - # The default behavior is that the tool shed is down. + # Since tool migration scripts can be executed any number of times, we need to + # make sure the appropriate tools are defined in tool_conf.xml. If no tools + # associated with the migration stage are defined, no repositories will be installed + # on disk. The default behavior is that the tool shed is down. tool_shed_accessible = False tool_panel_configs = common_util.get_non_shed_tool_panel_configs( app ) if tool_panel_configs: # The missing_tool_configs_dict contents are something like: # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} - tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, - tool_panel_configs, - latest_migration_script_number ) + tool_shed_accessible, missing_tool_configs_dict = \ + common_util.check_for_missing_tools( app, + tool_panel_configs, + latest_migration_script_number ) else: - # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but - # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in - # the database. + # It doesn't matter if the tool shed is accessible since there are no migrated + # tools defined in the local Galaxy instance, but we have to set the value of + # tool_shed_accessible to True so that the value of migrate_tools.version can + # be correctly set in the database. tool_shed_accessible = True missing_tool_configs_dict = odict() if tool_shed_accessible: @@ -93,15 +105,18 @@ if missing_tool_configs_dict: for proprietary_tool_conf in self.proprietary_tool_confs: # Create a backup of the tool configuration in the un-migrated state. - shutil.copy( proprietary_tool_conf, '%s-pre-stage-%04d' % ( proprietary_tool_conf, latest_migration_script_number ) ) + shutil.copy( proprietary_tool_conf, '%s-pre-stage-%04d' % ( proprietary_tool_conf, + latest_migration_script_number ) ) for repository_elem in root: # Make sure we have a valid repository tag. if self.__is_valid_repository_tag( repository_elem ): - # Get all repository dependencies for the repository defined by the current repository_elem. Repository dependency - # definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository - # dependency that contains a tool. The repository dependency can only contain items that are not loaded into the Galaxy - # tool panel (e.g., tool dependency definitions, custom datatypes, etc). This restriction must be followed down the - # entire dependency hierarchy. + # Get all repository dependencies for the repository defined by the + # current repository_elem. Repository dependency definitions contained + # in tool shed repositories with migrated tools must never define a + # relationship to a repository dependency that contains a tool. The + # repository dependency can only contain items that are not loaded into + # the Galaxy tool panel (e.g., tool dependency definitions, custom datatypes, + # etc). This restriction must be followed down the entire dependency hierarchy. name = repository_elem.get( 'name' ) changeset_revision = repository_elem.get( 'changeset_revision' ) tool_shed_accessible, repository_dependencies_dict = \ @@ -110,30 +125,38 @@ name, self.repository_owner, changeset_revision ) - # Make sure all repository dependency records exist (as tool_shed_repository table rows) in the Galaxy database. - created_tool_shed_repositories = self.create_or_update_tool_shed_repository_records( name, - changeset_revision, - repository_dependencies_dict ) + # Make sure all repository dependency records exist (as tool_shed_repository + # table rows) in the Galaxy database. + created_tool_shed_repositories = \ + self.create_or_update_tool_shed_repository_records( name, + changeset_revision, + repository_dependencies_dict ) # Order the repositories for proper installation. This process is similar to the # process used when installing tool shed repositories, but does not handle managing # tool panel sections and other components since repository dependency definitions # contained in tool shed repositories with migrated tools must never define a relationship # to a repository dependency that contains a tool. - ordered_tool_shed_repositories = self.order_repositories_for_installation( created_tool_shed_repositories, - repository_dependencies_dict ) + ordered_tool_shed_repositories = \ + self.order_repositories_for_installation( created_tool_shed_repositories, + repository_dependencies_dict ) for tool_shed_repository in ordered_tool_shed_repositories: - is_repository_dependency = self.__is_repository_dependency( name, changeset_revision, tool_shed_repository ) + is_repository_dependency = self.__is_repository_dependency( name, + changeset_revision, + tool_shed_repository ) self.install_repository( repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=is_repository_dependency ) else: - message = "\nNo tools associated with migration stage %s are defined in your " % str( latest_migration_script_number ) - message += "file%s named %s,\nso no repositories will be installed on disk.\n" % ( plural, file_names ) + message = "\nNo tools associated with migration stage %s are defined in your " % \ + str( latest_migration_script_number ) + message += "file%s named %s,\nso no repositories will be installed on disk.\n" % \ + ( plural, file_names ) print message else: - message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % str( latest_migration_script_number ) + message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % \ + str( latest_migration_script_number ) message += "Try again later.\n" print message @@ -354,16 +377,21 @@ repo_install_dir = relative_install_dir if not is_repository_dependency: for tool_elem in repository_elem: - # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> + # The tool_elem looks something like this: + # <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> tool_config = tool_elem.get( 'file' ) guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems. is_displayed, tool_sections = self.get_containing_tool_sections( tool_config ) if is_displayed: tool_panel_dict_for_tool_config = \ - tool_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) + self.tpm.generate_tool_panel_dict_for_tool_config( guid, + tool_config, + tool_sections=tool_sections ) # The tool-panel_dict has the following structure. - # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, + # {<Tool guid> : [{ tool_config : <tool_config_file>, + # id: <ToolSection id>, + # version : <ToolSection version>, # name : <TooSection name>}]} for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v @@ -433,15 +461,14 @@ tool_path=self.tool_path, sample_files_copied=sample_files_copied ) if not is_repository_dependency: - tool_util.add_to_tool_panel( self.app, - tool_shed_repository.name, - repository_clone_url, - tool_shed_repository.installed_changeset_revision, - repository_tools_tups, - self.repository_owner, - self.migrated_tools_config, - tool_panel_dict=tool_panel_dict_for_display, - new_install=True ) + self.tpm.add_to_tool_panel( tool_shed_repository.name, + repository_clone_url, + tool_shed_repository.installed_changeset_revision, + repository_tools_tups, + self.repository_owner, + self.migrated_tools_config, + tool_panel_dict=tool_panel_dict_for_display, + new_install=True ) if install_dependencies and tool_dependencies and has_tool_dependencies: # Install tool dependencies. suc.update_tool_shed_repository_status( self.app, diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/galaxy_install/tools/tool_panel_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/tools/tool_panel_manager.py @@ -0,0 +1,465 @@ +import logging +import os + +import galaxy.tools +from galaxy.tools.search import ToolBoxSearch +from xml.etree import ElementTree as XmlET + +from tool_shed.util import basic_util +from tool_shed.util import common_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util + +log = logging.getLogger( __name__ ) + + +class ToolPanelManager( object ): + + def __init__( self, app ): + self.app = app + + def add_to_shed_tool_config( self, shed_tool_conf_dict, elem_list ): + # A tool shed repository is being installed so change the shed_tool_conf file. Parse the + # config file to generate the entire list of config_elems instead of using the in-memory list + # since it will be a subset of the entire list if one or more repositories have been deactivated. + shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] + tool_path = shed_tool_conf_dict[ 'tool_path' ] + config_elems = [] + tree, error_message = xml_util.parse_xml( shed_tool_conf ) + if tree: + root = tree.getroot() + for elem in root: + config_elems.append( elem ) + # Add the elements to the in-memory list of config_elems. + for elem_entry in elem_list: + config_elems.append( elem_entry ) + # Persist the altered shed_tool_config file. + suc.config_elems_to_xml_file( self.app, config_elems, shed_tool_conf, tool_path ) + + def add_to_tool_panel( self, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, owner, + shed_tool_conf, tool_panel_dict, new_install=True ): + """A tool shed repository is being installed or updated so handle tool panel alterations accordingly.""" + # We need to change the in-memory version and the file system version of the shed_tool_conf file. + index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( self.app, shed_tool_conf ) + tool_path = shed_tool_conf_dict[ 'tool_path' ] + # Generate the list of ElementTree Element objects for each section or tool. + elem_list = self.generate_tool_panel_elem_list( repository_name, + repository_clone_url, + changeset_revision, + tool_panel_dict, + repository_tools_tups, + owner=owner ) + if new_install: + # Add the new elements to the shed_tool_conf file on disk. + self.add_to_shed_tool_config( shed_tool_conf_dict, elem_list ) + # Use the new elements to add entries to the + config_elems = shed_tool_conf_dict[ 'config_elems' ] + for config_elem in elem_list: + # Add the new elements to the in-memory list of config_elems. + config_elems.append( config_elem ) + # Load the tools into the in-memory tool panel. + if config_elem.tag == 'section': + self.app.toolbox.load_section_tag_set( config_elem, tool_path, load_panel_dict=True ) + elif config_elem.tag == 'workflow': + self.app.toolbox.load_workflow_tag_set( config_elem, + self.app.toolbox.tool_panel, + self.app.toolbox.integrated_tool_panel, + load_panel_dict=True ) + elif config_elem.tag == 'tool': + guid = config_elem.get( 'guid' ) + self.app.toolbox.load_tool_tag_set( config_elem, + self.app.toolbox.tool_panel, + self.app.toolbox.integrated_tool_panel, + tool_path, + load_panel_dict=True, + guid=guid ) + # Replace the old list of in-memory config_elems with the new list for this shed_tool_conf_dict. + shed_tool_conf_dict[ 'config_elems' ] = config_elems + self.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict + if self.app.config.update_integrated_tool_panel: + # Write the current in-memory version of the integrated_tool_panel.xml file to disk. + self.app.toolbox.write_integrated_tool_panel_config_file() + self.app.toolbox_search = ToolBoxSearch( self.app.toolbox ) + + def generate_tool_panel_dict_for_new_install( self, tool_dicts, tool_section=None ): + """ + When installing a repository that contains tools, all tools must currently be defined + within the same tool section in the tool panel or outside of any sections. + """ + tool_panel_dict = {} + if tool_section: + section_id = tool_section.id + section_name = tool_section.name + section_version = tool_section.version or '' + else: + section_id = '' + section_name = '' + section_version = '' + for tool_dict in tool_dicts: + if tool_dict.get( 'add_to_tool_panel', True ): + guid = tool_dict[ 'guid' ] + tool_config = tool_dict[ 'tool_config' ] + tool_section_dict = dict( tool_config=tool_config, id=section_id, name=section_name, version=section_version ) + if guid in tool_panel_dict: + tool_panel_dict[ guid ].append( tool_section_dict ) + else: + tool_panel_dict[ guid ] = [ tool_section_dict ] + return tool_panel_dict + + def generate_tool_panel_dict_for_tool_config( self, guid, tool_config, tool_sections=None ): + """ + Create a dictionary of the following type for a single tool config file name. + The intent is to call this method for every tool config in a repository and + append each of these as entries to a tool panel dictionary for the repository. + This enables each tool to be loaded into a different section in the tool panel. + {<Tool guid> : + [{ tool_config : <tool_config_file>, + id: <ToolSection id>, + version : <ToolSection version>, + name : <TooSection name>}]} + """ + tool_panel_dict = {} + file_name = basic_util.strip_path( tool_config ) + tool_section_dicts = self. generate_tool_section_dicts( tool_config=file_name, + tool_sections=tool_sections ) + tool_panel_dict[ guid ] = tool_section_dicts + return tool_panel_dict + + def generate_tool_panel_elem_list( self, repository_name, repository_clone_url, changeset_revision, + tool_panel_dict, repository_tools_tups, owner='' ): + """Generate a list of ElementTree Element objects for each section or tool.""" + elem_list = [] + tool_elem = None + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) + if not owner: + owner = suc.get_repository_owner( cleaned_repository_clone_url ) + tool_shed = cleaned_repository_clone_url.split( '/repos/' )[ 0 ].rstrip( '/' ) + for guid, tool_section_dicts in tool_panel_dict.items(): + for tool_section_dict in tool_section_dicts: + tool_section = None + inside_section = False + section_in_elem_list = False + if tool_section_dict[ 'id' ]: + inside_section = True + # Create a new section element only if we haven't already created it. + for index, elem in enumerate( elem_list ): + if elem.tag == 'section': + section_id = elem.get( 'id', None ) + if section_id == tool_section_dict[ 'id' ]: + section_in_elem_list = True + tool_section = elem + break + if tool_section is None: + tool_section = self.generate_tool_section_element_from_dict( tool_section_dict ) + # Find the tuple containing the current guid from the list of repository_tools_tups. + for repository_tool_tup in repository_tools_tups: + tool_file_path, tup_guid, tool = repository_tool_tup + if tup_guid == guid: + break + if inside_section: + tool_elem = suc.generate_tool_elem( tool_shed, + repository_name, + changeset_revision, + owner, + tool_file_path, + tool, + tool_section ) + else: + tool_elem = suc.generate_tool_elem( tool_shed, + repository_name, + changeset_revision, + owner, + tool_file_path, + tool, + None ) + if inside_section: + if section_in_elem_list: + elem_list[ index ] = tool_section + else: + elem_list.append( tool_section ) + else: + elem_list.append( tool_elem ) + return elem_list + + def generate_tool_section_dicts( self, tool_config=None, tool_sections=None ): + tool_section_dicts = [] + if tool_config is None: + tool_config = '' + if tool_sections: + for tool_section in tool_sections: + # The value of tool_section will be None if the tool is displayed outside + # of any sections in the tool panel. + if tool_section: + section_id = tool_section.id or '' + section_version = tool_section.version or '' + section_name = tool_section.name or '' + else: + section_id = '' + section_version = '' + section_name = '' + tool_section_dicts.append( dict( tool_config=tool_config, + id=section_id, + version=section_version, + name=section_name ) ) + else: + tool_section_dicts.append( dict( tool_config=tool_config, id='', version='', name='' ) ) + return tool_section_dicts + + def generate_tool_section_element_from_dict( self, tool_section_dict ): + # The value of tool_section_dict looks like the following. + # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} + if tool_section_dict[ 'id' ]: + # Create a new tool section. + tool_section = XmlET.Element( 'section' ) + tool_section.attrib[ 'id' ] = tool_section_dict[ 'id' ] + tool_section.attrib[ 'name' ] = tool_section_dict[ 'name' ] + tool_section.attrib[ 'version' ] = tool_section_dict[ 'version' ] + else: + tool_section = None + return tool_section + + def get_or_create_tool_section( self, toolbox, tool_panel_section_id, new_tool_panel_section_label=None ): + tool_panel_section_key = str( tool_panel_section_id ) + if tool_panel_section_key in toolbox.tool_panel: + # Appending a tool to an existing section in toolbox.tool_panel + tool_section = toolbox.tool_panel[ tool_panel_section_key ] + log.debug( "Appending to tool panel section: %s" % str( tool_section.name ) ) + else: + # Appending a new section to toolbox.tool_panel + if new_tool_panel_section_label is None: + # This might add an ugly section label to the tool panel, but, oh well... + new_tool_panel_section_label = tool_panel_section_id + elem = XmlET.Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section_label + elem.attrib[ 'id' ] = tool_panel_section_id + elem.attrib[ 'version' ] = '' + tool_section = galaxy.tools.ToolSection( elem ) + toolbox.tool_panel[ tool_panel_section_key ] = tool_section + log.debug( "Loading new tool panel section: %s" % str( tool_section.name ) ) + return tool_panel_section_key, tool_section + + def handle_tool_panel_section( self, toolbox, tool_panel_section_id=None, new_tool_panel_section_label=None ): + """Return a ToolSection object retrieved from the current in-memory tool_panel.""" + # If tool_panel_section_id is received, the section exists in the tool panel. In this + # case, the value of the received tool_panel_section_id must be the id retrieved from a + # tool panel config (e.g., tool_conf.xml, which may have getext). If new_tool_panel_section_label + # is received, a new section will be added to the tool panel. + if new_tool_panel_section_label: + section_id = str( new_tool_panel_section_label.lower().replace( ' ', '_' ) ) + tool_panel_section_key, tool_section = \ + self.get_or_create_tool_section( toolbox, + tool_panel_section_id=section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + elif tool_panel_section_id: + tool_panel_section_key = str( tool_panel_section_id ) + tool_section = toolbox.tool_panel[ tool_panel_section_key ] + else: + return None, None + return tool_panel_section_key, tool_section + + def handle_tool_panel_selection( self, toolbox, metadata, no_changes_checked, tool_panel_section_id, + new_tool_panel_section_label ): + """ + Handle the selected tool panel location for loading tools included in tool shed + repositories when installing or reinstalling them. + """ + # Get the location in the tool panel in which each tool was originally loaded. + tool_section = None + tool_panel_section_key = None + if 'tools' in metadata: + # This forces everything to be loaded into the same section (or no section) + # in the tool panel. + if no_changes_checked: + # Make sure the no_changes check box overrides the new_tool_panel_section_label + # if the user checked the check box and entered something into the field. + new_tool_panel_section_label = None + if 'tool_panel_section' in metadata: + tool_panel_dict = metadata[ 'tool_panel_section' ] + if not tool_panel_dict: + tool_panel_dict = self.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + else: + tool_panel_dict = self.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + if tool_panel_dict: + # The tool_panel_dict is empty when tools exist but are not installed into a tool panel section. + tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dict = tool_section_dicts[ 0 ] + original_section_id = tool_section_dict[ 'id' ] + original_section_name = tool_section_dict[ 'name' ] + if original_section_id: + tool_panel_section_key, tool_section = \ + self.get_or_create_tool_section( toolbox, + tool_panel_section_id=original_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + else: + # The user elected to change the tool panel section to contain the tools. + tool_panel_section_key, tool_section = \ + self.handle_tool_panel_section( toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + return tool_section, tool_panel_section_key + + def remove_from_shed_tool_config( self, shed_tool_conf_dict, guids_to_remove ): + # A tool shed repository is being uninstalled so change the shed_tool_conf file. + # Parse the config file to generate the entire list of config_elems instead of + # using the in-memory list since it will be a subset of the entire list if one + # or more repositories have been deactivated. + shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] + tool_path = shed_tool_conf_dict[ 'tool_path' ] + config_elems = [] + tree, error_message = xml_util.parse_xml( shed_tool_conf ) + if tree: + root = tree.getroot() + for elem in root: + config_elems.append( elem ) + config_elems_to_remove = [] + for config_elem in config_elems: + if config_elem.tag == 'section': + tool_elems_to_remove = [] + for tool_elem in config_elem: + if tool_elem.get( 'guid' ) in guids_to_remove: + tool_elems_to_remove.append( tool_elem ) + for tool_elem in tool_elems_to_remove: + # Remove all of the appropriate tool sub-elements from the section element. + config_elem.remove( tool_elem ) + if len( config_elem ) < 1: + # Keep a list of all empty section elements so they can be removed. + config_elems_to_remove.append( config_elem ) + elif config_elem.tag == 'tool': + if config_elem.get( 'guid' ) in guids_to_remove: + config_elems_to_remove.append( config_elem ) + for config_elem in config_elems_to_remove: + config_elems.remove( config_elem ) + # Persist the altered in-memory version of the tool config. + suc.config_elems_to_xml_file( self.app, config_elems, shed_tool_conf, tool_path ) + + def remove_from_tool_panel( self, repository, shed_tool_conf, uninstall ): + """ + A tool shed repository is being deactivated or uninstalled, so handle tool panel + alterations accordingly. + """ + # Determine where the tools are currently defined in the tool panel and store this + # information so the tools can be displayed in the same way when the repository is + # activated or reinstalled. + tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( self.app, repository ) + repository.metadata[ 'tool_panel_section' ] = tool_panel_dict + self.app.install_model.context.add( repository ) + self.app.install_model.context.flush() + # Create a list of guids for all tools that will be removed from the in-memory tool panel + # and config file on disk. + guids_to_remove = [ k for k in tool_panel_dict.keys() ] + # Remove the tools from the toolbox's tools_by_id dictionary. + for guid_to_remove in guids_to_remove: + if guid_to_remove in self.app.toolbox.tools_by_id: + del self.app.toolbox.tools_by_id[ guid_to_remove ] + index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( self.app, shed_tool_conf ) + if uninstall: + # Remove from the shed_tool_conf file on disk. + self.remove_from_shed_tool_config( shed_tool_conf_dict, guids_to_remove ) + config_elems = shed_tool_conf_dict[ 'config_elems' ] + config_elems_to_remove = [] + for config_elem in config_elems: + if config_elem.tag == 'section': + # Get the section key for the in-memory tool panel. + section_key = str( config_elem.get( "id" ) ) + # Generate the list of tool elements to remove. + tool_elems_to_remove = [] + for tool_elem in config_elem: + if tool_elem.get( 'guid' ) in guids_to_remove: + tool_elems_to_remove.append( tool_elem ) + for tool_elem in tool_elems_to_remove: + if tool_elem in config_elem: + # Remove the tool sub-element from the section element. + config_elem.remove( tool_elem ) + # Remove the tool from the section in the in-memory tool panel. + if section_key in self.app.toolbox.tool_panel: + tool_section = self.app.toolbox.tool_panel[ section_key ] + guid = tool_elem.get( 'guid' ) + tool_key = 'tool_%s' % str( guid ) + # Get the list of versions of this tool that are currently available in the toolbox. + available_tool_versions = self.app.toolbox.get_loaded_tools_by_lineage( guid ) + if tool_key in tool_section.elems: + if available_tool_versions: + available_tool_versions.reverse() + replacement_tool_key = None + replacement_tool_version = None + # Since we are going to remove the tool from the section, replace it with the + # newest loaded version of the tool. + for available_tool_version in available_tool_versions: + available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() + if available_tool_version.id in tool_section.elems.keys() or section_key == available_tool_section_id: + replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) + replacement_tool_version = available_tool_version + break + if replacement_tool_key and replacement_tool_version: + # Get the index of the tool_key in the tool_section. + for tool_section_elems_index, key in enumerate( tool_section.elems.keys() ): + if key == tool_key: + break + # Remove the tool from the tool section. + del tool_section.elems[ tool_key ] + # Add the replacement tool at the same location in the tool section. + tool_section.elems.insert( tool_section_elems_index, + replacement_tool_key, + replacement_tool_version ) + else: + del tool_section.elems[ tool_key ] + else: + del tool_section.elems[ tool_key ] + if uninstall: + # Remove the tool from the section in the in-memory integrated tool panel. + if section_key in self.app.toolbox.integrated_tool_panel: + tool_section = self.app.toolbox.integrated_tool_panel[ section_key ] + tool_key = 'tool_%s' % str( tool_elem.get( 'guid' ) ) + if tool_key in tool_section.elems: + del tool_section.elems[ tool_key ] + if len( config_elem ) < 1: + # Keep a list of all empty section elements so they can be removed. + config_elems_to_remove.append( config_elem ) + elif config_elem.tag == 'tool': + guid = config_elem.get( 'guid' ) + if guid in guids_to_remove: + tool_key = 'tool_%s' % str( config_elem.get( 'guid' ) ) + # Get the list of versions of this tool that are currently available in the toolbox. + available_tool_versions = self.app.toolbox.get_loaded_tools_by_lineage( guid ) + if tool_key in self.app.toolbox.tool_panel: + if available_tool_versions: + available_tool_versions.reverse() + replacement_tool_key = None + replacement_tool_version = None + # Since we are going to remove the tool from the section, replace it with + # the newest loaded version of the tool. + for available_tool_version in available_tool_versions: + available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() + if available_tool_version.id in self.app.toolbox.tool_panel.keys() or not available_tool_section_id: + replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) + replacement_tool_version = available_tool_version + break + if replacement_tool_key and replacement_tool_version: + # Get the index of the tool_key in the tool_section. + for tool_panel_index, key in enumerate( self.app.toolbox.tool_panel.keys() ): + if key == tool_key: + break + # Remove the tool from the tool panel. + del self.app.toolbox.tool_panel[ tool_key ] + # Add the replacement tool at the same location in the tool panel. + self.app.toolbox.tool_panel.insert( tool_panel_index, + replacement_tool_key, + replacement_tool_version ) + else: + del self.app.toolbox.tool_panel[ tool_key ] + else: + del self.app.toolbox.tool_panel[ tool_key ] + if uninstall: + if tool_key in self.app.toolbox.integrated_tool_panel: + del self.app.toolbox.integrated_tool_panel[ tool_key ] + config_elems_to_remove.append( config_elem ) + for config_elem in config_elems_to_remove: + # Remove the element from the in-memory list of elements. + config_elems.remove( config_elem ) + # Update the config_elems of the in-memory shed_tool_conf_dict. + shed_tool_conf_dict[ 'config_elems' ] = config_elems + self.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict + self.app.toolbox_search = ToolBoxSearch( self.app.toolbox ) + if uninstall and self.app.config.update_integrated_tool_panel: + # Write the current in-memory version of the integrated_tool_panel.xml file to disk. + self.app.toolbox.write_integrated_tool_panel_config_file() diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -10,6 +10,7 @@ from galaxy.web import url_for from tool_shed.repository_types import util as rt_util +from tool_shed.tools import tool_validator from tool_shed.util import basic_util from tool_shed.util import common_util @@ -128,7 +129,7 @@ log.debug( 'Loaded Data Manager tool_files: %s' % ( tool_file ) ) return metadata_dict - def generate_datatypes_metadata( self, repository, repository_clone_url, repository_files_dir, datatypes_config, + def generate_datatypes_metadata( self, tv, repository, repository_clone_url, repository_files_dir, datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed datatypes_config.""" tree, error_message = xml_util.parse_xml( datatypes_config ) @@ -178,7 +179,7 @@ tool_config_path = hg_util.get_config_from_disk( tool_config, repository_files_dir ) full_path = os.path.abspath( tool_config_path ) tool, valid, error_message = \ - tool_util.load_tool_from_config( self.app, self.app.security.encode_id( repository.id ), full_path ) + tv.load_tool_from_config( self.app.security.encode_id( repository.id ), full_path ) if tool is None: guid = None else: @@ -245,6 +246,7 @@ tool_data_table_conf.xml.sample file, in which case the entries should ultimately be persisted to the file referred to by self.app.config.shed_tool_data_table_config. """ + tv = tool_validator.ToolValidator( self.app ) if shed_config_dict is None: shed_config_dict = {} if updating_installed_repository: @@ -290,7 +292,8 @@ # Handle proprietary datatypes, if any. datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) if datatypes_config: - metadata_dict = self.generate_datatypes_metadata( repository, + metadata_dict = self.generate_datatypes_metadata( tv, + repository, repository_clone_url, files_dir, datatypes_config, @@ -361,20 +364,18 @@ is_tool = element_tree_root.tag == 'tool' if is_tool: tool, valid, error_message = \ - tool_util.load_tool_from_config( self.app, - self.app.security.encode_id( repository.id ), - full_path ) + tv.load_tool_from_config( self.app.security.encode_id( repository.id ), + full_path ) if tool is None: if not valid: invalid_tool_configs.append( name ) invalid_file_tups.append( ( name, error_message ) ) else: invalid_files_and_errors_tups = \ - tool_util.check_tool_input_params( self.app, - files_dir, - name, - tool, - sample_file_copy_paths ) + tv.check_tool_input_params( files_dir, + name, + tool, + sample_file_copy_paths ) can_set_metadata = True for tup in invalid_files_and_errors_tups: if name in tup: diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/metadata/repository_metadata_manager.py --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -2,11 +2,13 @@ import os import tempfile +from galaxy import util from galaxy.util import inflector -from galaxy import util +from galaxy.web.form_builder import SelectField from tool_shed.metadata import metadata_generator from tool_shed.repository_types.metadata import TipOnly +from tool_shed.repository_types import util as rt_util from tool_shed.util import basic_util from tool_shed.util import common_util @@ -20,9 +22,10 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app ): + def __init__( self, app, user ): super( RepositoryMetadataManager, self ).__init__( app ) self.app = app + self.user = user # Repository metadata comparisons for changeset revisions. self.EQUAL = 'equal' self.NO_METADATA = 'no metadata' @@ -47,6 +50,18 @@ self.sa_session.add( repository_metadata ) self.sa_session.flush() + def build_repository_ids_select_field( self, name='repository_ids', multiple=True, display='checkboxes', + my_writable=False ): + """Generate the current list of repositories for resetting metadata.""" + repositories_select_field = SelectField( name=name, multiple=multiple, display=display ) + query = self.get_query_for_setting_metadata_on_repositories( my_writable=my_writable, order=True ) + for repository in query: + owner = str( repository.user.username ) + option_label = '%s (%s)' % ( str( repository.name ), owner ) + option_value = '%s' % self.app.security.encode_id( repository.id ) + repositories_select_field.add_option( option_label, option_value ) + return repositories_select_field + def clean_repository_metadata( self, id, changeset_revisions ): # Delete all repository_metadata records associated with the repository that have # a changeset_revision that is not in changeset_revisions. We sometimes see multiple @@ -458,6 +473,54 @@ # The tool did not change through all of the changeset revisions. return old_id + def get_query_for_setting_metadata_on_repositories( self, my_writable=False, order=True ): + """ + Return a query containing repositories for resetting metadata. The order parameter + is used for displaying the list of repositories ordered alphabetically for display on + a page. When called from the Tool Shed API, order is False. + """ + # When called from the Tool Shed API, the metadata is reset on all repositories of types + # repository_suite_definition and tool_dependency_definition in addition to other selected + # repositories. + if my_writable: + username = self.user.username + clause_list = [] + for repository in self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.deleted == False ): + # Always reset metadata on all repositories of types repository_suite_definition and + # tool_dependency_definition. + if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION ]: + clause_list.append( self.app.model.Repository.table.c.id == repository.id ) + else: + allow_push = repository.allow_push( self.app ) + if allow_push: + # Include all repositories that are writable by the current user. + allow_push_usernames = allow_push.split( ',' ) + if username in allow_push_usernames: + clause_list.append( self.app.model.Repository.table.c.id == repository.id ) + if clause_list: + if order: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( or_( *clause_list ) ) \ + .order_by( self.app.model.Repository.table.c.name, + self.app.model.Repository.table.c.user_id ) + else: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( or_( *clause_list ) ) + else: + # Return an empty query. + return self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.id == -1 ) + else: + if order: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.deleted == False ) \ + .order_by( self.app.model.Repository.table.c.name, + self.app.model.Repository.table.c.user_id ) + else: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.deleted == False ) + def new_datatypes_metadata_required( self, repository_metadata, metadata_dict ): """ Compare the last saved metadata for each datatype in the repository with the new metadata @@ -732,13 +795,13 @@ # repository_metadata table record is not needed. return False - def reset_all_metadata_on_repository_in_tool_shed( self, user, id ): + def reset_all_metadata_on_repository_in_tool_shed( self, id ): """Reset all metadata on a single repository in a tool shed.""" repository = suc.get_repository_in_tool_shed( self.app, id ) log.debug( "Resetting all metadata on repository: %s" % repository.name ) repo_dir = repository.repo_path( self.app ) repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) # The list of changeset_revisions refers to repository_metadata records that have been created # or updated. When the following loop completes, we'll delete all repository_metadata records # for this repository that do not have a changeset_revision value in this list. @@ -875,7 +938,7 @@ self.sa_session.add( repository_metadata ) self.sa_session.flush() - def reset_metadata_on_selected_repositories( self, user, **kwd ): + def reset_metadata_on_selected_repositories( self, **kwd ): """ Inspect the repository changelog to reset metadata for all appropriate changeset revisions. This method is called from both Galaxy and the Tool Shed. @@ -892,7 +955,7 @@ repository = suc.get_repository_in_tool_shed( self.app, repository_id ) owner = str( repository.user.username ) invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_repository_in_tool_shed( user, repository_id ) + self.reset_all_metadata_on_repository_in_tool_shed( self.user, repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, invalid_file_tups, @@ -918,7 +981,7 @@ status = 'error' return message, status - def set_repository_metadata( self, host, user, repository, content_alert_str='', **kwd ): + def set_repository_metadata( self, host, repository, content_alert_str='', **kwd ): """ Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems. @@ -926,7 +989,7 @@ message = '' status = 'done' encoded_id = self.app.security.encode_id( repository.id ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) repo_dir = repository.repo_path( self.app ) repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) metadata_dict, invalid_file_tups = \ @@ -1027,10 +1090,9 @@ tool_util.reset_tool_data_tables( self.app ) return message, status - def set_repository_metadata_due_to_new_tip( self, host, user, repository, content_alert_str=None, **kwd ): + def set_repository_metadata_due_to_new_tip( self, host, repository, content_alert_str=None, **kwd ): """Set metadata on the repository tip in the tool shed.""" error_message, status = self.set_repository_metadata( host, - user, repository, content_alert_str=content_alert_str, **kwd ) diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/tools/tool_validator.py --- /dev/null +++ b/lib/tool_shed/tools/tool_validator.py @@ -0,0 +1,328 @@ +import filecmp +import logging +import os +import tempfile + +from galaxy.tools import parameters +from galaxy.tools.parameters import dynamic_options + +from tool_shed.util import basic_util +from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import tool_util + +log = logging.getLogger( __name__ ) + + +class ToolValidator( object ): + + def __init__( self, app ): + self.app = app + + def can_use_tool_config_disk_file( self, repository, repo, file_path, changeset_revision ): + """ + Determine if repository's tool config file on disk can be used. This method + is restricted to tool config files since, with the exception of tool config + files, multiple files with the same name will likely be in various directories + in the repository and we're comparing file names only (not relative paths). + """ + if not file_path or not os.path.exists( file_path ): + # The file no longer exists on disk, so it must have been deleted at some previous + # point in the change log. + return False + if changeset_revision == repository.tip( self.app ): + return True + file_name = basic_util.strip_path( file_path ) + latest_version_of_file = \ + self.get_latest_tool_config_revision_from_repository_manifest( repo, file_name, changeset_revision ) + can_use_disk_file = filecmp.cmp( file_path, latest_version_of_file ) + try: + os.unlink( latest_version_of_file ) + except: + pass + return can_use_disk_file + + def check_tool_input_params( self, repo_dir, tool_config_name, tool, sample_files ): + """ + Check all of the tool's input parameters, looking for any that are dynamically + generated using external data files to make sure the files exist. + """ + invalid_files_and_errors_tups = [] + correction_msg = '' + for input_param in tool.input_params: + if isinstance( input_param, parameters.basic.SelectToolParameter ) and input_param.is_dynamic: + # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, + # make sure all requirements exist. + options = input_param.dynamic_options or input_param.options + if options and isinstance( options, dynamic_options.DynamicOptions ): + if options.tool_data_table or options.missing_tool_data_table_name: + # Make sure the repository contains a tool_data_table_conf.xml.sample file. + sample_tool_data_table_conf = hg_util.get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir ) + if sample_tool_data_table_conf: + error, correction_msg = \ + tool_util.handle_sample_tool_data_table_conf_file( self.app, sample_tool_data_table_conf ) + if error: + invalid_files_and_errors_tups.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) ) + else: + options.missing_tool_data_table_name = None + else: + correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " + correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " + correction_msg += "that includes the required entry to correct this error.<br/>" + invalid_tup = ( tool_config_name, correction_msg ) + if invalid_tup not in invalid_files_and_errors_tups: + invalid_files_and_errors_tups.append( invalid_tup ) + if options.index_file or options.missing_index_file: + # Make sure the repository contains the required xxx.loc.sample file. + index_file = options.index_file or options.missing_index_file + index_file_name = basic_util.strip_path( index_file ) + sample_found = False + for sample_file in sample_files: + sample_file_name = basic_util.strip_path( sample_file ) + if sample_file_name == '%s.sample' % index_file_name: + options.index_file = index_file_name + options.missing_index_file = None + if options.tool_data_table: + options.tool_data_table.missing_index_file = None + sample_found = True + break + if not sample_found: + correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file_name ) + correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % \ + str( index_file_name ) + invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) + return invalid_files_and_errors_tups + + def concat_messages( self, msg1, msg2 ): + if msg1: + if msg2: + message = '%s %s' % ( msg1, msg2 ) + else: + message = msg1 + elif msg2: + message = msg2 + else: + message = '' + return message + + def copy_disk_sample_files_to_dir( self, repo_files_dir, dest_path ): + """ + Copy all files currently on disk that end with the .sample extension to the + directory to which dest_path refers. + """ + sample_files = [] + for root, dirs, files in os.walk( repo_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name.endswith( '.sample' ): + relative_path = os.path.join( root, name ) + tool_util.copy_sample_file( self.app, relative_path, dest_path=dest_path ) + sample_files.append( name ) + return sample_files + + def get_latest_tool_config_revision_from_repository_manifest( self, repo, filename, changeset_revision ): + """ + Get the latest revision of a tool config file named filename from the repository + manifest up to the value of changeset_revision. This method is restricted to tool_config + files rather than any file since it is likely that, with the exception of tool config + files, multiple files will have the same name in various directories within the repository. + """ + stripped_filename = basic_util.strip_path( filename ) + for changeset in hg_util.reversed_upper_bounded_changelog( repo, changeset_revision ): + manifest_ctx = repo.changectx( changeset ) + for ctx_file in manifest_ctx.files(): + ctx_file_name = basic_util.strip_path( ctx_file ) + if ctx_file_name == stripped_filename: + try: + fctx = manifest_ctx[ ctx_file ] + except LookupError: + # The ctx_file may have been moved in the change set. For example, + # 'ncbi_blastp_wrapper.xml' was moved to 'tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml', + # so keep looking for the file until we find the new location. + continue + fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-gltcrfrm" ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return tmp_filename + return None + + def get_list_of_copied_sample_files( self, repo, ctx, dir ): + """ + Find all sample files (files in the repository with the special .sample extension) + in the reversed repository manifest up to ctx. Copy each discovered file to dir and + return the list of filenames. If a .sample file was added in a changeset and then + deleted in a later changeset, it will be returned in the deleted_sample_files list. + The caller will set the value of app.config.tool_data_path to dir in order to load + the tools and generate metadata for them. + """ + deleted_sample_files = [] + sample_files = [] + for changeset in hg_util.reversed_upper_bounded_changelog( repo, ctx ): + changeset_ctx = repo.changectx( changeset ) + for ctx_file in changeset_ctx.files(): + ctx_file_name = basic_util.strip_path( ctx_file ) + # If we decide in the future that files deleted later in the changelog should + # not be used, we can use the following if statement. if ctx_file_name.endswith( '.sample' ) + # and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files: + if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files: + fctx = hg_util.get_file_context_from_ctx( changeset_ctx, ctx_file ) + if fctx in [ 'DELETED' ]: + # Since the possibly future used if statement above is commented out, the + # same file that was initially added will be discovered in an earlier changeset + # in the change log and fall through to the else block below. In other words, + # if a file named blast2go.loc.sample was added in change set 0 and then deleted + # in changeset 3, the deleted file in changeset 3 will be handled here, but the + # later discovered file in changeset 0 will be handled in the else block below. + # In this way, the file contents will always be found for future tools even though + # the file was deleted. + if ctx_file_name not in deleted_sample_files: + deleted_sample_files.append( ctx_file_name ) + else: + sample_files.append( ctx_file_name ) + tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) ) + fh = open( tmp_ctx_file_name, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return sample_files, deleted_sample_files + + def handle_sample_files_and_load_tool_from_disk( self, repo_files_dir, repository_id, tool_config_filepath, work_dir ): + """ + Copy all sample files from disk to a temporary directory since the sample files may + be in multiple directories. + """ + message = '' + sample_files = self.copy_disk_sample_files_to_dir( repo_files_dir, work_dir ) + if sample_files: + if 'tool_data_table_conf.xml.sample' in sample_files: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) + error, message = tool_util.handle_sample_tool_data_table_conf_file( self.app, tool_data_table_config ) + tool, valid, message2 = self.load_tool_from_config( repository_id, tool_config_filepath ) + message = self.concat_messages( message, message2 ) + return tool, valid, message, sample_files + + def handle_sample_files_and_load_tool_from_tmp_config( self, repo, repository_id, changeset_revision, + tool_config_filename, work_dir ): + tool = None + message = '' + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) + # We're not currently doing anything with the returned list of deleted_sample_files here. It is + # intended to help handle sample files that are in the manifest, but have been deleted from disk. + sample_files, deleted_sample_files = self.get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) + if sample_files: + self.app.config.tool_data_path = work_dir + if 'tool_data_table_conf.xml.sample' in sample_files: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) + if tool_data_table_config: + error, message = tool_util.handle_sample_tool_data_table_conf_file( self.app, tool_data_table_config ) + if error: + log.debug( message ) + manifest_ctx, ctx_file = hg_util.get_ctx_file_path_from_manifest( tool_config_filename, repo, changeset_revision ) + if manifest_ctx and ctx_file: + tool, message2 = self.load_tool_from_tmp_config( repo, repository_id, manifest_ctx, ctx_file, work_dir ) + message = self.concat_messages( message, message2 ) + return tool, message, sample_files + + def load_tool_from_changeset_revision( self, repository_id, changeset_revision, tool_config_filename ): + """ + Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value + of tool_config_filename. The value of changeset_revision is a valid (downloadable) + changeset revision. The tool config will be located in the repository manifest between + the received valid changeset revision and the first changeset revision in the repository, + searching backwards. + """ + original_tool_data_path = self.app.config.tool_data_path + repository = suc.get_repository_in_tool_shed( self.app, repository_id ) + repo_files_dir = repository.repo_path( self.app ) + repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_files_dir, create=False ) + message = '' + tool = None + can_use_disk_file = False + tool_config_filepath = suc.get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename ) + work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ltfcr" ) + can_use_disk_file = self.can_use_tool_config_disk_file( repository, + repo, + tool_config_filepath, + changeset_revision ) + if can_use_disk_file: + self.app.config.tool_data_path = work_dir + tool, valid, message, sample_files = \ + self.handle_sample_files_and_load_tool_from_disk( repo_files_dir, + repository_id, + tool_config_filepath, + work_dir ) + if tool is not None: + invalid_files_and_errors_tups = \ + self.check_tool_input_params( repo_files_dir, + tool_config_filename, + tool, + sample_files ) + if invalid_files_and_errors_tups: + message2 = tool_util.generate_message_for_invalid_tools( self.app, + invalid_files_and_errors_tups, + repository, + metadata_dict=None, + as_html=True, + displaying_invalid_tool=True ) + message = self.concat_messages( message, message2 ) + else: + tool, message, sample_files = \ + self.handle_sample_files_and_load_tool_from_tmp_config( repo, + repository_id, + changeset_revision, + tool_config_filename, + work_dir ) + basic_util.remove_dir( work_dir ) + self.app.config.tool_data_path = original_tool_data_path + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + tool_util.reset_tool_data_tables( self.app ) + return repository, tool, message + + def load_tool_from_config( self, repository_id, full_path ): + try: + tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id ) + valid = True + error_message = None + except KeyError, e: + tool = None + valid = False + error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) + error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' + error_message += 'this error. ' + except Exception, e: + tool = None + valid = False + error_message = str( e ) + return tool, valid, error_message + + def load_tool_from_tmp_config( self, repo, repository_id, ctx, ctx_file, work_dir ): + tool = None + message = '' + tmp_tool_config = hg_util.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) + if tmp_tool_config: + element_tree, error_message = xml_util.parse_xml( tmp_tool_config ) + if element_tree is None: + return tool, message + element_tree_root = element_tree.getroot() + # Look for code files required by the tool config. + tmp_code_files = [] + for code_elem in element_tree_root.findall( 'code' ): + code_file_name = code_elem.get( 'file' ) + tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) + if tmp_code_file_name: + tmp_code_files.append( tmp_code_file_name ) + tool, valid, message = self.load_tool_from_config( repository_id, tmp_tool_config ) + for tmp_code_file in tmp_code_files: + try: + os.unlink( tmp_code_file ) + except: + pass + try: + os.unlink( tmp_tool_config ) + except: + pass + return tool, message diff -r 9a63eaf328c6058bf046d48cbc947c76f390193c -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 lib/tool_shed/util/review_util.py --- a/lib/tool_shed/util/review_util.py +++ b/lib/tool_shed/util/review_util.py @@ -41,8 +41,8 @@ def get_component_by_name( app, name ): """Get a component from the database via a name.""" sa_session = app.model.context.current - return sa_session.query( app.app.model.Component ) \ - .filter( app.app.model.Component.table.c.name==name ) \ + return sa_session.query( app.model.Component ) \ + .filter( app.model.Component.table.c.name==name ) \ .first() def get_component_review_by_repository_review_id_component_id( app, repository_review_id, component_id ): This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/7be6bc6e26c9/ Changeset: 7be6bc6e26c9 User: martenson Date: 2014-07-21 23:48:47 Summary: permission API, some refactoring, changed return values (return permissions instead of dataset metadata) Affected #: 1 file diff -r d0a550fd70bb69ef79fd9e15aff3b7a66b5aa144 -r 7be6bc6e26c9f2530cddfd69d9acff95b8f3a7ff lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -160,6 +160,20 @@ return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) + def get_current_roles( self, trans, library_dataset): + dataset = library_dataset.library_dataset_dataset_association.dataset + + # Omit duplicated roles by converting to set + access_roles = set( dataset.get_access_roles( trans ) ) + modify_roles = set( trans.app.security_agent.get_roles_for_action( library_dataset, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) + manage_roles = set( dataset.get_manage_permissions_roles( trans ) ) + + access_dataset_role_list = [ access_role.name for access_role in access_roles ] + manage_dataset_role_list = [ manage_role.name for manage_role in manage_roles ] + modify_item_role_list = [ modify_role.name for modify_role in modify_roles ] + + return dict( access_dataset_roles=access_dataset_role_list, modify_item_roles=modify_item_role_list, manage_dataset_roles=manage_dataset_role_list ) + @expose_api def update( self, trans, encoded_dataset_id, **kwd ): """ @@ -174,13 +188,14 @@ :type action: string :rtype: dictionary - :returns: dict containing information about the dataset + :returns: dict of current roles for all permission types """ try: - dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) + library_dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) except Exception, e: raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) + dataset = library_dataset.library_dataset_dataset_association.dataset # User has to have manage permissions on dataset in order to remove access restrictions. current_user_roles = trans.get_current_user_roles() can_manage = trans.app.security_agent.can_manage_dataset( current_user_roles, dataset ) or trans.user_is_admin() @@ -192,18 +207,18 @@ raise exceptions.RequestParameterMissingException( 'The mandatory parameter "action" is missing.' ) elif action == 'remove_restrictions': trans.app.security_agent.make_dataset_public( dataset ) + if not trans.app.security_agent.dataset_is_public( dataset ): + raise exceptions.InternalServerError( 'An error occured while making dataset public.' ) elif action == 'make_private': trans.app.security_agent.make_dataset_public( dataset ) private_role = self.model.security_agent.get_private_user_role( trans.user ) dp = trans.model.DatasetPermissions( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, dataset, private_role ) trans.sa_session.add( dp ) trans.sa_session.flush() + if not trans.app.security_agent.dataset_is_private_to_user( dataset ): + raise exceptions.InternalServerError( 'An error occured while making dataset private.' ) - rval = trans.security.encode_all_ids( dataset.to_dict() ) - rval[ 'update_time' ] = dataset.update_time.strftime( "%Y-%m-%d %I:%M %p" ) - rval[ 'deleted' ] = dataset.deleted - rval[ 'folder_id' ] = 'F' + rval[ 'folder_id' ] - return rval + return self.get_current_roles( trans, library_dataset ) @expose_api def delete( self, trans, encoded_dataset_id, **kwd ): https://bitbucket.org/galaxy/galaxy-central/commits/7ac01ee81cd6/ Changeset: 7ac01ee81cd6 User: martenson Date: 2014-07-23 21:22:47 Summary: permissions API: connected the API to data libraries UI Affected #: 3 files diff -r 7be6bc6e26c9f2530cddfd69d9acff95b8f3a7ff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -68,6 +68,7 @@ rval[ 'file_size' ] = nice_size rval[ 'date_uploaded' ] = date_uploaded rval[ 'can_user_modify' ] = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset) or trans.user_is_admin() + rval[ 'is_unrestricted' ] = trans.app.security_agent.dataset_is_public( library_dataset.library_dataset_dataset_association.dataset ) # Manage dataset permission is always attached to the dataset itself, not the the ld or ldda to maintain consistency rval[ 'can_user_manage' ] = trans.app.security_agent.can_manage_dataset( current_user_roles, library_dataset.library_dataset_dataset_association.dataset) or trans.user_is_admin() @@ -107,13 +108,8 @@ scope = kwd.get( 'scope', None ) - # Return all roles currently set for relevant permissions. if scope == 'current' or scope is None: - # Omit duplicated roles by converting to set - access_roles = set( dataset.get_access_roles( trans ) ) - modify_roles = set( trans.app.security_agent.get_roles_for_action( library_dataset, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) - manage_roles = set( dataset.get_manage_permissions_roles( trans ) ) - + return self.get_current_roles( trans, library_dataset ) # legit_roles = trans.app.security_agent.get_legitimate_roles( trans, dataset, 'library_admin' ) # log.debug( 'CXXXXXCXCXCXCXCXCC legit roles: ' + str( [ legit_role.name for legit_role in legit_roles ] ) ) @@ -123,12 +119,6 @@ # log.debug( 'permission action: ' + str( k.action ) ) # log.debug( 'permission roles: ' + str( [ role.name for role in v ] ) ) - access_dataset_role_list = [ access_role.name for access_role in access_roles ] - manage_dataset_role_list = [ manage_role.name for manage_role in manage_roles ] - modify_item_role_list = [ modify_role.name for modify_role in modify_roles ] - - return dict( access_dataset_roles=access_dataset_role_list, modify_item_roles=modify_item_role_list, manage_dataset_roles=manage_dataset_role_list ) - # Return roles that are available to select. if scope == 'available': page = kwd.get( 'page', None ) @@ -161,21 +151,28 @@ return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) def get_current_roles( self, trans, library_dataset): - dataset = library_dataset.library_dataset_dataset_association.dataset - - # Omit duplicated roles by converting to set - access_roles = set( dataset.get_access_roles( trans ) ) - modify_roles = set( trans.app.security_agent.get_roles_for_action( library_dataset, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) - manage_roles = set( dataset.get_manage_permissions_roles( trans ) ) + """ + Find all roles currently connected to relevant permissions + on the library dataset and the underlying dataset. - access_dataset_role_list = [ access_role.name for access_role in access_roles ] - manage_dataset_role_list = [ manage_role.name for manage_role in manage_roles ] - modify_item_role_list = [ modify_role.name for modify_role in modify_roles ] + :param library_dataset: the model object + :type library_dataset: LibraryDataset + """ + dataset = library_dataset.library_dataset_dataset_association.dataset - return dict( access_dataset_roles=access_dataset_role_list, modify_item_roles=modify_item_role_list, manage_dataset_roles=manage_dataset_role_list ) + # Omit duplicated roles by converting to set + access_roles = set( dataset.get_access_roles( trans ) ) + modify_roles = set( trans.app.security_agent.get_roles_for_action( library_dataset, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) + manage_roles = set( dataset.get_manage_permissions_roles( trans ) ) + + access_dataset_role_list = [ access_role.name for access_role in access_roles ] + manage_dataset_role_list = [ manage_role.name for manage_role in manage_roles ] + modify_item_role_list = [ modify_role.name for modify_role in modify_roles ] + + return dict( access_dataset_roles=access_dataset_role_list, modify_item_roles=modify_item_role_list, manage_dataset_roles=manage_dataset_role_list ) @expose_api - def update( self, trans, encoded_dataset_id, **kwd ): + def update_permissions( self, trans, encoded_dataset_id, **kwd ): """ def update( self, trans, encoded_dataset_id, **kwd ): *POST /api/libraries/datasets/{encoded_dataset_id}/permissions @@ -196,7 +193,7 @@ raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) dataset = library_dataset.library_dataset_dataset_association.dataset - # User has to have manage permissions on dataset in order to remove access restrictions. + current_user_roles = trans.get_current_user_roles() can_manage = trans.app.security_agent.can_manage_dataset( current_user_roles, dataset ) or trans.user_is_admin() if not can_manage: @@ -211,12 +208,21 @@ raise exceptions.InternalServerError( 'An error occured while making dataset public.' ) elif action == 'make_private': trans.app.security_agent.make_dataset_public( dataset ) - private_role = self.model.security_agent.get_private_user_role( trans.user ) - dp = trans.model.DatasetPermissions( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, dataset, private_role ) + private_role = trans.app.security_agent.get_private_user_role( trans.user ) + dp = trans.app.model.DatasetPermissions( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, dataset, private_role ) trans.sa_session.add( dp ) trans.sa_session.flush() - if not trans.app.security_agent.dataset_is_private_to_user( dataset ): + if not trans.app.security_agent.dataset_is_private_to_user( trans, library_dataset ): raise exceptions.InternalServerError( 'An error occured while making dataset private.' ) + elif action == 'set_dataset_access_roles': + raise exceptions.NotImplemented() + elif action == 'set_dataset_manage_roles': + raise exceptions.NotImplemented() + elif action == 'set_library_dataset_modify_roles': + raise exceptions.NotImplemented() + else: + raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' + 'Allowed values are: "remove_restrictions", "make_private", "set_dataset_access_roles"' ) return self.get_current_roles( trans, library_dataset ) diff -r 7be6bc6e26c9f2530cddfd69d9acff95b8f3a7ff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -253,18 +253,12 @@ action='show_roles', conditions=dict( method=[ "GET" ] ) ) - webapp.mapper.connect( 'modify_permissions', + webapp.mapper.connect( 'update_lda_permissions', '/api/libraries/datasets/:encoded_dataset_id/permissions', controller='lda_datasets', - action='update', + action='update_permissions', conditions=dict( method=[ "POST" ] ) ) - # webapp.mapper.connect( 'show_legitimate_lda_roles', - # '/api/libraries/datasets/:encoded_dataset_id/permissions/current', - # controller='lda_datasets', - # action='get_roles', - # conditions=dict( method=[ "GET" ] ) ) - webapp.mapper.connect( 'delete_lda_item', '/api/libraries/datasets/:encoded_dataset_id', controller='lda_datasets', diff -r 7be6bc6e26c9f2530cddfd69d9acff95b8f3a7ff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -24,11 +24,12 @@ "click .toolbtn-download-dataset" : "downloadDataset", "click .toolbtn-import-dataset" : "importIntoHistory", "click .toolbtn-share-dataset" : "shareDataset", + "click .btn-copy-link-to-clipboard" : "copyToClipboard", + "click .btn-make-private" : "makeDatasetPrivate", + "click .btn-remove-restrictions" : "removeDatasetRestrictions", // missing features below "click .toolbtn_save_modifications" : "comingSoon", - "click .btn-remove-restrictions" : "comingSoon", - "click .btn-make-private" : "comingSoon", "click .btn-share-dataset" : "comingSoon" }, @@ -175,10 +176,9 @@ Galaxy.libraries.library_router.back(); }, - showPermissions: function(){ + showPermissions: function(options){ + this.options = _.extend(this.options, options); $(".tooltip").remove(); - var template = this.templateDatasetPermissions(); - this.$el.html(template({item: this.model})); // Select works different for admins var is_admin = false; @@ -186,11 +186,31 @@ is_admin = Galaxy.currUser.isAdmin(); } + var template = this.templateDatasetPermissions(); + this.$el.html(template({item: this.model, is_admin: is_admin})); + var self = this; + if (this.options.fetched_permissions === undefined){ + $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + self.prepareSelectBoxes({fetched_permissions:fetched_permissions, is_admin:is_admin}); + }).fail(function(){ + mod_toastr.error('An error occurred while fetching dataset permissions. :('); + }); + } else { + this.prepareSelectBoxes({is_admin:is_admin}); + } - // load all current permissions - $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { - var selected_access_dataset_roles = []; + $("#center [data-toggle]").tooltip(); + //hack to show scrollbars + $("#center").css('overflow','auto'); + }, + + prepareSelectBoxes: function(options){ + this.options = _.extend(this.options, options); + var fetched_permissions = this.options.fetched_permissions; + var is_admin = this.options.is_admin + var self = this; + var selected_access_dataset_roles = []; for (var i = 0; i < fetched_permissions.access_dataset_roles.length; i++) { selected_access_dataset_roles.push(fetched_permissions.access_dataset_roles[i] + ':' + fetched_permissions.access_dataset_roles[i]); } @@ -359,21 +379,39 @@ mod_toastr.error('An error occurred while fetching data with permissions. :('); }); } - }).fail(function(){ - mod_toastr.error('An error occurred while fetching data with permissions. :('); - }); - - //TODO add permissions for modification and management of datasets - - $("#center [data-toggle]").tooltip(); - //hack to show scrollbars - $("#center").css('overflow','auto'); }, comingSoon: function(){ mod_toastr.warning('Feature coming soon'); }, + copyToClipboard: function(){ + var href = Backbone.history.location.href; + if (href.lastIndexOf('/permissions') !== -1){ + href = href.substr(0, href.lastIndexOf('/permissions')); + } + window.prompt("Copy to clipboard: Ctrl+C, Enter", href); + }, + + makeDatasetPrivate: function(){ + var self = this; + $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { + self.model.set({is_unrestricted:false}); + self.showPermissions({fetched_permissions:fetched_permissions}) + }).fail(function(){ + mod_toastr.error('An error occurred while making dataset private. :('); + }); + }, + + removeDatasetRestrictions: function(){ + var self = this; + $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions").done(function(fetched_permissions) { + self.model.set({is_unrestricted:true}); + self.showPermissions({fetched_permissions:fetched_permissions}) + }).fail(function(){ + mod_toastr.error('An error occurred while making dataset unrestricted. :('); + }); + }, templateDataset : function(){ var tmpl_array = []; @@ -408,6 +446,13 @@ tmpl_array.push(' <% }); %>'); tmpl_array.push('</ol>'); + tmpl_array.push('<% if (item.get("is_unrestricted")) { %>'); + tmpl_array.push(' <p>'); + tmpl_array.push(' This dataset is unrestricted so everybody can access it. Just share the URL of this page. '); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> '); + tmpl_array.push(' </p>'); + tmpl_array.push('<% } %>'); + tmpl_array.push('<div class="dataset_table">'); tmpl_array.push(' <table class="grid table table-striped table-condensed">'); @@ -632,26 +677,37 @@ tmpl_array.push('<h1>Permissions: <%= _.escape(item.get("name")) %></h1>'); + tmpl_array.push('<div class="alert alert-warning">'); + tmpl_array.push('<% if (is_admin) { %>'); + tmpl_array.push('You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.'); + tmpl_array.push('<% } else { %>'); + tmpl_array.push('You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.'); + tmpl_array.push('<% } %>'); + tmpl_array.push('</div>'); tmpl_array.push('<div class="dataset_table">'); - tmpl_array.push('<p>You can remove all access restrictions on this dataset. '); - tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button"><span class="fa fa-globe"></span> Remove restrictions</span></button>'); - tmpl_array.push('</p>'); + tmpl_array.push('<% if (!item.get("is_unrestricted")) { %>'); + tmpl_array.push(' <p>You can remove all access restrictions on this dataset. '); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">'); + tmpl_array.push(' <span class="fa fa-globe"> Remove restrictions</span>'); + tmpl_array.push(' </button>'); + tmpl_array.push(' </p>'); + tmpl_array.push('<% } else { %>'); + tmpl_array.push(' This dataset is unrestricted so everybody can access it. Just share the URL of this page.'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> '); + tmpl_array.push(' <p>You can make this dataset private to you. '); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>'); + tmpl_array.push(' </p>'); + // tmpl_array.push(' <p>You can share this dataset privately with other Galaxy users. '); + // tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Only you and the suers you choose will be able to access the dataset." class="btn btn-default btn-share-dataset primary-button" type="button"><span class="fa fa-share"> Share Privately</span></button>'); + // tmpl_array.push(' </p>'); + tmpl_array.push('<% } %>'); - tmpl_array.push('<p>You can make this dataset private to you. '); - tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"></span> Make private</span></button>'); - tmpl_array.push('</p>'); - - tmpl_array.push('<p>You can share this dataset with another Galaxy user. '); - tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Only you and the other user will be able to access the dataset." class="btn btn-default btn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); - tmpl_array.push('</p>'); - - tmpl_array.push('<p>You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.</p>'); tmpl_array.push('<hr/>'); tmpl_array.push('<h2>Library-related permissions</h2>'); - tmpl_array.push('<div class="alert alert-success">You have the permission to modify this Library item. This includes changing its metadata and other information. It does not include modifying the underlying dataset.</div>'); + tmpl_array.push('<div class="alert alert-success">You have the permission to modify this Library item. This includes changing its metadata and other information.</div>'); tmpl_array.push('<h4>Roles that can modify the library item</h4>'); tmpl_array.push('<div id="modify_perm" class="modify_perm roles-selection"></div>'); tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify the information about this library item.</div>'); @@ -660,7 +716,7 @@ tmpl_array.push('<h2>Dataset-related permissions</h2>'); tmpl_array.push('<div class="alert alert-success">You have the permission to manage permissions on this dataset. That means you can control who can access it and also appoint others that can manage permissions on it.</div>'); - tmpl_array.push('<div class="alert alert-danger">Changes made here will affect <strong>every</strong> library item and every history this dataset is part of.</div>'); + tmpl_array.push('<div class="alert alert-warning">Changes made here will affect <strong>every</strong> library item and every history this dataset is part of.</div>'); tmpl_array.push('<h4>Roles that can access dataset</h4>'); tmpl_array.push('<div id="access_perm" class="access_perm roles-selection"></div>'); tmpl_array.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>'); https://bitbucket.org/galaxy/galaxy-central/commits/ec1d03be24f7/ Changeset: ec1d03be24f7 User: martenson Date: 2014-07-23 21:23:04 Summary: Merge Affected #: 185 files diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -86,6 +86,11 @@ err_code = error_codes.USER_REQUEST_INVALID_PARAMETER +class AuthenticationFailed( MessageException ): + status_code = 401 + err_code = error_codes.USER_AUTHENTICATION_FAILED + + class AuthenticationRequired( MessageException ): status_code = 403 #TODO: as 401 and send WWW-Authenticate: ??? diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/exceptions/error_codes.json --- a/lib/galaxy/exceptions/error_codes.json +++ b/lib/galaxy/exceptions/error_codes.json @@ -60,6 +60,11 @@ "message": "Supplied incorrect or incompatible tool meta parameters." }, { + "name": "USER_AUTHENTICATION_FAILED", + "code": 401001, + "message": "Authentication failed, invalid credentials supplied." + }, + { "name": "USER_NO_API_KEY", "code": 403001, "message": "API authentication required for this request" diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/webapps/galaxy/api/authenticate.py --- a/lib/galaxy/webapps/galaxy/api/authenticate.py +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -12,11 +12,10 @@ """ from base64 import b64decode -from paste.httpexceptions import HTTPBadRequest from urllib import unquote -from galaxy import web -from galaxy.exceptions import ObjectNotFound +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy import exceptions from galaxy.web.base.controller import BaseAPIController, CreatesApiKeysMixin import logging @@ -25,7 +24,7 @@ class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ): - @web.expose_api_anonymous + @expose_api_anonymous def get_api_key( self, trans, **kwd ): """ def get_api_key( self, trans, **kwd ) @@ -43,7 +42,7 @@ if ( len( user ) is not 1 ): # DB is inconsistent and we have more users with same email - raise ObjectNotFound + raise exceptions.ObjectNotFound() else: user = user[0] is_valid_user = user.check_password( password ) @@ -54,8 +53,7 @@ key = self.create_api_key( trans, user ) return dict( api_key=key ) else: - trans.response.status = 500 - return "invalid password" + raise exceptions.AuthenticationFailed() def _decode_baseauth( self, encoded_str ): """ @@ -81,7 +79,7 @@ try: email, password = b64decode( split[ 0 ] ).split( ':' ) except: - raise HTTPBadRequest + raise exceptions.ActionInputError() # If there are only two elements, check the first and ensure it says # 'basic' so that we know we're about to decode the right thing. If not, @@ -91,13 +89,13 @@ try: email, password = b64decode( split[ 1 ] ).split( ':' ) except: - raise HTTPBadRequest + raise exceptions.ActionInputError() else: - raise HTTPBadRequest + raise exceptions.ActionInputError() # If there are more than 2 elements, something crazy must be happening. # Bail. else: - raise HTTPBadRequest + raise exceptions.ActionInputError() return unquote( email ), unquote( password ) diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -13,6 +13,7 @@ from tool_shed.galaxy_install.install_manager import InstallRepositoryManager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager + from tool_shed.util import common_util from tool_shed.util import encoding_util from tool_shed.util import hg_util diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -12,12 +12,10 @@ import tool_shed.repository_types.util as rt_util from tool_shed.util import common_util -from tool_shed.util import data_manager_util -from tool_shed.util import datatype_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import readme_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util @@ -26,12 +24,16 @@ from tool_shed.galaxy_install import dependency_display from tool_shed.galaxy_install import install_manager +from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.grids import admin_toolshed_grids from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import data_manager from tool_shed.galaxy_install.tools import tool_panel_manager +from tool_shed.tools import tool_version_manager + log = logging.getLogger( __name__ ) @@ -46,7 +48,7 @@ def activate_repository( self, trans, **kwd ): """Activate a repository that was deactivated but not uninstalled.""" repository_id = kwd[ 'id' ] - repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) try: trans.app.installed_repository_manager.activate_repository( repository ) except Exception, e: @@ -72,7 +74,7 @@ def browse_repository( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako', repository=repository, message=message, @@ -105,7 +107,7 @@ action='purge_repository', **kwd ) ) if operation == "activate or reinstall": - repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) if repository.uninstalled: # Since we're reinstalling the repository we need to find the latest changeset revision to which it can # be updated so that we can reset the metadata if necessary. This will ensure that information about @@ -206,7 +208,7 @@ def check_for_updates( self, trans, **kwd ): """Send a request to the relevant tool shed to see if there are any updates.""" repository_id = kwd.get( 'id', None ) - repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) params = '?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ ( web.url_for( '/', qualified=True ), @@ -232,7 +234,7 @@ status = kwd.get( 'status', 'done' ) remove_from_disk = kwd.get( 'remove_from_disk', '' ) remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) - tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = \ suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) if relative_install_dir: @@ -250,20 +252,21 @@ shed_tool_conf, uninstall=remove_from_disk_checked ) if tool_shed_repository.includes_data_managers: - data_manager_util.remove_from_data_manager( trans.app, tool_shed_repository ) + dmh = data_manager.DataManagerHandler( trans.app ) + dmh.remove_from_data_manager( tool_shed_repository ) if tool_shed_repository.includes_datatypes: # Deactivate proprietary datatypes. - installed_repository_dict = datatype_util.load_installed_datatypes( trans.app, - tool_shed_repository, - repository_install_dir, - deactivate=True ) + cdl = custom_datatype_manager.CustomDatatypeLoader( trans.app ) + installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository, + repository_install_dir, + deactivate=True ) if installed_repository_dict: converter_path = installed_repository_dict.get( 'converter_path' ) if converter_path is not None: - datatype_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) + cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=True ) display_path = installed_repository_dict.get( 'display_path' ) if display_path is not None: - datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=True ) + cdl.load_installed_display_applications( installed_repository_dict, deactivate=True ) if remove_from_disk_checked: try: # Remove the repository from disk. @@ -394,7 +397,7 @@ of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which it was installed. """ - repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None: message = "Unable to retrieve tool dependencies from the Tool Shed because one or more of the following required " @@ -419,7 +422,7 @@ Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an uninstalled tool shed repository. """ - repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None: message = "Unable to retrieve updated repository information from the Tool Shed because one or more of the following " @@ -513,7 +516,7 @@ status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) if repository_id is not None: - repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) if repository is not None: tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) name = str( repository.name ) @@ -571,7 +574,7 @@ dependencies are included in the updated revision. """ updating_repository_id = kwd.get( 'updating_repository_id', None ) - repository = suc.get_installed_tool_shed_repository( trans.app, updating_repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, updating_repository_id ) # All received dependencies need to be installed - confirmed by the caller. encoded_tool_dependencies_dict = kwd.get( 'encoded_tool_dependencies_dict', None ) if encoded_tool_dependencies_dict is not None: @@ -747,7 +750,7 @@ if repository_id is None: return trans.show_error_message( 'Missing required encoded repository id.' ) operation = kwd.get( 'operation', None ) - repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) if repository is None: return trans.show_error_message( 'Invalid repository specified.' ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) @@ -866,15 +869,15 @@ message += ' and restart your Galaxy server to install tool dependencies.' status = 'error' installed_tool_dependencies_select_field = \ - suc.build_tool_dependencies_select_field( trans.app, - tool_shed_repository=tool_shed_repository, - name='inst_td_ids', - uninstalled_only=False ) + tool_dependency_util.build_tool_dependencies_select_field( trans.app, + tool_shed_repository=tool_shed_repository, + name='inst_td_ids', + uninstalled_only=False ) uninstalled_tool_dependencies_select_field = \ - suc.build_tool_dependencies_select_field( trans.app, - tool_shed_repository=tool_shed_repository, - name='uninstalled_tool_dependency_ids', - uninstalled_only=True ) + tool_dependency_util.build_tool_dependencies_select_field( trans.app, + tool_shed_repository=tool_shed_repository, + name='uninstalled_tool_dependency_ids', + uninstalled_only=True ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository_tool_dependencies.mako', repository=tool_shed_repository, installed_tool_dependencies_select_field=installed_tool_dependencies_select_field, @@ -1276,7 +1279,7 @@ repository_id = kwd.get( 'id', None ) new_kwd = {} if repository_id is not None: - repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) if repository: if repository.is_new: if kwd.get( 'purge_repository_button', False ): @@ -1314,7 +1317,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd[ 'id' ] - tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) no_changes = kwd.get( 'no_changes', '' ) no_changes_checked = CheckboxField.is_checked( no_changes ) install_repository_dependencies = CheckboxField.is_checked( kwd.get( 'install_repository_dependencies', '' ) ) @@ -1384,14 +1387,14 @@ tool_dependencies = metadata.get( 'tool_dependencies', None ) else: tool_dependencies = None - repo_info_dict = repository_maintenance_util.create_repo_info_dict( trans.app, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.changeset_revision, - ctx_rev=ctx_rev, - repository_owner=tool_shed_repository.owner, - repository_name=tool_shed_repository.name, - tool_dependencies=tool_dependencies, - repository_dependencies=repository_dependencies ) + repo_info_dict = repository_util.create_repo_info_dict( trans.app, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.changeset_revision, + ctx_rev=ctx_rev, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) if repo_info_dict not in repo_info_dicts: repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. @@ -1457,7 +1460,7 @@ action='browse_repositories', message=message, status=status ) ) - tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) rrm = RepairRepositoryManager( trans.app ) if kwd.get( 'repair_repository_button', False ): encoded_repair_dict = kwd.get( 'repair_dict', None ) @@ -1475,7 +1478,7 @@ repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) repositories_for_repair.append( repository ) return self.repair_tool_shed_repositories( trans, rrm, repositories_for_repair, ordered_repo_info_dicts ) - tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) repair_dict = rrm.get_repair_dict( tool_shed_repository ) encoded_repair_dict = encoding_util.tool_shed_encode( repair_dict ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) @@ -1537,7 +1540,7 @@ repository_id = kwd.get( 'id', None ) latest_changeset_revision = kwd.get( 'latest_changeset_revision', None ) latest_ctx_rev = kwd.get( 'latest_ctx_rev', None ) - tool_shed_repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) metadata = tool_shed_repository.metadata tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( tool_shed_repository.tool_shed ) ) @@ -1597,14 +1600,14 @@ repository_dependencies = \ rdim.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, tool_shed_repository ) - repo_info_dict = repository_maintenance_util.create_repo_info_dict( trans.app, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, - ctx_rev=tool_shed_repository.ctx_rev, - repository_owner=tool_shed_repository.owner, - repository_name=tool_shed_repository.name, - tool_dependencies=tool_dependencies, - repository_dependencies=repository_dependencies ) + repo_info_dict = repository_util.create_repo_info_dict( trans.app, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.installed_changeset_revision, + ctx_rev=tool_shed_repository.ctx_rev, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) irm = trans.app.installed_repository_manager dependencies_for_repository_dict = irm.get_dependencies_for_repository( tool_shed_url, repo_info_dict, @@ -1724,7 +1727,7 @@ @web.require_admin def reset_repository_metadata( self, trans, id ): """Reset all metadata on a single installed tool shed repository.""" - repository = suc.get_installed_tool_shed_repository( trans.app, id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: @@ -1742,7 +1745,7 @@ persist=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: - suc.update_in_shed_tool_config( trans.app, repository ) + irmm.update_in_shed_tool_config( repository ) trans.install_model.context.add( repository ) trans.install_model.context.flush() message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name @@ -1763,7 +1766,7 @@ @web.require_admin def reset_to_install( self, trans, **kwd ): """An error occurred while cloning the repository, so reset everything necessary to enable another attempt.""" - repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) if kwd.get( 'reset_repository', False ): suc.set_repository_attributes( trans.app, repository, @@ -1789,7 +1792,7 @@ Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed repository and update the metadata for the repository's revision in the Galaxy database. """ - repository = suc.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ), str( repository.owner ), @@ -1799,7 +1802,8 @@ text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) if text: tool_version_dicts = json.from_json_string( text ) - tool_util.handle_tool_versions( trans.app, tool_version_dicts, repository ) + tvm = tool_version_manager.ToolVersionManager( trans.app ) + tvm.handle_tool_versions( tool_version_dicts, repository ) message = "Tool versions have been set for all included tools." status = 'done' else: @@ -1930,9 +1934,11 @@ hg_util.update_repository( repo, latest_ctx_rev ) # Remove old Data Manager entries if repository.includes_data_managers: - data_manager_util.remove_from_data_manager( trans.app, repository ) + dmh = data_manager.DataManagerHandler( trans.app ) + dmh.remove_from_data_manager( repository ) # Update the repository metadata. - irmm = InstalledRepositoryMetadataManager( trans.app ) + tpm = tool_panel_manager.ToolPanelManager( trans.app ) + irmm = InstalledRepositoryMetadataManager( trans.app, tpm ) metadata_dict, invalid_file_tups = \ irmm.generate_metadata_for_changeset_revision( repository=repository, changeset_revision=latest_changeset_revision, @@ -1944,11 +1950,10 @@ updating_installed_repository=True, persist=True ) if 'tools' in metadata_dict: - tpm = tool_panel_manager.ToolPanelManager( trans.app ) tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: - tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository ) - repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) + tool_panel_dict = tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) + repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) tpm.add_to_tool_panel( repository_name=str( repository.name ), repository_clone_url=repository_clone_url, changeset_revision=str( repository.installed_changeset_revision ), @@ -1959,13 +1964,13 @@ new_install=False ) # Add new Data Manager entries if 'data_manager' in metadata_dict: - new_data_managers = data_manager_util.install_data_managers( trans.app, - trans.app.config.shed_data_manager_config_file, - metadata_dict, - repository.get_shed_config_dict( trans.app ), - os.path.join( relative_install_dir, name ), - repository, - repository_tools_tups ) + dmh = data_manager.DataManagerHandler( trans.app ) + new_data_managers = dmh.install_data_managers( trans.app.config.shed_data_manager_config_file, + metadata_dict, + repository.get_shed_config_dict( trans.app ), + os.path.join( relative_install_dir, name ), + repository, + repository_tools_tups ) if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict: new_repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) new_repository_dependencies = new_repository_dependencies_dict.get( 'repository_dependencies', [] ) @@ -2069,8 +2074,9 @@ repository_names_not_updated = [] updated_count = 0 for repository in trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ - .filter( trans.install_model.ToolShedRepository.table.c.deleted == False ): - ok, updated = suc.check_or_update_tool_shed_status_for_installed_repository( trans.app, repository ) + .filter( trans.install_model.ToolShedRepository.table.c.deleted == False ): + ok, updated = \ + repository_util.check_or_update_tool_shed_status_for_installed_repository( trans.app, repository ) if ok: success_count += 1 else: @@ -2085,7 +2091,8 @@ else: repository_id = kwd.get( 'id', None ) repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id ) - ok, updated = suc.check_or_update_tool_shed_status_for_installed_repository( trans.app, repository ) + ok, updated = \ + repository_util.check_or_update_tool_shed_status_for_installed_repository( trans.app, repository ) if ok: if updated: message = "The tool shed status for repository <b>%s</b> has been updated." % str( repository.name ) @@ -2104,7 +2111,7 @@ def view_tool_metadata( self, trans, repository_id, tool_id, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = suc.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) repository_metadata = repository.metadata shed_config_dict = repository.get_shed_config_dict( trans.app ) tool_metadata = {} @@ -2119,7 +2126,8 @@ tool_config = os.path.join( shed_config_dict.get( 'tool_path' ), tool_config ) tool = trans.app.toolbox.load_tool( os.path.abspath( tool_config ), guid=tool_metadata[ 'guid' ] ) if tool: - tool_version = tool_util.get_tool_version( trans.app, str( tool.id ) ) + tvm = tool_version_manager.ToolVersionManager( trans.app ) + tool_version = tvm.get_tool_version( str( tool.id ) ) tool_lineage = tool_version.get_version_ids( trans.app, reverse=True ) break return trans.fill_template( "/admin/tool_shed_repository/view_tool_metadata.mako", diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -195,6 +195,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, ExportsHistoryMixin, ImportsHistoryMixin ): + def __init__( self, app ): super( HistoryController, self ).__init__( app ) self.mgrs = util.bunch.Bunch( diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -1,5 +1,6 @@ from sqlalchemy import desc, and_ from galaxy import model, web +from galaxy import managers from galaxy.web import error, url_for from galaxy.model.item_attrs import UsesItemRatings from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesHistoryMixin, UsesStoredWorkflowMixin, UsesVisualizationMixin @@ -285,6 +286,12 @@ _page_selection_grid = PageSelectionGrid() _visualization_selection_grid = VisualizationSelectionGrid() + def __init__( self, app ): + super( PageController, self ).__init__( app ) + self.mgrs = util.bunch.Bunch( + histories=managers.histories.HistoryManager() + ) + @web.expose @web.require_login() def list( self, trans, *args, **kwargs ): @@ -718,6 +725,7 @@ """ Returns html suitable for embedding in another page. """ + #TODO: should be moved to history controller and/or called via ajax from the template history = self.get_history( trans, id, False, True ) if not history: return None @@ -729,15 +737,22 @@ hda_dicts = [] datasets = self.get_history_datasets( trans, history ) - for hda in datasets: - hda_dict = self.get_hda_dict( trans, hda ) - hda_dict[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, hda ) - hda_dicts.append( hda_dict ) - history_dict = self.get_history_dict( trans, history, hda_dictionaries=hda_dicts ) - history_dict[ 'annotation' ] = history.annotation + #for hda in datasets: + # hda_dict = self.get_hda_dict( trans, hda ) + # hda_dict[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, hda ) + # hda_dicts.append( hda_dict ) + #history_dict = self.get_history_dict( trans, history, hda_dictionaries=hda_dicts ) + #history_dict[ 'annotation' ] = history.annotation + + # include all datasets: hidden, deleted, and purged + #TODO!: doubled query (hda_dictionaries + datasets) + history_data = self.mgrs.histories._get_history_data( trans, history ) + history_dictionary = history_data[ 'history' ] + hda_dictionaries = history_data[ 'contents' ] + history_dictionary[ 'annotation' ] = history.annotation filled = trans.fill_template( "history/embed.mako", item=history, item_data=datasets, - user_is_owner=user_is_owner, history_dict=history_dict, hda_dicts=hda_dicts ) + user_is_owner=user_is_owner, history_dict=history_dictionary, hda_dicts=hda_dictionaries ) return filled def _get_embed_html( self, trans, item_class, item_id ): diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -19,7 +19,7 @@ from tool_shed.util import basic_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util @@ -194,10 +194,10 @@ includes_tools_for_display_in_tool_panel, \ has_repository_dependencies, \ has_repository_dependencies_only_if_compiling_contained_td = \ - repository_maintenance_util.get_repo_info_dict( trans.app, - trans.user, - encoded_repository_id, - changeset_revision ) + repository_util.get_repo_info_dict( trans.app, + trans.user, + encoded_repository_id, + changeset_revision ) return repository_dict, repository_metadata_dict, repo_info_dict else: log.debug( "Unable to locate repository_metadata record for repository id %s and changeset_revision %s" % \ diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -11,7 +11,7 @@ from tool_shed.metadata import repository_metadata_manager from tool_shed.util import metadata_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import shed_util_common as suc log = logging.getLogger( __name__ ) @@ -320,14 +320,14 @@ def manage_role_associations( self, trans, **kwd ): """Manage users, groups and repositories associated with a role.""" role_id = kwd.get( 'id', None ) - role = repository_maintenance_util.get_role_by_id( trans.app, role_id ) + role = repository_util.get_role_by_id( trans.app, role_id ) # We currently only have a single role associated with a repository, the repository admin role. repository_role_association = role.repositories[ 0 ] repository = repository_role_association.repository - associations_dict = repository_maintenance_util.handle_role_associations( trans.app, - role, - repository, - **kwd ) + associations_dict = repository_util.handle_role_associations( trans.app, + role, + repository, + **kwd ) in_users = associations_dict.get( 'in_users', [] ) out_users = associations_dict.get( 'out_users', [] ) in_groups = associations_dict.get( 'in_groups', [] ) diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -20,7 +20,9 @@ from tool_shed.galaxy_install import dependency_display from tool_shed.metadata import repository_metadata_manager + from tool_shed.tools import tool_validator +from tool_shed.tools import tool_version_manager from tool_shed.util import basic_util from tool_shed.util import common_util @@ -29,7 +31,7 @@ from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import readme_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import search_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util @@ -1060,7 +1062,7 @@ action='browse_repositories', message=message, status=status ) ) - name = kwd.get( 'name', '' ) + name = kwd.get( 'name', '' ).strip() description = kwd.get( 'description', '' ) long_description = kwd.get( 'long_description', '' ) category_ids = util.listify( kwd.get( 'category_id', '' ) ) @@ -1068,7 +1070,7 @@ repository_type = kwd.get( 'repository_type', rt_util.UNRESTRICTED ) if kwd.get( 'create_repository_button', False ): error = False - message = repository_maintenance_util.validate_repository_name( trans.app, name, trans.user ) + message = repository_util.validate_repository_name( trans.app, name, trans.user ) if message: error = True if not description: @@ -1077,13 +1079,13 @@ if error: status = 'error' else: - repository, message = repository_maintenance_util.create_repository( trans.app, - name, - repository_type, - description, - long_description, - user_id=trans.user.id, - category_ids=category_ids ) + repository, message = repository_util.create_repository( trans.app, + name, + repository_type, + description, + long_description, + user_id=trans.user.id, + category_ids=category_ids ) trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', message=message, @@ -1818,7 +1820,7 @@ repository_id, changeset_revision = tup repo_info_dict, cur_includes_tools, cur_includes_tool_dependencies, cur_includes_tools_for_display_in_tool_panel, \ cur_has_repository_dependencies, cur_has_repository_dependencies_only_if_compiling_contained_td = \ - repository_maintenance_util.get_repo_info_dict( trans.app, trans.user, repository_id, changeset_revision ) + repository_util.get_repo_info_dict( trans.app, trans.user, repository_id, changeset_revision ) if cur_has_repository_dependencies and not has_repository_dependencies: has_repository_dependencies = True if cur_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td: @@ -1949,16 +1951,16 @@ after_changeset_revision=changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = repository_maintenance_util.create_repo_info_dict( app=trans.app, - repository_clone_url=repository_clone_url, - changeset_revision=changeset_revision, - ctx_rev=str( ctx.rev() ), - repository_owner=repository.user.username, - repository_name=repository.name, - repository=repository, - repository_metadata=repository_metadata, - tool_dependencies=None, - repository_dependencies=None ) + repo_info_dict = repository_util.create_repo_info_dict( app=trans.app, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + ctx_rev=str( ctx.rev() ), + repository_owner=repository.user.username, + repository_name=repository.name, + repository=repository, + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) includes_data_managers = False includes_datatypes = False includes_tools = False @@ -2272,7 +2274,7 @@ repository.long_description = long_description flush_needed = True if repository.times_downloaded == 0 and repo_name != repository.name: - message = repository_maintenance_util.validate_repository_name( trans.app, repo_name, user ) + message = repository_util.validate_repository_name( trans.app, repo_name, user ) if message: error = True else: @@ -2282,12 +2284,12 @@ trans.app.hgweb_config_manager.change_entry( old_lhs, new_lhs, repo_dir ) # Change the entry in the repository's hgrc file. hgrc_file = os.path.join( repo_dir, '.hg', 'hgrc' ) - repository_maintenance_util.change_repository_name_in_hgrc_file( hgrc_file, repo_name ) + repository_util.change_repository_name_in_hgrc_file( hgrc_file, repo_name ) # Rename the repository's admin role to match the new repository name. repository_admin_role = repository.admin_role repository_admin_role.name = \ - repository_maintenance_util.get_repository_admin_role_name( str( repo_name ), - str( repository.user.username ) ) + repository_util.get_repository_admin_role_name( str( repo_name ), + str( repository.user.username ) ) trans.sa_session.add( repository_admin_role ) repository.name = repo_name flush_needed = True @@ -2377,7 +2379,7 @@ current_allow_push_list = current_allow_push.split( ',' ) else: current_allow_push_list = [] - allow_push_select_field = repository_maintenance_util.build_allow_push_select_field( trans, current_allow_push_list ) + allow_push_select_field = repository_util.build_allow_push_select_field( trans, current_allow_push_list ) checked = alerts_checked or user.email in email_alerts alerts_check_box = CheckboxField( 'alerts', checked=checked ) changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, @@ -2519,10 +2521,10 @@ if repository_metadata: metadata = repository_metadata.metadata role = repository.admin_role - associations_dict = repository_maintenance_util.handle_role_associations( trans.app, - role, - repository, - **kwd ) + associations_dict = repository_util.handle_role_associations( trans.app, + role, + repository, + **kwd ) in_users = associations_dict.get( 'in_users', [] ) out_users = associations_dict.get( 'out_users', [] ) in_groups = associations_dict.get( 'in_groups', [] ) @@ -2755,7 +2757,7 @@ # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( id, **kwd ) + rmm.reset_all_metadata_on_repository_in_tool_shed( id ) if invalid_file_tups: repository = suc.get_repository_in_tool_shed( trans.app, id ) message = tool_util.generate_message_for_invalid_tools( trans.app, @@ -3432,10 +3434,10 @@ basic_util.remove_dir( work_dir ) break if guid: - tool_lineage = tool_util.get_version_lineage_for_tool( trans.app, - repository_id, - repository_metadata, - guid ) + tvm = tool_version_manager.ToolVersionManager( trans.app ) + tool_lineage = tvm.get_version_lineage_for_tool( repository_id, + repository_metadata, + guid ) else: repository_metadata_id = None metadata = None diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -13,13 +13,13 @@ from tool_shed.dependencies import attribute_handlers from tool_shed.galaxy_install import dependency_display from tool_shed.metadata import repository_metadata_manager -import tool_shed.repository_types.util as rt_util +from tool_shed.repository_types import util as rt_util +from tool_shed.tools import data_table_manager from tool_shed.util import basic_util from tool_shed.util import commit_util from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc -from tool_shed.util import tool_util from tool_shed.util import xml_util from galaxy import eggs @@ -100,6 +100,7 @@ if uploaded_file or uploaded_directory: rdah = attribute_handlers.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False ) tdah = attribute_handlers.ToolDependencyAttributeHandler( trans.app, unpopulate=False ) + tdtm = data_table_manager.ToolDataTableManager( trans.app ) ok = True isgzip = False isbz2 = False @@ -221,7 +222,7 @@ # Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded # by parsing the file and adding new entries to the in-memory trans.app.tool_data_tables # dictionary. - error, error_message = tool_util.handle_sample_tool_data_table_conf_file( trans.app, full_path ) + error, error_message = tdtm.handle_sample_tool_data_table_conf_file( full_path, persist=False ) if error: message = '%s<br/>%s' % ( message, error_message ) # See if the content of the change set was valid. @@ -309,7 +310,7 @@ message += invalid_repository_dependencies_message status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - tool_util.reset_tool_data_tables( trans.app ) + tdtm.reset_tool_data_tables() if uploaded_directory: basic_util.remove_dir( uploaded_directory ) trans.response.send_redirect( web.url_for( controller='repository', @@ -323,7 +324,7 @@ basic_util.remove_dir( uploaded_directory ) status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - tool_util.reset_tool_data_tables( trans.app ) + tdtm.reset_tool_data_tables() selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/tool_shed/repository/upload.mako', repository=repository, diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -9,6 +9,7 @@ from time import strftime from galaxy import web +from galaxy.model.orm import and_ from galaxy.util import asbool from galaxy.util import CHUNK_SIZE from galaxy.util.odict import odict @@ -24,7 +25,7 @@ from tool_shed.util import common_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import shed_util_common as suc from tool_shed.util import xml_util @@ -408,7 +409,7 @@ flush = True # Do not allow dependent repository revisions to be automatically installed if population # resulted in errors. - dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( self.app, repository_metadata ) + dependent_downloadable_revisions = self.get_dependent_downloadable_revisions( repository_metadata ) for dependent_downloadable_revision in dependent_downloadable_revisions: if dependent_downloadable_revision.downloadable: dependent_downloadable_revision.downloadable = False @@ -462,13 +463,13 @@ else: category_ids.append( self.app.security.encode_id( category.id ) ) # Create the repository record in the database. - repository, create_message = repository_maintenance_util.create_repository( self.app, - name, - type, - description, - long_description, - user_id=user_id, - category_ids=category_ids ) + repository, create_message = repository_util.create_repository( self.app, + name, + type, + description, + long_description, + user_id=user_id, + category_ids=category_ids ) if create_message: results_message += create_message # Populate the new repository with the contents of exported repository archive. @@ -541,6 +542,66 @@ archives.append( archive_file_name ) return archives, error_message + def get_dependent_downloadable_revisions( self, repository_metadata ): + """ + Return all repository_metadata records that are downloadable and that depend upon the received + repository_metadata record. + """ + # This method is called only from the tool shed. + sa_session = self.app.model.context.current + rm_changeset_revision = repository_metadata.changeset_revision + rm_repository = repository_metadata.repository + rm_repository_name = str( rm_repository.name ) + rm_repository_owner = str( rm_repository.user.username ) + dependent_downloadable_revisions = [] + for repository in sa_session.query( self.app.model.Repository ) \ + .filter( and_( self.app.model.Repository.table.c.id != rm_repository.id, + self.app.model.Repository.table.c.deleted == False, + self.app.model.Repository.table.c.deprecated == False ) ): + downloadable_revisions = repository.downloadable_revisions + if downloadable_revisions: + for downloadable_revision in downloadable_revisions: + if downloadable_revision.has_repository_dependencies: + metadata = downloadable_revision.metadata + if metadata: + repository_dependencies_dict = metadata.get( 'repository_dependencies', {} ) + repository_dependencies_tups = repository_dependencies_dict.get( 'repository_dependencies', [] ) + for repository_dependencies_tup in repository_dependencies_tups: + tool_shed, \ + name, \ + owner, \ + changeset_revision, \ + prior_installation_required, \ + only_if_compiling_contained_td = \ + common_util.parse_repository_dependency_tuple( repository_dependencies_tup ) + if name == rm_repository_name and owner == rm_repository_owner: + # We've discovered a repository revision that depends upon the repository associated + # with the received repository_metadata record, but we need to make sure it depends + # upon the revision. + if changeset_revision == rm_changeset_revision: + dependent_downloadable_revisions.append( downloadable_revision ) + else: + # Make sure the defined changeset_revision is current. + defined_repository_metadata = \ + sa_session.query( self.app.model.RepositoryMetadata ) \ + .filter( self.app.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) \ + .first() + if defined_repository_metadata is None: + # The defined changeset_revision is not associated with a repository_metadata + # record, so updates must be necessary. + defined_repository = suc.get_repository_by_name_and_owner( self.app, name, owner ) + defined_repo = hg_util.get_repo_for_repository( self.app, + repository=defined_repository, + repo_path=None, + create=False ) + updated_changeset_revision = \ + suc.get_next_downloadable_changeset_revision( defined_repository, + defined_repo, + changeset_revision ) + if updated_changeset_revision == rm_changeset_revision: + dependent_downloadable_revisions.append( downloadable_revision ) + return dependent_downloadable_revisions + def get_export_info_dict( self, export_info_file_path ): """ Parse the export_info.xml file contained within the capsule and return a dictionary diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py @@ -0,0 +1,218 @@ +import logging +import os +import tempfile + +from galaxy.util import asbool + +from tool_shed.util import basic_util +from tool_shed.util import hg_util +from tool_shed.util import tool_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util + +log = logging.getLogger( __name__ ) + + +class CustomDatatypeLoader( object ): + + def __init__( self, app ): + self.app = app + + def alter_config_and_load_prorietary_datatypes( self, datatypes_config, relative_install_dir, + deactivate=False, override=True ): + """ + Parse a custom datatypes config (a datatypes_conf.xml file included in an installed + tool shed repository) and add information to appropriate element attributes that will + enable custom datatype class modules, datatypes converters and display applications + to be discovered and properly imported by the datatypes registry. The value of override + will be False when a tool shed repository is being installed. Since installation is + occurring after the datatypes registry has been initialized, the registry's contents + cannot be overridden by conflicting data types. + """ + tree, error_message = xml_util.parse_xml( datatypes_config ) + if tree is None: + return None, None + datatypes_config_root = tree.getroot() + registration = datatypes_config_root.find( 'registration' ) + if registration is None: + # We have valid XML, but not a valid custom datatypes definition. + return None, None + sniffers = datatypes_config_root.find( 'sniffers' ) + converter_path, display_path = self.get_converter_and_display_paths( registration, + relative_install_dir ) + if converter_path: + # Path to datatype converters + registration.attrib[ 'proprietary_converter_path' ] = converter_path + if display_path: + # Path to datatype display applications + registration.attrib[ 'proprietary_display_path' ] = display_path + relative_path_to_datatype_file_name = None + datatype_files = datatypes_config_root.find( 'datatype_files' ) + datatype_class_modules = [] + if datatype_files is not None: + # The <datatype_files> tag set contains any number of <datatype_file> tags. + # <datatype_files> + # <datatype_file name="gmap.py"/> + # <datatype_file name="metagenomics.py"/> + # </datatype_files> + # We'll add attributes to the datatype tag sets so that the modules can be properly imported + # by the datatypes registry. + for elem in datatype_files.findall( 'datatype_file' ): + datatype_file_name = elem.get( 'name', None ) + if datatype_file_name: + # Find the file in the installed repository. + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == datatype_file_name: + datatype_class_modules.append( os.path.join( root, name ) ) + break + break + if datatype_class_modules: + for relative_path_to_datatype_file_name in datatype_class_modules: + datatype_file_name_path, datatype_file_name = os.path.split( relative_path_to_datatype_file_name ) + for elem in registration.findall( 'datatype' ): + # Handle 'type' attribute which should be something like one of the following: + # type="gmap:GmapDB" + # type="galaxy.datatypes.gmap:GmapDB" + dtype = elem.get( 'type', None ) + if dtype: + fields = dtype.split( ':' ) + proprietary_datatype_module = fields[ 0 ] + if proprietary_datatype_module.find( '.' ) >= 0: + # Handle the case where datatype_module is "galaxy.datatypes.gmap". + proprietary_datatype_module = proprietary_datatype_module.split( '.' )[ -1 ] + # The value of proprietary_path must be an absolute path due to job_working_directory. + elem.attrib[ 'proprietary_path' ] = os.path.abspath( datatype_file_name_path ) + elem.attrib[ 'proprietary_datatype_module' ] = proprietary_datatype_module + # Temporarily persist the custom datatypes configuration file so it can be loaded into the + # datatypes registry. + fd, proprietary_datatypes_config = tempfile.mkstemp( prefix="tmp-toolshed-acalpd" ) + os.write( fd, '<?xml version="1.0"?>\n' ) + os.write( fd, '<datatypes>\n' ) + os.write( fd, '%s' % xml_util.xml_to_string( registration ) ) + if sniffers is not None: + os.write( fd, '%s' % xml_util.xml_to_string( sniffers ) ) + os.write( fd, '</datatypes>\n' ) + os.close( fd ) + os.chmod( proprietary_datatypes_config, 0644 ) + # Load custom datatypes + self.app.datatypes_registry.load_datatypes( root_dir=self.app.config.root, + config=proprietary_datatypes_config, + deactivate=deactivate, + override=override ) + if deactivate: + # Reload the upload tool to eliminate deactivated datatype extensions from the file_type + # select list. + tool_util.reload_upload_tools( self.app ) + else: + self.append_to_datatypes_registry_upload_file_formats( registration ) + tool_util.reload_upload_tools( self.app ) + if datatype_files is not None: + try: + os.unlink( proprietary_datatypes_config ) + except: + pass + return converter_path, display_path + + def append_to_datatypes_registry_upload_file_formats( self, elem ): + # See if we have any datatypes that should be displayed in the upload tool's file_type select list. + for datatype_elem in elem.findall( 'datatype' ): + extension = datatype_elem.get( 'extension', None ) + display_in_upload = datatype_elem.get( 'display_in_upload', None ) + if extension is not None and display_in_upload is not None: + display_in_upload = asbool( str( display_in_upload ) ) + if display_in_upload and extension not in self.app.datatypes_registry.upload_file_formats: + self.app.datatypes_registry.upload_file_formats.append( extension ) + + def create_repository_dict_for_proprietary_datatypes( self, tool_shed, name, owner, installed_changeset_revision, + tool_dicts, converter_path=None, display_path=None ): + return dict( tool_shed=tool_shed, + repository_name=name, + repository_owner=owner, + installed_changeset_revision=installed_changeset_revision, + tool_dicts=tool_dicts, + converter_path=converter_path, + display_path=display_path ) + + def get_converter_and_display_paths( self, registration_elem, relative_install_dir ): + """ + Find the relative path to data type converters and display applications included + in installed tool shed repositories. + """ + converter_path = None + display_path = None + for elem in registration_elem.findall( 'datatype' ): + if not converter_path: + # If any of the <datatype> tag sets contain <converter> tags, set the converter_path + # if it is not already set. This requires developers to place all converters in the + # same subdirectory within the repository hierarchy. + for converter in elem.findall( 'converter' ): + converter_config = converter.get( 'file', None ) + if converter_config: + converter_config_file_name = basic_util.strip_path( converter_config ) + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == converter_config_file_name: + # The value of converter_path must be absolute due to job_working_directory. + converter_path = os.path.abspath( root ) + break + if converter_path: + break + if not display_path: + # If any of the <datatype> tag sets contain <display> tags, set the display_path + # if it is not already set. This requires developers to place all display acpplications + # in the same subdirectory within the repository hierarchy. + for display_app in elem.findall( 'display' ): + display_config = display_app.get( 'file', None ) + if display_config: + display_config_file_name = basic_util.strip_path( display_config ) + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == display_config_file_name: + # The value of display_path must be absolute due to job_working_directory. + display_path = os.path.abspath( root ) + break + if display_path: + break + if converter_path and display_path: + break + return converter_path, display_path + + def load_installed_datatype_converters( self, installed_repository_dict, deactivate=False ): + """Load or deactivate proprietary datatype converters.""" + self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, + installed_repository_dict=installed_repository_dict, + deactivate=deactivate ) + + def load_installed_datatypes( self, repository, relative_install_dir, deactivate=False ): + """ + Load proprietary datatypes and return information needed for loading custom + datatypes converters and display applications later. + """ + metadata = repository.metadata + repository_dict = None + datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, relative_install_dir ) + if datatypes_config: + converter_path, display_path = \ + self.alter_config_and_load_prorietary_datatypes( datatypes_config, + relative_install_dir, + deactivate=deactivate ) + if converter_path or display_path: + # Create a dictionary of tool shed repository related information. + repository_dict = \ + self.create_repository_dict_for_proprietary_datatypes( tool_shed=repository.tool_shed, + name=repository.name, + owner=repository.owner, + installed_changeset_revision=repository.installed_changeset_revision, + tool_dicts=metadata.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) + return repository_dict + + def load_installed_display_applications( self, installed_repository_dict, deactivate=False ): + """Load or deactivate custom datatype display applications.""" + self.app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, + deactivate=deactivate ) diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/tool_shed/galaxy_install/dependency_display.py --- a/lib/tool_shed/galaxy_install/dependency_display.py +++ b/lib/tool_shed/galaxy_install/dependency_display.py @@ -1,3 +1,4 @@ +import json import logging import os import threading @@ -461,7 +462,7 @@ url = common_util.url_join( tool_shed_url, 'repository/get_readme_files%s' % params ) raw_text = common_util.tool_shed_get( self.app, tool_shed_url, url ) - readme_files_dict = json.from_json_string( raw_text ) + readme_files_dict = json.loads( raw_text ) else: readme_files_dict = readme_util.build_readme_files_dict( self.app, repository, diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -18,8 +18,6 @@ from tool_shed.util import basic_util from tool_shed.util import common_util -from tool_shed.util import data_manager_util -from tool_shed.util import datatype_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc @@ -27,14 +25,19 @@ from tool_shed.util import tool_util from tool_shed.util import xml_util +from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder from tool_shed.galaxy_install.tool_dependencies.recipe.install_environment import InstallEnvironment from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager +from tool_shed.galaxy_install.tools import data_manager from tool_shed.galaxy_install.tools import tool_panel_manager +from tool_shed.tools import data_table_manager +from tool_shed.tools import tool_version_manager + log = logging.getLogger( __name__ ) @@ -42,6 +45,7 @@ def __init__( self, app ): self.app = app + self.install_model = self.app.install_model self.INSTALL_ACTIONS = [ 'download_binary', 'download_by_url', 'download_file', 'setup_perl_environment', 'setup_python_environment', 'setup_r_environment', 'setup_ruby_environment', 'shell_command' ] @@ -118,7 +122,7 @@ work_dir=work_dir, current_dir=current_dir, initial_download=False ) - if tool_dependency.status in [ self.app.install_model.ToolDependency.installation_status.ERROR ]: + if tool_dependency.status in [ self.install_model.ToolDependency.installation_status.ERROR ]: # If the tool_dependency status is in an error state, return it with no additional # processing. return tool_dependency @@ -130,7 +134,6 @@ return tool_dependency def install_and_build_package_via_fabric( self, tool_shed_repository, tool_dependency, actions_dict ): - sa_session = self.app.install_model.context try: # There is currently only one fabric method. tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) @@ -221,8 +224,8 @@ tool_dependency, error_message, remove_installation_path=False ) - if tool_dependency and tool_dependency.status in [ self.app.install_model.ToolDependency.installation_status.INSTALLED, - self.app.install_model.ToolDependency.installation_status.ERROR ]: + if tool_dependency and tool_dependency.status in [ self.install_model.ToolDependency.installation_status.INSTALLED, + self.install_model.ToolDependency.installation_status.ERROR ]: installed_packages.append( tool_dependency ) if self.app.config.manage_dependency_relationships: # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. @@ -237,7 +240,6 @@ self.install_and_build_package(). The use of fabric is being eliminated, so some of these functions may need to be renamed at some point. """ - sa_session = self.app.install_model.context if not os.path.exists( install_dir ): os.makedirs( install_dir ) actions_dict = dict( install_dir=install_dir ) @@ -353,7 +355,7 @@ package_name=package_name, actions_elem=actions_elem, action_elem=None ) - if tool_dependency.status == self.app.install_model.ToolDependency.installation_status.INSTALLED: + if tool_dependency.status == self.install_model.ToolDependency.installation_status.INSTALLED: # If an <actions> tag was found that matches the current platform, and # self.install_via_fabric() did not result in an error state, set binary_installed # to True in order to skip any remaining platform-specific <actions> tags. @@ -396,7 +398,7 @@ actions_elem=actions_elem, action_elem=None ) if actions_elem.tag == 'action' and \ - tool_dependency.status != self.app.install_model.ToolDependency.installation_status.ERROR: + tool_dependency.status != self.install_model.ToolDependency.installation_status.ERROR: # If the tool dependency is not in an error state, perform any final actions that have been # defined within the actions_group tag set, but outside of an <actions> tag, which defines # the recipe for installing and compiling from source. @@ -416,19 +418,19 @@ package_name=package_name, actions_elem=actions_elems, action_elem=None ) - if tool_dependency.status != self.app.install_model.ToolDependency.installation_status.ERROR: + if tool_dependency.status != self.install_model.ToolDependency.installation_status.ERROR: log.debug( 'Tool dependency %s version %s has been installed in %s.' % \ ( str( package_name ), str( package_version ), str( install_dir ) ) ) return tool_dependency def mark_tool_dependency_installed( self, tool_dependency ): - if tool_dependency.status not in [ self.app.install_model.ToolDependency.installation_status.ERROR, - self.app.install_model.ToolDependency.installation_status.INSTALLED ]: + if tool_dependency.status not in [ self.install_model.ToolDependency.installation_status.ERROR, + self.install_model.ToolDependency.installation_status.INSTALLED ]: log.debug( 'Changing status for tool dependency %s from %s to %s.' % \ ( str( tool_dependency.name ), str( tool_dependency.status ), - str( self.app.install_model.ToolDependency.installation_status.INSTALLED ) ) ) - status = self.app.install_model.ToolDependency.installation_status.INSTALLED + str( self.install_model.ToolDependency.installation_status.INSTALLED ) ) ) + status = self.install_model.ToolDependency.installation_status.INSTALLED tool_dependency = tool_dependency_util.set_tool_dependency_attributes( self.app, tool_dependency=tool_dependency, status=status, @@ -439,8 +441,13 @@ class InstallRepositoryManager( object ): - def __init__( self, app ): + def __init__( self, app, tpm=None ): self.app = app + self.install_model = self.app.install_model + if tpm is None: + self.tpm = tool_panel_manager.ToolPanelManager( self.app ) + else: + self.tpm = tpm def get_repository_components_for_installation( self, encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys ): @@ -497,12 +504,13 @@ def handle_repository_contents( self, tool_shed_repository, tool_path, repository_clone_url, relative_install_dir, tool_shed=None, tool_section=None, shed_tool_conf=None, reinstalling=False ): """ - Generate the metadata for the installed tool shed repository, among other things. This method is called from Galaxy - (never the tool shed) when an administrator is installing a new repository or reinstalling an uninstalled repository. + Generate the metadata for the installed tool shed repository, among other things. + This method is called when an administrator is installing a new repository or + reinstalling an uninstalled repository. """ - install_model = self.app.install_model shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) - irmm = InstalledRepositoryMetadataManager( self.app ) + tdtm = data_table_manager.ToolDataTableManager( self.app ) + irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) metadata_dict, invalid_file_tups = \ irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, changeset_revision=tool_shed_repository.changeset_revision, @@ -518,8 +526,8 @@ tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository ) if tool_shed_status_dict: tool_shed_repository.tool_shed_status = tool_shed_status_dict - install_model.context.add( tool_shed_repository ) - install_model.context.flush() + self.install_model.context.add( tool_shed_repository ) + self.install_model.context.flush() if 'tool_dependencies' in metadata_dict and not reinstalling: tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, tool_shed_repository, @@ -527,28 +535,26 @@ set_status=True ) if 'sample_files' in metadata_dict: sample_files = metadata_dict.get( 'sample_files', [] ) - tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) + tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_data_table_conf_filename, tool_data_table_elems = \ - tool_util.install_tool_data_tables( self.app, tool_shed_repository, tool_index_sample_files ) + tdtm.install_tool_data_tables( tool_shed_repository, tool_index_sample_files ) if tool_data_table_elems: self.app.tool_data_tables.add_new_entries_from_config_file( tool_data_table_conf_filename, None, self.app.config.shed_tool_data_table_config, persist=True ) if 'tools' in metadata_dict: - tpm = tool_panel_manager.ToolPanelManager( self.app ) - tool_panel_dict = tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) + tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) sample_files = metadata_dict.get( 'sample_files', [] ) - tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) + tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] - repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = tool_util.handle_missing_data_table_entry( self.app, - relative_install_dir, - tool_path, - repository_tools_tups ) + repository_tools_tups = tdtm.handle_missing_data_table_entry( relative_install_dir, + tool_path, + repository_tools_tups ) # Handle missing index files for tool parameters that are dynamically generated select lists. repository_tools_tups, sample_files_copied = tool_util.handle_missing_index_file( self.app, tool_path, @@ -561,45 +567,46 @@ sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) - tpm.add_to_tool_panel( repository_name=tool_shed_repository.name, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, - repository_tools_tups=repository_tools_tups, - owner=tool_shed_repository.owner, - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=True ) + self.tpm.add_to_tool_panel( repository_name=tool_shed_repository.name, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.installed_changeset_revision, + repository_tools_tups=repository_tools_tups, + owner=tool_shed_repository.owner, + shed_tool_conf=shed_tool_conf, + tool_panel_dict=tool_panel_dict, + new_install=True ) if 'data_manager' in metadata_dict: - new_data_managers = data_manager_util.install_data_managers( self.app, - self.app.config.shed_data_manager_config_file, - metadata_dict, - shed_config_dict, - relative_install_dir, - tool_shed_repository, - repository_tools_tups ) + dmh = data_manager.DataManagerHandler( self.app ) + new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, + metadata_dict, + shed_config_dict, + relative_install_dir, + tool_shed_repository, + repository_tools_tups ) if 'datatypes' in metadata_dict: - tool_shed_repository.status = install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES + tool_shed_repository.status = self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: tool_shed_repository.includes_datatypes = True - install_model.context.add( tool_shed_repository ) - install_model.context.flush() + self.install_model.context.add( tool_shed_repository ) + self.install_model.context.flush() files_dir = relative_install_dir if shed_config_dict.get( 'tool_path' ): files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) # Load data types required by tools. + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) converter_path, display_path = \ - datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, files_dir, override=False ) + cdl.alter_config_and_load_prorietary_datatypes( datatypes_config, files_dir, override=False ) if converter_path or display_path: # Create a dictionary of tool shed repository related information. repository_dict = \ - datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, - name=tool_shed_repository.name, - owner=tool_shed_repository.owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) + cdl.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, + name=tool_shed_repository.name, + owner=tool_shed_repository.owner, + installed_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dicts=metadata_dict.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) if converter_path: # Load proprietary datatype converters self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, installed_repository_dict=repository_dict ) @@ -628,7 +635,6 @@ return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts def initiate_repository_installation( self, installation_dict ): - install_model = self.app.install_model # The following installation_dict entries are all required. created_or_updated_tool_shed_repositories = installation_dict[ 'created_or_updated_tool_shed_repositories' ] filtered_repo_info_dicts = installation_dict[ 'filtered_repo_info_dicts' ] @@ -648,11 +654,10 @@ tool_shed_url = installation_dict[ 'tool_shed_url' ] # Handle contained tools. if includes_tools_for_display_in_tool_panel and ( new_tool_panel_section_label or tool_panel_section_id ): - tpm = tool_panel_manager.ToolPanelManager( self.app ) tool_panel_section_key, tool_section = \ - tpm.handle_tool_panel_section( self.app.toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + self.tpm.handle_tool_panel_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) else: tool_panel_section_key = None tool_section = None @@ -675,12 +680,12 @@ tsr_ids = [ r.id for r in created_or_updated_tool_shed_repositories ] tool_shed_repositories = [] for tsr_id in tsr_ids: - tsr = install_model.context.query( install_model.ToolShedRepository ).get( tsr_id ) + tsr = self.install_model.context.query( self.install_model.ToolShedRepository ).get( tsr_id ) tool_shed_repositories.append( tsr ) clause_list = [] for tsr_id in tsr_ids: - clause_list.append( install_model.ToolShedRepository.table.c.id == tsr_id ) - query = install_model.context.query( install_model.ToolShedRepository ).filter( or_( *clause_list ) ) + clause_list.append( self.install_model.ToolShedRepository.table.c.id == tsr_id ) + query = self.install_model.context.query( self.install_model.ToolShedRepository ).filter( or_( *clause_list ) ) return encoded_kwd, query, tool_shed_repositories, encoded_repository_ids def install( self, tool_shed_url, name, owner, changeset_revision, install_options ): @@ -726,7 +731,7 @@ shed_tool_conf = install_options.get( 'shed_tool_conf', None ) if shed_tool_conf: # Get the tool_path setting. - index, shed_conf_dict = suc.get_shed_tool_conf_dict( self.app, shed_tool_conf ) + index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( shed_tool_conf ) tool_path = shed_conf_dict[ 'tool_path' ] else: # Pick a semi-random shed-related tool panel configuration file and get the tool_path setting. @@ -792,11 +797,10 @@ self.order_components_for_installation( tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys ) # Install the repositories, keeping track of each one for later display. for index, tsr_id in enumerate( ordered_tsr_ids ): - install_model = self.app.install_model - tool_shed_repository = install_model.context.query( install_model.ToolShedRepository ) \ - .get( self.app.security.decode_id( tsr_id ) ) - if tool_shed_repository.status in [ install_model.ToolShedRepository.installation_status.NEW, - install_model.ToolShedRepository.installation_status.UNINSTALLED ]: + tool_shed_repository = self.install_model.context.query( self.install_model.ToolShedRepository ) \ + .get( self.app.security.decode_id( tsr_id ) ) + if tool_shed_repository.status in [ self.install_model.ToolShedRepository.installation_status.NEW, + self.install_model.ToolShedRepository.installation_status.UNINSTALLED ]: repo_info_dict = ordered_repo_info_dicts[ index ] tool_panel_section_key = ordered_tool_panel_section_keys[ index ] self.install_tool_shed_repository( tool_shed_repository, @@ -814,7 +818,6 @@ def install_tool_shed_repository( self, tool_shed_repository, repo_info_dict, tool_panel_section_key, shed_tool_conf, tool_path, install_tool_dependencies, reinstalling=False ): - install_model = self.app.install_model if tool_panel_section_key: try: tool_section = self.app.toolbox.tool_panel[ tool_panel_section_key ] @@ -827,9 +830,8 @@ if isinstance( repo_info_dict, basestring ): repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) # Clone each repository to the configured location. - suc.update_tool_shed_repository_status( self.app, - tool_shed_repository, - install_model.ToolShedRepository.installation_status.CLONING ) + self.update_tool_shed_repository_status( tool_shed_repository, + self.install_model.ToolShedRepository.installation_status.CLONING ) repo_info_tuple = repo_info_dict[ tool_shed_repository.name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple relative_clone_dir = suc.generate_tool_shed_repository_install_dir( repository_clone_url, @@ -859,13 +861,12 @@ tool_section=tool_section, shed_tool_conf=shed_tool_conf, reinstalling=reinstalling ) - install_model.context.refresh( tool_shed_repository ) + self.install_model.context.refresh( tool_shed_repository ) metadata = tool_shed_repository.metadata if 'tools' in metadata: # Get the tool_versions from the tool shed for each tool in the installed change set. - suc.update_tool_shed_repository_status( self.app, - tool_shed_repository, - install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) + self.update_tool_shed_repository_status( tool_shed_repository, + self.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, str( tool_shed_repository.tool_shed ) ) params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( tool_shed_repository.name ), str( tool_shed_repository.owner ), @@ -875,7 +876,8 @@ text = common_util.tool_shed_get( self.app, tool_shed_url, url ) if text: tool_version_dicts = json.loads( text ) - tool_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository ) + tvm = tool_version_manager.ToolVersionManager( self.app ) + tvm.handle_tool_versions( tool_version_dicts, tool_shed_repository ) else: if not error_message: error_message = "" @@ -885,9 +887,8 @@ if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata: work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-itsr" ) # Install tool dependencies. - suc.update_tool_shed_repository_status( self.app, - tool_shed_repository, - install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + self.update_tool_shed_repository_status( tool_shed_repository, + self.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = hg_util.get_config_from_disk( 'tool_dependencies.xml', install_dir ) itdm = InstallToolDependencyManager( self.app ) @@ -896,9 +897,8 @@ tool_dependencies=tool_shed_repository.tool_dependencies, from_tool_migration_manager=False ) basic_util.remove_dir( work_dir ) - suc.update_tool_shed_repository_status( self.app, - tool_shed_repository, - install_model.ToolShedRepository.installation_status.INSTALLED ) + self.update_tool_shed_repository_status( tool_shed_repository, + self.install_model.ToolShedRepository.installation_status.INSTALLED ) if self.app.config.manage_dependency_relationships: # Add the installed repository and any tool dependencies to the in-memory dictionaries # in the installed_repository_manager. @@ -907,7 +907,7 @@ # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. suc.set_repository_attributes( self.app, tool_shed_repository, - status=install_model.ToolShedRepository.installation_status.ERROR, + status=self.install_model.ToolShedRepository.installation_status.ERROR, error_message=error_message, deleted=False, uninstalled=False, @@ -962,3 +962,13 @@ ordered_repo_info_dicts.append( repo_info_dict ) ordered_tool_panel_section_keys.append( tool_panel_section_key ) return ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys + + def update_tool_shed_repository_status( self, tool_shed_repository, status, error_message=None ): + """ + Update the status of a tool shed repository in the process of being installed into Galaxy. + """ + tool_shed_repository.status = status + if error_message: + tool_shed_repository.error_message = str( error_message ) + self.install_model.context.add( tool_shed_repository ) + self.install_model.context.flush() diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -7,14 +7,15 @@ from galaxy import util from tool_shed.util import common_util from tool_shed.util import container_util -from tool_shed.util import data_manager_util -from tool_shed.util import datatype_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import xml_util from galaxy.model.orm import and_ +from tool_shed.galaxy_install.datatypes import custom_datatype_manager +from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import data_manager from tool_shed.galaxy_install.tools import tool_panel_manager log = logging.getLogger( __name__ ) @@ -81,8 +82,9 @@ repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools_for_display_in_tool_panel: tpm = tool_panel_manager.ToolPanelManager( self.app ) + irmm = InstalledRepositoryMetadataManager( self.app, tpm ) metadata = repository.metadata - repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata ) + repository_tools_tups = irmm.get_repository_tools_tups( metadata ) # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] tpm.add_to_tool_panel( repository.name, @@ -97,13 +99,13 @@ tp, data_manager_relative_install_dir = repository.get_tool_relative_path( self.app ) # Hack to add repository.name here, which is actually the root of the installed repository data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name ) - new_data_managers = data_manager_util.install_data_managers( self.app, - self.app.config.shed_data_manager_config_file, - metadata, - repository.get_shed_config_dict( self.app ), - data_manager_relative_install_dir, - repository, - repository_tools_tups ) + dmh = data_manager.DataManagerHandler( self.app ) + new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, + metadata, + repository.get_shed_config_dict( self.app ), + data_manager_relative_install_dir, + repository, + repository_tools_tups ) self.install_model.context.add( repository ) self.install_model.context.flush() if repository.includes_datatypes: @@ -112,17 +114,17 @@ else: repository_install_dir = os.path.abspath( relative_install_dir ) # Activate proprietary datatypes. - installed_repository_dict = datatype_util.load_installed_datatypes( self.app, - repository, - repository_install_dir, - deactivate=False ) + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) + installed_repository_dict = cdl.load_installed_datatypes( repository, + repository_install_dir, + deactivate=False ) if installed_repository_dict: converter_path = installed_repository_dict.get( 'converter_path' ) if converter_path is not None: - datatype_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=False ) + cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=False ) display_path = installed_repository_dict.get( 'display_path' ) if display_path is not None: - datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=False ) + cdl.load_installed_display_applications( installed_repository_dict, deactivate=False ) def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ): """ @@ -340,8 +342,8 @@ installed_rd_tups = [] missing_rd_tups = [] for tsr in repository.repository_dependencies: - prior_installation_required = suc.set_prior_installation_required( self.app, repository, tsr ) - only_if_compiling_contained_td = suc.set_only_if_compiling_contained_td( repository, tsr ) + prior_installation_required = self.set_prior_installation_required( repository, tsr ) + only_if_compiling_contained_td = self.set_only_if_compiling_contained_td( repository, tsr ) rd_tup = [ tsr.tool_shed, tsr.name, tsr.owner, @@ -730,22 +732,24 @@ self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) def load_proprietary_datatypes( self ): + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) for tool_shed_repository in self.context.query( self.install_model.ToolShedRepository ) \ - .filter( and_( self.install_model.ToolShedRepository.table.c.includes_datatypes==True, - self.install_model.ToolShedRepository.table.c.deleted==False ) ) \ - .order_by( self.install_model.ToolShedRepository.table.c.id ): + .filter( and_( self.install_model.ToolShedRepository.table.c.includes_datatypes==True, + self.install_model.ToolShedRepository.table.c.deleted==False ) ) \ + .order_by( self.install_model.ToolShedRepository.table.c.id ): relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) if relative_install_dir: - installed_repository_dict = datatype_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) + installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository, relative_install_dir ) if installed_repository_dict: self.installed_repository_dicts.append( installed_repository_dict ) def load_proprietary_converters_and_display_applications( self, deactivate=False ): + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) for installed_repository_dict in self.installed_repository_dicts: if installed_repository_dict[ 'converter_path' ]: - datatype_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) + cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=deactivate ) if installed_repository_dict[ 'display_path' ]: - datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) + cdl.load_installed_display_applications( installed_repository_dict, deactivate=deactivate ) def purge_repository( self, repository ): """Purge a repository with status New (a white ghost) from the database.""" @@ -955,6 +959,47 @@ return True return False + def set_only_if_compiling_contained_td( self, repository, required_repository ): + """ + Return True if the received required_repository is only needed to compile a tool + dependency defined for the received repository. + """ + # This method is called only from Galaxy when rendering repository dependencies + # for an installed tool shed repository. + # TODO: Do we need to check more than changeset_revision here? + required_repository_tup = [ required_repository.tool_shed, \ + required_repository.name, \ + required_repository.owner, \ + required_repository.changeset_revision ] + for tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td: + partial_tup = tup[ 0:4 ] + if partial_tup == required_repository_tup: + return 'True' + return 'False' + + def set_prior_installation_required( self, repository, required_repository ): + """ + Return True if the received required_repository must be installed before the + received repository. + """ + tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, + str( required_repository.tool_shed ) ) + required_repository_tup = [ tool_shed_url, + str( required_repository.name ), + str( required_repository.owner ), + str( required_repository.changeset_revision ) ] + # Get the list of repository dependency tuples associated with the received repository + # where prior_installation_required is True. + required_rd_tups_that_must_be_installed = repository.requires_prior_installation_of + for required_rd_tup in required_rd_tups_that_must_be_installed: + # Repository dependency tuples in metadata include a prior_installation_required value, + # so strip it for comparision. + partial_required_rd_tup = required_rd_tup[ 0:4 ] + if partial_required_rd_tup == required_repository_tup: + # Return the string value of prior_installation_required, which defaults to 'False'. + return str( required_rd_tup[ 4 ] ) + return 'False' + def update_existing_tool_dependency( self, repository, original_dependency_dict, new_dependencies_dict ): """ Update an exsiting tool dependency whose definition was updated in a change set diff -r 7ac01ee81cd6379ae78555cf8070239be3527d65 -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -5,20 +5,27 @@ from galaxy.util import inflector from galaxy.web.form_builder import SelectField +from tool_shed.galaxy_install.tools import tool_panel_manager from tool_shed.metadata import metadata_generator from tool_shed.util import common_util +from tool_shed.util import repository_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util +from tool_shed.util import xml_util log = logging.getLogger( __name__ ) class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app ): + def __init__( self, app, tpm=None ): super( InstalledRepositoryMetadataManager, self ).__init__( app ) self.app = app + if tpm is None: + self.tpm = tool_panel_manager.ToolPanelManager( self.app ) + else: + self.tpm = tpm def build_repository_ids_select_field( self, name='repository_ids', multiple=True, display='checkboxes' ): """Generate the current list of repositories for resetting metadata.""" @@ -46,11 +53,32 @@ return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) + def get_repository_tools_tups( self, metadata_dict ): + """ + Return a list of tuples of the form (relative_path, guid, tool) for each tool defined + in the received tool shed repository metadata. + """ + repository_tools_tups = [] + index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( metadata_dict.get( 'shed_config_filename' ) ) + if 'tools' in metadata_dict: + for tool_dict in metadata_dict[ 'tools' ]: + load_relative_path = relative_path = tool_dict.get( 'tool_config', None ) + if shed_conf_dict.get( 'tool_path' ): + load_relative_path = os.path.join( shed_conf_dict.get( 'tool_path' ), relative_path ) + guid = tool_dict.get( 'guid', None ) + if relative_path and guid: + tool = self.app.toolbox.load_tool( os.path.abspath( load_relative_path ), guid=guid ) + else: + tool = None + if tool: + repository_tools_tups.append( ( relative_path, guid, tool ) ) + return repository_tools_tups + def reset_all_metadata_on_installed_repository( self, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" invalid_file_tups = [] metadata_dict = {} - repository = suc.get_installed_tool_shed_repository( self.app, id ) + repository = repository_util.get_installed_tool_shed_repository( self.app, id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( self.app ) if relative_install_dir: @@ -67,7 +95,7 @@ persist=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: - suc.update_in_shed_tool_config( self.app, repository ) + self.update_in_shed_tool_config( repository ) self.app.install_model.context.add( repository ) self.app.install_model.context.flush() log.debug( 'Metadata has been reset on repository %s.' % repository.name ) @@ -90,7 +118,7 @@ unsuccessful_count = 0 for repository_id in repository_ids: try: - repository = suc.get_installed_tool_shed_repository( self.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id ) owner = str( repository.owner ) invalid_file_tups, metadata_dict = \ self.reset_all_metadata_on_installed_repository( repository_id ) @@ -117,3 +145,49 @@ message = 'Select at least one repository to on which to reset all metadata.' status = 'error' return message, status + + def tool_shed_from_repository_clone_url( self, repository_clone_url ): + """Given a repository clone URL, return the tool shed that contains the repository.""" + return common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) + + def update_in_shed_tool_config( self, repository ): + """ + A tool shed repository is being updated so change the shed_tool_conf file. Parse the config + file to generate the entire list of config_elems instead of using the in-memory list. + """ + shed_conf_dict = repository.get_shed_config_dict( self.app ) + shed_tool_conf = shed_conf_dict[ 'config_filename' ] + tool_path = shed_conf_dict[ 'tool_path' ] + tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) + repository_tools_tups = self.get_repository_tools_tups( repository.metadata ) + clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) + tool_shed = self.tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) + owner = repository.owner + if not owner: + owner = suc.get_repository_owner( cleaned_repository_clone_url ) + guid_to_tool_elem_dict = {} + for tool_config_filename, guid, tool in repository_tools_tups: + guid_to_tool_elem_dict[ guid ] = self.tpm.generate_tool_elem( tool_shed, + repository.name, + repository.changeset_revision, + repository.owner or '', + tool_config_filename, + tool, + None ) + config_elems = [] + tree, error_message = xml_util.parse_xml( shed_tool_conf ) + if tree: + root = tree.getroot() + for elem in root: + if elem.tag == 'section': + for i, tool_elem in enumerate( elem ): + guid = tool_elem.attrib.get( 'guid' ) + if guid in guid_to_tool_elem_dict: + elem[i] = guid_to_tool_elem_dict[ guid ] + elif elem.tag == 'tool': + guid = elem.attrib.get( 'guid' ) + if guid in guid_to_tool_elem_dict: + elem = guid_to_tool_elem_dict[ guid ] + config_elems.append( elem ) + self.tpm.config_elems_to_xml_file( config_elems, shed_tool_conf, tool_path ) This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/e6f9927e064e/ Changeset: e6f9927e064e User: martenson Date: 2014-07-23 21:48:59 Summary: pack JS Affected #: 2 files diff -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 -r e6f9927e064eb0836b159cc04f20df350003adfc static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -30,7 +30,7 @@ // missing features below "click .toolbtn_save_modifications" : "comingSoon", - "click .btn-share-dataset" : "comingSoon" + // "click .btn-share-dataset" : "comingSoon" }, diff -r ec1d03be24f7d98fb28ad6792b61e89ebb3f1632 -r e6f9927e064eb0836b159cc04f20df350003adfc static/scripts/packed/mvc/library/library-dataset-view.js --- a/static/scripts/packed/mvc/library/library-dataset-view.js +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .toolbtn_save_modifications":"comingSoon","click .btn-remove-restrictions":"comingSoon","click .btn-make-private":"comingSoon","click .btn-share-dataset":"comingSoon"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){f(e)},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var g=new c.HistoryItem();g.url=g.urlRoot+f+"/contents";var e="/api/histories/"+f+"/set_as_current";$.ajax({url:e,type:"PUT"});g.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(i,h){if(typeof h.responseJSON!=="undefined"){d.error("Dataset not imported. "+h.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(){$(".tooltip").remove();var f=this.templateDatasetPermissions();this.$el.html(f({item:this.model}));var g=false;if(Galaxy.currUser){g=Galaxy.currUser.isAdmin()}var e=this;$.get("/api/libraries/datasets/"+e.id+"/permissions/current").done(function(j){var k=[];for(var m=0;m<j.length;m++){k.push(j[m]+":"+j[m])}if(g){var h={minimumInputLength:1,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:e.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+e.id+"/permissions",dataType:"json",quietMillis:100,data:function(i,p){return{q:i,page_limit:10,page:p}},results:function(q,p){var i=(p*10)<q.total;return{results:q.roles,more:i}}},formatResult:function l(i){return i.name+" type: "+i.type},formatSelection:function o(i){return i.name},initSelection:function(i,q){var p=[];$(i.val().split(",")).each(function(){var r=this.split(":");p.push({id:r[1],name:r[1]})});q(p)},initialData:k.join(","),dropdownCssClass:"bigdrop"};this.accessSelectObject=new b.View(h)}else{var n=this.templateAccessSelect();$.get("/api/libraries/datasets/"+e.id+"/permissions",function(i){$(".access_perm").html(n({options:i.roles}));this.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")});$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},comingSoon:function(){d.warning("Feature coming soon")},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify dataset" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Change permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> go to Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> see the Dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1><%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-success">You have rights to change permissions on this dataset. That means you can control who can access it, who can modify it and also appoint others that can manage permissions on it.</div>');e.push('<div class="dataset_table">');e.push("<h2>Basic permissions</h2>");e.push("<p>You can remove all access restrictions on this dataset. ");e.push('<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to see the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button"><span class="fa fa-globe"></span> Remove restrictions</span></button>');e.push("</p>");e.push("<p>You can make this dataset private to you. ");e.push('<button data-toggle="tooltip" data-placement="top" title="Only you will be able to see the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"></span> Make private</span></button>');e.push("</p>");e.push("<p>You can share this dataset with another Galaxy user. ");e.push('<button data-toggle="tooltip" data-placement="top" title="Only you and the other user will be able to see the dataset." class="btn btn-default btn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push("</p>");e.push("<h2>Advanced permissions</h2>");e.push("<p>You can assign any number of roles to any of the following three dataset permission types. However please read carefully the implications of such actions.</p>");e.push("<h3>Access Roles</h3>");e.push('<div class="alert alert-info">User has to have <strong>all these roles</strong> in order to see this dataset.</div>');e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("<h3>Modify Roles</h3>");e.push('<div class="alert alert-info">Users with <strong>any</strong> of these roles can modify the information about this dataset.</div>');e.push('<div id="modify_perm" class="modify_perm"></div>');e.push("<h3>Manage Roles</h3>");e.push('<div class="alert alert-info">Users with <strong>any</strong> of these roles can change permissions of this dataset.</div>');e.push('<div id="manage_perm" class="manage_perm"></div>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){f(e)},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var g=new c.HistoryItem();g.url=g.urlRoot+f+"/contents";var e="/api/histories/"+f+"/set_as_current";$.ajax({url:e,type:"PUT"});g.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(i,h){if(typeof h.responseJSON!=="undefined"){d.error("Dataset not imported. "+h.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while fetching dataset permissions. :(")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};this.accessSelectObject=new b.View(o);this.modifySelectObject=new b.View(l);this.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));this.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f})}).fail(function(){d.error("An error occurred while making dataset private. :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f})}).fail(function(){d.error("An error occurred while making dataset unrestricted. :(")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Permissions: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<hr/>");e.push("<h2>Library-related permissions</h2>");e.push('<div class="alert alert-success">You have the permission to modify this Library item. This includes changing its metadata and other information.</div>');e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify the information about this library item.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-success">You have the permission to manage permissions on this dataset. That means you can control who can access it and also appoint others that can manage permissions on it.</div>');e.push('<div class="alert alert-warning">Changes made here will affect <strong>every</strong> library item and every history this dataset is part of.</div>');e.push("<h4>Roles that can access dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/e78b03ee1740/ Changeset: e78b03ee1740 User: martenson Date: 2014-07-24 23:26:41 Summary: permission API, set permissions Affected #: 3 files diff -r e6f9927e064eb0836b159cc04f20df350003adfc -r e78b03ee17402b722930538e1b93335c28e075e6 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -851,8 +851,8 @@ def set_all_dataset_permissions( self, dataset, permissions={} ): """ - Set new permissions on a dataset, eliminating all current permissions - permissions looks like: { Action : [ Role, Role ] } + Set new full permissions on a dataset, eliminating all current permissions. + Permission looks like: { Action : [ Role, Role ] } """ # Make sure that DATASET_MANAGE_PERMISSIONS is associated with at least 1 role has_dataset_manage_permissions = False @@ -884,8 +884,8 @@ def set_dataset_permission( self, dataset, permission={} ): """ - Set a specific permission on a dataset, leaving all other current permissions on the dataset alone - permissions looks like: { Action : [ Role, Role ] } + Set a specific permission on a dataset, leaving all other current permissions on the dataset alone. + Permission looks like: { Action : [ Role, Role ] } """ flush_needed = False for action, roles in permission.items(): diff -r e6f9927e064eb0836b159cc04f20df350003adfc -r e78b03ee17402b722930538e1b93335c28e075e6 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -181,7 +181,7 @@ :type encoded_dataset_id: an encoded id string :param action: (required) describes what action should be performed - available actions: make_private, remove_restrictions + available actions: make_private, remove_restrictions, set_permissions :type action: string :rtype: dictionary @@ -199,6 +199,16 @@ if not can_manage: raise exceptions.InsufficientPermissionsException( 'You do not have proper permissions to manage permissions on this dataset.' ) + new_access_roles_ids = kwd.get( 'access_ids[]', None ) + new_manage_roles_ids = kwd.get( 'manage_ids[]', None ) + new_modify_roles_ids = kwd.get( 'modify_ids[]', None ) + # if new_access_roles_ids is None: + # new_access_roles_ids = kwd.get( 'access_ids', None ) + # if new_manage_roles_ids is None: + # new_manage_roles_ids = kwd.get( 'manage_ids', None ) + # if new_modify_roles_ids is None: + # new_modify_roles_ids = kwd.get( 'modify_ids', None ) + action = kwd.get( 'action', None ) if action is None: raise exceptions.RequestParameterMissingException( 'The mandatory parameter "action" is missing.' ) @@ -214,11 +224,12 @@ trans.sa_session.flush() if not trans.app.security_agent.dataset_is_private_to_user( trans, library_dataset ): raise exceptions.InternalServerError( 'An error occured while making dataset private.' ) - elif action == 'set_dataset_access_roles': - raise exceptions.NotImplemented() - elif action == 'set_dataset_manage_roles': - raise exceptions.NotImplemented() - elif action == 'set_library_dataset_modify_roles': + elif action == 'set_permissions': + # permission = { Action : [ Role, Role ] } + # trans.app.security_agent.set_dataset_permission( dataset, permission ) + + + raise exceptions.NotImplemented() else: raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' diff -r e6f9927e064eb0836b159cc04f20df350003adfc -r e78b03ee17402b722930538e1b93335c28e075e6 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -27,6 +27,7 @@ "click .btn-copy-link-to-clipboard" : "copyToClipboard", "click .btn-make-private" : "makeDatasetPrivate", "click .btn-remove-restrictions" : "removeDatasetRestrictions", + "click .toolbtn_save_permissions" : "savePermissions", // missing features below "click .toolbtn_save_modifications" : "comingSoon", @@ -367,14 +368,14 @@ dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller }; - this.accessSelectObject = new mod_select.View(access_select_options); - this.modifySelectObject = new mod_select.View(modify_select_options); - this.manageSelectObject = new mod_select.View(manage_select_options); + self.accessSelectObject = new mod_select.View(access_select_options); + self.modifySelectObject = new mod_select.View(modify_select_options); + self.manageSelectObject = new mod_select.View(manage_select_options); } else { // Non-admins have select with pre-loaded options var template = self.templateAccessSelect(); $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) { $('.access_perm').html(template({options:data.roles})); - this.accessSelectObject = $('#access_select').select2(); + self.accessSelectObject = $('#access_select').select2(); }).fail(function() { mod_toastr.error('An error occurred while fetching data with permissions. :('); }); @@ -398,21 +399,59 @@ $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { self.model.set({is_unrestricted:false}); self.showPermissions({fetched_permissions:fetched_permissions}) + mod_toastr.success('The dataset is now private to you'); }).fail(function(){ - mod_toastr.error('An error occurred while making dataset private. :('); + mod_toastr.error('An error occurred while making dataset private :('); }); }, removeDatasetRestrictions: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions").done(function(fetched_permissions) { + $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") + .done(function(fetched_permissions) { self.model.set({is_unrestricted:true}); self.showPermissions({fetched_permissions:fetched_permissions}) - }).fail(function(){ - mod_toastr.error('An error occurred while making dataset unrestricted. :('); + mod_toastr.success('Access to this dataset is now unrestricted'); + }) + .fail(function(){ + mod_toastr.error('An error occurred while making dataset unrestricted :('); }); }, + savePermissions: function(event){ + var self = this; + var access_roles = this.accessSelectObject.$el.select2('data'); + var manage_roles = this.manageSelectObject.$el.select2('data'); + var modify_roles = this.modifySelectObject.$el.select2('data'); + + var access_ids = []; + var manage_ids = []; + var modify_ids = []; + + for (var i = access_roles.length - 1; i >= 0; i--) { + access_ids.push(access_roles[i].id); + }; + for (var i = manage_roles.length - 1; i >= 0; i--) { + manage_ids.push(manage_roles[i].id); + }; + for (var i = modify_roles.length - 1; i >= 0; i--) { + modify_ids.push(modify_roles[i].id); + }; + + // access_ids = typeof access_ids === 'string' ? access_ids : $.param(access_ids) + // manage_ids = typeof manage_ids === 'string' ? manage_ids : $.param(manage_ids) + // modify_ids = typeof modify_ids === 'string' ? modify_ids : $.param(modify_ids) + + $.post("/api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + .done(function(fetched_permissions){ + //fetch dataset again + self.showPermissions({fetched_permissions:fetched_permissions}) + }) + .fail(function(){ + mod_toastr.error('An error occurred while setting dataset permissions :('); + }) + }, + templateDataset : function(){ var tmpl_array = []; // CONTAINER START @@ -687,6 +726,17 @@ tmpl_array.push('<div class="dataset_table">'); + tmpl_array.push('<h2>Library-related permissions</h2>'); + // tmpl_array.push('<p>You have the permission to modify this Library item. This includes changing its name, metadata, and other information.</p>'); + tmpl_array.push('<h4>Roles that can modify the library item</h4>'); + tmpl_array.push('<div id="modify_perm" class="modify_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>'); + // tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); + tmpl_array.push('<hr/>'); + + tmpl_array.push('<h2>Dataset-related permissions</h2>'); + tmpl_array.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>'); + tmpl_array.push('<% if (!item.get("is_unrestricted")) { %>'); tmpl_array.push(' <p>You can remove all access restrictions on this dataset. '); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">'); @@ -703,28 +753,16 @@ // tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Only you and the suers you choose will be able to access the dataset." class="btn btn-default btn-share-dataset primary-button" type="button"><span class="fa fa-share"> Share Privately</span></button>'); // tmpl_array.push(' </p>'); tmpl_array.push('<% } %>'); - - tmpl_array.push('<hr/>'); - tmpl_array.push('<h2>Library-related permissions</h2>'); - tmpl_array.push('<div class="alert alert-success">You have the permission to modify this Library item. This includes changing its metadata and other information.</div>'); - tmpl_array.push('<h4>Roles that can modify the library item</h4>'); - tmpl_array.push('<div id="modify_perm" class="modify_perm roles-selection"></div>'); - tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify the information about this library item.</div>'); - tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); - tmpl_array.push('<hr/>'); - - tmpl_array.push('<h2>Dataset-related permissions</h2>'); - tmpl_array.push('<div class="alert alert-success">You have the permission to manage permissions on this dataset. That means you can control who can access it and also appoint others that can manage permissions on it.</div>'); - tmpl_array.push('<div class="alert alert-warning">Changes made here will affect <strong>every</strong> library item and every history this dataset is part of.</div>'); - tmpl_array.push('<h4>Roles that can access dataset</h4>'); + // tmpl_array.push('<p>You have the permission to manage permissions on this dataset. That means you can control who can access it and also appoint others that can manage permissions on it.</p>'); + tmpl_array.push('<h4>Roles that can access the dataset</h4>'); tmpl_array.push('<div id="access_perm" class="access_perm roles-selection"></div>'); tmpl_array.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>'); - tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); + // tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); tmpl_array.push('<h4>Roles that can manage permissions on the dataset</h4>'); tmpl_array.push('<div id="manage_perm" class="manage_perm roles-selection"></div>'); tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>'); - tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); https://bitbucket.org/galaxy/galaxy-central/commits/3fd7bfda6be3/ Changeset: 3fd7bfda6be3 User: martenson Date: 2014-07-24 23:27:02 Summary: Merge Affected #: 11 files diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1712,10 +1712,15 @@ if self.__display_multirun_option(): # Select multiple datasets, run multiple jobs. multirun_key = "%s|__multirun__" % self.name + collection_multirun_key = "%s|__collection_multirun__" % self.name if multirun_key in (other_values or {}): multirun_value = listify( other_values[ multirun_key ] ) if multirun_value and len( multirun_value ) > 1: default_field = "select_multiple" + elif collection_multirun_key in (other_values or {}): + multirun_value = listify( other_values[ collection_multirun_key ] ) + if multirun_value: + default_field = "select_collection" else: multirun_value = value multi_dataset_matcher = DatasetMatcher( trans, self, multirun_value, other_values ) @@ -2014,9 +2019,17 @@ default_field = "select_single_collection" fields = odict() + collection_multirun_key = "%s|__collection_multirun__" % self.name + if collection_multirun_key in (other_values or {}): + multirun_value = other_values[ collection_multirun_key ] + if multirun_value: + default_field = "select_map_over_collections" + else: + multirun_value = value + history = self._get_history( trans ) fields[ "select_single_collection" ] = self._get_single_collection_field( trans=trans, history=history, value=value, other_values=other_values ) - fields[ "select_map_over_collections" ] = self._get_select_dataset_collection_field( trans=trans, history=history, value=value, other_values=other_values ) + fields[ "select_map_over_collections" ] = self._get_select_dataset_collection_field( trans=trans, history=history, value=multirun_value, other_values=other_values ) return self._switch_fields( fields, default_field=default_field ) diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1514,7 +1514,7 @@ @web.expose def delete_address( self, trans, cntrller, address_id=None, user_id=None ): try: - user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decod_id( address_id ) ) + user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) except: message = 'Invalid address is (%s)' % address_id status = 'error' @@ -1522,7 +1522,7 @@ user_address.deleted = True trans.sa_session.add( user_address ) trans.sa_session.flush() - 'Address (%s) deleted' % user_address.desc + message = 'Address (%s) deleted' % user_address.desc status = 'done' return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1262,7 +1262,11 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) metadata = repository_metadata.metadata toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) + # Initialize the repository dependency RelationBuilder. rb = relation_builder.RelationBuilder( trans.app, repository, repository_metadata, toolshed_base_url ) + # Work-around to ensure repositories that contain packages needed only for compiling + # a dependent package are included in the capsule. + rb.set_filter_dependencies_needed_for_compiling( False ) # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = rb.get_repository_dependencies_for_changeset_revision() if repository_dependencies: diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -245,9 +245,13 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, self.repository_id, self.changeset_revision ) - # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. + # Get a dictionary of all repositories upon which the contents of the current + # repository_metadata record depend. toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) rb = RelationBuilder( self.app, repository, repository_metadata, toolshed_base_url ) + # Work-around to ensure repositories that contain packages needed only for compiling + # a dependent package are included in the capsule. + rb.set_filter_dependencies_needed_for_compiling( False ) repository_dependencies = rb.get_repository_dependencies_for_changeset_revision() repo = hg_util.get_repo_for_repository( self.app, repository=self.repository, diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f lib/tool_shed/dependencies/repository/relation_builder.py --- a/lib/tool_shed/dependencies/repository/relation_builder.py +++ b/lib/tool_shed/dependencies/repository/relation_builder.py @@ -23,6 +23,11 @@ self.handled_key_rd_dicts = [] self.key_rd_dicts_to_be_processed = [] self.tool_shed_url = tool_shed_url + # This is a temporary work-around for handling repository dependencies that are needed + # only if compiling a dependent package. This value should be True unless exporting + # a repository capsule, in which case the set_filter_dependencies_needed_for_compiling() + # function is called. + self.filter_dependencies_needed_for_compiling = True def can_add_to_key_rd_dicts( self, key_rd_dict, key_rd_dicts ): """Handle the case where an update to the changeset revision was done.""" @@ -389,9 +394,12 @@ current_repository_key_rd_dicts = \ self.get_updated_changeset_revisions_for_repository_dependencies( current_repository_key_rd_dicts ) for key_rd_dict in current_repository_key_rd_dicts: - # Filter out repository dependencies that are required only if compiling the dependent - # repository's tool dependency. - key_rd_dict = self.filter_only_if_compiling_contained_td( key_rd_dict ) + if self.filter_dependencies_needed_for_compiling: + # Filter out repository dependencies that are required only if compiling the dependent + # repository's tool dependency. + # TODO: this temporary work-around should be removed when the underlying framework + # support for handling only_if_compiling_contained_td-flagged repositories is completed. + key_rd_dict = self.filter_only_if_compiling_contained_td( key_rd_dict ) if key_rd_dict: is_circular = False in_handled_key_rd_dicts = self.in_key_rd_dicts( key_rd_dict, self.handled_key_rd_dicts ) @@ -483,6 +491,9 @@ clean_key_rd_dicts.append( new_key_rd_dict ) return clean_key_rd_dicts + def set_filter_dependencies_needed_for_compiling( self, value ): + self.filter_dependencies_needed_for_compiling = asbool( value ) + def update_circular_repository_dependencies( self, repository_key, repository_dependency, repository_dependencies ): repository_dependency_as_key = self.get_repository_dependency_as_key( repository_dependency ) repository_key_as_repository_dependency = repository_key.split( container_util.STRSEP ) diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -12,6 +12,7 @@ from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util +from tool_shed.util import xml_util log = logging.getLogger( __name__ ) diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f static/scripts/galaxy.tools.js --- a/static/scripts/galaxy.tools.js +++ b/static/scripts/galaxy.tools.js @@ -86,7 +86,7 @@ }).attr( 'title', selectionType['select_by'] - ); + ).data( "index", iIndex ); view.formRow().find( "label" ).append( button ); } }); @@ -114,11 +114,13 @@ } else { $("div#remap-row").css("display", "none"); } - this.formRow().find( "i" ).each(function(index, iElement) { + this.formRow().find( "i" ).each(function(_, iElement) { + var $iElement = $(iElement); + var index = $iElement.data("index"); if(index == enableIndex) { - $(iElement).css('color', 'black'); + $iElement.css('color', 'black'); } else { - $(iElement).css('color', 'Gray'); + $iElement.css('color', 'Gray'); } }); var $select = this.$( "select" ); diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -103,8 +103,9 @@ var self = this, menu = create_icon_buttons_menu([ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { - visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) { - _.each(tracks, function(track) { + visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, + function(new_tracks) { + _.each(new_tracks, function(track) { view.add_drawable( tracks.object_from_template(track, view, view) ); }); }); diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f test/functional/tools/collection_two_paired.xml --- /dev/null +++ b/test/functional/tools/collection_two_paired.xml @@ -0,0 +1,69 @@ +<tool id="collection_two_paired" name="collection_two_paired" version="0.1.0"> + <command> + #if $kind.collection_type == "paired" + cat $kind.f1.forward $kind.f1['reverse'] >> $out1; + cat $kind.f2.forward $kind.f2['reverse'] >> $out1; + #else + #for $i, $_ in enumerate($kind.f1): + cat $kind.f1[$i] $kind.f2[$i] >> $out1; + #end for + #end if + </command> + <inputs> + <conditional name="kind"> + <param type="select" name="collection_type"> + <option value="paired">Paired Datasets</option> + <option value="list">List of Datasets</option> + </param> + <when value="paired"> + <param name="f1" type="data_collection" collection_type="paired" /> + <param name="f2" type="data_collection" collection_type="paired" /> + </when> + <when value="list"> + <param name="f1" type="data_collection" collection_type="list" /> + <param name="f2" type="data_collection" collection_type="list" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="out1" /> + </outputs> + <tests> + <test> + <conditional name="kind"> + <param name="collection_type" value="paired" /> + <param name="f1"> + <collection type="paired"> + <element name="forward" value="simple_line.txt" /> + <element name="reverse" value="simple_line_alternative.txt" /> + </collection> + </param> + <param name="f2"> + <collection type="paired"> + <element name="forward" value="simple_line.txt" /> + <element name="reverse" value="simple_line_alternative.txt" /> + </collection> + </param> + </conditional> + <output name="out1" file="simple_lines_interleaved.txt"/> + </test> + <test> + <conditional name="kind"> + <param name="collection_type" value="list" /> + <param name="f1"> + <collection type="list"> + <element name="l11" value="simple_line.txt" /> + <element name="l12" value="simple_line.txt" /> + </collection> + </param> + <param name="f2"> + <collection type="list"> + <element name="l21" value="simple_line_alternative.txt" /> + <element name="l22" value="simple_line_alternative.txt" /> + </collection> + </param> + </conditional> + <output name="out1" file="simple_lines_interleaved.txt"/> + </test> + </tests> +</tool> diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -21,4 +21,5 @@ <tool file="collection_paired_test.xml" /><tool file="collection_nested_test.xml" /><tool file="collection_mixed_param.xml" /> + <tool file="collection_two_paired.xml" /></toolbox> \ No newline at end of file diff -r e78b03ee17402b722930538e1b93335c28e075e6 -r 3fd7bfda6be315b569db0053dea5b834417e719f test/unit/tools/test_execution.py --- a/test/unit/tools/test_execution.py +++ b/test/unit/tools/test_execution.py @@ -16,13 +16,12 @@ eggs.require( "Paste" ) from paste import httpexceptions -# Tool with a repeat parameter, to test state update. -REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"> +BASE_REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"><command>echo "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1</command><inputs><param type="text" name="param1" value="" /><repeat name="repeat1" label="Repeat 1"> - <param type="text" name="param2" value="" /> + %s </repeat></inputs><outputs> @@ -31,6 +30,10 @@ </tool> ''' +# Tool with a repeat parameter, to test state update. +REPEAT_TOOL_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % '''<param type="text" name="param2" value="" />''' +REPEAT_COLLECTION_PARAM_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % '''<param type="data_collection" name="param2" collection_type="paired" />''' + class ToolExecutionTestCase( TestCase, tools_support.UsesApp, tools_support.UsesTools ): @@ -287,13 +290,48 @@ } ) self.__assert_exeuted( template, template_vars ) - def __history_dataset_collection_for( self, hdas, id=1234 ): - collection = galaxy.model.DatasetCollection() + def test_subcollection_multirun_with_state_updates( self ): + self._init_tool( REPEAT_COLLECTION_PARAM_CONTENTS ) + hda1, hda2 = self.__add_dataset( 1 ), self.__add_dataset( 2 ) + collection = self.__history_dataset_collection_for( [ hda1, hda2 ], collection_type="list:paired" ) + collection_id = self.app.security.encode_id( collection.id ) + self.app.dataset_collections_service = Bunch( + match_collections=lambda collections: None + ) + template, template_vars = self.__handle_with_incoming( + repeat1_add="dummy", + ) + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert len( state.inputs[ "repeat1" ] ) == 1 + template, template_vars = self.__handle_with_incoming( state, **{ + "repeat1_0|param2|__collection_multirun__": "%s|paired" % collection_id, + "repeat1_add": "dummy", + } ) + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert state.inputs[ "repeat1" ][ 0 ][ "param2|__collection_multirun__" ] == "%s|paired" % collection_id + + def __history_dataset_collection_for( self, hdas, collection_type="list", id=1234 ): + collection = galaxy.model.DatasetCollection( + collection_type=collection_type, + ) to_element = lambda hda: galaxy.model.DatasetCollectionElement( collection=collection, element=hda, ) - collection.datasets = map(to_element, hdas) + elements = map(to_element, hdas) + if collection_type == "list:paired": + paired_collection = galaxy.model.DatasetCollection( + collection_type="paired", + ) + paired_collection.elements = elements + list_dce = galaxy.model.DatasetCollectionElement( + collection=collection, + element=paired_collection, + ) + elements = [ list_dce ] + + collection.elements = elements + history_dataset_collection_association = galaxy.model.HistoryDatasetCollectionAssociation( id=id, collection=collection, @@ -349,13 +387,13 @@ self.history.datasets.append( hda ) return hda - def __add_collection_dataset( self, id, *hdas ): + def __add_collection_dataset( self, id, collection_type="paired", *hdas ): hdca = galaxy.model.HistoryDatasetCollectionAssociation() hdca.id = id collection = galaxy.model.DatasetCollection() hdca.collection = collection collection.elements = [ galaxy.model.DatasetCollectionElement(element=self.__add_dataset( 1 )) ] - + collection.type = collection_type self.trans.sa_session.model_objects[ galaxy.model.HistoryDatasetCollectionAssociation ][ id ] = hdca self.history.dataset_collections.append( hdca ) return hdca https://bitbucket.org/galaxy/galaxy-central/commits/09c372c6ec5f/ Changeset: 09c372c6ec5f User: martenson Date: 2014-07-24 23:27:32 Summary: Merge Affected #: 1 file diff -r 3fd7bfda6be315b569db0053dea5b834417e719f -r 09c372c6ec5f4b9381787fd4ecbde38deb8736e0 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1391,7 +1391,7 @@ # Load parameters (optional) input_elem = root.find("inputs") enctypes = set() - if input_elem: + if input_elem is not None: # Handle properties of the input form self.check_values = string_as_bool( input_elem.get("check_values", self.check_values ) ) self.nginx_upload = string_as_bool( input_elem.get( "nginx_upload", self.nginx_upload ) ) https://bitbucket.org/galaxy/galaxy-central/commits/c6afab452541/ Changeset: c6afab452541 User: martenson Date: 2014-07-29 20:38:44 Summary: another piece of permission API for datasets and library datasets Affected #: 5 files diff -r 09c372c6ec5f4b9381787fd4ecbde38deb8736e0 -r c6afab452541a54c1755b54f2e93c47950b8ae75 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -221,7 +221,7 @@ roles.append( item_permission.role ) return roles - def get_valid_dataset_roles( self, trans, dataset, query, page, page_limit ): + def get_valid_dataset_roles( self, trans, dataset, query=None, page=None, page_limit=None ): """ This method retrieves the list of possible roles that user can select in the dataset permissions form. Admins can select any role so the @@ -237,7 +237,12 @@ log.debug('search_query: ' + str(search_query)) # Limit the query only to get the page needed - limit = page * page_limit + if page is not None and page_limit is not None: + paginated = True + limit = page * page_limit + else: + paginated = False + total_count = None # For public datasets admins can choose from all roles @@ -247,16 +252,19 @@ if query is not None: db_query = db_query.filter( self.model.Role.table.c.name.like( search_query, escape='/' ) ) total_count = db_query.count() - # Takes the least number of results from beginning that includes the requested page - roles = db_query.order_by( self.model.Role.table.c.name ).limit( limit ).all() + if paginated: + # Takes the least number of results from beginning that includes the requested page + roles = db_query.order_by( self.model.Role.table.c.name ).limit( limit ).all() + page_start = ( page * page_limit ) - page_limit + page_end = page_start + page_limit + if total_count < page_start: + # Return empty list if there are less results than the requested position + roles = [] + else: + roles = roles[ page_start:page_end ] + else: + roles = db_query.order_by( self.model.Role.table.c.name ) - page_start = ( page * page_limit ) - page_limit - page_end = page_start + page_limit - if total_count < page_start: - # Return empty list if there are less results than the requested position - roles = [] - else: - roles = roles[ page_start:page_end ] # Non-admin and public dataset elif self.dataset_is_public( dataset ): # Add the current user's private role @@ -885,7 +893,7 @@ def set_dataset_permission( self, dataset, permission={} ): """ Set a specific permission on a dataset, leaving all other current permissions on the dataset alone. - Permission looks like: { Action : [ Role, Role ] } + Permission looks like: { Action.action : [ Role, Role ] } """ flush_needed = False for action, roles in permission.items(): @@ -1010,6 +1018,27 @@ if flush_needed: self.sa_session.flush() + def set_library_item_permission( self, library_dataset, permission={} ): + """ + Set a specific permission on a library item, leaving all other current permissions on the item alone. + Permission looks like: { Action.action : [ Role, Role ] } + """ + flush_needed = False + for action, roles in permission.items(): + if isinstance( action, Action ): + action = action.action + # Delete the current specific permission on the library_dataset if one exists + for dp in library_dataset.actions: + if dp.action == action: + self.sa_session.delete( dp ) + flush_needed = True + # Add the new specific permission on the library_dataset + for dp in [ self.model.LibraryDatasetPermissions( action, library_dataset, role ) for role in roles ]: + self.sa_session.add( dp ) + flush_needed = True + if flush_needed: + self.sa_session.flush() + def library_is_public( self, library, contents=False ): if contents: # Check all contained folders and datasets to find any that are not public diff -r 09c372c6ec5f4b9381787fd4ecbde38deb8736e0 -r c6afab452541a54c1755b54f2e93c47950b8ae75 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -22,6 +22,8 @@ from galaxy.security import Action from galaxy.util.streamball import StreamBall from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin +from sqlalchemy.orm.exc import MultipleResultsFound +from sqlalchemy.orm.exc import NoResultFound import logging log = logging.getLogger( __name__ ) @@ -202,12 +204,6 @@ new_access_roles_ids = kwd.get( 'access_ids[]', None ) new_manage_roles_ids = kwd.get( 'manage_ids[]', None ) new_modify_roles_ids = kwd.get( 'modify_ids[]', None ) - # if new_access_roles_ids is None: - # new_access_roles_ids = kwd.get( 'access_ids', None ) - # if new_manage_roles_ids is None: - # new_manage_roles_ids = kwd.get( 'manage_ids', None ) - # if new_modify_roles_ids is None: - # new_modify_roles_ids = kwd.get( 'modify_ids', None ) action = kwd.get( 'action', None ) if action is None: @@ -225,18 +221,99 @@ if not trans.app.security_agent.dataset_is_private_to_user( trans, library_dataset ): raise exceptions.InternalServerError( 'An error occured while making dataset private.' ) elif action == 'set_permissions': - # permission = { Action : [ Role, Role ] } - # trans.app.security_agent.set_dataset_permission( dataset, permission ) + # ACCESS DATASET ROLES + valid_access_roles = [] + invalid_access_roles_names = [] + if new_access_roles_ids is None: + trans.app.security_agent.make_dataset_public( dataset ) + else: + # Check whether we receive only one role, then it is not a list so we make it into one. + if isinstance(new_access_roles_ids, basestring): + new_access_roles_ids = [ new_access_roles_ids ] + for role_id in new_access_roles_ids: + role = self._load_role( trans, role_id ) + + # Check whether role is in the set of allowed roles + valid_roles, total_roles = trans.app.security_agent.get_valid_dataset_roles( trans, dataset ) + if role in valid_roles: + valid_access_roles.append( role ) + else: + invalid_access_roles_names.append( role_id ) + if len( invalid_access_roles_names ) > 0: + log.debug( "The following roles could not be added to the dataset access permission: " + str( invalid_access_roles_names ) ) + access_permission = dict( access=valid_access_roles ) + trans.app.security_agent.set_dataset_permission( dataset, access_permission ) + + # MANAGE DATASET ROLES + valid_manage_roles = [] + invalid_manage_roles_names = [] + new_manage_roles_ids = util.listify( new_manage_roles_ids ) + log.debug("new_manage_roles_ids: " + str(new_manage_roles_ids)) - raise exceptions.NotImplemented() + # Load all access roles to check + active_access_roles = dataset.get_access_roles( trans ) + + for role_id in new_manage_roles_ids: + role = self._load_role( trans, role_id ) + + # Check whether role is in the set of access roles + if role in active_access_roles: + valid_manage_roles.append( role ) + else: + invalid_manage_roles_names.append( role_id ) + + if len( invalid_manage_roles_names ) > 0: + log.debug( "The following roles could not be added to the dataset manage permission: " + str( invalid_manage_roles_names ) ) + + manage_permission = { trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS : valid_manage_roles } + trans.app.security_agent.set_dataset_permission( dataset, manage_permission ) + + # MODIFY LIBRARY ITEM ROLES + valid_modify_roles = [] + invalid_modify_roles_names = [] + new_modify_roles_ids = util.listify( new_modify_roles_ids ) + log.debug("new_modify_roles_ids: " + str(new_modify_roles_ids)) + + # Load all access roles to check + active_access_roles = dataset.get_access_roles( trans ) + + for role_id in new_modify_roles_ids: + role = self._load_role( trans, role_id ) + + # Check whether role is in the set of access roles + if role in active_access_roles: + valid_modify_roles.append( role ) + else: + invalid_modify_roles_names.append( role_id ) + + if len( invalid_modify_roles_names ) > 0: + log.debug( "The following roles could not be added to the dataset manage permission: " + str( invalid_modify_roles_names ) ) + + modify_permission = { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY : valid_modify_roles } + trans.app.security_agent.set_library_item_permission( library_dataset, modify_permission ) + else: raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' 'Allowed values are: "remove_restrictions", "make_private", "set_dataset_access_roles"' ) return self.get_current_roles( trans, library_dataset ) + def _load_role( self, trans, role_name ): + """ + Method loads the role from the DB based on the given role name. + """ + try: + role = trans.sa_session.query( trans.app.model.Role ).filter( trans.model.Role.table.c.name == role_name ).one() + except MultipleResultsFound: + raise exceptions.InconsistentDatabase( 'Multiple roles found with the same name. Name: ' + str( role_name ) ) + except NoResultFound: + raise exceptions.RequestParameterInvalidException( 'No role found with the name provided. Name: ' + str( role_name ) ) + except Exception, e: + raise exceptions.InternalServerError( 'Error loading from the database.' + str(e)) + return role + @expose_api def delete( self, trans, encoded_dataset_id, **kwd ): """ diff -r 09c372c6ec5f4b9381787fd4ecbde38deb8736e0 -r c6afab452541a54c1755b54f2e93c47950b8ae75 static/scripts/packed/galaxy.tools.js --- a/static/scripts/packed/galaxy.tools.js +++ b/static/scripts/packed/galaxy.tools.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/tools"],function(c,b){var a=function(g,f){$("input[name='"+g+"'][type='checkbox']").attr("checked",!!f)};$("div.checkUncheckAllPlaceholder").each(function(){var f=$(this).attr("checkbox_name");select_link=$("<a class='action-button'></a>").text("Select All").click(function(){a(f,true)});unselect_link=$("<a class='action-button'></a>").text("Unselect All").click(function(){a(f,false)});$(this).append(select_link).append(" ").append(unselect_link)});var e={select_single:{icon_class:"fa-file-o",select_by:"Run tool on single input",allow_remap:true},select_multiple:{icon_class:"fa-files-o",select_by:"Run tool in parallel across multiple datasets",allow_remap:false,min_option_count:2},select_collection:{icon_class:"fa-folder-o",select_by:"Run tool in parallel across dataset collection",allow_remap:false},multiselect_single:{icon_class:"fa-list-alt",select_by:"Run tool over multiple datasets",allow_remap:true},multiselect_collection:{icon_class:"fa-folder-o",select_by:"Run tool over dataset collection",allow_remap:false,},select_single_collection:{icon_class:"fa-file-o",select_by:"Run tool on single collection",allow_remap:true},select_map_over_collections:{icon_class:"fa-folder-o",select_by:"Map tool over compontents of nested collection",allow_remap:false,}};var d=Backbone.View.extend({initialize:function(l){var g=l.default_option;var m=null;var k=l.switch_options;this.switchOptions=k;this.prefix=l.prefix;var j=this.$el;var f=this;var h=0;var i=0;c.each(this.switchOptions,function(r,t){var n=c.size(r.options);var q=e[t];var p=h++;var s=false;if(g==t){m=p}else{if(n<(q.min_option_count||1)){s=true}}if(!s){i++;var o=$('<i class="fa '+q.icon_class+' runOptionIcon" style="padding-left: 5px; 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Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while fetching dataset permissions. :(")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};this.accessSelectObject=new b.View(o);this.modifySelectObject=new b.View(l);this.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));this.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f})}).fail(function(){d.error("An error occurred while making dataset private. :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f})}).fail(function(){d.error("An error occurred while making dataset unrestricted. :(")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Permissions: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<hr/>");e.push("<h2>Library-related permissions</h2>");e.push('<div class="alert alert-success">You have the permission to modify this Library item. This includes changing its metadata and other information.</div>');e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify the information about this library item.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-success">You have the permission to manage permissions on this dataset. That means you can control who can access it and also appoint others that can manage permissions on it.</div>');e.push('<div class="alert alert-warning">Changes made here will affect <strong>every</strong> library item and every history this dataset is part of.</div>');e.push("<h4>Roles that can access dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){f(e)},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var g=new c.HistoryItem();g.url=g.urlRoot+f+"/contents";var e="/api/histories/"+f+"/set_as_current";$.ajax({url:e,type:"PUT"});g.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(i,h){if(typeof h.responseJSON!=="undefined"){d.error("Dataset not imported. "+h.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while fetching dataset permissions. :(")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you")}).fail(function(){d.error("An error occurred while making dataset private :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted")}).fail(function(){d.error("An error occurred while making dataset unrestricted :(")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i})}).fail(function(){d.error("An error occurred while setting dataset permissions :(")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Permissions: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 09c372c6ec5f4b9381787fd4ecbde38deb8736e0 -r c6afab452541a54c1755b54f2e93c47950b8ae75 static/scripts/packed/viz/trackster.js --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1,1 +1,1 @@ -var ui=null;var view=null;var browser_router=null;require(["utils/utils","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/underscore","base","viz/trackster/tracks","viz/visualization"],function(b,e,a,c){var d=e.Base.extend({initialize:function(g){this.baseURL=g},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var g=[];$(".bookmark").each(function(){g.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var h=(view.overview_drawable?view.overview_drawable.config.get_value("name"):null),j={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:h},bookmarks:g};return $.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(j)}}).success(function(k){Galaxy.modal.hide();view.vis_id=k.vis_id;view.has_changes=false;window.history.pushState({},"",k.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var g=this,h=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(j){b.each(j,function(k){view.add_drawable(j.object_from_template(k,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new a.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=g.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){g.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){g.handle_unsaved_changes(view)}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=h;return h},add_bookmarks:function(){var g=this,h=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(j){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:j,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var k,l=$(this).val();if($(this).attr("name")==="id"){k={hda_id:l}}else{k={ldda_id:l}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:k,dataType:"json"}).then(function(m){for(i=0;i<m.data.length;i++){var n=m.data[i];g.add_bookmark(n[0],n[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(l,j,g){var n=$("#right .unified-panel-body"),p=$("<div/>").addClass("bookmark").appendTo(n);var q=$("<div/>").addClass("position").appendTo(p),m=$("<a href=''/>").text(l).appendTo(q).click(function(){view.go_to(l);return false}),k=$("<div/>").text(j).appendTo(p);if(g){var o=$("<div/>").addClass("delete-icon-container").prependTo(p).click(function(){p.slideUp("fast");p.remove();view.has_changes=true;return false}),h=$("<a href=''/>").addClass("icon-button delete").appendTo(o);k.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return p},create_visualization:function(m,g,l,n,k){var j=this,h=new a.TracksterView(b.extend(m,{header:false}));h.editor=true;$.when(h.load_chroms_deferred).then(function(y){if(g){var w=g.chrom,o=g.start,t=g.end,q=g.overview;if(w&&(o!==undefined)&&t){h.change_chrom(w,o,t)}else{h.change_chrom(y[0].chrom)}}else{h.change_chrom(y[0].chrom)}if(l){var r,p,s;for(var u=0;u<l.length;u++){h.add_drawable(a.object_from_template(l[u],h,h))}}var x;for(var u=0;u<h.drawables.length;u++){if(h.drawables[u].config.get_value("name")===q){h.set_overview(h.drawables[u]);break}}if(n){var v;for(var u=0;u<n.length;u++){v=n[u];j.add_bookmark(v.position,v.annotation,k)}}h.has_changes=false});this.set_up_router({view:h});return h},set_up_router:function(g){new c.TrackBrowserRouter(g);Backbone.history.start()},init_keyboard_nav:function(g){$(document).keyup(function(h){if($(h.srcElement).is(":input")){return}switch(h.which){case 37:g.move_fraction(0.25);break;case 38:var j=Math.round(g.viewport_container.height()/15);g.viewport_container.scrollTop(g.viewport_container.scrollTop()-20);break;case 39:g.move_fraction(-0.25);break;case 40:var j=Math.round(g.viewport_container.height()/15);g.viewport_container.scrollTop(g.viewport_container.scrollTop()+20);break}})},handle_unsaved_changes:function(g){if(g.has_changes){var h=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){$(window).off("beforeunload");window.location=galaxy_config.root+"visualization"},Save:function(){$.when(h.save_viz()).then(function(){window.location=galaxy_config.root+"visualization"})}}})}else{window.location=galaxy_config.root+"visualization"}}});var f=e.Backbone.View.extend({initialize:function(){ui=new d(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},view_existing:function(){var g=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:g.title,vis_id:g.vis_id,dbkey:g.dbkey},g.viewport,g.tracks,g.bookmarks,true);this.init_editor()},view_new:function(){var g=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(h){Galaxy.modal.show({title:"New Visualization",body:g.template_view_new(h),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){g.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey").val(galaxy_config.app.default_dbkey)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(g){var j='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var h=0;h<g.length;h++){j+='<option value="'+g[h][1]+'">'+g[h][0]+"</option>"}j+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return j},create_browser:function(h,g){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:h,dbkey:g},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.config.get_value("name")+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(g){view.add_drawable(a.object_from_template(g,view,view))}})}$("#add-bookmark-button").click(function(){var h=view.chrom+":"+view.low+"-"+view.high,g="Bookmark description";return ui.add_bookmark(h,g,true)});ui.init_keyboard_nav(view);$(window).on("beforeunload",function(){if(view.has_changes){return"There are unsaved changes to your visualization that will be lost if you leave this page."}})}});return{TracksterUI:d,GalaxyApp:f}}); \ No newline at end of file +var ui=null;var view=null;var browser_router=null;require(["utils/utils","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/underscore","base","viz/trackster/tracks","viz/visualization"],function(b,e,a,c){var d=e.Base.extend({initialize:function(g){this.baseURL=g},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var g=[];$(".bookmark").each(function(){g.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var h=(view.overview_drawable?view.overview_drawable.config.get_value("name"):null),j={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:h},bookmarks:g};return $.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(j)}}).success(function(k){Galaxy.modal.hide();view.vis_id=k.vis_id;view.has_changes=false;window.history.pushState({},"",k.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var g=this,h=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){c.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(j){b.each(j,function(k){view.add_drawable(a.object_from_template(k,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new a.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=g.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){g.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){g.handle_unsaved_changes(view)}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=h;return h},add_bookmarks:function(){var g=this,h=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(j){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:j,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var k,l=$(this).val();if($(this).attr("name")==="id"){k={hda_id:l}}else{k={ldda_id:l}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:k,dataType:"json"}).then(function(m){for(i=0;i<m.data.length;i++){var n=m.data[i];g.add_bookmark(n[0],n[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(l,j,g){var n=$("#right .unified-panel-body"),p=$("<div/>").addClass("bookmark").appendTo(n);var q=$("<div/>").addClass("position").appendTo(p),m=$("<a href=''/>").text(l).appendTo(q).click(function(){view.go_to(l);return false}),k=$("<div/>").text(j).appendTo(p);if(g){var o=$("<div/>").addClass("delete-icon-container").prependTo(p).click(function(){p.slideUp("fast");p.remove();view.has_changes=true;return false}),h=$("<a href=''/>").addClass("icon-button delete").appendTo(o);k.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return p},create_visualization:function(m,g,l,n,k){var j=this,h=new a.TracksterView(b.extend(m,{header:false}));h.editor=true;$.when(h.load_chroms_deferred).then(function(y){if(g){var w=g.chrom,o=g.start,t=g.end,q=g.overview;if(w&&(o!==undefined)&&t){h.change_chrom(w,o,t)}else{h.change_chrom(y[0].chrom)}}else{h.change_chrom(y[0].chrom)}if(l){var r,p,s;for(var u=0;u<l.length;u++){h.add_drawable(a.object_from_template(l[u],h,h))}}var x;for(var u=0;u<h.drawables.length;u++){if(h.drawables[u].config.get_value("name")===q){h.set_overview(h.drawables[u]);break}}if(n){var v;for(var u=0;u<n.length;u++){v=n[u];j.add_bookmark(v.position,v.annotation,k)}}h.has_changes=false});this.set_up_router({view:h});return h},set_up_router:function(g){new c.TrackBrowserRouter(g);Backbone.history.start()},init_keyboard_nav:function(g){$(document).keyup(function(h){if($(h.srcElement).is(":input")){return}switch(h.which){case 37:g.move_fraction(0.25);break;case 38:var j=Math.round(g.viewport_container.height()/15);g.viewport_container.scrollTop(g.viewport_container.scrollTop()-20);break;case 39:g.move_fraction(-0.25);break;case 40:var j=Math.round(g.viewport_container.height()/15);g.viewport_container.scrollTop(g.viewport_container.scrollTop()+20);break}})},handle_unsaved_changes:function(g){if(g.has_changes){var h=this;Galaxy.modal.show({title:"Close visualization",body:"There are unsaved changes to your visualization which will be lost if you do not save them.",buttons:{Cancel:function(){Galaxy.modal.hide()},"Leave without Saving":function(){$(window).off("beforeunload");window.location=galaxy_config.root+"visualization"},Save:function(){$.when(h.save_viz()).then(function(){window.location=galaxy_config.root+"visualization"})}}})}else{window.location=galaxy_config.root+"visualization"}}});var f=e.Backbone.View.extend({initialize:function(){ui=new d(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},view_existing:function(){var g=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:g.title,vis_id:g.vis_id,dbkey:g.dbkey},g.viewport,g.tracks,g.bookmarks,true);this.init_editor()},view_new:function(){var g=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(h){Galaxy.modal.show({title:"New Visualization",body:g.template_view_new(h),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){g.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey").val(galaxy_config.app.default_dbkey)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(g){var j='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var h=0;h<g.length;h++){j+='<option value="'+g[h][1]+'">'+g[h][0]+"</option>"}j+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return j},create_browser:function(h,g){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:h,dbkey:g},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.config.get_value("name")+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(g){view.add_drawable(a.object_from_template(g,view,view))}})}$("#add-bookmark-button").click(function(){var h=view.chrom+":"+view.low+"-"+view.high,g="Bookmark description";return ui.add_bookmark(h,g,true)});ui.init_keyboard_nav(view);$(window).on("beforeunload",function(){if(view.has_changes){return"There are unsaved changes to your visualization that will be lost if you leave this page."}})}});return{TracksterUI:d,GalaxyApp:f}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/5d46cecbd1b3/ Changeset: 5d46cecbd1b3 User: martenson Date: 2014-07-29 20:39:11 Summary: Merge Affected #: 96 files diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 .hgignore --- a/.hgignore +++ b/.hgignore @@ -16,6 +16,7 @@ # Database stuff database/beaker_sessions +database/citations database/community_files database/compiled_templates database/files diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" 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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#portlet-header-text");var n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa 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n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return 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n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" 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src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job 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No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - 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Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function tt(e){var t=+(e=="e"),n=t?1:-1,r=I/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function nt(){h.empty()||h.extent(x),Y.data([h.empty()?k.domain():x]).each(function(e,t){var n=k(e[0])-k.range()[0],r=k.range()[1]-k(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",k(e[1])).attr("width",r<0?0:r)})}function rt(){x=h.empty()?null:h.extent(),S=h.empty()?k.domain():h.extent(),D.brush({extent:S,brush:h}),nt(),r.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&e[n].bar})),t.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&!e[n].bar}));var n=$.select(".nv-focus .nv-barsWrap").datum(R.length?R.map(function(e,t){return{key:e.key,values:e.values.filter(function(e,t){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(d=e,B):d},B.showDistY=function(e){return arguments.length?(v=e,B):v},B.showControls=function(e){return arguments.length?(w=e,B):w},B.showLegend=function(e){return arguments.length?(m=e,B):m},B.showXAxis=function(e){return arguments.length?(g=e,B):g},B.showYAxis=function(e){return arguments.length?(y=e,B):y},B.rightAlignYAxis=function(e){return arguments.length?(b=e,r.orient(e?"right":"left"),B):b},B.fisheye=function(e){return arguments.length?(E=e,B):E},B.tooltips=function(e){return arguments.length?(x=e,B):x},B.tooltipContent=function(e){return arguments.length?(C=e,B):C},B.tooltipXContent=function(e){return arguments.length?(T=e,B):T},B.tooltipYContent=function(e){return arguments.length?(N=e,B):N},B.state=function(e){return arguments.length?(k=e,B):k},B.defaultState=function(e){return arguments.length?(L=e,B):L},B.noData=function(e){return arguments.length?(O=e,B):O},B.transitionDuration=function(e){return arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 config/plugins/visualizations/charts/static/views/settings.js --- a/config/plugins/visualizations/charts/static/views/settings.js +++ b/config/plugins/visualizations/charts/static/views/settings.js @@ -19,6 +19,7 @@ // create settings this.form = new TableForm.View(app, { + title : 'Configuration', content : 'This chart type does not provide any options.' }); diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -21,6 +21,9 @@ ## shared css ${h.css( 'base' )} + ## crossfilter + ${h.javascript_link( app_root + "plugins/crossfilter/crossfilter.js" )} + ## canvg ${h.javascript_link( app_root + "plugins/canvg/rgbcolor.js" )} ${h.javascript_link( app_root + "plugins/canvg/canvg.js" )} diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -177,6 +177,7 @@ <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/><datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/><datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/> @@ -262,6 +263,7 @@ --><sniffer type="galaxy.datatypes.tabular:Vcf"/><sniffer type="galaxy.datatypes.binary:TwoBit"/> + <sniffer type="galaxy.datatypes.binary:SQlite"/><sniffer type="galaxy.datatypes.binary:Bam"/><sniffer type="galaxy.datatypes.binary:Sff"/><sniffer type="galaxy.datatypes.xml:Phyloxml"/> diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 display_applications/igb/bam.xml --- a/display_applications/igb/bam.xml +++ b/display_applications/igb/bam.xml @@ -7,8 +7,8 @@ #set nm=$bam_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bai_file" url="${niceName}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="data" name="bam_file" url="${niceName}.bam" strip_https="True" /> + <param type="data" name="bai_file" url="${niceName}.bam.bai" metadata="bam_index" /> + <param type="data" name="bam_file" url="${niceName}.bam" /></link></display> diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 display_applications/igb/bb.xml --- a/display_applications/igb/bb.xml +++ b/display_applications/igb/bb.xml @@ -8,7 +8,7 @@ #set nm=$bigbed_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigbed_file" url="${niceName}.bigbed" strip_https="True" /> + <param type="data" name="bigbed_file" url="${niceName}.bigbed" /></link></display> diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 display_applications/igb/bed.xml --- a/display_applications/igb/bed.xml +++ b/display_applications/igb/bed.xml @@ -8,7 +8,7 @@ #set nm=$bed_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bed_file" url="${niceName}.bed" strip_https="True" /> + <param type="data" name="bed_file" url="${niceName}.bed" /><param type="template" name="bioviz" strip="True" > http://bioviz.org/igb/galaxy.html?version=${bed_file.dbkey}&loadresidues=false&feature_url_0=${bed_file.url}&sym_name_0=${niceName}&sym_method_0=${bed_file.url}&query_url=${bed_file.url}&server_url=galaxy diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 display_applications/igb/bedgraph.xml --- a/display_applications/igb/bedgraph.xml +++ b/display_applications/igb/bedgraph.xml @@ -8,7 +8,7 @@ #set nm=$bedgraph_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bedgraph_file" url="${niceName}.bed.bedgraph" strip_https="True" /> + <param type="data" name="bedgraph_file" url="${niceName}.bed.bedgraph" /><param type="template" name="bioviz" strip="True" > http://bioviz.org/igb/galaxy.html?version=${bedgraph_file.dbkey}&loadresidues=false&feature_url_0=${bedgraph_file.url}&sym_name_0=${niceName}&sym_method_0=${bedgraph_file.url}&query_url=${bedgraph_file.url}&server_url=galaxy diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 display_applications/igb/bigwig.xml --- a/display_applications/igb/bigwig.xml +++ b/display_applications/igb/bigwig.xml @@ -8,7 +8,7 @@ #set nm=$bigwig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigwig_file" url="${niceName}.bigwig" strip_https="True" /> + <param type="data" name="bigwig_file" url="${niceName}.bigwig" /><!--<param type="template" name="position" strip="True" > #set chrom, start, end = $bigwig_file.datatype.get_estimated_display_viewport( $bigwig_file ) #if $chrom is not None: diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 display_applications/igb/gtf.xml --- a/display_applications/igb/gtf.xml +++ b/display_applications/igb/gtf.xml @@ -8,7 +8,7 @@ #set nm=$gtf_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + <param type="data" name="gtf_file" url="${niceName}.gtf" /><param type="template" name="bioviz" strip="True" > http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidues=false&feature_url_0=${gtf_file.url}&sym_name_0=${niceName}&sym_method_0=${gtf_file.url}&query_url=${gtf_file.url}&server_url=galaxy diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 display_applications/igb/wig.xml --- a/display_applications/igb/wig.xml +++ b/display_applications/igb/wig.xml @@ -8,7 +8,7 @@ #set nm=$wig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="wig_file" url="${niceName}.wig" strip_https="True" /> + <param type="data" name="wig_file" url="${niceName}.wig" /><param type="template" name="position" strip="True" > #set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file ) #if $chrom is not None: diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -64,8 +64,6 @@ tempfile.tempdir = self.new_file_path self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) - self.genome_data_path = kwargs.get( "genome_data_path", "tool-data/genome" ) - self.rsync_url = kwargs.get( "rsync_url", "rsync://datacache.galaxyproject.org/indexes" ) # Galaxy OpenID settings self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) self.openid_config = kwargs.get( 'openid_config_file', 'openid_conf.xml' ) @@ -378,6 +376,10 @@ # Default chunk size for chunkable datatypes -- 64k self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) ) + self.citation_cache_type = kwargs.get( "citation_cache_type", "file" ) + self.citation_cache_data_dir = self.resolve_path( kwargs.get( "citation_cache_data_dir", "database/citations/data" ) ) + self.citation_cache_lock_dir = self.resolve_path( kwargs.get( "citation_cache_lock_dir", "database/citations/locks" ) ) + @property def sentry_dsn_public( self ): """ @@ -572,6 +574,10 @@ tool_configs = self.config.tool_configs if self.config.migrated_tools_config not in tool_configs: tool_configs.append( self.config.migrated_tools_config ) + + from galaxy.managers.citations import CitationsManager + self.citations_manager = CitationsManager( self ) + from galaxy import tools self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) # Search support for tools diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -12,6 +12,7 @@ import subprocess import tempfile import zipfile +import sqlite3 from urllib import urlencode, quote_plus from galaxy import eggs @@ -545,3 +546,45 @@ return "Binary TwoBit format nucleotide file (%s)" % (data.nice_size(dataset.get_size())) Binary.register_sniffable_binary_format("twobit", "twobit", TwoBit) + + +@dataproviders.decorators.has_dataproviders +class SQlite ( Binary ): + file_ext = "sqlite" + + # Connects and runs a query that should work on any real database + # If the file is not sqlite, an exception will be thrown and the sniffer will return false + def sniff( self, filename ): + try: + conn = sqlite3.connect(filename) + schema_version=conn.cursor().execute("pragma schema_version").fetchone() + conn.close() + if schema_version is not None: + return True + return False + except: + return False + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + dataset.peek = "SQLite Database" + dataset.blurb = data.nice_size( dataset.get_size() ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def display_peek( self, dataset ): + try: + return dataset.peek + except: + return "SQLite Database (%s)" % ( data.nice_size( dataset.get_size() ) ) + + + @dataproviders.decorators.dataprovider_factory( 'sqlite', dataproviders.dataset.SQliteDataProvider.settings ) + def sqlite_dataprovider( self, dataset, **settings ): + dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) + return dataproviders.dataset.SQliteDataProvider( dataset_source, **settings ) + + +Binary.register_sniffable_binary_format("sqlite","sqlite",SQlite) + diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -11,6 +11,8 @@ import line import column import external +import sqlite3 +import re from galaxy import eggs eggs.require( 'bx-python' ) @@ -700,3 +702,39 @@ #TODO: as samtools - need more info on output format raise NotImplementedError() super( BGzipTabixDataProvider, self ).__init__( dataset, **kwargs ) + + + +class SQliteDataProvider ( base.DataProvider ): + """ + Data provider that uses a sqlite database file as its source. + + Allows any query to be run and returns the resulting rows as sqlite3 row objects + """ + settings = { + 'query' : 'str' + } + + def __init__( self, source, query=None, **kwargs ): + self.query=query + self.connection = sqlite3.connect(source.dataset.file_name); + self.connection.row_factory = sqlite3.Row + super( SQliteDataProvider, self ).__init__( source, **kwargs ) + + def query_matches_whitelist(self,query): + if re.match("select ",query,re.IGNORECASE): + if re.search("^([^\"]|\"[^\"]*\")*?;",query) or re.search("^([^\']|\'[^\']*\')*?;",query): + return False + else: + return True + return False + + + + def __iter__( self ): + if (self.query is not None) and self.query_matches_whitelist(self.query): + for row in self.connection.cursor().execute(self.query): + yield row + else: + yield + diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -90,19 +90,19 @@ f.close() return False -def convert_newlines( fname, in_place=True ): +def convert_newlines( fname, in_place=True, tmp_dir=None, tmp_prefix=None ): """ Converts in place a file from universal line endings to Posix line endings. >>> fname = get_test_fname('temp.txt') >>> file(fname, 'wt').write("1 2\\r3 4") - >>> convert_newlines(fname) + >>> convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir()) (2, None) >>> file(fname).read() '1 2\\n3 4\\n' """ - fd, temp_name = tempfile.mkstemp() + fd, temp_name = tempfile.mkstemp( prefix=tmp_prefix, dir=tmp_dir ) fp = os.fdopen( fd, "wt" ) i = None for i, line in enumerate( file( fname, "U" ) ): @@ -150,20 +150,20 @@ else: return ( i, temp_name ) -def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+" ): +def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+", tmp_dir=None, tmp_prefix=None ): """ Combines above methods: convert_newlines() and sep2tabs() so that files do not need to be read twice >>> fname = get_test_fname('temp.txt') >>> file(fname, 'wt').write("1 2\\r3 4") - >>> convert_newlines_sep2tabs(fname) + >>> convert_newlines_sep2tabs(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir()) (2, None) >>> file(fname).read() '1\\t2\\n3\\t4\\n' """ regexp = re.compile( patt ) - fd, temp_name = tempfile.mkstemp() + fd, temp_name = tempfile.mkstemp( prefix=tmp_prefix, dir=tmp_dir ) fp = os.fdopen( fd, "wt" ) for i, line in enumerate( file( fname, "U" ) ): line = line.rstrip( '\r\n' ) diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/managers/citations.py --- /dev/null +++ b/lib/galaxy/managers/citations.py @@ -0,0 +1,170 @@ +import pkg_resources + +import functools +import os +import urllib2 + +pkg_resources.require('Beaker') +from beaker.cache import CacheManager +from beaker.util import parse_cache_config_options + +import logging +log = logging.getLogger( __name__ ) + + +class CitationsManager( object ): + + def __init__( self, app ): + self.app = app + self.doi_cache = DoiCache( app.config ) + + def citations_for_tool( self, tool ): + return tool.citations + + def citations_for_tool_ids( self, tool_ids ): + citation_collection = CitationCollection() + for tool_id in tool_ids: + tool = self._get_tool( tool_id ) + for citation in self.citations_for_tool( tool ): + citation_collection.add( citation ) + return citation_collection.citations + + def parse_citation( self, citation_elem, tool_directory ): + return parse_citation( citation_elem, tool_directory, self ) + + def _get_tool( self, tool_id ): + tool = self.app.toolbox.get_tool( tool_id ) + return tool + + +class DoiCache( object ): + + def __init__( self, config ): + cache_opts = { + 'cache.type': getattr( config, 'citation_cache_type', 'file'), + 'cache.data_dir': getattr( config, 'citation_cache_data_dir', None), + 'cache.lock_dir': getattr( config, 'citation_cache_lock_dir', None), + } + self._cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache('doi') + + def _raw_get_bibtex( self, doi ): + dx_url = "http://dx.doi.org/" + doi + headers = {'Accept': "text/bibliography; style=bibtex" } + req = urllib2.Request(dx_url, data="", headers=headers) + response = urllib2.urlopen(req) + bibtex = response.read() + return bibtex + + def get_bibtex( self, doi ): + createfunc = functools.partial(self._raw_get_bibtex, doi) + return self._cache.get(key=doi, createfunc=createfunc) + + +def parse_citation( elem, directory, citation_manager ): + """ Parse an abstract citation entry from the specified XML element. + The directory parameter should be used to find external files for this + citation. + """ + citation_type = elem.attrib.get( 'type', None ) + citation_class = CITATION_CLASSES.get( citation_type, None ) + if not citation_class: + log.warn("Unknown or unspecified citation type: %s" % citation_type) + return None + return citation_class( elem, directory, citation_manager ) + + +class CitationCollection( object ): + + def __init__( self ): + self.citations = [] + + def __iter__( self ): + return self.citations.__iter__() + + def __len__( self ): + return len( self.citations ) + + def add( self, new_citation ): + for citation in self.citations: + if citation.equals( new_citation ): + # TODO: We have two equivalent citations, pick the more + # informative/complete/correct. + return False + + self.citations.append( new_citation ) + return True + + +class BaseCitation( object ): + + def to_dict( self, citation_format ): + if citation_format == "bibtex": + return dict( + format="bibtex", + content=self.to_bibtex(), + ) + else: + raise Exception("Unknown citation format %s" % citation_format) + + def equals( self, other_citation ): + if self.has_doi() and other_citation.has_doi(): + return self.doi() == other_citation.doi() + else: + # TODO: Do a better job figuring out if this is the same citation. + return self.to_bibtex() == other_citation.to_bibtex() + + def has_doi( self ): + return False + + +class BibtexCitation( BaseCitation ): + + def __init__( self, elem, directory, citation_manager ): + bibtex_file = elem.attrib.get("file", None) + if bibtex_file: + raw_bibtex = open(os.path.join(directory, bibtex_file), "r").read() + else: + raw_bibtex = elem.text.strip() + self._set_raw_bibtex( raw_bibtex ) + + def _set_raw_bibtex( self, raw_bibtex ): + self.raw_bibtex = raw_bibtex + + def to_bibtex( self ): + return self.raw_bibtex + + +class DoiCitation( BaseCitation ): + BIBTEX_UNSET = object() + + def __init__( self, elem, directory, citation_manager ): + self.__doi = elem.text.strip() + self.doi_cache = citation_manager.doi_cache + self.raw_bibtex = DoiCitation.BIBTEX_UNSET + + def has_doi( self ): + return True + + def doi( self ): + return self.__doi + + def to_bibtex( self ): + if self.raw_bibtex is DoiCitation.BIBTEX_UNSET: + try: + self.raw_bibtex = self.doi_cache.get_bibtex(self.__doi) + except Exception: + log.exception("Failed to fetch bibtex for DOI %s" % self.__doi) + + if self.raw_bibtex is DoiCitation.BIBTEX_UNSET: + return """@MISC{%s, + DOI = '%s', + note = 'Failed to fetch BibTeX for DOI.' + }""" % (self.__doi, self.__doi) + else: + return self.raw_bibtex + + +CITATION_CLASSES = dict( + bibtex=BibtexCitation, + doi=DoiCitation, +) diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -34,6 +34,7 @@ from galaxy.util.bunch import Bunch from galaxy.util.hash_util import new_secure_hash from galaxy.util.directory_hash import directory_hash_id +from galaxy.util.sanitize_html import sanitize_html from galaxy.web.framework.helpers import to_unicode from galaxy.web.form_builder import (AddressField, CheckboxField, HistoryField, PasswordField, SelectField, TextArea, TextField, WorkflowField, @@ -873,7 +874,7 @@ class History( object, Dictifiable, UsesAnnotations, HasName ): dict_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' ) - dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged', 'importable', 'slug' ) + dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged', 'importable', 'slug', 'empty' ) default_name = 'Unnamed history' def __init__( self, id=None, name=None, user=None ): @@ -890,6 +891,10 @@ self.galaxy_sessions = [] self.tags = [] + @property + def empty( self ): + return self.hid_counter == 1 + def _next_hid( self ): # this is overriden in mapping.py db_next_hid() method if len( self.datasets ) == 0: @@ -2589,8 +2594,8 @@ class DatasetCollection( object, Dictifiable, UsesAnnotations ): """ """ - dict_collection_visible_keys = ( 'id', 'name', 'collection_type' ) - dict_element_visible_keys = ( 'id', 'name', 'collection_type' ) + dict_collection_visible_keys = ( 'id', 'collection_type' ) + dict_element_visible_keys = ( 'id', 'collection_type' ) def __init__( self, @@ -3703,23 +3708,27 @@ self.country = country self.phone = phone def get_html(self): + # This should probably be deprecated eventually. It should currently + # sanitize. + # TODO Find out where else uses this and replace with + # templates html = '' if self.name: - html = html + self.name + html = html + sanitize_html(self.name) if self.institution: - html = html + '<br/>' + self.institution + html = html + '<br/>' + sanitize_html(self.institution) if self.address: - html = html + '<br/>' + self.address + html = html + '<br/>' + sanitize_html(self.address) if self.city: - html = html + '<br/>' + self.city + html = html + '<br/>' + sanitize_html(self.city) if self.state: - html = html + ' ' + self.state + html = html + ' ' + sanitize_html(self.state) if self.postal_code: - html = html + ' ' + self.postal_code + html = html + ' ' + sanitize_html(self.postal_code) if self.country: - html = html + '<br/>' + self.country + html = html + '<br/>' + sanitize_html(self.country) if self.phone: - html = html + '<br/>' + 'Phone: ' + self.phone + html = html + '<br/>' + 'phone: ' + sanitize_html(self.phone) return html class UserOpenID( object ): diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1360,6 +1360,9 @@ requirements, containers = parse_requirements_from_xml( root ) self.requirements = requirements self.containers = containers + + self.citations = self._parse_citations( root ) + # Determine if this tool can be used in workflows self.is_workflow_compatible = self.check_workflow_compatible(root) # Trackster configuration. @@ -1686,6 +1689,20 @@ trace_msg = repr( traceback.format_tb( trace ) ) log.error( "Traceback: %s" % trace_msg ) + def _parse_citations( self, root ): + citations = [] + citations_elem = root.find("citations") + if not citations_elem: + return citations + + for citation_elem in citations_elem: + if citation_elem.tag != "citation": + pass + citation = self.app.citations_manager.parse_citation( citation_elem, self.tool_dir ) + if citation: + citations.append( citation ) + return citations + # TODO: This method doesn't have to be part of the Tool class. def parse_error_level( self, err_level ): """ diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -114,6 +114,8 @@ #allow explicit conversion to be stored in job_parameter table target_dict[ conversion_name ] = conversion_data.id # a more robust way to determine JSONable value is desired elif isinstance( input, DataCollectionToolParameter ): + if not value: + return for i, v in enumerate( value.collection.dataset_instances ): data = v current_user_roles = trans.get_current_user_roles() diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -53,7 +53,7 @@ value = incoming_value error = None try: - if value is not None or isinstance( param, DataToolParameter ): + if value is not None or isinstance( param, DataToolParameter ) or isinstance( param, DataCollectionToolParameter ): # Convert value from HTML representation if source == 'html': value = param.from_html( value, trans, param_values ) diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2078,7 +2078,7 @@ def from_html( self, value, trans, other_values={} ): if not value and not self.optional: - raise ValueError( "History does not include a dataset of the required format / build" ) + raise ValueError( "History does not include a dataset collection of the correct type or containing the correct types of datasets" ) if value in [None, "None"]: return None if isinstance( value, str ) and value.find( "," ) > 0: diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -269,6 +269,12 @@ def __init__( self, has_collection, dataset_paths=[], **kwargs ): super(DatasetCollectionWrapper, self).__init__() + if has_collection is None: + self.__input_supplied = False + return + else: + self.__input_supplied = True + if hasattr( has_collection, "name" ): # It is a HistoryDatasetCollectionAssociation collection = has_collection.collection @@ -294,24 +300,41 @@ element_instances[element_identifier] = element_wrapper element_instance_list.append( element_wrapper ) - self.element_instances = element_instances - self.element_instance_list = element_instance_list + self.__element_instances = element_instances + self.__element_instance_list = element_instance_list def keys( self ): - return self.element_instances.keys() + if not self.__input_supplied: + return [] + return self.__element_instances.keys() @property def is_collection( self ): return True + @property + def is_input_supplied( self ): + return self.__input_supplied + def __getitem__( self, key ): + if not self.__input_supplied: + return None if isinstance( key, int ): - return self.element_instance_list[ key ] + return self.__element_instance_list[ key ] else: - return self.element_instances[ key ] + return self.__element_instances[ key ] def __getattr__( self, key ): - return self.element_instances[ key ] + if not self.__input_supplied: + return None + return self.__element_instances[ key ] def __iter__( self ): - return self.element_instance_list.__iter__() + if not self.__input_supplied: + return [].__iter__() + return self.__element_instance_list.__iter__() + + def __nonzero__( self ): + # Fail `#if $param` checks in cheetah is optional input + # not specified or if resulting collection is empty. + return self.__input_supplied and bool( self.__element_instance_list ) diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -48,10 +48,10 @@ from .inflection import Inflector, English inflector = Inflector(English) -log = logging.getLogger(__name__) +log = logging.getLogger(__name__) _lock = threading.RLock() -CHUNK_SIZE = 65536 #64k +CHUNK_SIZE = 65536 # 64k DATABASE_MAX_STRING_SIZE = 32768 DATABASE_MAX_STRING_SIZE_PRETTY = '32K' @@ -62,6 +62,7 @@ NULL_CHAR = '\000' BINARY_CHARS = [ NULL_CHAR ] + def is_multi_byte( chars ): for char in chars: try: @@ -69,18 +70,15 @@ except UnicodeDecodeError: # Probably binary return False - if wchartype.is_asian( char ) or \ - wchartype.is_full_width( char ) or \ - wchartype.is_kanji( char ) or \ - wchartype.is_hiragana( char ) or \ - wchartype.is_katakana( char ) or \ - wchartype.is_half_katakana( char ) or \ - wchartype.is_hangul( char ) or \ - wchartype.is_full_digit( char ) or \ - wchartype.is_full_letter( char ): + if ( wchartype.is_asian( char ) or wchartype.is_full_width( char ) or + wchartype.is_kanji( char ) or wchartype.is_hiragana( char ) or + wchartype.is_katakana( char ) or wchartype.is_half_katakana( char ) + or wchartype.is_hangul( char ) or wchartype.is_full_digit( char ) + or wchartype.is_full_letter( char )): return True return False + def is_binary( value, binary_chars=None ): """ File is binary if it contains a null-byte by default (e.g. behavior of grep, etc.). @@ -99,6 +97,7 @@ return True return False + def get_charset_from_http_headers( headers, default=None ): rval = headers.get('content-type', None ) if rval and 'charset=' in rval: @@ -107,16 +106,18 @@ return rval return default + def synchronized(func): """This wrapper will serialize access to 'func' to a single thread. Use it as a decorator.""" def caller(*params, **kparams): - _lock.acquire(True) # Wait + _lock.acquire(True) # Wait try: return func(*params, **kparams) finally: _lock.release() return caller + def file_iter(fname, sep=None): """ This generator iterates over a file and yields its lines @@ -131,6 +132,7 @@ if line and line[0] != '#': yield line.split(sep) + def file_reader( fp, chunk_size=CHUNK_SIZE ): """This generator yields the open fileobject in chunks (default 64k). Closes the file at the end""" while 1: @@ -140,6 +142,7 @@ yield data fp.close() + def unique_id(KEY_SIZE=128): """ Generates an unique id @@ -148,8 +151,8 @@ >>> len(set(ids)) 1000 """ - id = str( random.getrandbits( KEY_SIZE ) ) - return md5(id).hexdigest() + return md5(str( random.getrandbits( KEY_SIZE ) )).hexdigest() + def parse_xml(fname): """Returns a parsed xml tree""" @@ -163,6 +166,7 @@ tree = ElementTree.fromstring(xml_string) return tree + def xml_to_string( elem, pretty=False ): """Returns a string from an xml tree""" if pretty: @@ -170,12 +174,13 @@ try: return ElementTree.tostring( elem ) except TypeError, e: - #assume this is a comment + # we assume this is a comment if hasattr( elem, 'text' ): return "<!-- %s -->\n" % ( elem.text ) else: raise e + def xml_element_compare( elem1, elem2 ): if not isinstance( elem1, dict ): elem1 = xml_element_to_dict( elem1 ) @@ -183,9 +188,11 @@ elem2 = xml_element_to_dict( elem2 ) return elem1 == elem2 + def xml_element_list_compare( elem_list1, elem_list2 ): return [ xml_element_to_dict( elem ) for elem in elem_list1 ] == [ xml_element_to_dict( elem ) for elem in elem_list2 ] + def xml_element_to_dict( elem ): rval = {} if elem.attrib: @@ -220,7 +227,6 @@ return rval - def pretty_print_xml( elem, level=0 ): pad = ' ' i = "\n" + level * pad @@ -238,26 +244,28 @@ elem.tail = i + pad return elem + def get_file_size( value, default=None ): try: - #try built-in + # try built-in return os.path.getsize( value ) except: try: - #try built-in one name attribute + # try built-in one name attribute return os.path.getsize( value.name ) except: try: - #try tell() of end of object + # try tell() of end of object offset = value.tell() value.seek( 0, 2 ) rval = value.tell() value.seek( offset ) return rval except: - #return default value + # return default value return default + def shrink_stream_by_size( value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False ): rval = '' if get_file_size( value ) > size: @@ -292,6 +300,7 @@ rval += data return rval + def shrink_string_by_size( value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False ): if len( value ) > size: len_join_by = len( join_by ) @@ -311,29 +320,30 @@ value = "%s%s%s" % ( value[:left_index], join_by, value[-right_index:] ) return value + def pretty_print_json(json_data, is_json_string=False): if is_json_string: json_data = json.from_json_string(json_data) return json.to_json_string(json_data, sort_keys=True, indent=4) # characters that are valid -valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!") +valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!") # characters that are allowed but need to be escaped -mapped_chars = { '>' :'__gt__', - '<' :'__lt__', - "'" :'__sq__', - '"' :'__dq__', - '[' :'__ob__', - ']' :'__cb__', - '{' :'__oc__', - '}' :'__cc__', - '@' : '__at__', - '\n' : '__cn__', - '\r' : '__cr__', - '\t' : '__tc__', - '#' : '__pd__' - } +mapped_chars = { '>': '__gt__', + '<': '__lt__', + "'": '__sq__', + '"': '__dq__', + '[': '__ob__', + ']': '__cb__', + '{': '__oc__', + '}': '__cc__', + '@': '__at__', + '\n': '__cn__', + '\r': '__cr__', + '\t': '__tc__', + '#': '__pd__'} + def restore_text(text): """Restores sanitized text""" @@ -343,6 +353,7 @@ text = text.replace(value, key) return text + def sanitize_text(text): """ Restricts the characters that are allowed in text; accepts both strings @@ -353,6 +364,7 @@ elif isinstance( text, list ): return [ _sanitize_text_helper(t) for t in text ] + def _sanitize_text_helper(text): """Restricts the characters that are allowed in a string""" @@ -363,9 +375,10 @@ elif c in mapped_chars: out.append(mapped_chars[c]) else: - out.append('X') # makes debugging easier + out.append('X') # makes debugging easier return ''.join(out) + def sanitize_param(value): """Clean incoming parameters (strings or lists)""" if isinstance( value, basestring ): @@ -373,10 +386,12 @@ elif isinstance( value, list ): return map(sanitize_text, value) else: - raise Exception, 'Unknown parameter type (%s)' % ( type( value ) ) + raise Exception('Unknown parameter type (%s)' % ( type( value ) )) valid_filename_chars = set( string.ascii_letters + string.digits + '_.' ) invalid_filenames = [ '', '.', '..' ] + + def sanitize_for_filename( text, default=None ): """ Restricts the characters that are allowed in a filename portion; Returns default value or a unique id string if result is not a valid name. @@ -512,7 +527,7 @@ def __init__( self, params, sanitize=True ): if sanitize: for key, value in params.items(): - if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: #sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed. + if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: # sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed. self.__dict__[ key ] = sanitize_param( value ) else: self.__dict__[ key ] = value @@ -525,7 +540,7 @@ """ flat = [] for key, value in self.__dict__.items(): - if type(value) == type([]): + if isinstance(value, list): for v in value: flat.append( (key, v) ) else: @@ -551,16 +566,19 @@ def update(self, values): self.__dict__.update(values) + def rst_to_html( s ): """Convert a blob of reStructuredText to HTML""" log = logging.getLogger( "docutils" ) + class FakeStream( object ): def write( self, str ): if len( str ) > 0 and not str.isspace(): log.warn( str ) return unicodify( docutils.core.publish_string( s, - writer=docutils.writers.html4css1.Writer(), - settings_overrides={ "embed_stylesheet": False, "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), "warning_stream": FakeStream() } ) ) + writer=docutils.writers.html4css1.Writer(), + settings_overrides={ "embed_stylesheet": False, "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), "warning_stream": FakeStream() } ) ) + def xml_text(root, name=None): """Returns the text inside an element""" @@ -582,6 +600,8 @@ # asbool implementation pulled from PasteDeploy truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1']) falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0']) + + def asbool(obj): if isinstance(obj, basestring): obj = obj.strip().lower() @@ -600,6 +620,7 @@ else: return False + def string_as_bool_or_none( string ): """ Returns True, None or False based on the argument: @@ -618,6 +639,7 @@ else: return False + def listify( item, do_strip=False ): """ Make a single item a single item list, or return a list if passed a @@ -635,6 +657,7 @@ else: return [ item ] + def commaify(amount): orig = amount new = re.sub("^(-?\d+)(\d{3})", '\g<1>,\g<2>', amount) @@ -643,7 +666,8 @@ else: return commaify(new) -def roundify(amount, sfs = 2): + +def roundify(amount, sfs=2): """ Take a number in string form and truncate to 'sfs' significant figures. """ @@ -652,6 +676,7 @@ else: return amount[0:sfs] + '0'*(len(amount) - sfs) + def unicodify( value, encoding=DEFAULT_ENCODING, error='replace', default=None ): """ Returns a unicode string or None @@ -691,6 +716,7 @@ def object_to_string( obj ): return binascii.hexlify( pickle.dumps( obj, 2 ) ) + def string_to_object( s ): return pickle.loads( binascii.unhexlify( s ) ) @@ -743,19 +769,23 @@ return False return True + def get_ucsc_by_build(build): sites = [] for site in ucsc_build_sites: if build in site['builds']: - sites.append((site['name'],site['url'])) + sites.append((site['name'], site['url'])) return sites + + def get_gbrowse_sites_by_build(build): sites = [] for site in gbrowse_build_sites: if build in site['builds']: - sites.append((site['name'],site['url'])) + sites.append((site['name'], site['url'])) return sites + def read_dbnames(filename): """ Read build names from file """ class DBNames( list ): @@ -764,48 +794,54 @@ db_names = DBNames() try: ucsc_builds = {} - man_builds = [] #assume these are integers + man_builds = [] # assume these are integers name_to_db_base = {} for line in open(filename): try: - if line[0:1] == "#": continue - fields = line.replace("\r","").replace("\n","").split("\t") - #Special case of unspecified build is at top of list + if line[0:1] == "#": + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") + # Special case of unspecified build is at top of list if fields[0] == "?": - db_names.insert(0,(fields[0],fields[1])) + db_names.insert(0, (fields[0], fields[1])) continue - try: #manual build (i.e. microbes) + try: # manual build (i.e. microbes) int(fields[0]) man_builds.append((fields[1], fields[0])) - except: #UCSC build + except: # UCSC build db_base = fields[0].rstrip('0123456789') if db_base not in ucsc_builds: ucsc_builds[db_base] = [] name_to_db_base[fields[1]] = db_base - #we want to sort within a species numerically by revision number + # we want to sort within a species numerically by revision number build_rev = re.compile(r'\d+$') - try: build_rev = int(build_rev.findall(fields[0])[0]) - except: build_rev = 0 - ucsc_builds[db_base].append((build_rev, fields[0],fields[1])) - except: continue + try: + build_rev = int(build_rev.findall(fields[0])[0]) + except: + build_rev = 0 + ucsc_builds[db_base].append((build_rev, fields[0], fields[1])) + except: + continue sort_names = name_to_db_base.keys() sort_names.sort() for name in sort_names: db_base = name_to_db_base[name] ucsc_builds[db_base].sort() ucsc_builds[db_base].reverse() - ucsc_builds[db_base] = [(build, name) for build_rev, build, name in ucsc_builds[db_base]] + ucsc_builds[db_base] = [(build, name) for _, build, name in ucsc_builds[db_base]] db_names = DBNames( db_names + ucsc_builds[db_base] ) - if len( db_names ) > 1 and len( man_builds ) > 0: db_names.append( ( db_names.default_value, '----- Additional Species Are Below -----' ) ) + if len( db_names ) > 1 and len( man_builds ) > 0: + db_names.append( ( db_names.default_value, '----- Additional Species Are Below -----' ) ) man_builds.sort() - man_builds = [(build, name) for name, build in man_builds] + man_builds = [(build, name) for name, build in man_builds] db_names = DBNames( db_names + man_builds ) except Exception, e: print "ERROR: Unable to read builds file:", e - if len(db_names)<1: + if len(db_names) < 1: db_names = DBNames( [( db_names.default_value, db_names.default_name )] ) return db_names + def read_ensembl( filename, ucsc ): """ Read Ensembl build names from file """ ucsc_builds = [] @@ -814,47 +850,55 @@ ensembl_builds = list() try: for line in open( filename ): - if line[0:1] in [ '#', '\t' ]: continue - fields = line.replace("\r","").replace("\n","").split("\t") - if fields[0] in ucsc_builds: continue + if line[0:1] in [ '#', '\t' ]: + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") + if fields[0] in ucsc_builds: + continue ensembl_builds.append( dict( dbkey=fields[0], release=fields[1], name=fields[2].replace( '_', ' ' ) ) ) except Exception, e: print "ERROR: Unable to read builds file:", e return ensembl_builds + def read_ncbi( filename ): """ Read NCBI build names from file """ ncbi_builds = list() try: for line in open( filename ): - if line[0:1] in [ '#', '\t' ]: continue - fields = line.replace("\r","").replace("\n","").split("\t") + if line[0:1] in [ '#', '\t' ]: + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") ncbi_builds.append( dict( dbkey=fields[0], name=fields[1] ) ) except Exception, e: print "ERROR: Unable to read builds file:", e return ncbi_builds + def read_build_sites( filename, check_builds=True ): """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ build_sites = [] try: for line in open(filename): try: - if line[0:1] == "#": continue - fields = line.replace("\r","").replace("\n","").split("\t") + if line[0:1] == "#": + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") site_name = fields[0] site = fields[1] if check_builds: site_builds = fields[2].split(",") - site_dict = {'name':site_name, 'url':site, 'builds':site_builds} + site_dict = {'name': site_name, 'url': site, 'builds': site_builds} else: - site_dict = {'name':site_name, 'url':site} + site_dict = {'name': site_name, 'url': site} build_sites.append( site_dict ) - except: continue + except: + continue except: - print "ERROR: Unable to read builds for site file %s" %filename + print "ERROR: Unable to read builds for site file %s" % filename return build_sites + def relativize_symlinks( path, start=None, followlinks=False): for root, dirs, files in os.walk( path, followlinks=followlinks ): rel_start = None @@ -871,23 +915,26 @@ os.remove( symlink_file_name ) os.symlink( rel_path, symlink_file_name ) + def stringify_dictionary_keys( in_dict ): - #returns a new dictionary - #changes unicode keys into strings, only works on top level (does not recurse) - #unicode keys are not valid for expansion into keyword arguments on method calls + # returns a new dictionary + # changes unicode keys into strings, only works on top level (does not recurse) + # unicode keys are not valid for expansion into keyword arguments on method calls out_dict = {} for key, value in in_dict.iteritems(): out_dict[ str( key ) ] = value return out_dict + def recursively_stringify_dictionary_keys( d ): if isinstance(d, dict): - return dict([(k.encode( DEFAULT_ENCODING ), recursively_stringify_dictionary_keys(v)) for k,v in d.iteritems()]) + return dict([(k.encode( DEFAULT_ENCODING ), recursively_stringify_dictionary_keys(v)) for k, v in d.iteritems()]) elif isinstance(d, list): return [recursively_stringify_dictionary_keys(x) for x in d] else: return d + def mkstemp_ln( src, prefix='mkstemp_ln_' ): """ From tempfile._mkstemp_inner, generate a hard link in the same dir with a @@ -904,9 +951,10 @@ return (os.path.abspath(file)) except OSError, e: if e.errno == errno.EEXIST: - continue # try again + continue # try again raise - raise IOError, (errno.EEXIST, "No usable temporary file name found") + raise IOError(errno.EEXIST, "No usable temporary file name found") + def umask_fix_perms( path, umask, unmasked_perms, gid=None ): """ @@ -923,7 +971,7 @@ try: os.chmod( path, perms ) except Exception, e: - log.warning( 'Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % ( oct( umask ), \ + log.warning( 'Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % ( oct( umask ), path, oct( perms ), oct( stat.S_IMODE( st.st_mode ) ), @@ -939,11 +987,12 @@ except: desired_group = gid current_group = st.st_gid - log.warning( 'Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % ( desired_group, \ + log.warning( 'Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % ( desired_group, path, current_group, e ) ) + def docstring_trim(docstring): """Trimming python doc strings. Taken from: http://www.python.org/dev/peps/pep-0257/""" if not docstring: @@ -970,6 +1019,7 @@ # Return a single string: return '\n'.join(trimmed) + def nice_size(size): """ Returns a readably formatted string with the size @@ -989,14 +1039,15 @@ except: return '??? bytes' for ind, word in enumerate(words): - step = 1024 ** (ind + 1) + step = 1024 ** (ind + 1) if step > size: size = size / float(1024 ** ind) - if word == 'bytes': # No decimals for bytes + if word == 'bytes': # No decimals for bytes return "%d bytes" % size return "%.1f %s" % (size, word) return '??? bytes' + def size_to_bytes( size ): """ Returns a number of bytes if given a reasonably formatted string with the size @@ -1023,6 +1074,7 @@ elif multiple.startswith( 'b' ): return int( size ) + def send_mail( frm, to, subject, body, config ): """ Sends an email. @@ -1072,6 +1124,7 @@ s.sendmail( frm, to, msg.as_string() ) s.quit() + def force_symlink( source, link_name ): try: os.symlink( source, link_name ) @@ -1082,12 +1135,13 @@ else: raise e + def move_merge( source, target ): - #when using shutil and moving a directory, if the target exists, - #then the directory is placed inside of it - #if the target doesn't exist, then the target is made into the directory - #this makes it so that the target is always the target, and if it exists, - #the source contents are moved into the target + # when using shutil and moving a directory, if the target exists, + # then the directory is placed inside of it + # if the target doesn't exist, then the target is made into the directory + # this makes it so that the target is always the target, and if it exists, + # the source contents are moved into the target if os.path.isdir( source ) and os.path.exists( target ) and os.path.isdir( target ): for name in os.listdir( source ): move_merge( os.path.join( source, name ), os.path.join( target, name ) ) @@ -1103,7 +1157,7 @@ rv |= ord(x) ^ ord(y) return rv == 0 -galaxy_root_path = os.path.join(__path__[0], "..","..","..") +galaxy_root_path = os.path.join(__path__[0], "..", "..", "..") # The dbnames list is used in edit attributes and the upload tool dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) ) @@ -1114,6 +1168,7 @@ gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) ) dlnames = dict(ucsc=ucsc_names, ensembl=ensembl_names, ncbi=ncbi_names) + def galaxy_directory(): return os.path.abspath(galaxy_root_path) diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -18,7 +18,7 @@ from galaxy.web.base.controller import ExportsHistoryMixin from galaxy.web.base.controller import ImportsHistoryMixin -from galaxy.managers import histories +from galaxy.managers import histories, citations from galaxy import util from galaxy.util import string_as_bool @@ -34,6 +34,7 @@ def __init__( self, app ): super( HistoriesController, self ).__init__( app ) + self.citations_manager = citations.CitationsManager( app ) self.mgrs = util.bunch.Bunch( histories=histories.HistoryManager() ) @@ -117,6 +118,20 @@ history_data[ 'contents_url' ] = url_for( 'history_contents', history_id=history_id ) return history_data + @expose_api_anonymous + def citations( self, trans, history_id, **kwd ): + history = self.mgrs.histories.get( trans, self._decode_id( trans, history_id ), check_ownership=False, check_accessible=True ) + tool_ids = set([]) + for dataset in history.datasets: + job = dataset.creating_job + if not job: + continue + tool_id = job.tool_id + if not tool_id: + continue + tool_ids.add(tool_id) + return map( lambda citation: citation.to_dict( "bibtex" ), self.citations_manager.citations_for_tool_ids( tool_ids ) ) + @expose_api def set_as_current( self, trans, id, **kwd ): """ diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,6 +1,8 @@ import urllib +from galaxy import exceptions from galaxy import web, util +from galaxy.web import _future_expose_api_anonymous from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import UsesVisualizationMixin from galaxy.web.base.controller import UsesHistoryMixin @@ -44,7 +46,7 @@ trans.response.status = 500 return { 'error': str( exc ) } - @web.expose_api + @_future_expose_api_anonymous def show( self, trans, id, **kwd ): """ GET /api/tools/{tool_id} @@ -52,18 +54,16 @@ """ io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) link_details = util.string_as_bool( kwd.get( 'link_details', False ) ) - try: - id = urllib.unquote_plus( id ) - tool = self.app.toolbox.get_tool( id ) - if not tool: - trans.response.status = 404 - return { 'error': 'tool not found', 'id': id } - return tool.to_dict( trans, io_details=io_details, link_details=link_details ) + tool = self._get_tool( id ) + return tool.to_dict( trans, io_details=io_details, link_details=link_details ) - except Exception, exc: - log.error( 'could not convert tool (%s) to dictionary: %s', id, str( exc ), exc_info=True ) - trans.response.status = 500 - return { 'error': str( exc ) } + @_future_expose_api_anonymous + def citations( self, trans, id, **kwds ): + tool = self._get_tool( id ) + rval = [] + for citation in tool.citations: + rval.append( citation.to_dict( 'bibtex' ) ) + return rval @web.expose_api_anonymous def create( self, trans, payload, **kwd ): @@ -170,6 +170,12 @@ # # -- Helper methods -- # + def _get_tool( self, id ): + id = urllib.unquote_plus( id ) + tool = self.app.toolbox.get_tool( id ) + if not tool: + raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id) + return tool def _rerun_tool( self, trans, payload, **kwargs ): """ diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -82,11 +82,17 @@ latest_workflow = stored_workflow.latest_workflow inputs = {} for step in latest_workflow.steps: - if step.type == 'data_input': + step_type = step.type + if step_type in ['data_input', 'data_collection_input']: if step.tool_inputs and "name" in step.tool_inputs: - inputs[step.id] = {'label': step.tool_inputs['name'], 'value': ""} + label = step.tool_inputs['name'] + elif step_type == "data_input": + label = "Input Dataset" + elif step_type == "data_collection_input": + label = "Input Dataset Collection" else: - inputs[step.id] = {'label': "Input Dataset", 'value': ""} + raise ValueError("Invalid step_type %s" % step_type) + inputs[step.id] = {'label': label, 'value': ""} else: pass # Eventually, allow regular tool parameters to be inserted and modified at runtime. @@ -194,7 +200,27 @@ # Pull other parameters out of payload. param_map = payload.get( 'parameters', {} ) - ds_map = payload.get( 'ds_map', {} ) + inputs = payload.get( 'inputs', None ) + inputs_by = payload.get( 'inputs_by', None ) + if inputs is None: + # Default to legacy behavior - read ds_map and reference steps + # by unencoded step id (a raw database id). + inputs = payload.get( 'ds_map', {} ) + inputs_by = inputs_by or 'step_id' + else: + inputs = inputs or {} + # New default is to reference steps by index of workflow step + # which is intrinsic to the workflow and independent of the state + # of Galaxy at the time of workflow import. + inputs_by = inputs_by or 'step_index' + + valid_inputs_by = [ 'step_id', 'step_index', 'name' ] + if inputs_by not in valid_inputs_by: + trans.response.status = 403 + error_message_template = "Invalid inputs_by specified '%s' must be one of %s" + error_message = error_message_template % ( inputs_by, valid_inputs_by ) + raise ValueError( error_message ) + add_to_history = 'no_add_to_history' not in payload history_param = payload.get('history', '') @@ -234,33 +260,42 @@ trans.sa_session.flush() # Set workflow inputs. - for k in ds_map: + for k in inputs: try: - if ds_map[k]['src'] == 'ldda': + if inputs[k]['src'] == 'ldda': ldda = trans.sa_session.query(self.app.model.LibraryDatasetDatasetAssociation).get( - trans.security.decode_id(ds_map[k]['id'])) + trans.security.decode_id(inputs[k]['id'])) assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) - hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - elif ds_map[k]['src'] == 'ld': + content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) + elif inputs[k]['src'] == 'ld': ldda = trans.sa_session.query(self.app.model.LibraryDataset).get( - trans.security.decode_id(ds_map[k]['id'])).library_dataset_dataset_association + trans.security.decode_id(inputs[k]['id'])).library_dataset_dataset_association assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) - hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - elif ds_map[k]['src'] == 'hda': + content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) + elif inputs[k]['src'] == 'hda': # Get dataset handle, add to dict and history if necessary - hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get( - trans.security.decode_id(ds_map[k]['id'])) - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + content = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get( + trans.security.decode_id(inputs[k]['id'])) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) + elif inputs[k]['src'] == 'hdca': + content = self.app.dataset_collections_service.get_dataset_collection_instance( + trans, + 'history', + inputs[k]['id'] + ) else: trans.response.status = 400 - return "Unknown dataset source '%s' specified." % ds_map[k]['src'] - if add_to_history and hda.history != history: - hda = hda.copy() - history.add_dataset(hda) - ds_map[k]['hda'] = hda + return "Unknown dataset source '%s' specified." % inputs[k]['src'] + if add_to_history and content.history != history: + content = content.copy() + if isinstance( content, self.app.model.HistoryDatasetAssociation ): + history.add_dataset( content ) + else: + history.add_dataset_collection( content ) + inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly except AssertionError: trans.response.status = 400 - return "Invalid Dataset '%s' Specified" % ds_map[k]['id'] + return "Invalid Dataset '%s' Specified" % inputs[k]['id'] # Run each step, connecting outputs to inputs replacement_dict = payload.get('replacement_params', {}) @@ -268,7 +303,8 @@ run_config = WorkflowRunConfig( target_history=history, replacement_dict=replacement_dict, - ds_map=ds_map, + inputs=inputs, + inputs_by=inputs_by, param_map=param_map, ) diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -174,6 +174,7 @@ webapp.mapper.resource( 'ftp_file', 'ftp_files', path_prefix='/api' ) webapp.mapper.resource( 'group', 'groups', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) + webapp.mapper.connect( '/api/tools/{id:.+?}/citations', action='citations', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}', action='show', controller="tools" ) webapp.mapper.resource( 'tool', 'tools', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) @@ -181,6 +182,7 @@ webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' ) webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) + webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" ) webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) webapp.mapper.resource( 'datatype', 'datatypes', diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -448,6 +448,13 @@ # ......................................................................... html @web.expose + def citations( self, trans ): + # Get history + history = trans.history + history_id = trans.security.encode_id( history.id ) + return trans.fill_template( "history/citations.mako", history=history, history_id=history_id ) + + @web.expose def display_structured( self, trans, id=None ): """ Display a history as a nested structure showing the jobs and workflow diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -32,19 +32,26 @@ target_history. (Defaults to False) :type copy_inputs_to_history: bool - :param ds_map: Map from step ids to dict's containing HDA for these steps. - :type ds_map: dict + :param inputs: Map from step ids to dict's containing HDA for these steps. + :type inputs: dict + + :param inputs_by: How inputs maps to inputs (datasets/collections) to workflows + steps - by unencoded database id ('step_id'), index in workflow + 'step_index' (independent of database), or by input name for + that step ('name'). + :type inputs_by: str :param param_map: Override tool and/or step parameters (see documentation on _update_step_parameters below). :type param_map: """ - def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, ds_map={}, param_map={} ): + def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, inputs_by='step_id', param_map={} ): self.target_history = target_history self.replacement_dict = replacement_dict self.copy_inputs_to_history = copy_inputs_to_history - self.ds_map = ds_map + self.inputs = inputs + self.inputs_by = inputs_by self.param_map = param_map @@ -66,7 +73,9 @@ self.target_history = workflow_run_config.target_history self.replacement_dict = workflow_run_config.replacement_dict self.copy_inputs_to_history = workflow_run_config.copy_inputs_to_history - self.ds_map = workflow_run_config.ds_map + self.inputs = workflow_run_config.inputs + self.inputs_by = workflow_run_config.inputs_by + self.inputs_by_step_id = {} self.param_map = workflow_run_config.param_map self.outputs = odict() @@ -200,7 +209,7 @@ outputs[ step.id ] = out_data # Web controller may set copy_inputs_to_history, API controller always sets - # ds_map. + # inputs. if self.copy_inputs_to_history: for input_dataset_hda in out_data.values(): content_type = input_dataset_hda.history_content_type @@ -214,8 +223,8 @@ outputs[ step.id ][ 'input_ds_copy' ] = new_hdca else: raise Exception("Unknown history content encountered") - if self.ds_map: - outputs[ step.id ][ 'output' ] = self.ds_map[ str( step.id ) ][ 'hda' ] + if self.inputs: + outputs[ step.id ][ 'output' ] = self.inputs_by_step_id[ step.id ][ 'hda' ] return job @@ -277,14 +286,23 @@ message = "Workflow cannot be run because of step upgrade messages: %s" % step.upgrade_messages raise exceptions.MessageException( message ) else: - # This is an input step. Make sure we have an available input. - if step.type == 'data_input' and str( step.id ) not in self.ds_map: - message = "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id - raise exceptions.MessageException( message ) - step.module = modules.module_factory.from_workflow_step( self.trans, step ) step.state = step.module.get_runtime_state() + # This is an input step. Make sure we have an available input. + if step.type in [ 'data_input', 'data_collection_input' ]: + if self.inputs_by == "step_id": + key = str( step.id ) + elif self.inputs_by == "name": + key = step.tool_inputs.get( 'name', None ) + else: + key = str( step.order_index ) + if key not in self.inputs: + message = "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id + raise exceptions.MessageException( message ) + else: + self.inputs_by_step_id[ step.id ] = self.inputs[ key ] + def _update_step_parameters(step, param_map): """ diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py @@ -0,0 +1,48 @@ +""" +The following tools have been eliminated from the distribution: + +1: Compute an expression on every row +2: Correlation for numeric columns +3: Count GFF Features +4: Filter on ambiguities in polymorphism datasets +5: Generate A Matrix for using PC and LDA +6: Histogram of a numeric column +7: Perform Linear Discriminant Analysis +8: Maximal Information-based Nonparametric Exploration +9: Pearson and apos Correlation between any two numeric columns +10: Convert from pgSnp to gd_snp +11: Draw ROC plot on "Perform LDA" output +12: Scatterplot of two numeric columns +13: snpFreq significant SNPs in case-control data +14: Build custom track for UCSC genome browser +15: VCF to pgSnp + +The tools are now available in the repositories respectively: + +1: column_maker +2: correlation +3: count_gff_features +4: dna_filtering +5: generate_pc_lda_matrix +6: histogram +7: lda_analysis +8: mine +9: pearson_correlation +10: pgsnp2gd_snp +11: plot_from_lda +12: scatterplot +13: snpfreq +14: ucsc_custom_track +15: vcf2pgsnp + +from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu +and will be installed into your local Galaxy instance at the +location discussed above by running the following command. + +""" + +def upgrade( migrate_engine ): + print __doc__ + +def downgrade( migrate_engine ): + pass diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh --- a/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh @@ -73,12 +73,11 @@ fi done -echo -n "Retrieving admin user's API key..." -api_key_json=`curl -s --user $admin_user_email:$admin_user_password $local_shed_url/api/authenticate/baseauth/` -api_key=`echo $api_key_json | grep api_key | awk 'BEGIN { FS="\"" } ; { print \$4 }' | sed 's/\\s\+//'` +echo -n "Retrieving admin user's API key from $local_shed_url..." +api_key=`curl -s --user $admin_user_email:$admin_user_password $local_shed_url/api/authenticate/baseauth/ | sed 's/.\+api_key[^0-9a-f]\+\([0-9a-f]\+\).\+/\1/'` if [[ -z $api_key && ${api_key+x} ]] ; then - stop_err "Error getting API key for user $admin_user_email." + stop_err "Error getting API key for user $admin_user_email." fi echo " done." diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 run_tests.sh --- a/run_tests.sh +++ b/run_tests.sh @@ -88,7 +88,7 @@ shift 1 fi ;; - -with_framework_test_tools|--with_framework_test_tools) + -with_framework_test_tools|--with_framework_test_tools) with_framework_test_tools_arg="-with_framework_test_tools" shift ;; diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 scripts/migrate_tools/0012_tools.sh --- /dev/null +++ b/scripts/migrate_tools/0012_tools.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml $@ diff -r c6afab452541a54c1755b54f2e93c47950b8ae75 -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 scripts/migrate_tools/0012_tools.xml --- /dev/null +++ b/scripts/migrate_tools/0012_tools.xml @@ -0,0 +1,48 @@ +<?xml version="1.0"?> +<toolshed name="toolshed.g2.bx.psu.edu"> + <repository changeset_revision="08a01b2ce4cd" owner="devteam" name="column_maker" description="Compute an expression on every row"> + <tool file="stats/column_maker.xml" id="Add_a_column1" version="1.1.0" /> + </repository> + <repository changeset_revision="24e01abf9e34" owner="devteam" name="correlation" description="Correlation for numeric columns"> + <tool file="stats/cor.xml" id="cor2" version="1.0.0" /> + </repository> + <repository changeset_revision="fabda887a71f" owner="devteam" name="count_gff_features" description="Count GFF Features"> + <tool file="stats/count_gff_features.xml" id="count_gff_features" version="0.1" /> + </repository> + <repository changeset_revision="a6f0d355b05f" owner="devteam" name="dna_filtering" description="Filter on ambiguities in polymorphism datasets"> + <tool file="stats/dna_filtering.xml" id="dna_filter" version="1.0.0" /> + </repository> + <repository changeset_revision="04cdbd00dcec" owner="devteam" name="generate_pc_lda_matrix" description="Generate A Matrix for using PC and LDA"> + <tool file="stats/generate_matrix_for_pca_lda.xml" id="generate_matrix_for_pca_and_lda1" version="1.0.0" /> + </repository> + <repository changeset_revision="6ff47de059a0" owner="devteam" name="histogram" description="Histogram of a numeric column"> + <tool file="plotting/histogram2.xml" id="histogram_rpy" version="1.0.3" /> + </repository> + <repository changeset_revision="f38763b52f33" owner="devteam" name="lda_analysis" description="Perform Linear Discriminant Analysis"> + <tool file="stats/lda_analy.xml" id="lda_analy1" version="1.0.1" /> + </repository> + <repository changeset_revision="783d91de9e6d" owner="devteam" name="mine" description="Maximal Information-based Nonparametric Exploration"> + <tool file="stats/MINE.xml" id="maximal_information_based_nonparametric_exploration" version="0.0.1" /> + </repository> + <repository changeset_revision="5ebbb889236a" owner="devteam" name="pearson_correlation" description="Pearson and apos Correlation between any two numeric columns"> + <tool file="stats/correlation.xml" id="Pearson_and_apos_Correlation1" version="1.0.0" /> + </repository> + <repository changeset_revision="d281062566f9" owner="devteam" name="pgsnp2gd_snp" description="Convert from pgSnp to gd_snp"> + <tool file="phenotype_association/pgSnp2gd_snp.xml" id="pgSnp2gd_snp" version="1.0.0" /> + </repository> + <repository changeset_revision="c5ab37076128" owner="devteam" name="plot_from_lda" description="Draw ROC plot on "Perform LDA" output"> + <tool file="stats/plot_from_lda.xml" id="plot_for_lda_output1" version="1.0.1" /> + </repository> + <repository changeset_revision="c12b0759203b" owner="devteam" name="scatterplot" description="Scatterplot of two numeric columns"> + <tool file="plotting/scatterplot.xml" id="scatterplot_rpy" version="1.0.0" /> + </repository> + <repository changeset_revision="72ea0d13dd66" owner="devteam" name="snpfreq" description="snpFreq significant SNPs in case-control data"> + <tool file="phenotype_association/snpFreq.xml" id="hgv_snpFreq" version="1.0.1" /> + </repository> + <repository changeset_revision="618e56c3109b" owner="devteam" name="ucsc_custom_track" description="Build custom track for UCSC genome browser"> + <tool file="visualization/build_ucsc_custom_track.xml" id="build_ucsc_custom_track_1" version="1.0.0" /> + </repository> + <repository changeset_revision="5fca46616675" owner="devteam" name="vcf2pgsnp" description="VCF to pgSnp"> + <tool file="phenotype_association/vcf2pgSnp.xml" id="vcf2pgSnp" version="1.0.0" /> + </repository> +</toolshed> \ No newline at end of file This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/25772fa9e947/ Changeset: 25772fa9e947 User: martenson Date: 2014-08-02 00:29:03 Summary: permision API: working permissions for libraries including UI Affected #: 8 files diff -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -95,6 +95,9 @@ def set_all_library_permissions( self, trans, dataset, permissions ): raise "Unimplemented Method" + def set_library_item_permission( self, library_item, permission ): + raise "Unimplemented Method" + def library_is_public( self, library ): raise "Unimplemented Method" @@ -221,10 +224,10 @@ roles.append( item_permission.role ) return roles - def get_valid_dataset_roles( self, trans, dataset, query=None, page=None, page_limit=None ): + def get_valid_roles( self, trans, item, query=None, page=None, page_limit=None, is_library_access=False ): """ This method retrieves the list of possible roles that user can select - in the dataset permissions form. Admins can select any role so the + in the item permissions form. Admins can select any role so the results are paginated in order to save the bandwidth and to speed things up. Standard users can select their own private role, any of their @@ -245,8 +248,15 @@ total_count = None - # For public datasets admins can choose from all roles - if trans.user_is_admin() and self.dataset_is_public( dataset ): + if isinstance( item, self.model.Library ) and self.library_is_public( item ): + is_public_item = True + elif isinstance( item, self.model.Dataset ) and self.dataset_is_public( item ): + is_public_item = True + else: + is_public_item = False + + # For public items and for library access admins can choose from all roles + if trans.user_is_admin() and ( is_public_item or is_library_access ): # Add all non-deleted roles that fit the query db_query = trans.sa_session.query( trans.app.model.Role ).filter( self.model.Role.table.c.deleted == False ) if query is not None: @@ -265,8 +275,8 @@ else: roles = db_query.order_by( self.model.Role.table.c.name ) - # Non-admin and public dataset - elif self.dataset_is_public( dataset ): + # Non-admin and public item + elif is_public_item: # Add the current user's private role roles.append( self.get_private_user_role( trans.user ) ) # Add the current user's sharing roles @@ -279,10 +289,10 @@ self.model.Role.table.c.type != self.model.Role.types.SHARING ) ) \ .order_by( self.model.Role.table.c.name ): roles.append( role ) - # User is not admin and dataset is not public + # User is not admin and item is not public else: # If item has roles associated with the access permission, we need to start with them. - access_roles = dataset.get_access_roles( trans ) + access_roles = item.get_access_roles( trans ) for role in access_roles: if trans.user_is_admin() or self.ok_to_display( trans.user, role ): roles.append( role ) @@ -1018,7 +1028,7 @@ if flush_needed: self.sa_session.flush() - def set_library_item_permission( self, library_dataset, permission={} ): + def set_library_item_permission( self, library_item, permission={} ): """ Set a specific permission on a library item, leaving all other current permissions on the item alone. Permission looks like: { Action.action : [ Role, Role ] } @@ -1027,15 +1037,20 @@ for action, roles in permission.items(): if isinstance( action, Action ): action = action.action - # Delete the current specific permission on the library_dataset if one exists - for dp in library_dataset.actions: - if dp.action == action: - self.sa_session.delete( dp ) + # Delete the current specific permission on the library item if one exists + for item_permission in library_item.actions: + if item_permission.action == action: + self.sa_session.delete( item_permission ) flush_needed = True - # Add the new specific permission on the library_dataset - for dp in [ self.model.LibraryDatasetPermissions( action, library_dataset, role ) for role in roles ]: - self.sa_session.add( dp ) - flush_needed = True + # Add the new specific permission on the library item + if isinstance( library_item, self.model.LibraryDataset ): + for item_permission in [ self.model.LibraryDatasetPermissions( action, library_item, role ) for role in roles ]: + self.sa_session.add( item_permission ) + flush_needed = True + elif isinstance ( library_item, self.model.LibraryPermissions): + for item_permission in [ self.model.LibraryPermissions( action, library_item, role ) for role in roles ]: + self.sa_session.add( item_permission ) + flush_needed = True if flush_needed: self.sa_session.flush() diff -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -103,26 +103,18 @@ raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) dataset = library_dataset.library_dataset_dataset_association.dataset - # User has to have manage permissions in order to see the roles. + # User has to have manage permissions permission in order to see the roles. can_manage = trans.app.security_agent.can_manage_dataset( current_user_roles, dataset ) or trans.user_is_admin() if not can_manage: - raise exceptions.InsufficientPermissionsException( 'You do not have proper permissions to access permissions.' ) + raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to access permissions.' ) scope = kwd.get( 'scope', None ) if scope == 'current' or scope is None: return self.get_current_roles( trans, library_dataset ) - # legit_roles = trans.app.security_agent.get_legitimate_roles( trans, dataset, 'library_admin' ) - # log.debug( 'CXXXXXCXCXCXCXCXCC legit roles: ' + str( [ legit_role.name for legit_role in legit_roles ] ) ) - - # all_permissions = trans.app.security_agent.get_permissions( library_dataset ) - # for k,v in all_permissions.items(): - # log.debug( '*******************************************' ) - # log.debug( 'permission action: ' + str( k.action ) ) - # log.debug( 'permission roles: ' + str( [ role.name for role in v ] ) ) # Return roles that are available to select. - if scope == 'available': + elif scope == 'available': page = kwd.get( 'page', None ) if page is not None: page = int( page ) @@ -137,20 +129,14 @@ query = kwd.get( 'q', None ) - # try: - # library_dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) - # except Exception, e: - # raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) - # dataset = library_dataset.library_dataset_dataset_association.dataset - # library = library_dataset.folder.parent_library - - roles, total_roles = trans.app.security_agent.get_valid_dataset_roles( trans, dataset, query, page, page_limit ) + roles, total_roles = trans.app.security_agent.get_valid_roles( trans, dataset, query, page, page_limit ) return_roles = [] for role in roles: return_roles.append( dict( id=role.name, name=role.name, type=role.type ) ) - return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) + else: + raise exceptions.RequestParameterInvalidException( "The value of 'scope' parameter is invalid. Alllowed values: current, available" ) def get_current_roles( self, trans, library_dataset): """ @@ -159,6 +145,9 @@ :param library_dataset: the model object :type library_dataset: LibraryDataset + + :rtype: dictionary + :returns: dict of current roles for all available permission types """ dataset = library_dataset.library_dataset_dataset_association.dataset @@ -179,15 +168,25 @@ def update( self, trans, encoded_dataset_id, **kwd ): *POST /api/libraries/datasets/{encoded_dataset_id}/permissions - :param encoded_dataset_id: the encoded id of the dataset to make private + :param encoded_dataset_id: the encoded id of the dataset to update permissions of :type encoded_dataset_id: an encoded id string :param action: (required) describes what action should be performed available actions: make_private, remove_restrictions, set_permissions :type action: string + :param access_ids[]: list of Role.name defining roles that should have access permission on the dataset + :type access_ids[]: string or list + :param manage_ids[]: list of Role.name defining roles that should have manage permission on the dataset + :type manage_ids[]: string or list + :param modify_ids[]: list of Role.name defining roles that should have modify permission on the library dataset item + :type modify_ids[]: string or list + :rtype: dictionary - :returns: dict of current roles for all permission types + :returns: dict of current roles for all available permission types + + :raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError + RequestParameterMissingException """ try: library_dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=False ) @@ -235,13 +234,13 @@ role = self._load_role( trans, role_id ) # Check whether role is in the set of allowed roles - valid_roles, total_roles = trans.app.security_agent.get_valid_dataset_roles( trans, dataset ) + valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, dataset ) if role in valid_roles: valid_access_roles.append( role ) else: invalid_access_roles_names.append( role_id ) if len( invalid_access_roles_names ) > 0: - log.debug( "The following roles could not be added to the dataset access permission: " + str( invalid_access_roles_names ) ) + log.warning( "The following roles could not be added to the dataset access permission: " + str( invalid_access_roles_names ) ) access_permission = dict( access=valid_access_roles ) trans.app.security_agent.set_dataset_permission( dataset, access_permission ) @@ -250,7 +249,6 @@ valid_manage_roles = [] invalid_manage_roles_names = [] new_manage_roles_ids = util.listify( new_manage_roles_ids ) - log.debug("new_manage_roles_ids: " + str(new_manage_roles_ids)) # Load all access roles to check active_access_roles = dataset.get_access_roles( trans ) @@ -265,7 +263,7 @@ invalid_manage_roles_names.append( role_id ) if len( invalid_manage_roles_names ) > 0: - log.debug( "The following roles could not be added to the dataset manage permission: " + str( invalid_manage_roles_names ) ) + log.warning( "The following roles could not be added to the dataset manage permission: " + str( invalid_manage_roles_names ) ) manage_permission = { trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS : valid_manage_roles } trans.app.security_agent.set_dataset_permission( dataset, manage_permission ) @@ -274,7 +272,6 @@ valid_modify_roles = [] invalid_modify_roles_names = [] new_modify_roles_ids = util.listify( new_modify_roles_ids ) - log.debug("new_modify_roles_ids: " + str(new_modify_roles_ids)) # Load all access roles to check active_access_roles = dataset.get_access_roles( trans ) @@ -289,7 +286,7 @@ invalid_modify_roles_names.append( role_id ) if len( invalid_modify_roles_names ) > 0: - log.debug( "The following roles could not be added to the dataset manage permission: " + str( invalid_modify_roles_names ) ) + log.warning( "The following roles could not be added to the dataset modify permission: " + str( invalid_modify_roles_names ) ) modify_permission = { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY : valid_modify_roles } trans.app.security_agent.set_library_item_permission( library_dataset, modify_permission ) @@ -303,6 +300,14 @@ def _load_role( self, trans, role_name ): """ Method loads the role from the DB based on the given role name. + + :param role_name: name of the role to load from the DB + :type role_name: string + + :rtype: Role + :returns: the loaded Role object + + :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError """ try: role = trans.sa_session.query( trans.app.model.Role ).filter( trans.model.Role.table.c.name == role_name ).one() diff -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -7,6 +7,8 @@ from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.model.orm import and_, not_, or_ from galaxy.web.base.controller import BaseAPIController +from sqlalchemy.orm.exc import MultipleResultsFound +from sqlalchemy.orm.exc import NoResultFound import logging log = logging.getLogger( __name__ ) @@ -95,8 +97,14 @@ """ library_id = id deleted = util.string_as_bool( deleted ) + library = self._load_library( trans, library_id, deleted ) + if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( trans.get_current_user_roles(), library ) ): + raise exceptions.ObjectNotFound( 'Library with the id provided ( %s ) was not found' % id ) + return library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) + + def _load_library( self, trans, encoded_library_id, deleted=False ): try: - decoded_library_id = trans.security.decode_id( library_id ) + decoded_library_id = trans.security.decode_id( encoded_library_id ) except TypeError: raise exceptions.MalformedId( 'Malformed library id ( %s ) specified, unable to decode.' % id ) try: @@ -104,9 +112,7 @@ assert library.deleted == deleted except Exception: library = None - if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( trans.get_current_user_roles(), library ) ): - raise exceptions.ObjectNotFound( 'Library with the id provided ( %s ) was not found' % id ) - return library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) + return library @expose_api def create( self, trans, payload, **kwd ): @@ -250,3 +256,231 @@ trans.sa_session.add( library ) trans.sa_session.flush() return library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) + + @expose_api + def get_permissions( self, trans, encoded_library_id, **kwd ): + """ + * GET /api/libraries/{id}/permissions + + Load all permissions for the given library id and return it. + + :param encoded_library_id: the encoded id of the library + :type encoded_library_id: an encoded id string + + :param scope: either 'current' or 'available' + :type scope: string + + :param is_library_access: indicates whether the roles available for the library access are requested + :type is_library_access: bool + + :returns: dictionary with all applicable permissions' values + :rtype: dictionary + + :raises: ObjectNotFound, InsufficientPermissionsException + """ + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() + library = self._load_library( trans, encoded_library_id ) + if not library or not ( is_admin or trans.app.security_agent.can_access_library( current_user_roles, library ) ): + raise exceptions.ObjectNotFound( 'Library with the id provided ( %s ) was not found' % id ) + if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, library ) ): + raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to access permissions of this library.' ) + + scope = kwd.get( 'scope', None ) + is_library_access = kwd.get( 'is_library_access', False ) + + if scope == 'current' or scope is None: + return self._get_current_roles( trans, library ) + + # Return roles that are available to select. + elif scope == 'available': + page = kwd.get( 'page', None ) + if page is not None: + page = int( page ) + else: + page = 1 + + page_limit = kwd.get( 'page_limit', None ) + if page_limit is not None: + page_limit = int( page_limit ) + else: + page_limit = 10 + + query = kwd.get( 'q', None ) + + roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library, query, page, page_limit, is_library_access ) + + return_roles = [] + for role in roles: + return_roles.append( dict( id=role.name, name=role.name, type=role.type ) ) + return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) + else: + raise exceptions.RequestParameterInvalidException( "The value of 'scope' parameter is invalid. Alllowed values: current, available" ) + + def _load_role( self, trans, role_name ): + """ + Method loads the role from the DB based on the given role name. + + :param role_name: name of the role to load from the DB + :type role_name: string + + :rtype: Role + :returns: the loaded Role object + + :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError + """ + try: + role = trans.sa_session.query( trans.app.model.Role ).filter( trans.model.Role.table.c.name == role_name ).one() + except MultipleResultsFound: + raise exceptions.InconsistentDatabase( 'Multiple roles found with the same name. Name: ' + str( role_name ) ) + except NoResultFound: + raise exceptions.RequestParameterInvalidException( 'No role found with the name provided. Name: ' + str( role_name ) ) + except Exception, e: + raise exceptions.InternalServerError( 'Error loading from the database.' + str(e)) + return role + + @expose_api + def set_permissions( self, trans, encoded_library_id, **kwd ): + """ + def set_permissions( self, trans, encoded_dataset_id, **kwd ): + *POST /api/libraries/{encoded_library_id}/permissions + + :param encoded_library_id: the encoded id of the library to set the permissions of + :type encoded_library_id: an encoded id string + + :param action: (required) describes what action should be performed + available actions: remove_restrictions, set_permissions + :type action: string + + :param access_ids[]: list of Role.name defining roles that should have access permission on the library + :type access_ids[]: string or list + :param add_ids[]: list of Role.name defining roles that should have add item permission on the library + :type add_ids[]: string or list + :param manage_ids[]: list of Role.name defining roles that should have manage permission on the library + :type manage_ids[]: string or list + :param modify_ids[]: list of Role.name defining roles that should have modify permission on the library + :type modify_ids[]: string or list + + :rtype: dictionary + :returns: dict of current roles for all available permission types + + :raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError + RequestParameterMissingException + """ + is_admin = trans.user_is_admin() + current_user_roles = trans.get_current_user_roles() + library = self._load_library( trans, encoded_library_id ) + if not library or not ( is_admin or trans.app.security_agent.can_access_library( current_user_roles, library ) ): + raise exceptions.ObjectNotFound( 'Library with the id provided ( %s ) was not found' % id ) + if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, library ) ): + raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to modify permissions of this library.' ) + + new_access_roles_ids = util.listify( kwd.get( 'access_ids[]', None ) ) + new_add_roles_ids = util.listify( kwd.get( 'add_ids[]', None ) ) + new_manage_roles_ids = util.listify( kwd.get( 'manage_ids[]', None ) ) + new_modify_roles_ids = util.listify( kwd.get( 'modify_ids[]', None ) ) + + action = kwd.get( 'action', None ) + if action is None: + raise exceptions.RequestParameterMissingException( 'The mandatory parameter "action" is missing.' ) + elif action == 'remove_restrictions': + trans.app.security_agent.make_library_public( library ) + if not trans.app.security_agent.library_is_public( library ): + raise exceptions.InternalServerError( 'An error occured while making library public.' ) + elif action == 'set_permissions': + + # ACCESS LIBRARY ROLES + valid_access_roles = [] + invalid_access_roles_names = [] + for role_id in new_access_roles_ids: + role = self._load_role( trans, role_id ) + # Check whether role is in the set of allowed roles + valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library, is_library_access=True ) + if role in valid_roles: + valid_access_roles.append( role ) + else: + invalid_access_roles_names.append( role_id ) + if len( invalid_access_roles_names ) > 0: + log.warning( "The following roles could not be added to the library access permission: " + str( invalid_access_roles_names ) ) + + # ADD TO LIBRARY ROLES + valid_add_roles = [] + invalid_add_roles_names = [] + for role_id in new_add_roles_ids: + role = self._load_role( trans, role_id ) + # Check whether role is in the set of allowed roles + valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library ) + if role in valid_roles: + valid_add_roles.append( role ) + else: + invalid_add_roles_names.append( role_id ) + if len( invalid_add_roles_names ) > 0: + log.warning( "The following roles could not be added to the add library item permission: " + str( invalid_add_roles_names ) ) + + # MANAGE LIBRARY ROLES + valid_manage_roles = [] + invalid_manage_roles_names = [] + for role_id in new_manage_roles_ids: + role = self._load_role( trans, role_id ) + # Check whether role is in the set of allowed roles + valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library ) + if role in valid_roles: + valid_manage_roles.append( role ) + else: + invalid_manage_roles_names.append( role_id ) + if len( invalid_manage_roles_names ) > 0: + log.warning( "The following roles could not be added to the manage library permission: " + str( invalid_manage_roles_names ) ) + + # MODIFY LIBRARY ROLES + valid_modify_roles = [] + invalid_modify_roles_names = [] + for role_id in new_modify_roles_ids: + role = self._load_role( trans, role_id ) + # Check whether role is in the set of allowed roles + valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library ) + if role in valid_roles: + valid_modify_roles.append( role ) + else: + invalid_modify_roles_names.append( role_id ) + if len( invalid_modify_roles_names ) > 0: + log.warning( "The following roles could not be added to the modify library permission: " + str( invalid_modify_roles_names ) ) + + permissions = { trans.app.security_agent.permitted_actions.LIBRARY_ACCESS : valid_access_roles } + permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_ADD : valid_add_roles } ) + permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MANAGE : valid_manage_roles } ) + permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY : valid_modify_roles } ) + + # trans.app.security_agent.set_library_item_permission( library, permissions ) + trans.app.security_agent.set_all_library_permissions( trans, library, permissions ) + else: + raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' + 'Allowed values are: "remove_restrictions", set_dataset_access_roles"' ) + + return self._get_current_roles( trans, library ) + + + def _get_current_roles( self, trans, library): + """ + Find all roles currently connected to relevant permissions + on the library. + + :param library: the model object + :type library: Library + + :rtype: dictionary + :returns: dict of current roles for all available permission types + """ + # Omit duplicated roles by converting to set + access_roles = set( library.get_access_roles( trans ) ) + modify_roles = set( trans.app.security_agent.get_roles_for_action( library, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) + manage_roles = set( trans.app.security_agent.get_roles_for_action( library, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ) ) + add_roles = set( trans.app.security_agent.get_roles_for_action( library, trans.app.security_agent.permitted_actions.LIBRARY_ADD ) ) + + access_library_role_list = [ access_role.name for access_role in access_roles ] + modify_library_role_list = [ modify_role.name for modify_role in modify_roles ] + manage_library_role_list = [ manage_role.name for manage_role in manage_roles ] + add_library_item_role_list = [ add_role.name for add_role in add_roles ] + + return dict( access_library_role_list=access_library_role_list, modify_library_role_list=modify_library_role_list, manage_library_role_list=manage_library_role_list, add_library_item_role_list=add_library_item_role_list ) + + diff -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -241,7 +241,19 @@ '/api/libraries/:id', controller='libraries', action='update', - conditions=dict( method=[ "PATCH", 'PUT' ] ) ) + conditions=dict( method=[ "PATCH", "PUT" ] ) ) + + webapp.mapper.connect( 'show_library_permissions', + '/api/libraries/:encoded_library_id/permissions', + controller='libraries', + action='get_permissions', + conditions=dict( method=[ "GET" ] ) ) + + webapp.mapper.connect( 'set_library_permissions', + '/api/libraries/:encoded_library_id/permissions', + controller='libraries', + action='set_permissions', + conditions=dict( method=[ "POST" ] ) ) webapp.mapper.connect( 'show_lda_item', '/api/libraries/datasets/:id', diff -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -12,7 +12,8 @@ "mvc/library/library-librarylist-view", "mvc/library/library-librarytoolbar-view", "mvc/library/library-foldertoolbar-view", - "mvc/library/library-dataset-view" + "mvc/library/library-dataset-view", + "mvc/library/library-library-view" ], function(mod_masthead, mod_utils, @@ -23,7 +24,8 @@ mod_librarylist_view, mod_librarytoolbar_view, mod_foldertoolbar_view, - mod_library_dataset_view + mod_library_dataset_view, + mod_library_library_view ) { // ============================================================================ @@ -37,6 +39,7 @@ routes: { "" : "libraries", + "library/:library_id/permissions" : "library_permissions", "folders/:id" : "folder_content", "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", "folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions", @@ -72,6 +75,7 @@ libraryToolbarView: null, libraryListView: null, library_router: null, + libraryView: null, folderToolbarView: null, folderListView: null, datasetView: null, @@ -120,6 +124,13 @@ Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}); }); + this.library_router.on('route:library_permissions', function(library_id){ + if (Galaxy.libraries.LibraryView){ + Galaxy.libraries.libraryView.$el.unbind('click'); + } + Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); + }); + Backbone.history.start({pushState: false}); } }); diff -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -181,12 +181,18 @@ this.options = _.extend(this.options, options); $(".tooltip").remove(); + if (this.options.fetched_permissions !== undefined){ + if (this.options.fetched_permissions.access_dataset_roles.length === 0){ + this.model.set({is_unrestricted:true}); + } else{ + this.model.set({is_unrestricted:false}); + } + } // Select works different for admins var is_admin = false; if (Galaxy.currUser){ is_admin = Galaxy.currUser.isAdmin(); } - var template = this.templateDatasetPermissions(); this.$el.html(template({item: this.model, is_admin: is_admin})); @@ -438,14 +444,11 @@ modify_ids.push(modify_roles[i].id); }; - // access_ids = typeof access_ids === 'string' ? access_ids : $.param(access_ids) - // manage_ids = typeof manage_ids === 'string' ? manage_ids : $.param(manage_ids) - // modify_ids = typeof modify_ids === 'string' ? modify_ids : $.param(modify_ids) - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) + mod_toastr.success('Permissions saved'); }) .fail(function(){ mod_toastr.error('An error occurred while setting dataset permissions :('); @@ -470,6 +473,9 @@ tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); tmpl_array.push(' <% } %>'); + // tmpl_array.push(' <% if (item.get("has_versions")) { %>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Show previous versions" class="btn btn-default toolbtn-previous-versions primary-button" type="button"><span class="fa fa-clock-o"></span> Versions</span></button>'); + // tmpl_array.push(' <% } %>'); tmpl_array.push(' </div>'); @@ -727,11 +733,9 @@ tmpl_array.push('<div class="dataset_table">'); tmpl_array.push('<h2>Library-related permissions</h2>'); - // tmpl_array.push('<p>You have the permission to modify this Library item. This includes changing its name, metadata, and other information.</p>'); tmpl_array.push('<h4>Roles that can modify the library item</h4>'); tmpl_array.push('<div id="modify_perm" class="modify_perm roles-selection"></div>'); tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>'); - // tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); tmpl_array.push('<hr/>'); tmpl_array.push('<h2>Dataset-related permissions</h2>'); @@ -754,19 +758,14 @@ // tmpl_array.push(' </p>'); tmpl_array.push('<% } %>'); - // tmpl_array.push('<p>You have the permission to manage permissions on this dataset. That means you can control who can access it and also appoint others that can manage permissions on it.</p>'); tmpl_array.push('<h4>Roles that can access the dataset</h4>'); tmpl_array.push('<div id="access_perm" class="access_perm roles-selection"></div>'); tmpl_array.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>'); - // tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); tmpl_array.push('<h4>Roles that can manage permissions on the dataset</h4>'); tmpl_array.push('<div id="manage_perm" class="manage_perm roles-selection"></div>'); tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>'); tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); - - - tmpl_array.push('</div>'); // CONTAINER END diff -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 static/scripts/mvc/library/library-library-view.js --- /dev/null +++ b/static/scripts/mvc/library/library-library-view.js @@ -0,0 +1,340 @@ +define([ + "libs/toastr", + "mvc/library/library-model", + 'mvc/ui/ui-select' + ], +function( + mod_toastr, + mod_library_model, + mod_select + ) { + +var LibraryView = Backbone.View.extend({ + el: '#center', + + model: null, + + options: { + + }, + + events: { + "click .toolbtn_save_permissions" : "savePermissions" + }, + + initialize: function(options){ + this.options = _.extend(this.options, options); + if (this.options.id){ + this.fetchLibrary(); + } + }, + + fetchLibrary: function(options){ + this.options = _.extend(this.options, options); + this.model = new mod_library_model.Library({id:this.options.id}); + var that = this; + this.model.fetch({ + success: function() { + if (that.options.show_permissions){ + that.showPermissions(); + } else { + that.render(); + } + }, + error: function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error(response.responseJSON.err_msg + ' Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}}); + } else { + mod_toastr.error('An error ocurred :(. Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}}); + } + } + }); + }, + + render: function(options){ + // $(".tooltip").remove(); + this.options = _.extend(this.options, options); + var template = this.templateDataset(); + this.$el.html(template({item: this.model})); + $(".peek").html(this.model.get("peek")); + $("#center [data-toggle]").tooltip(); + }, + + enableModification: function(){ + $(".tooltip").remove(); + var template = this.templateModifyDataset(); + this.$el.html(template({item: this.model})); + $(".peek").html(this.model.get("peek")); + $("#center [data-toggle]").tooltip(); + }, + + shareDataset: function(){ + mod_toastr.info('Feature coming soon.'); + }, + + goBack: function(){ + Galaxy.libraries.library_router.back(); + }, + + showPermissions: function(options){ + this.options = _.extend(this.options, options); + // $(".tooltip").remove(); + + if (this.options.fetched_permissions !== undefined){ + if (this.options.fetched_permissions.access_dataset_roles.length === 0){ + this.model.set({is_unrestricted:true}); + } else{ + this.model.set({is_unrestricted:false}); + } + } + var template = this.templateLibraryPermissions(); + this.$el.html(template({library: this.model})); + + var self = this; + if (this.options.fetched_permissions === undefined){ + $.get( "/api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + self.prepareSelectBoxes({fetched_permissions:fetched_permissions}); + }).fail(function(){ + mod_toastr.error('An error occurred while fetching library permissions. :('); + }); + } else { + this.prepareSelectBoxes({}); + } + + $("#center [data-toggle]").tooltip(); + //hack to show scrollbars + $("#center").css('overflow','auto'); + }, + + _serializeRoles : function(role_list){ + var selected_roles = []; + for (var i = 0; i < role_list.length; i++) { + selected_roles.push(role_list[i] + ':' + role_list[i]); + } + return selected_roles; + }, + + prepareSelectBoxes: function(options){ + this.options = _.extend(this.options, options); + var fetched_permissions = this.options.fetched_permissions; + var self = this; + + var selected_access_library_roles = this._serializeRoles(fetched_permissions.access_library_role_list); + var selected_add_item_roles = this._serializeRoles(fetched_permissions.add_library_item_role_list); + var selected_manage_library_roles = this._serializeRoles(fetched_permissions.manage_library_role_list); + var selected_modify_library_roles = this._serializeRoles(fetched_permissions.modify_library_role_list); + + self.accessSelectObject = new mod_select.View(this._createSelectOptions(this, 'access_perm', selected_access_library_roles)); + self.addSelectObject = new mod_select.View(this._createSelectOptions(this, 'add_perm', selected_add_item_roles)); + self.manageSelectObject = new mod_select.View(this._createSelectOptions(this, 'manage_perm', selected_manage_library_roles)); + self.modifySelectObject = new mod_select.View(this._createSelectOptions(this, 'modify_perm', selected_modify_library_roles)); + }, + + _createSelectOptions: function(self, id, init_data){ + var select_options = { + minimumInputLength: 0, + css: id, + multiple:true, + placeholder: 'Click to select a role', + container: self.$el.find('#' + id), + ajax: { + url: "/api/libraries/" + self.id + "/permissions?scope=available", + dataType: 'json', + quietMillis: 100, + data: function (term, page) { // page is the one-based page number tracked by Select2 + return { + q: term, //search term + page_limit: 10, // page size + page: page // page number + }; + }, + results: function (data, page) { + var more = (page * 10) < data.total; // whether or not there are more results available + // notice we return the value of more so Select2 knows if more results can be loaded + return {results: data.roles, more: more}; + } + }, + formatResult : function roleFormatResult(role) { + return role.name + ' type: ' + role.type; + }, + + formatSelection: function roleFormatSelection(role) { + return role.name; + }, + initSelection: function(element, callback) { + // the input tag has a value attribute preloaded that points to a preselected role's id + // this function resolves that id attribute to an object that select2 can render + // using its formatResult renderer - that way the role name is shown preselected + var data = []; + $(element.val().split(",")).each(function() { + var item = this.split(':'); + data.push({ + id: item[1], + name: item[1] + }); + }); + callback(data); + }, + initialData: init_data.join(','), + dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller + }; + + return select_options; + }, + + comingSoon: function(){ + mod_toastr.warning('Feature coming soon'); + }, + + copyToClipboard: function(){ + var href = Backbone.history.location.href; + if (href.lastIndexOf('/permissions') !== -1){ + href = href.substr(0, href.lastIndexOf('/permissions')); + } + window.prompt("Copy to clipboard: Ctrl+C, Enter", href); + }, + + makeDatasetPrivate: function(){ + var self = this; + $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { + self.model.set({is_unrestricted:false}); + self.showPermissions({fetched_permissions:fetched_permissions}) + mod_toastr.success('The dataset is now private to you'); + }).fail(function(){ + mod_toastr.error('An error occurred while making dataset private :('); + }); + }, + + removeDatasetRestrictions: function(){ + var self = this; + $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") + .done(function(fetched_permissions) { + self.model.set({is_unrestricted:true}); + self.showPermissions({fetched_permissions:fetched_permissions}) + mod_toastr.success('Access to this dataset is now unrestricted'); + }) + .fail(function(){ + mod_toastr.error('An error occurred while making dataset unrestricted :('); + }); + }, + + _extractIds: function(roles_list){ + ids_list = []; + for (var i = roles_list.length - 1; i >= 0; i--) { + ids_list.push(roles_list[i].id); + }; + return ids_list; + }, + savePermissions: function(event){ + var self = this; + + var access_ids = this._extractIds(this.accessSelectObject.$el.select2('data')); + var add_ids = this._extractIds(this.addSelectObject.$el.select2('data')); + var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data')); + var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data')); + + $.post("/api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + .done(function(fetched_permissions){ + //fetch dataset again + self.showPermissions({fetched_permissions:fetched_permissions}) + mod_toastr.success('Permissions saved'); + }) + .fail(function(){ + mod_toastr.error('An error occurred while setting library permissions :('); + }) + }, + + templateLibrary : function(){ + var tmpl_array = []; + // CONTAINER START + tmpl_array.push('<div class="library_style_container">'); + + tmpl_array.push(' <div id="library_toolbar">'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>'); + tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); + tmpl_array.push(' </div>'); + + // tmpl_array.push('<% if (item.get("is_unrestricted")) { %>'); + tmpl_array.push(' <p>'); + tmpl_array.push(' This dataset is unrestricted so everybody can access it. Just share the URL of this page. '); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> '); + tmpl_array.push(' </p>'); + // tmpl_array.push('<% } %>'); + + tmpl_array.push('<div class="dataset_table">'); + + tmpl_array.push(' <table class="grid table table-striped table-condensed">'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); + tmpl_array.push(' </tr>'); + + tmpl_array.push(' <% if (item.get("data_type")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data type</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' </table>'); + tmpl_array.push('</div>'); + + // CONTAINER END + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + }, + + templateLibraryPermissions : function(){ + var tmpl_array = []; + // CONTAINER START + tmpl_array.push('<div class="library_style_container">'); + + tmpl_array.push(' <div id="library_toolbar">'); + tmpl_array.push(' <a href="#"><button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Libraries</span></button></a>'); + tmpl_array.push(' </div>'); + + tmpl_array.push('<h1>Permissions: <%= _.escape(library.get("name")) %></h1>'); + + tmpl_array.push('<div class="alert alert-warning">'); + tmpl_array.push('You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.'); + tmpl_array.push('</div>'); + + tmpl_array.push('<div class="dataset_table">'); + + tmpl_array.push('<h2>Library permissions</h2>'); + + tmpl_array.push('<h4>Roles that can access the library</h4>'); + tmpl_array.push('<div id="access_perm" class="access_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can access this library. If there are no access roles set on the library it is considered <strong>unrestricted</strong>.</div>'); + + tmpl_array.push('<h4>Roles that can manage permissions on this library</h4>'); + tmpl_array.push('<div id="manage_perm" class="manage_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this library (includes giving access).</div>'); + + tmpl_array.push('<h4>Roles that can add items to this library</h4>'); + tmpl_array.push('<div id="add_perm" class="add_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this library (folders and datasets).</div>'); + + tmpl_array.push('<h4>Roles that can modify this library</h4>'); + tmpl_array.push('<div id="modify_perm" class="modify_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this library (name, synopsis, etc.).</div>'); + + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); + + tmpl_array.push('</div>'); + + // CONTAINER END + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + } + +}); + +return { + LibraryView: LibraryView +}; + +}); diff -r 5d46cecbd1b3bbb5a0183d01fba7b54d0a608093 -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 static/scripts/mvc/library/library-libraryrow-view.js --- a/static/scripts/mvc/library/library-libraryrow-view.js +++ b/static/scripts/mvc/library/library-libraryrow-view.js @@ -103,8 +103,10 @@ this.element_visibility_config = vis_config; }, - permissions_on_library: function(){ - mod_toastr.info('Coming soon. Stay tuned.'); + permissions_on_library: function(options){ + this.options = _.extend(this.options, options); + $(".tooltip").remove(); + }, /* User clicked the 'edit' button on row so we render a new row @@ -248,7 +250,11 @@ tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>'); tmpl_array.push(' <% }%>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>'); + + // tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>'); + + + tmpl_array.push(' <a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button></a>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>'); https://bitbucket.org/galaxy/galaxy-central/commits/482de41429fc/ Changeset: 482de41429fc User: martenson Date: 2014-08-02 00:29:25 Summary: Merge Affected #: 84 files diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed .hgtags --- a/.hgtags +++ b/.hgtags @@ -7,6 +7,13 @@ 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 -68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02 +8c30e91bc9ae19ee4dc7ec2c22fa825979497108 latest_2014.06.02 +9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 +9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 +81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 +2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -52,12 +52,9 @@ migrated_tools_conf.xml.sample data_manager_conf.xml.sample shed_data_manager_conf.xml.sample -tool-data/shared/ensembl/builds.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample -tool-data/shared/ncbi/builds.txt.sample tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/shared/ucsc/builds.txt.sample -tool-data/shared/ucsc/publicbuilds.txt.sample tool-data/shared/ucsc/ucsc_build_sites.txt.sample " diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed cron/get_ensembl.py --- a/cron/get_ensembl.py +++ /dev/null @@ -1,23 +0,0 @@ -from galaxy import eggs -import pkg_resources -pkg_resources.require("SQLAlchemy >= 0.4") -pkg_resources.require("MySQL_python") -from sqlalchemy import * - - -engine = create_engine( 'mysql://anonymous@ensembldb.ensembl.org:5306', pool_recycle=3600 ) -conn = engine.connect() -dbs = conn.execute( "SHOW DATABASES LIKE 'ensembl_website_%%'" ) -builds = {} -lines = [] -for res in dbs: - dbname = res[0] - release = dbname.split('_')[-1] - genomes = conn.execute( "SELECT RS.assembly_code, S.name, S.common_name, %s FROM ensembl_website_%s.release_species RS LEFT JOIN ensembl_website_%s.species S on RS.species_id = S.species_id" % ( release, release, release ) ) - for genome in genomes: - builds[genome[0]] = dict( release=genome[3], species='%s (%s/%s)' % ( genome[1], genome[2], genome[0] ) ) -for build in builds.items(): - if build[0]: - lines.append( '\t'.join( [ build[0], '%d' % build[1]['release'], build[1]['species'] ] ) ) - -print '\n'.join( lines ) diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed cron/get_ncbi.py --- a/cron/get_ncbi.py +++ /dev/null @@ -1,93 +0,0 @@ -import urllib, pkg_resources, os -pkg_resources.require( 'elementtree' ) -from elementtree import ElementTree, ElementInclude -from xml.parsers.expat import ExpatError as XMLParseErrorThing -import sys - -import pkg_resources - -class GetListing: - def __init__( self, data ): - self.tree = ElementTree.parse( data ) - self.root = self.tree.getroot() - ElementInclude.include(self.root) - - def xml_text(self, name=None): - """Returns the text inside an element""" - root = self.root - if name is not None: - # Try attribute first - val = root.get(name) - if val: - return val - # Then try as element - elem = root.find(name) - else: - elem = root - if elem is not None and elem.text: - text = ''.join(elem.text.splitlines()) - return text.strip() - # No luck, return empty string - return '' - -def dlcachefile( webenv, querykey, i, results ): - url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&usehistory=y&term=nuccore_assembly[filter]%20AND%20refseq[filter]' - fp = urllib.urlopen( url ) - search = GetListing( fp ) - fp.close() - webenv = search.xml_text( 'WebEnv' ) - querykey = search.xml_text( 'QueryKey' ) - url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nuccore&WebEnv=%s&query_key=%s&retstart=%d&retmax=%d' % ( webenv, querykey, i, results ) - fp = urllib.urlopen( url ) - cachefile = os.tmpfile() - for line in fp: - cachefile.write( line ) - fp.close() - cachefile.flush() - cachefile.seek(0) - return cachefile - - -url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&usehistory=y&term=nuccore_assembly[filter]%20AND%20refseq[filter]' -fp = urllib.urlopen( url ) -results = GetListing( fp ) -fp.close() - -webenv = results.xml_text( 'WebEnv' ) -querykey = results.xml_text( 'QueryKey' ) -counts = int( results.xml_text( 'Count' ) ) -results = 10000 -found = 0 - -for i in range(0, counts + results, results): - rets = dict() - cache = dlcachefile( webenv, querykey, i, results ) - try: - xmldoc = GetListing( cache ) - except (IOError, XMLParseErrorThing): - cache = dlcachefile( webenv, querykey, i, results ) - try: - xmldoc = GetListing( cache ) - except (IOError, XMLParseErrorThing): - cache.close() - exit() - pass - finally: - cache.close() - entries = xmldoc.root.findall( 'DocSum' ) - for entry in entries: - dbkey = None - children = entry.findall('Item') - for item in children: - rets[ item.get('Name') ] = item.text - if not rets['Caption'].startswith('NC_'): - continue - - for ret in rets['Extra'].split('|'): - if not ret.startswith('NC_'): - continue - else: - dbkey = ret - break - if dbkey is not None: - print '\t'.join( [ dbkey, rets['Title'] ] ) diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed cron/parse_builds.py --- a/cron/parse_builds.py +++ b/cron/parse_builds.py @@ -15,7 +15,7 @@ import pkg_resources; pkg_resources.require( "elementtree" ) from elementtree import ElementTree -URL = "http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn" +URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn" def getbuilds(url): try: @@ -33,7 +33,7 @@ print "?\tunspecified (?)" sys.exit(1) - print "#Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn" + print "#Harvested from http://genome.cse.ucsc.edu/cgi-bin/das/dsn" print "?\tunspecified (?)" for dsn in tree: build = dsn.find("SOURCE").attrib['id'] diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed cron/parse_publicbuilds.py --- a/cron/parse_publicbuilds.py +++ /dev/null @@ -1,57 +0,0 @@ -#!/usr/bin/env python - -""" -Connects to the URL specified and outputs builds available at that -DSN in tabular format. USCS Test gateway is used as default. -build description -""" - -import sys -import urllib -if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.ElementTree as ElementTree -else: - from galaxy import eggs - import pkg_resources; pkg_resources.require( "elementtree" ) - from elementtree import ElementTree - -URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn" - -def getbuilds(url): - try: - page = urllib.urlopen(URL) - except: - print "#Unable to open " + URL - print "?\tunspecified (?)" - sys.exit(1) - - text = page.read() - try: - tree = ElementTree.fromstring(text) - except: - print "#Invalid xml passed back from " + URL - print "?\tunspecified (?)" - sys.exit(1) - - print "#Harvested from http://genome.cse.ucsc.edu/cgi-bin/das/dsn" - print "?\tunspecified (?)" - for dsn in tree: - build = dsn.find("SOURCE").attrib['id'] - description = dsn.find("DESCRIPTION").text.replace(" - Genome at UCSC","").replace(" Genome at UCSC","") - - fields = description.split(" ") - temp = fields[0] - for i in range(len(fields)-1): - if temp == fields[i+1]: - fields.pop(i+1) - else: - temp = fields[i+1] - description = " ".join(fields) - yield [build,description] - -if __name__ == "__main__": - if len(sys.argv) > 1: - URL = sys.argv[1] - for build in getbuilds(URL): - print build[0]+"\t"+build[1]+" ("+build[0]+")" - diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed cron/updateensembl.sh.sample --- a/cron/updateensembl.sh.sample +++ /dev/null @@ -1,42 +0,0 @@ -#!/bin/sh -# -# Script to update Ensembl shared data tables. The idea is to update, but if -# the update fails, not replace current data/tables with error -# messages. - -# Edit this line to refer to galaxy's path: -GALAXY=/path/to/galaxy -PYTHONPATH=${GALAXY}/lib -export PYTHONPATH - -# setup directories -echo "Creating required directories." -DIRS=" -${GALAXY}/tool-data/shared/ensembl -${GALAXY}/tool-data/shared/ensembl/new -" -for dir in $DIRS; do - if [ ! -d $dir ]; then - echo "Creating $dir" - mkdir $dir - else - echo "$dir already exists, continuing." - fi -done - -date -echo "Updating Ensembl shared data tables." - -# Try to build "builds.txt" -echo "Updating builds.txt" -python ${GALAXY}/cron/get_ensembl.py > ${GALAXY}/tool-data/shared/ensembl/new/builds.txt -if [ $? -eq 0 ] -then - diff ${GALAXY}/tool-data/shared/ensembl/new/builds.txt ${GALAXY}/tool-data/shared/ensembl/builds.txt > /dev/null 2>&1 - if [ $? -ne 0 ] - then - cp -f ${GALAXY}/tool-data/shared/ensembl/new/builds.txt ${GALAXY}/tool-data/shared/ensembl/builds.txt - fi -else - echo "Failed to update builds.txt" >&2 -fi diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed cron/updatencbi.sh.sample --- a/cron/updatencbi.sh.sample +++ /dev/null @@ -1,42 +0,0 @@ -#!/bin/sh -# -# Script to update NCBI shared data tables. The idea is to update, but if -# the update fails, not replace current data/tables with error -# messages. - -# Edit this line to refer to galaxy's path: -GALAXY=/path/to/galaxy -PYTHONPATH=${GALAXY}/lib -export PYTHONPATH - -# setup directories -echo "Creating required directories." -DIRS=" -${GALAXY}/tool-data/shared/ncbi -${GALAXY}/tool-data/shared/ncbi/new -" -for dir in $DIRS; do - if [ ! -d $dir ]; then - echo "Creating $dir" - mkdir $dir - else - echo "$dir already exists, continuing." - fi -done - -date -echo "Updating NCBI shared data tables." - -# Try to build "builds.txt" -echo "Updating builds.txt" -python ${GALAXY}/cron/get_ncbi.py > ${GALAXY}/tool-data/shared/ncbi/new/builds.txt -if [ $? -eq 0 ] -then - diff ${GALAXY}/tool-data/shared/ncbi/new/builds.txt ${GALAXY}/tool-data/shared/ncbi/builds.txt > /dev/null 2>&1 - if [ $? -ne 0 ] - then - cp -f ${GALAXY}/tool-data/shared/ncbi/new/builds.txt ${GALAXY}/tool-data/shared/ncbi/builds.txt - fi -else - echo "Failed to update builds.txt" >&2 -fi diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample +++ b/cron/updateucsc.sh.sample @@ -28,20 +28,6 @@ date echo "Updating UCSC shared data tables." -# Try to build "publicbuilds.txt" -echo "Updating publicbuilds.txt" -python ${GALAXY}/cron/parse_publicbuilds.py > ${GALAXY}/tool-data/shared/ucsc/new/publicbuilds.txt -if [ $? -eq 0 ] -then - diff ${GALAXY}/tool-data/shared/ucsc/new/publicbuilds.txt ${GALAXY}/tool-data/shared/ucsc/publicbuilds.txt > /dev/null 2>&1 - if [ $? -ne 0 ] - then - cp -f ${GALAXY}/tool-data/shared/ucsc/new/publicbuilds.txt ${GALAXY}/tool-data/shared/ucsc/publicbuilds.txt - fi -else - echo "Failed to update publicbuilds.txt" >&2 -fi - # Try to build "builds.txt" echo "Updating builds.txt" python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed doc/Makefile --- a/doc/Makefile +++ b/doc/Makefile @@ -17,22 +17,9 @@ # the i18n builder cannot share the environment and doctrees with the others I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source -# Galaxy Local variables - -TOOLDATASHAREDDIR = ../tool-data/shared -TOOLDATABUILDFILES = $(TOOLDATASHAREDDIR)/ensembl/builds.txt \ - $(TOOLDATASHAREDDIR)/ncbi/builds.txt \ - $(TOOLDATASHAREDDIR)/ucsc/publicbuilds.txt - .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext updaterst -# Sphinx wants the build files to be there; Copy the sample files into -# place if we don't already have the build files. -$(TOOLDATABUILDFILES) : - /bin/cp $@.sample $@ - - help: @echo "Please use \`make <target>' where <target> is one of" @echo " html to make standalone HTML files" diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -64,6 +64,9 @@ # Load dbkey / genome build manager self._configure_genome_builds( data_table_name="__dbkeys__", load_old_style=True ) + # Load build sites (old-style) + self._configure_build_sites() + # Genomes self.genomes = Genomes( self ) # Data providers registry. diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -16,6 +16,7 @@ from galaxy.util import string_as_bool from galaxy.util import listify from galaxy.util.dbkeys import GenomeBuilds +from galaxy.util.build_sites import BuildSites from galaxy import eggs log = logging.getLogger( __name__ ) @@ -72,6 +73,7 @@ self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) ) self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root ) self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() ) + self.builds_file_path = resolve_path( kwargs.get( "builds_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'builds.txt') ), self.root ) self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'chrom') ), self.root ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) # The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution @@ -83,6 +85,7 @@ tcf = kwargs[ 'tool_config_files' ] else: tcf = 'tool_conf.xml,shed_tool_conf.xml' + self.integrated_tool_panel_config = resolve_path( kwargs.get( 'integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.root ) self.tool_filters = listify( kwargs.get( "tool_filters", [] ), do_strip=True ) self.tool_label_filters = listify( kwargs.get( "tool_label_filters", [] ), do_strip=True ) self.tool_section_filters = listify( kwargs.get( "tool_section_filters", [] ), do_strip=True ) @@ -221,7 +224,9 @@ self.sanitize_all_html = string_as_bool( kwargs.get( 'sanitize_all_html', True ) ) self.serve_xss_vulnerable_mimetypes = string_as_bool( kwargs.get( 'serve_xss_vulnerable_mimetypes', False ) ) self.enable_old_display_applications = string_as_bool( kwargs.get( "enable_old_display_applications", "True" ) ) + self.ucsc_build_sites = resolve_path( kwargs.get( 'ucsc_build_sites', os.path.join( self.tool_data_path, 'shared', 'ucsc', 'ucsc_build_sites.txt') ), self.root ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") + self.gbrowse_build_sites = resolve_path( kwargs.get( 'gbrowse_build_sites', os.path.join( self.tool_data_path, 'shared', 'gbrowse', 'gbrowse_build_sites.txt') ), self.root ) self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225" ).lower().split(",") self.brand = kwargs.get( 'brand', None ) self.welcome_url = kwargs.get( 'welcome_url', '/static/welcome.html' ) @@ -455,13 +460,13 @@ except Exception, e: raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) # Create the directories that it makes sense to create - for path in (self.file_path, self.new_file_path, - self.job_working_directory, self.cluster_files_directory, - self.template_cache, self.ftp_upload_dir, + if self.object_store_config_file is None: + for path in (self.file_path, self.job_working_directory): + self._ensure_directory( path ) + for path in (self.new_file_path, self.template_cache, self.ftp_upload_dir, self.library_import_dir, self.user_library_import_dir, - self.nginx_upload_store, './static/genetrack/plots', - self.whoosh_index_dir, self.object_store_cache_path, - os.path.join( self.tool_data_path, 'shared', 'jars' )): + self.nginx_upload_store, self.whoosh_index_dir, + self.object_store_cache_path): self._ensure_directory( path ) # Check that required files exist tool_configs = self.tool_configs @@ -569,6 +574,9 @@ def _configure_genome_builds( self, data_table_name="__dbkeys__", load_old_style=True ): self.genome_builds = GenomeBuilds( self, data_table_name=data_table_name, load_old_style=load_old_style ) + def _configure_build_sites( self ): + self.build_sites = BuildSites( self ) + def _configure_toolbox( self ): # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. tool_configs = self.config.tool_configs diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -11,7 +11,7 @@ import line import column import external -import sqlite3 +from galaxy.util import sqlite import re from galaxy import eggs @@ -704,35 +704,23 @@ super( BGzipTabixDataProvider, self ).__init__( dataset, **kwargs ) - -class SQliteDataProvider ( base.DataProvider ): +class SQliteDataProvider( base.DataProvider ): """ Data provider that uses a sqlite database file as its source. Allows any query to be run and returns the resulting rows as sqlite3 row objects """ settings = { - 'query' : 'str' + 'query': 'str' } def __init__( self, source, query=None, **kwargs ): - self.query=query - self.connection = sqlite3.connect(source.dataset.file_name); - self.connection.row_factory = sqlite3.Row + self.query = query + self.connection = sqlite.connect(source.dataset.file_name) super( SQliteDataProvider, self ).__init__( source, **kwargs ) - def query_matches_whitelist(self,query): - if re.match("select ",query,re.IGNORECASE): - if re.search("^([^\"]|\"[^\"]*\")*?;",query) or re.search("^([^\']|\'[^\']*\')*?;",query): - return False - else: - return True - return False - - - def __iter__( self ): - if (self.query is not None) and self.query_matches_whitelist(self.query): + if (self.query is not None) and sqlite.is_read_only_query(self.query): for row in self.connection.cursor().execute(self.query): yield row else: diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -85,7 +85,7 @@ if not dataset.dbkey: dataset.dbkey = 'hg18' # punt! if dataset.has_data(): - for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): + for site_name, site_url in app.build_sites.get_ucsc_by_build(dataset.dbkey): if site_name in app.config.ucsc_display_sites: site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs internal_url = "%s" % url_for( controller='dataset', diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -234,7 +234,7 @@ # Filter UCSC sites to only those that are supported by this build and # enabled. valid_sites = [ ( name, url ) - for name, url in util.get_ucsc_by_build( dataset.dbkey ) + for name, url in app.build_sites.get_ucsc_by_build( dataset.dbkey ) if name in app.config.ucsc_display_sites ] if not valid_sites: return [] @@ -750,7 +750,7 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in util.get_ucsc_by_build( dataset.dbkey ): + for site_name, site_url in app.build_sites.get_ucsc_by_build( dataset.dbkey ): if site_name in app.config.ucsc_display_sites: redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % @@ -762,7 +762,7 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in util.get_gbrowse_sites_by_build( dataset.dbkey ): + for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ): if site_name in app.config.gbrowse_display_sites: if seqid.startswith( 'chr' ) and len ( seqid ) > 3: seqid = seqid[3:] @@ -1091,7 +1091,7 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in util.get_gbrowse_sites_by_build( dataset.dbkey ): + for site_name, site_url in app.build_sites.get_gbrowse_sites_by_build( dataset.dbkey ): if site_name in app.config.gbrowse_display_sites: if chrom.startswith( 'chr' ) and len ( chrom ) > 3: chrom = chrom[3:] @@ -1103,7 +1103,7 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in util.get_ucsc_by_build( dataset.dbkey ): + for site_name, site_url in app.build_sites.get_ucsc_by_build( dataset.dbkey ): if site_name in app.config.ucsc_display_sites: redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) ) link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) @@ -1285,7 +1285,7 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport(dataset) if chrom is not None: - for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): + for site_name, site_url in app.build_sites.get_ucsc_by_build(dataset.dbkey): if site_name in app.config.ucsc_display_sites: internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py +++ b/lib/galaxy/eggs/__init__.py @@ -11,6 +11,7 @@ import pkg_resources galaxy_dir = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..', '..', '..' ) ) +eggs_dir = os.environ.get( 'GALAXY_EGGS_PATH', os.path.join( galaxy_dir, 'eggs' ) ) py = 'py%s' % sys.version[:3] class EggNotFetchable( Exception ): @@ -49,7 +50,8 @@ if self.name is not None and self.version is not None: self.set_distribution() def set_dir( self ): - self.dir = os.path.join( galaxy_dir, 'eggs' ) + global eggs_dir + self.dir = eggs_dir if not os.path.exists( self.dir ): os.makedirs( self.dir ) def set_distribution( self ): @@ -395,7 +397,7 @@ def get_env(): env = pkg_resources.Environment( search_path='', platform=pkg_resources.get_platform() ) - for dist in pkg_resources.find_distributions( os.path.join( galaxy_dir, 'eggs' ), False ): + for dist in pkg_resources.find_distributions( eggs_dir, False ): env.add( dist ) return env env = get_env() diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -79,6 +79,9 @@ def get_sharable_url( self, app ): tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, self.tool_shed ) if tool_shed_url: + # Append a slash to the tool shed URL, because urlparse.urljoin will eliminate + # the last part of a URL if it does not end with a forward slash. + tool_shed_url = '%s/' % tool_shed_url return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) return tool_shed_url diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -132,7 +132,7 @@ # File that contains the XML section and tool tags from all tool panel config files integrated into a # single file that defines the tool panel layout. This file can be changed by the Galaxy administrator # (in a way similar to the single tool_conf.xml file in the past) to alter the layout of the tool panel. - self.integrated_tool_panel_config = os.path.join( app.config.root, 'integrated_tool_panel.xml' ) + self.integrated_tool_panel_config = app.config.integrated_tool_panel_config # In-memory dictionary that defines the layout of the tool_panel.xml file on disk. self.integrated_tool_panel = odict() self.integrated_tool_panel_config_has_contents = os.path.exists( self.integrated_tool_panel_config ) and os.stat( self.integrated_tool_panel_config ).st_size > 0 diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1002,7 +1002,7 @@ >>> # Create a mock transaction with 'hg17' as the current build >>> from galaxy.util.bunch import Bunch - >>> trans = Bunch( history=Bunch( genome_build='hg17' ), db_builds=util.dbnames ) + >>> trans = Bunch( history=Bunch( genome_build='hg17' ), db_builds=util.read_dbnames( None ) ) >>> p = GenomeBuildParameter( None, XML( ... ''' @@ -1071,7 +1071,7 @@ def _get_dbkey_names( self, trans=None ): if not self.tool: # Hack for unit tests, since we have no tool - return util.dbnames + return util.read_dbnames( None ) return self.tool.app.genome_builds.get_genome_build_names( trans=trans ) diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py +++ b/lib/galaxy/tools/util/maf_utilities.py @@ -9,6 +9,8 @@ import bx.interval_index_file import sys, os, string, tempfile import logging +from errno import EMFILE +import resource from copy import deepcopy assert sys.version_info[:2] >= ( 2, 4 ) @@ -45,15 +47,96 @@ print >> sys.stderr, "Fatal Error: %s" % msg sys.exit() + +class TempFileHandler( object ): + ''' + Handles creating, opening, closing, and deleting of Temp files, with a + maximum number of files open at one time. + ''' + + DEFAULT_MAX_OPEN_FILES = max( resource.getrlimit( resource.RLIMIT_NOFILE )[0] / 2, 1 ) + + def __init__( self, max_open_files=None, **kwds ): + if max_open_files is None: + max_open_files = self.DEFAULT_MAX_OPEN_FILES + self.max_open_files = max_open_files + self.files = [] + self.open_file_indexes = [] + self.kwds = kwds + + def get_open_tempfile( self, index=None, **kwds ): + if index is not None and index in self.open_file_indexes: + self.open_file_indexes.remove( index ) + else: + if self.max_open_files: + while len( self.open_file_indexes ) >= self.max_open_files: + self.close( self.open_file_indexes[0] ) + if index is None: + index = len( self.files ) + temp_kwds = dict( self.kwds ) + temp_kwds.update( kwds ) + # Being able to use delete=True here, would simplify a bit, + # but we support python2.4 in these tools + while True: + try: + tmp_file = tempfile.NamedTemporaryFile( **temp_kwds ) + filename = tmp_file.name + break + except OSError, e: + if self.open_file_indexes and e.errno == EMFILE: + self.max_open_files = len( self.open_file_indexes ) + self.close( self.open_file_indexes[0] ) + else: + raise e + tmp_file.close() + self.files.append( open( filename, 'w+b' ) ) + else: + while True: + try: + self.files[ index ] = open( self.files[ index ].name, 'r+b' ) + break + except OSError, e: + if self.open_file_indexes and e.errno == EMFILE: + self.max_open_files = len( self.open_file_indexes ) + self.close( self.open_file_indexes[0] ) + else: + raise e + self.files[ index ].seek( 0, 2 ) + self.open_file_indexes.append( index ) + return index, self.files[ index ] + + def close( self, index, delete=False ): + if index in self.open_file_indexes: + self.open_file_indexes.remove( index ) + rval = self.files[ index ].close() + if delete: + try: + os.unlink( self.files[ index ].name ) + except OSError: + pass + return rval + + def flush( self, index ): + if index in self.open_file_indexes: + self.files[ index ].flush() + + def __del__( self ): + for i in xrange( len( self.files ) ): + self.close( i, delete=True ) + + #an object corresponding to a reference layered alignment class RegionAlignment( object ): DNA_COMPLEMENT = string.maketrans( "ACGTacgt", "TGCAtgca" ) MAX_SEQUENCE_SIZE = sys.maxint #Maximum length of sequence allowed - def __init__( self, size, species = [] ): + def __init__( self, size, species = [], temp_file_handler = None ): assert size <= self.MAX_SEQUENCE_SIZE, "Maximum length allowed for an individual sequence has been exceeded (%i > %i)." % ( size, self.MAX_SEQUENCE_SIZE ) self.size = size + if not temp_file_handler: + temp_file_handler = TempFileHandler() + self.temp_file_handler = temp_file_handler self.sequences = {} if not isinstance( species, list ): species = [species] @@ -63,8 +146,9 @@ #add a species to the alignment def add_species( self, species ): #make temporary sequence files - self.sequences[species] = tempfile.TemporaryFile() - self.sequences[species].write( "-" * self.size ) + file_index, fh = self.temp_file_handler.get_open_tempfile() + self.sequences[species] = file_index + fh.write( "-" * self.size ) #returns the names for species found in alignment, skipping names as requested def get_species_names( self, skip = [] ): @@ -77,8 +161,9 @@ #returns the sequence for a species def get_sequence( self, species ): - self.sequences[species].seek( 0 ) - return self.sequences[species].read() + file_index, fh = self.temp_file_handler.get_open_tempfile( self.sequences[species] ) + fh.seek( 0 ) + return fh.read() #returns the reverse complement of the sequence for a species def get_sequence_reverse_complement( self, species ): @@ -95,8 +180,9 @@ if index >= self.size or index < 0: raise Exception( "Your index (%i) is out of range (0 - %i)." % ( index, self.size - 1 ) ) if len( bases ) == 0: raise Exception( "A set of genomic positions can only have a positive length." ) if species not in self.sequences.keys(): self.add_species( species ) - self.sequences[species].seek( index ) - self.sequences[species].write( bases ) + file_index, fh = self.temp_file_handler.get_open_tempfile( self.sequences[species] ) + fh.seek( index ) + fh.write( bases ) #Flush temp file of specified species, or all species def flush( self, species = None ): @@ -105,12 +191,12 @@ elif not isinstance( species, list ): species = [species] for spec in species: - self.sequences[spec].flush() + self.temp_file_handler.flush( self.sequences[spec] ) class GenomicRegionAlignment( RegionAlignment ): - def __init__( self, start, end, species = [] ): - RegionAlignment.__init__( self, end - start, species ) + def __init__( self, start, end, species = [], temp_file_handler = None ): + RegionAlignment.__init__( self, end - start, species, temp_file_handler=temp_file_handler ) self.start = start self.end = end @@ -118,15 +204,18 @@ DNA_COMPLEMENT = string.maketrans( "ACGTacgt", "TGCAtgca" ) - def __init__( self, exon_starts, exon_ends, species = [] ): + def __init__( self, exon_starts, exon_ends, species = [], temp_file_handler = None ): if not isinstance( exon_starts, list ): exon_starts = [exon_starts] if not isinstance( exon_ends, list ): exon_ends = [exon_ends] assert len( exon_starts ) == len( exon_ends ), "The number of starts does not match the number of sizes." self.exons = [] + if not temp_file_handler: + temp_file_handler = TempFileHandler() + self.temp_file_handler = temp_file_handler for i in range( len( exon_starts ) ): - self.exons.append( GenomicRegionAlignment( exon_starts[i], exon_ends[i], species ) ) + self.exons.append( GenomicRegionAlignment( exon_starts[i], exon_ends[i], species, temp_file_handler=temp_file_handler ) ) #returns the names for species found in alignment, skipping names as requested def get_species_names( self, skip = [] ): @@ -140,14 +229,20 @@ #returns the sequence for a species def get_sequence( self, species ): - sequence = tempfile.TemporaryFile() + index, fh = self.temp_file_handler.get_open_tempfile() for exon in self.exons: if species in exon.get_species_names(): - sequence.write( exon.get_sequence( species ) ) + seq = exon.get_sequence( species ) + # we need to refetch fh here, since exon.get_sequence( species ) uses a tempfile + # and if max==1, it would close fh + index, fh = self.temp_file_handler.get_open_tempfile( index ) + fh.write( seq ) else: - sequence.write( "-" * exon.size ) - sequence.seek( 0 ) - return sequence.read() + fh.write( "-" * exon.size ) + fh.seek( 0 ) + rval = fh.read() + self.temp_file_handler.close( index, delete=True ) + return rval #returns the reverse complement of the sequence for a species def get_sequence_reverse_complement( self, species ): @@ -366,9 +461,9 @@ yield block, idx, offset #returns a filled region alignment for specified regions -def get_region_alignment( index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): - if species is not None: alignment = RegionAlignment( end - start, species ) - else: alignment = RegionAlignment( end - start, primary_species ) +def get_region_alignment( index, primary_species, chrom, start, end, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True, temp_file_handler = None ): + if species is not None: alignment = RegionAlignment( end - start, species, temp_file_handler=temp_file_handler ) + else: alignment = RegionAlignment( end - start, primary_species, temp_file_handler=temp_file_handler ) return fill_region_alignment( alignment, index, primary_species, chrom, start, end, strand, species, mincols, overwrite_with_gaps ) #reduces a block to only positions exisiting in the src provided @@ -437,10 +532,10 @@ return alignment #returns a filled spliced region alignment for specified region with start and end lists -def get_spliced_region_alignment( index, primary_species, chrom, starts, ends, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True ): +def get_spliced_region_alignment( index, primary_species, chrom, starts, ends, strand = '+', species = None, mincols = 0, overwrite_with_gaps = True, temp_file_handler = None ): #create spliced alignment object - if species is not None: alignment = SplicedAlignment( starts, ends, species ) - else: alignment = SplicedAlignment( starts, ends, [primary_species] ) + if species is not None: alignment = SplicedAlignment( starts, ends, species, temp_file_handler=temp_file_handler ) + else: alignment = SplicedAlignment( starts, ends, [primary_species], temp_file_handler=temp_file_handler ) for exon in alignment.exons: fill_region_alignment( exon, index, primary_species, chrom, exon.start, exon.end, strand, species, mincols, overwrite_with_gaps ) return alignment diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -714,11 +714,11 @@ def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) class ParamsWithSpecs( collections.defaultdict ): @@ -770,22 +770,6 @@ return True -def get_ucsc_by_build(build): - sites = [] - for site in ucsc_build_sites: - if build in site['builds']: - sites.append((site['name'], site['url'])) - return sites - - -def get_gbrowse_sites_by_build(build): - sites = [] - for site in gbrowse_build_sites: - if build in site['builds']: - sites.append((site['name'], site['url'])) - return sites - - def read_dbnames(filename): """ Read build names from file """ class DBNames( list ): @@ -796,6 +780,9 @@ ucsc_builds = {} man_builds = [] # assume these are integers name_to_db_base = {} + if filename is None: + # Should only be happening with the galaxy.tools.parameters.basic:GenomeBuildParameter docstring unit test + filename = os.path.join( 'tool-data', 'shared', 'ucsc', 'builds.txt.sample' ) for line in open(filename): try: if line[0:1] == "#": @@ -842,63 +829,6 @@ return db_names -def read_ensembl( filename, ucsc ): - """ Read Ensembl build names from file """ - ucsc_builds = [] - for build in ucsc: - ucsc_builds.append( build[0] ) - ensembl_builds = list() - try: - for line in open( filename ): - if line[0:1] in [ '#', '\t' ]: - continue - fields = line.replace("\r", "").replace("\n", "").split("\t") - if fields[0] in ucsc_builds: - continue - ensembl_builds.append( dict( dbkey=fields[0], release=fields[1], name=fields[2].replace( '_', ' ' ) ) ) - except Exception, e: - print "ERROR: Unable to read builds file:", e - return ensembl_builds - - -def read_ncbi( filename ): - """ Read NCBI build names from file """ - ncbi_builds = list() - try: - for line in open( filename ): - if line[0:1] in [ '#', '\t' ]: - continue - fields = line.replace("\r", "").replace("\n", "").split("\t") - ncbi_builds.append( dict( dbkey=fields[0], name=fields[1] ) ) - except Exception, e: - print "ERROR: Unable to read builds file:", e - return ncbi_builds - - -def read_build_sites( filename, check_builds=True ): - """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ - build_sites = [] - try: - for line in open(filename): - try: - if line[0:1] == "#": - continue - fields = line.replace("\r", "").replace("\n", "").split("\t") - site_name = fields[0] - site = fields[1] - if check_builds: - site_builds = fields[2].split(",") - site_dict = {'name': site_name, 'url': site, 'builds': site_builds} - else: - site_dict = {'name': site_name, 'url': site} - build_sites.append( site_dict ) - except: - continue - except: - print "ERROR: Unable to read builds for site file %s" % filename - return build_sites - - def relativize_symlinks( path, start=None, followlinks=False): for root, dirs, files in os.walk( path, followlinks=followlinks ): rel_start = None @@ -1159,15 +1089,6 @@ galaxy_root_path = os.path.join(__path__[0], "..", "..", "..") -# The dbnames list is used in edit attributes and the upload tool -dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) ) -ucsc_names = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "publicbuilds.txt" ) ) -ensembl_names = read_ensembl( os.path.join( galaxy_root_path, "tool-data", "shared", "ensembl", "builds.txt" ), ucsc_names ) -ncbi_names = read_ncbi( os.path.join( galaxy_root_path, "tool-data", "shared", "ncbi", "builds.txt" ) ) -ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "ucsc_build_sites.txt" ) ) -gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) ) -dlnames = dict(ucsc=ucsc_names, ensembl=ensembl_names, ncbi=ncbi_names) - def galaxy_directory(): return os.path.abspath(galaxy_root_path) diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/util/build_sites.py --- /dev/null +++ b/lib/galaxy/util/build_sites.py @@ -0,0 +1,52 @@ +""" +Functionality for dealing with build sites for legacy display applications. +""" +import os.path + + +class BuildSites( object ): + + def __init__( self, app ): + self._app = app + self._build_sites = {} + self.load_build_sites() + + def read_build_sites( self, filename, check_builds=True ): + """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ + build_sites = [] + try: + for line in open(filename): + try: + if line[0:1] == "#": + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") + site_name = fields[0] + site = fields[1] + if check_builds: + site_builds = fields[2].split(",") + site_dict = {'name': site_name, 'url': site, 'builds': site_builds} + else: + site_dict = {'name': site_name, 'url': site} + build_sites.append( site_dict ) + except: + continue + except: + print "ERROR: Unable to read builds for site file %s" % filename + return build_sites + + def load_build_sites( self ): + self._build_sites['ucsc'] = self.read_build_sites( self._app.config.ucsc_build_sites ) + self._build_sites['gbrowse'] = self.read_build_sites( self._app.config.gbrowse_build_sites ) + + def get_site_by_build( self, site_type, build ): + sites = [] + for site in self._build_sites[site_type]: + if build in site['builds']: + sites.append((site['name'], site['url'])) + return sites + + def get_ucsc_sites_by_build( self, build ): + return self._get_site_by_build( 'ucsc', build ) + + def get_gbrowse_sites_by_build( self, build ): + return self._get_site_by_build( 'gbrowse', build ) diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -2,7 +2,7 @@ Functionality for dealing with dbkeys. """ #dbkeys read from disk using builds.txt -from galaxy.util import dbnames +from galaxy.util import read_dbnames from galaxy.util.json import from_json_string import os.path @@ -17,7 +17,7 @@ self._static_chrom_info_path = app.config.len_file_path # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups if load_old_style: - self._static_dbkeys = list( dbnames ) + self._static_dbkeys = list( read_dbnames( app.config.builds_file_path ) ) else: self._static_dbkeys = [] diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/util/sqlite.py --- /dev/null +++ b/lib/galaxy/util/sqlite.py @@ -0,0 +1,32 @@ +import sqlite3 +import re + +try: + import sqlparse + def is_read_only_query(query): + statements = sqlparse.parse(query) + for statement in statements: + if statement.get_type() != "SELECT": + return False + return True + +except ImportError: + # Without sqlparse we use a very weak regex check + def is_read_only_query(query): + if re.match("select ", query, re.IGNORECASE): + if re.search("^([^\"]|\"[^\"]*\")*?;", query) or re.search("^([^\']|\'[^\']*\')*?;", query): + return False + else: + return True + return False + + + + + +def connect(path): + connection = sqlite3.connect(path) + connection.row_factory = sqlite3.Row + return connection + + diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -1260,18 +1260,6 @@ return self.app.genome_builds.get_genome_build_names( trans=self ) @property - def ucsc_builds( self ): - return util.dlnames['ucsc'] - - @property - def ensembl_builds( self ): - return util.dlnames['ensembl'] - - @property - def ncbi_builds( self ): - return util.dlnames['ncbi'] - - @property def user_ftp_dir( self ): identifier = self.app.config.ftp_upload_dir_identifier return os.path.join( self.app.config.ftp_upload_dir, getattr(self.user, identifier) ) diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -52,6 +52,9 @@ # because the Tool Shed should always have an empty dictionary! self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path ) self.genome_builds = GenomeBuilds( self ) + # Citation manager needed to load tools. + from galaxy.managers.citations import CitationsManager + self.citations_manager = CitationsManager( self ) # The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required. self.toolbox = tools.ToolBox( [], self.config.tool_path, self ) # Initialize the Tool Shed security agent. diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -130,6 +130,9 @@ if global_conf and "__file__" in global_conf: global_conf_parser.read(global_conf['__file__']) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) + self.citation_cache_type = kwargs.get( "citation_cache_type", "file" ) + self.citation_cache_data_dir = resolve_path( kwargs.get( "citation_cache_data_dir", "database/tool_shed_citations/data" ), self.root ) + self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root ) def get( self, key, default ): return self.config_dict.get( key, default ) diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -20,13 +20,13 @@ from tool_shed.galaxy_install import dependency_display from tool_shed.metadata import repository_metadata_manager +from tool_shed.utility_containers import ToolShedUtilityContainerManager from tool_shed.tools import tool_validator from tool_shed.tools import tool_version_manager from tool_shed.util import basic_util from tool_shed.util import common_util -from tool_shed.util import container_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import metadata_util @@ -1273,12 +1273,12 @@ # Only display repository dependencies if they exist. exclude = [ 'datatypes', 'invalid_repository_dependencies', 'invalid_tool_dependencies', 'invalid_tools', 'readme_files', 'tool_dependencies', 'tools', 'tool_test_results', 'workflows', 'data_manager' ] - containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, - repository, - changeset_revision, - repository_dependencies, - repository_metadata, - exclude=exclude ) + tsucm = ToolShedUtilityContainerManager( trans.app ) + containers_dict = tsucm.build_repository_containers( repository, + changeset_revision, + repository_dependencies, + repository_metadata, + exclude=exclude ) export_repository_dependencies_check_box = CheckboxField( 'export_repository_dependencies', checked=True ) else: containers_dict = None @@ -2458,11 +2458,11 @@ skip_tool_tests_check_box = CheckboxField( 'skip_tool_tests', checked=skip_tool_tests_checked ) categories = suc.get_categories( trans.app ) selected_categories = [ rca.category_id for rca in repository.categories ] - containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, - repository, - changeset_revision, - repository_dependencies, - repository_metadata ) + tsucm = ToolShedUtilityContainerManager( trans.app ) + containers_dict = tsucm.build_repository_containers( repository, + changeset_revision, + repository_dependencies, + repository_metadata ) heads = hg_util.get_repository_heads( repo ) deprecated_repository_dependency_tups = \ metadata_util.get_repository_dependency_tups_from_repository_metadata( trans.app, @@ -2653,11 +2653,11 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, - repository, - changeset_revision, - repository_dependencies, - repository_metadata ) + tsucm = ToolShedUtilityContainerManager( trans.app ) + containers_dict = tsucm.build_repository_containers( repository, + changeset_revision, + repository_dependencies, + repository_metadata ) return trans.fill_template( '/webapps/tool_shed/repository/preview_tools_in_changeset.mako', repository=repository, containers_dict=containers_dict, @@ -3360,11 +3360,11 @@ else: message += malicious_error status = 'error' - containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, - repository, - changeset_revision, - repository_dependencies, - repository_metadata ) + tsucm = ToolShedUtilityContainerManager( trans.app ) + containers_dict = tsucm.build_repository_containers( repository, + changeset_revision, + repository_dependencies, + repository_metadata ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) heads = hg_util.get_repository_heads( repo ) return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -1,17 +1,26 @@ -import os, logging -from galaxy import web, util +import logging +import os + +from sqlalchemy.sql.expression import func + +from galaxy import util +from galaxy import web + +from galaxy.model.orm import and_ +from galaxy.util.odict import odict from galaxy.web.base.controller import BaseUIController -from galaxy.web.form_builder import SelectField, CheckboxField -from sqlalchemy.sql.expression import func -from galaxy.model.orm import and_ +from galaxy.web.form_builder import CheckboxField +from galaxy.web.form_builder import SelectField + from galaxy.webapps.tool_shed.util import ratings_util + +import tool_shed.grids.repository_review_grids as repository_review_grids +import tool_shed.grids.util as grids_util + from tool_shed.util.container_util import STRSEP -import tool_shed.util.shed_util_common as suc from tool_shed.util import hg_util from tool_shed.util import review_util -from galaxy.util.odict import odict -import tool_shed.grids.repository_review_grids as repository_review_grids -import tool_shed.grids.util as grids_util +from tool_shed.util import shed_util_common as suc log = logging.getLogger( __name__ ) diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/galaxy/webapps/tool_shed/framework/middleware/hg.py --- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py +++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py @@ -22,6 +22,7 @@ CHUNK_SIZE = 65536 + class Hg( object ): def __init__( self, app, config ): @@ -35,12 +36,20 @@ self.db_url = self.config[ 'database_connection' ] else: self.db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config[ 'database_file' ] + # Keep track of whether we're setting repository metadata so that we do not increment the times_downloaded + # count for the repository. + self.setting_repository_metadata = False def __call__( self, environ, start_response ): + if 'PATH_INFO' in environ: + path_info = environ[ 'PATH_INFO' ].lstrip( '/' ) + if path_info == 'repository/reset_all_metadata': + self.setting_repository_metadata = True cmd = self.__get_hg_command( **environ ) # The 'getbundle' command indicates that a mercurial client is getting a bundle of one or more changesets, indicating - # a clone or a pull. - if cmd == 'getbundle': + # a clone or a pull. However, we do not want to increment the times_downloaded count if we're only setting repository + # metadata. + if cmd == 'getbundle' and not self.setting_repository_metadata: common, _ = environ[ 'HTTP_X_HGARG_1' ].split( '&' ) # The 'common' parameter indicates the full sha-1 hash of the changeset the client currently has checked out. If # this is 0000000000000000000000000000000000000000, then the client is performing a fresh checkout. If it has any diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/tool_shed/dependencies/repository/relation_builder.py --- a/lib/tool_shed/dependencies/repository/relation_builder.py +++ b/lib/tool_shed/dependencies/repository/relation_builder.py @@ -3,6 +3,7 @@ from galaxy.util import asbool from galaxy.util import listify + from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import hg_util diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/tool_shed/galaxy_install/dependency_display.py --- a/lib/tool_shed/galaxy_install/dependency_display.py +++ b/lib/tool_shed/galaxy_install/dependency_display.py @@ -3,6 +3,11 @@ import os import threading +from galaxy import util + +from tool_shed.galaxy_install.utility_containers import GalaxyUtilityContainerManager +from tool_shed.utility_containers import utility_container_manager + from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import readme_util @@ -274,22 +279,23 @@ old_container_repository_dependencies_root = old_container_dict[ 'repository_dependencies' ] if old_container_repository_dependencies_root: if repository_dependencies_root_folder is None: - repository_dependencies_root_folder = container_util.Folder( id=folder_id, - key='root', - label='root', - parent=None ) + repository_dependencies_root_folder = utility_container_manager.Folder( id=folder_id, + key='root', + label='root', + parent=None ) folder_id += 1 - repository_dependencies_folder = container_util.Folder( id=folder_id, - key='merged', - label='Repository dependencies', - parent=repository_dependencies_root_folder ) + repository_dependencies_folder = utility_container_manager.Folder( id=folder_id, + key='merged', + label='Repository dependencies', + parent=repository_dependencies_root_folder ) folder_id += 1 # The old_container_repository_dependencies_root will be a root folder containing a single sub_folder. old_container_repository_dependencies_folder = old_container_repository_dependencies_root.folders[ 0 ] # Change the folder id so it won't confict with others being merged. old_container_repository_dependencies_folder.id = folder_id folder_id += 1 - repository_components_tuple = container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) + repository_components_tuple = \ + container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) components_list = suc.extract_components_from_tuple( repository_components_tuple ) name = components_list[ 1 ] # Generate the label by retrieving the repository name. @@ -299,15 +305,15 @@ old_container_tool_dependencies_root = old_container_dict[ 'tool_dependencies' ] if old_container_tool_dependencies_root: if tool_dependencies_root_folder is None: - tool_dependencies_root_folder = container_util.Folder( id=folder_id, - key='root', - label='root', - parent=None ) + tool_dependencies_root_folder = utility_container_manager.Folder( id=folder_id, + key='root', + label='root', + parent=None ) folder_id += 1 - tool_dependencies_folder = container_util.Folder( id=folder_id, - key='merged', - label='Tool dependencies', - parent=tool_dependencies_root_folder ) + tool_dependencies_folder = utility_container_manager.Folder( id=folder_id, + key='merged', + label='Tool dependencies', + parent=tool_dependencies_root_folder ) folder_id += 1 else: td_list = [ td.listify for td in tool_dependencies_folder.tool_dependencies ] @@ -408,23 +414,22 @@ repository_missing_tool_dependencies=missing_tool_dependencies, required_repo_info_dicts=None ) # Most of the repository contents are set to None since we don't yet know what they are. - containers_dict = \ - container_util.build_repository_containers_for_galaxy( app=self.app, - repository=None, - datatypes=None, - invalid_tools=None, - missing_repository_dependencies=missing_repository_dependencies, - missing_tool_dependencies=missing_tool_dependencies, - readme_files_dict=readme_files_dict, - repository_dependencies=installed_repository_dependencies, - tool_dependencies=installed_tool_dependencies, - valid_tools=None, - workflows=None, - valid_data_managers=None, - invalid_data_managers=None, - data_managers_errors=None, - new_install=True, - reinstalling=False ) + gucm = GalaxyUtilityContainerManager( self.app ) + containers_dict = gucm.build_repository_containers( repository=None, + datatypes=None, + invalid_tools=None, + missing_repository_dependencies=missing_repository_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=installed_repository_dependencies, + tool_dependencies=installed_tool_dependencies, + valid_tools=None, + workflows=None, + valid_data_managers=None, + invalid_data_managers=None, + data_managers_errors=None, + new_install=True, + reinstalling=False ) if not updating: # If we installing a new repository and not updaing an installed repository, we can merge # the missing_repository_dependencies container contents to the installed_repository_dependencies @@ -506,23 +511,22 @@ valid_data_managers = metadata['data_manager'].get( 'data_managers', None ) invalid_data_managers = metadata['data_manager'].get( 'invalid_data_managers', None ) data_managers_errors = metadata['data_manager'].get( 'messages', None ) - containers_dict = \ - container_util.build_repository_containers_for_galaxy( app=self.app, - repository=repository, - datatypes=datatypes, - invalid_tools=invalid_tools, - missing_repository_dependencies=missing_repository_dependencies, - missing_tool_dependencies=missing_tool_dependencies, - readme_files_dict=readme_files_dict, - repository_dependencies=installed_repository_dependencies, - tool_dependencies=installed_tool_dependencies, - valid_tools=valid_tools, - workflows=workflows, - valid_data_managers=valid_data_managers, - invalid_data_managers=invalid_data_managers, - data_managers_errors=data_managers_errors, - new_install=False, - reinstalling=reinstalling ) + gucm = GalaxyUtilityContainerManager( self.app ) + containers_dict = gucm.build_repository_containers( repository=repository, + datatypes=datatypes, + invalid_tools=invalid_tools, + missing_repository_dependencies=missing_repository_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=installed_repository_dependencies, + tool_dependencies=installed_tool_dependencies, + valid_tools=valid_tools, + workflows=workflows, + valid_data_managers=valid_data_managers, + invalid_data_managers=invalid_data_managers, + data_managers_errors=data_managers_errors, + new_install=False, + reinstalling=reinstalling ) else: containers_dict = dict( datatypes=None, invalid_tools=None, diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/tool_shed/galaxy_install/utility_containers/__init__.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py @@ -0,0 +1,145 @@ +import logging +import os +import threading + +from tool_shed.utility_containers import utility_container_manager + +log = logging.getLogger( __name__ ) + + +class GalaxyUtilityContainerManager( utility_container_manager.UtilityContainerManager ): + + def __init__( self, app ): + self.app = app + + def build_repository_containers( self, repository, datatypes, invalid_tools, missing_repository_dependencies, + missing_tool_dependencies, readme_files_dict, repository_dependencies, + tool_dependencies, valid_tools, workflows, valid_data_managers, + invalid_data_managers, data_managers_errors, new_install=False, + reinstalling=False ): + """ + Return a dictionary of containers for the received repository's dependencies and readme files for + display during installation to Galaxy. + """ + containers_dict = dict( datatypes=None, + invalid_tools=None, + missing_tool_dependencies=None, + readme_files=None, + repository_dependencies=None, + missing_repository_dependencies=None, + tool_dependencies=None, + valid_tools=None, + workflows=None, + valid_data_managers=None, + invalid_data_managers=None ) + # Some of the tool dependency folders will include links to display tool dependency information, and + # some of these links require the repository id. However we need to be careful because sometimes the + # repository object is None. + if repository: + repository_id = repository.id + changeset_revision = repository.changeset_revision + else: + repository_id = None + changeset_revision = None + lock = threading.Lock() + lock.acquire( True ) + try: + folder_id = 0 + # Datatypes container. + if datatypes: + folder_id, datatypes_root_folder = self.build_datatypes_folder( folder_id, datatypes ) + containers_dict[ 'datatypes' ] = datatypes_root_folder + # Invalid tools container. + if invalid_tools: + folder_id, invalid_tools_root_folder = \ + self.build_invalid_tools_folder( folder_id, + invalid_tools, + changeset_revision, + repository=repository, + label='Invalid tools' ) + containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder + # Readme files container. + if readme_files_dict: + folder_id, readme_files_root_folder = self.build_readme_files_folder( folder_id, readme_files_dict ) + containers_dict[ 'readme_files' ] = readme_files_root_folder + # Installed repository dependencies container. + if repository_dependencies: + if new_install: + label = 'Repository dependencies' + else: + label = 'Installed repository dependencies' + folder_id, repository_dependencies_root_folder = \ + self.build_repository_dependencies_folder( folder_id=folder_id, + repository_dependencies=repository_dependencies, + label=label, + installed=True ) + containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder + # Missing repository dependencies container. + if missing_repository_dependencies: + folder_id, missing_repository_dependencies_root_folder = \ + self.build_repository_dependencies_folder( folder_id=folder_id, + repository_dependencies=missing_repository_dependencies, + label='Missing repository dependencies', + installed=False ) + containers_dict[ 'missing_repository_dependencies' ] = missing_repository_dependencies_root_folder + # Installed tool dependencies container. + if tool_dependencies: + if new_install: + label = 'Tool dependencies' + else: + label = 'Installed tool dependencies' + # We only want to display the Status column if the tool_dependency is missing. + folder_id, tool_dependencies_root_folder = \ + self.build_tool_dependencies_folder( folder_id, + tool_dependencies, + label=label, + missing=False, + new_install=new_install, + reinstalling=reinstalling ) + containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder + # Missing tool dependencies container. + if missing_tool_dependencies: + # We only want to display the Status column if the tool_dependency is missing. + folder_id, missing_tool_dependencies_root_folder = \ + self.build_tool_dependencies_folder( folder_id, + missing_tool_dependencies, + label='Missing tool dependencies', + missing=True, + new_install=new_install, + reinstalling=reinstalling ) + containers_dict[ 'missing_tool_dependencies' ] = missing_tool_dependencies_root_folder + # Valid tools container. + if valid_tools: + folder_id, valid_tools_root_folder = self.build_tools_folder( folder_id, + valid_tools, + repository, + changeset_revision, + label='Valid tools' ) + containers_dict[ 'valid_tools' ] = valid_tools_root_folder + # Workflows container. + if workflows: + folder_id, workflows_root_folder = \ + self.build_workflows_folder( folder_id=folder_id, + workflows=workflows, + repository_metadata_id=None, + repository_id=repository_id, + label='Workflows' ) + containers_dict[ 'workflows' ] = workflows_root_folder + if valid_data_managers: + folder_id, valid_data_managers_root_folder = \ + self.build_data_managers_folder( folder_id=folder_id, + data_managers=valid_data_managers, + label='Valid Data Managers' ) + containers_dict[ 'valid_data_managers' ] = valid_data_managers_root_folder + if invalid_data_managers or data_managers_errors: + folder_id, invalid_data_managers_root_folder = \ + self.build_invalid_data_managers_folder( folder_id=folder_id, + data_managers=invalid_data_managers, + error_messages=data_managers_errors, + label='Invalid Data Managers' ) + containers_dict[ 'invalid_data_managers' ] = invalid_data_managers_root_folder + except Exception, e: + log.debug( "Exception in build_repository_containers: %s" % str( e ) ) + finally: + lock.release() + return containers_dict diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/tool_shed/grids/repository_grid_filter_manager.py --- a/lib/tool_shed/grids/repository_grid_filter_manager.py +++ b/lib/tool_shed/grids/repository_grid_filter_manager.py @@ -27,7 +27,7 @@ return "Certified 2 Repository Suites %s" % trailing_string if filter == self.filters.SUITES: return "Repository Suites %s" % trailing_string - return "%s" % default + return "%s %s" % ( default, trailing_string ) def get_filter( self, trans ): filter = trans.get_cookie( name='toolshedrepogridfilter' ) diff -r 25772fa9e9476dc0ab621d700e043312c2ae89e5 -r 482de41429fce74a9aac990b992c42eb8ed109ed lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -7,6 +7,7 @@ from galaxy.datatypes import checkers from galaxy.model.orm import and_ from galaxy.tools.data_manager.manager import DataManager +from galaxy.tools.test import TestCollectionDef from galaxy.web import url_for from tool_shed.repository_types import util as rt_util @@ -621,7 +622,13 @@ # </test> inputs.append( ( param_name, values ) ) else: - if len( values ) == 1: + if isinstance( values, TestCollectionDef ): + # Nested required files are being populated correctly, + # not sure we need the value here to be anything else? + collection_type = values.collection_type + metadata_display_value = "%s collection" % collection_type + inputs.append( ( param_name, metadata_display_value ) ) + elif len( values ) == 1: inputs.append( ( param_name, values[ 0 ] ) ) else: inputs.append( ( param_name, values ) ) This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/f521140aef30/ Changeset: f521140aef30 User: martenson Date: 2014-08-05 18:23:44 Summary: permission API for folders, libraries, library datasets/datasets close to finish Affected #: 21 files diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -252,6 +252,8 @@ is_public_item = True elif isinstance( item, self.model.Dataset ) and self.dataset_is_public( item ): is_public_item = True + elif isinstance( item, self.model.LibraryFolder ): + is_public_item = True else: is_public_item = False @@ -289,7 +291,8 @@ self.model.Role.table.c.type != self.model.Role.types.SHARING ) ) \ .order_by( self.model.Role.table.c.name ): roles.append( role ) - # User is not admin and item is not public + # User is not admin and item is not public + # User will see all the roles derived from the access roles on the item else: # If item has roles associated with the access permission, we need to start with them. access_roles = item.get_access_roles( trans ) diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -44,6 +44,7 @@ :raises: MalformedId, InconsistentDatabase, ObjectNotFound, InternalServerError """ + is_admin = trans.user_is_admin() deleted = kwd.get( 'include_deleted', 'missing' ) try: deleted = util.asbool( deleted ) @@ -105,7 +106,7 @@ folder_contents = [] update_time = '' create_time = '' - # Go through every accessible item (folders, datasets) in the folder and include its meta-data. + # Go through every accessible item (folders, datasets) in the folder and include its metadata. for content_item in self._load_folder_contents( trans, folder, deleted ): return_item = {} encoded_id = trans.security.encode_id( content_item.id ) @@ -114,37 +115,27 @@ if content_item.api_type == 'folder': encoded_id = 'F' + encoded_id - # Check whether user can modify current folder - can_modify = False - if trans.user_is_admin(): - can_modify = True - elif trans.user: - can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, folder ) - return_item.update( dict( can_modify=can_modify ) ) + can_modify = is_admin or ( trans.user and trans.app.security_agent.can_modify_library_item( current_user_roles, folder ) ) + can_manage = is_admin or ( trans.user and trans.app.security_agent.can_manage_library_item( current_user_roles, folder ) ) + return_item.update( dict( can_modify=can_modify, can_manage=can_manage ) ) if content_item.api_type == 'file': - # Is the dataset public or private? - # When both are False the dataset is 'restricted' - is_private = False - is_unrestricted = False - # Access rights are checked on the dataset level, not on the ld or ldda level to maintain consistency - if trans.app.security_agent.dataset_is_public( content_item.library_dataset_dataset_association.dataset ): - is_unrestricted = True + # Is the dataset public or private? + # When both are False the dataset is 'restricted' + # Access rights are checked on the dataset level, not on the ld or ldda level to maintain consistency + is_unrestricted = trans.app.security_agent.dataset_is_public( content_item.library_dataset_dataset_association.dataset ) + if trans.user and trans.app.security_agent.dataset_is_private_to_user( trans, content_item ): + is_private = True else: - is_unrestricted = False - if trans.user: - is_private = trans.app.security_agent.dataset_is_private_to_user( trans, content_item ) + is_private = False # Can user manage the permissions on the dataset? - can_manage = False - if trans.user_is_admin(): - can_manage = True - elif trans.user: - can_manage = trans.app.security_agent.can_manage_dataset( current_user_roles, content_item.library_dataset_dataset_association.dataset ) + can_manage = is_admin or (trans.user and trans.app.security_agent.can_manage_dataset( current_user_roles, content_item.library_dataset_dataset_association.dataset ) ) nice_size = util.nice_size( int( content_item.library_dataset_dataset_association.get_size() ) ) library_dataset_dict = content_item.to_dict() + return_item.update( dict( data_type=library_dataset_dict[ 'data_type' ], date_uploaded=library_dataset_dict[ 'date_uploaded' ], is_unrestricted=is_unrestricted, @@ -152,7 +143,7 @@ can_manage=can_manage, file_size=nice_size ) ) - # For every item include the default meta-data + # For every item include the default metadata return_item.update( dict( id=encoded_id, type=content_item.api_type, name=content_item.name, @@ -166,10 +157,10 @@ full_path = self.build_path( trans, folder )[ ::-1 ] # Check whether user can add items to the current folder - can_add_library_item = trans.user_is_admin() or trans.app.security_agent.can_add_library_item( current_user_roles, folder ) + can_add_library_item = is_admin or trans.app.security_agent.can_add_library_item( current_user_roles, folder ) - # Check whether user can modify current folder - can_modify_folder = trans.app.security_agent.can_modify_library_item( current_user_roles, folder ) + # Check whether user can modify the current folder + can_modify_folder = is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, folder ) metadata = dict( full_path=full_path, can_add_library_item=can_add_library_item, diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c lib/galaxy/webapps/galaxy/api/folders.py --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -8,6 +8,7 @@ # import socket # import traceback # import string +from galaxy import util from galaxy import web from galaxy import exceptions from galaxy.web import _future_expose_api as expose_api @@ -86,27 +87,15 @@ elif name is None: raise exceptions.RequestParameterMissingException( "Missing required parameter 'name'." ) - # encoded_parent_folder_id should be prefixed by 'F' encoded_parent_folder_id = self.__cut_the_prefix( encoded_parent_folder_id ) - try: - decoded_parent_folder_id = trans.security.decode_id( encoded_parent_folder_id ) - except ValueError: - raise exceptions.MalformedId( "Malformed folder id ( %s ) specified, unable to decode" % ( str( id ) ) ) - - try: - parent_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == decoded_parent_folder_id ).one() - except MultipleResultsFound: - raise exceptions.InconsistentDatabase( 'Multiple folders found with the same id.' ) - except NoResultFound: - raise exceptions.RequestParameterInvalidException( 'No folder found with the id provided.' ) - except Exception, e: - raise exceptions.InternalServerError( 'Error loading from the database.' + str( e ) ) - + decoded_parent_folder_id = self.__decode_folder_id( trans, encoded_parent_folder_id ) + parent_folder = self.__load_folder( trans, decoded_parent_folder_id ) + library = parent_folder.parent_library if library.deleted: raise exceptions.ObjectAttributeInvalidException( 'You cannot create folder within a deleted library. Undelete it first.' ) - # TODO: refactor the functionality for use here instead of calling another controller + # TODO: refactor the functionality for use in manager instead of calling another controller params = dict( [ ( "name", name ), ( "description", description ) ] ) status, output = trans.webapp.controllers['library_common'].create_folder( trans, 'api', encoded_parent_folder_id, '', **params ) @@ -126,6 +115,160 @@ else: raise exceptions.InternalServerError( 'Error while creating a folder.' + str( e ) ) + @expose_api + def get_permissions( self, trans, encoded_folder_id, **kwd ): + """ + * GET /api/folders/{id}/permissions + + Load all permissions for the given folder id and return it. + + :param encoded_folder_id: the encoded id of the folder + :type encoded_folder_id: an encoded id string + + :param scope: either 'current' or 'available' + :type scope: string + + :returns: dictionary with all applicable permissions' values + :rtype: dictionary + + :raises: ObjectNotFound, InsufficientPermissionsException + """ + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() + + encoded_folder_id = self.__cut_the_prefix( encoded_folder_id ) + decoded_folder_id = self.__decode_folder_id( trans, encoded_folder_id ) + folder = self.__load_folder( trans, decoded_folder_id ) + + if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, library ) ): + raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to access permissions of this folder.' ) + + scope = kwd.get( 'scope', None ) + + if scope == 'current' or scope is None: + return self._get_current_roles( trans, folder ) + + # Return roles that are available to select. + elif scope == 'available': + page = kwd.get( 'page', None ) + if page is not None: + page = int( page ) + else: + page = 1 + + page_limit = kwd.get( 'page_limit', None ) + if page_limit is not None: + page_limit = int( page_limit ) + else: + page_limit = 10 + + query = kwd.get( 'q', None ) + + roles, total_roles = trans.app.security_agent.get_valid_roles( trans, folder, query, page, page_limit ) + + return_roles = [] + for role in roles: + return_roles.append( dict( id=role.name, name=role.name, type=role.type ) ) + return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) + else: + raise exceptions.RequestParameterInvalidException( "The value of 'scope' parameter is invalid. Alllowed values: current, available" ) + + @expose_api + def set_permissions( self, trans, encoded_folder_id, **kwd ): + """ + def set_permissions( self, trans, encoded_folder_id, **kwd ): + *POST /api/folders/{encoded_folder_id}/permissions + + :param encoded_folder_id: the encoded id of the folder to set the permissions of + :type encoded_folder_id: an encoded id string + + :param action: (required) describes what action should be performed + available actions: set_permissions + :type action: string + + :param add_ids[]: list of Role.name defining roles that should have add item permission on the folder + :type add_ids[]: string or list + :param manage_ids[]: list of Role.name defining roles that should have manage permission on the folder + :type manage_ids[]: string or list + :param modify_ids[]: list of Role.name defining roles that should have modify permission on the folder + :type modify_ids[]: string or list + + :rtype: dictionary + :returns: dict of current roles for all available permission types + + :raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError + RequestParameterMissingException + """ + is_admin = trans.user_is_admin() + current_user_roles = trans.get_current_user_roles() + + decoded_folder_id = self.__decode_folder_id( trans, self.__cut_the_prefix( encoded_folder_id ) ) + folder = self.__load_folder( trans, decoded_folder_id ) + if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, folder ) ): + raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to modify permissions of this folder.' ) + + new_add_roles_ids = util.listify( kwd.get( 'add_ids[]', None ) ) + new_manage_roles_ids = util.listify( kwd.get( 'manage_ids[]', None ) ) + new_modify_roles_ids = util.listify( kwd.get( 'modify_ids[]', None ) ) + + action = kwd.get( 'action', None ) + if action is None: + raise exceptions.RequestParameterMissingException( 'The mandatory parameter "action" is missing.' ) + elif action == 'set_permissions': + + # ADD TO LIBRARY ROLES + valid_add_roles = [] + invalid_add_roles_names = [] + for role_id in new_add_roles_ids: + role = self._load_role( trans, role_id ) + # Check whether role is in the set of allowed roles + valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, folder ) + if role in valid_roles: + valid_add_roles.append( role ) + else: + invalid_add_roles_names.append( role_id ) + if len( invalid_add_roles_names ) > 0: + log.warning( "The following roles could not be added to the add library item permission: " + str( invalid_add_roles_names ) ) + + # MANAGE FOLDER ROLES + valid_manage_roles = [] + invalid_manage_roles_names = [] + for role_id in new_manage_roles_ids: + role = self._load_role( trans, role_id ) + # Check whether role is in the set of allowed roles + valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, folder ) + if role in valid_roles: + valid_manage_roles.append( role ) + else: + invalid_manage_roles_names.append( role_id ) + if len( invalid_manage_roles_names ) > 0: + log.warning( "The following roles could not be added to the manage folder permission: " + str( invalid_manage_roles_names ) ) + + # MODIFY FOLDER ROLES + valid_modify_roles = [] + invalid_modify_roles_names = [] + for role_id in new_modify_roles_ids: + role = self._load_role( trans, role_id ) + # Check whether role is in the set of allowed roles + valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, folder ) + if role in valid_roles: + valid_modify_roles.append( role ) + else: + invalid_modify_roles_names.append( role_id ) + if len( invalid_modify_roles_names ) > 0: + log.warning( "The following roles could not be added to the modify folder permission: " + str( invalid_modify_roles_names ) ) + + permissions = { trans.app.security_agent.permitted_actions.LIBRARY_ADD : valid_add_roles } + permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MANAGE : valid_manage_roles } ) + permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY : valid_modify_roles } ) + + trans.app.security_agent.set_all_library_permissions( trans, folder, permissions ) + else: + raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' + 'Allowed values are: "set_permissions"' ) + + return self._get_current_roles( trans, folder ) + @web.expose_api def update( self, trans, id, library_id, payload, **kwd ): """ @@ -134,9 +277,81 @@ """ raise exceptions.NotImplemented( 'Updating folder through this endpoint is not implemented yet.' ) - def __cut_the_prefix(self, encoded_id): - + def __cut_the_prefix( self, encoded_id ): + """ + Remove the prefix from the encoded folder id. + """ if ( ( len( encoded_id ) % 16 == 1 ) and encoded_id.startswith( 'F' ) ): - return encoded_id[ 1: ] + cut_id = encoded_id[ 1: ] else: raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_id ) ) + return cut_id + + def __decode_folder_id( self, trans, encoded_id ): + """ + Decode the folder id given that it has already lost the prefixed 'F'. + """ + try: + decoded_id = trans.security.decode_id( encoded_id ) + except ValueError: + raise exceptions.MalformedId( "Malformed folder id ( %s ) specified, unable to decode" % ( str( encoded_id ) ) ) + return decoded_id + + def __load_folder( self, trans, folder_id ): + """ + Load the folder from the DB. + """ + try: + folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == folder_id ).one() + except MultipleResultsFound: + raise exceptions.InconsistentDatabase( 'Multiple folders found with the same id.' ) + except NoResultFound: + raise exceptions.RequestParameterInvalidException( 'No folder found with the id provided.' ) + except Exception, e: + raise exceptions.InternalServerError( 'Error loading from the database.' + str( e ) ) + return folder + + + def _get_current_roles( self, trans, folder ): + """ + Find all roles currently connected to relevant permissions + on the folder. + + :param folder: the model object + :type folder: LibraryFolder + + :rtype: dictionary + :returns: dict of current roles for all available permission types + """ + # Omit duplicated roles by converting to set + modify_roles = set( trans.app.security_agent.get_roles_for_action( folder, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) + manage_roles = set( trans.app.security_agent.get_roles_for_action( folder, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ) ) + add_roles = set( trans.app.security_agent.get_roles_for_action( folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD ) ) + + modify_folder_role_list = [ modify_role.name for modify_role in modify_roles ] + manage_folder_role_list = [ manage_role.name for manage_role in manage_roles ] + add_library_item_role_list = [ add_role.name for add_role in add_roles ] + + return dict( modify_folder_role_list=modify_folder_role_list, manage_folder_role_list=manage_folder_role_list, add_library_item_role_list=add_library_item_role_list ) + + def _load_role( self, trans, role_name ): + """ + Method loads the role from the DB based on the given role name. + + :param role_name: name of the role to load from the DB + :type role_name: string + + :rtype: Role + :returns: the loaded Role object + + :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError + """ + try: + role = trans.sa_session.query( trans.app.model.Role ).filter( trans.model.Role.table.c.name == role_name ).one() + except MultipleResultsFound: + raise exceptions.InconsistentDatabase( 'Multiple roles found with the same name. Name: ' + str( role_name ) ) + except NoResultFound: + raise exceptions.RequestParameterInvalidException( 'No role found with the name provided. Name: ' + str( role_name ) ) + except Exception, e: + raise exceptions.InternalServerError( 'Error loading from the database.' + str(e)) + return role diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -111,7 +111,7 @@ scope = kwd.get( 'scope', None ) if scope == 'current' or scope is None: - return self.get_current_roles( trans, library_dataset ) + return self._get_current_roles( trans, library_dataset ) # Return roles that are available to select. elif scope == 'available': @@ -138,7 +138,7 @@ else: raise exceptions.RequestParameterInvalidException( "The value of 'scope' parameter is invalid. Alllowed values: current, available" ) - def get_current_roles( self, trans, library_dataset): + def _get_current_roles( self, trans, library_dataset): """ Find all roles currently connected to relevant permissions on the library dataset and the underlying dataset. @@ -293,9 +293,9 @@ else: raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' - 'Allowed values are: "remove_restrictions", "make_private", "set_dataset_access_roles"' ) + 'Allowed values are: "remove_restrictions", "make_private", "set_permissions"' ) - return self.get_current_roles( trans, library_dataset ) + return self._get_current_roles( trans, library_dataset ) def _load_role( self, trans, role_name ): """ diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -32,10 +32,11 @@ .. seealso:: :attr:`galaxy.model.Library.dict_collection_visible_keys` """ + is_admin = trans.user_is_admin() query = trans.sa_session.query( trans.app.model.Library ) deleted = kwd.get( 'deleted', 'missing' ) try: - if not trans.user_is_admin(): + if not is_admin: # non-admins can't see deleted libraries deleted = False else: @@ -48,15 +49,17 @@ # given value wasn't true/false but the user is admin so we don't filter on this parameter at all pass - current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ] - library_access_action = trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action - restricted_library_ids = [ lp.library_id for lp in ( trans.sa_session.query( trans.model.LibraryPermissions ) - .filter( trans.model.LibraryPermissions.table.c.action == library_access_action ) - .distinct() ) ] - accessible_restricted_library_ids = [ lp.library_id for lp in ( trans.sa_session.query( trans.model.LibraryPermissions ) - .filter( and_( trans.model.LibraryPermissions.table.c.action == library_access_action, - trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids ) ) ) ) ] - query = query.filter( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ), trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) + if not is_admin: + # non-admins can see only allowed and public libraries + current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ] + library_access_action = trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action + restricted_library_ids = [ lp.library_id for lp in ( trans.sa_session.query( trans.model.LibraryPermissions ) + .filter( trans.model.LibraryPermissions.table.c.action == library_access_action ) + .distinct() ) ] + accessible_restricted_library_ids = [ lp.library_id for lp in ( trans.sa_session.query( trans.model.LibraryPermissions ) + .filter( and_( trans.model.LibraryPermissions.table.c.action == library_access_action, + trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids ) ) ) ) ] + query = query.filter( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ), trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) libraries = [] for library in query: item = library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) @@ -287,7 +290,7 @@ raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to access permissions of this library.' ) scope = kwd.get( 'scope', None ) - is_library_access = kwd.get( 'is_library_access', False ) + is_library_access = util.string_as_bool( kwd.get( 'is_library_access', False ) ) if scope == 'current' or scope is None: return self._get_current_roles( trans, library ) @@ -450,11 +453,10 @@ permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MANAGE : valid_manage_roles } ) permissions.update( { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY : valid_modify_roles } ) - # trans.app.security_agent.set_library_item_permission( library, permissions ) trans.app.security_agent.set_all_library_permissions( trans, library, permissions ) else: raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' - 'Allowed values are: "remove_restrictions", set_dataset_access_roles"' ) + 'Allowed values are: "remove_restrictions", set_permissions"' ) return self._get_current_roles( trans, library ) diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -325,6 +325,18 @@ 'folders', path_prefix='/api' ) + webapp.mapper.connect( 'show_folder_permissions', + '/api/folders/:encoded_folder_id/permissions', + controller='folders', + action='get_permissions', + conditions=dict( method=[ "GET" ] ) ) + + webapp.mapper.connect( 'set_folder_permissions', + '/api/folders/:encoded_folder_id/permissions', + controller='folders', + action='set_permissions', + conditions=dict( method=[ "POST" ] ) ) + webapp.mapper.resource( 'content', 'contents', controller='folder_contents', diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -13,7 +13,8 @@ "mvc/library/library-librarytoolbar-view", "mvc/library/library-foldertoolbar-view", "mvc/library/library-dataset-view", - "mvc/library/library-library-view" + "mvc/library/library-library-view", + "mvc/library/library-folder-view" ], function(mod_masthead, mod_utils, @@ -25,7 +26,8 @@ mod_librarytoolbar_view, mod_foldertoolbar_view, mod_library_dataset_view, - mod_library_library_view + mod_library_library_view, + mod_library_folder_view ) { // ============================================================================ @@ -40,6 +42,7 @@ routes: { "" : "libraries", "library/:library_id/permissions" : "library_permissions", + "folders/:folder_id/permissions" : "folder_permissions", "folders/:id" : "folder_content", "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", "folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions", @@ -125,12 +128,19 @@ }); this.library_router.on('route:library_permissions', function(library_id){ - if (Galaxy.libraries.LibraryView){ + if (Galaxy.libraries.libraryView){ Galaxy.libraries.libraryView.$el.unbind('click'); } Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({id: library_id, show_permissions: true}); }); + this.library_router.on('route:folder_permissions', function(folder_id){ + if (Galaxy.libraries.folderView){ + Galaxy.libraries.folderView.$el.unbind('click'); + } + Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({id: folder_id, show_permissions: true}); + }); + Backbone.history.start({pushState: false}); } }); diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -720,7 +720,7 @@ tmpl_array.push(' <% }); %>'); tmpl_array.push('</ol>'); - tmpl_array.push('<h1>Permissions: <%= _.escape(item.get("name")) %></h1>'); + tmpl_array.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>'); tmpl_array.push('<div class="alert alert-warning">'); tmpl_array.push('<% if (is_admin) { %>'); diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/mvc/library/library-folder-view.js --- /dev/null +++ b/static/scripts/mvc/library/library-folder-view.js @@ -0,0 +1,303 @@ +define([ + "libs/toastr", + "mvc/library/library-model", + 'mvc/ui/ui-select' + ], +function( + mod_toastr, + mod_library_model, + mod_select + ) { + +var FolderView = Backbone.View.extend({ + el: '#center', + + model: null, + + options: { + + }, + + events: { + "click .toolbtn_save_permissions" : "savePermissions" + }, + + initialize: function(options){ + this.options = _.extend(this.options, options); + if (this.options.id){ + this.fetchFolder(); + } + }, + + fetchFolder: function(options){ + this.options = _.extend(this.options, options); + this.model = new mod_library_model.FolderAsModel({id:this.options.id}); + var that = this; + this.model.fetch({ + success: function() { + if (that.options.show_permissions){ + that.showPermissions(); + } else { + that.render(); + } + }, + error: function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error(response.responseJSON.err_msg + ' Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}}); + } else { + mod_toastr.error('An error ocurred :(. Click this to go back.', '', {onclick: function() {Galaxy.libraries.library_router.back();}}); + } + } + }); + }, + + render: function(options){ + $(".tooltip").remove(); + this.options = _.extend(this.options, options); + var template = this.templateFolder(); + this.$el.html(template({item: this.model})); + $(".peek").html(this.model.get("peek")); + $("#center [data-toggle]").tooltip(); + }, + + shareFolder: function(){ + mod_toastr.info('Feature coming soon.'); + }, + + goBack: function(){ + Galaxy.libraries.library_router.back(); + }, + + showPermissions: function(options){ + this.options = _.extend(this.options, options); + $(".tooltip").remove(); + + var is_admin = false; + if (Galaxy.currUser){ + is_admin = Galaxy.currUser.isAdmin(); + } + var template = this.templateFolderPermissions(); + this.$el.html(template({folder: this.model, is_admin:is_admin})); + + var self = this; + if (this.options.fetched_permissions === undefined){ + $.get( "/api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + self.prepareSelectBoxes({fetched_permissions:fetched_permissions}); + }).fail(function(){ + mod_toastr.error('An error occurred while fetching folder permissions. :('); + }); + } else { + this.prepareSelectBoxes({}); + } + + $("#center [data-toggle]").tooltip(); + //hack to show scrollbars + $("#center").css('overflow','auto'); + }, + + _serializeRoles : function(role_list){ + var selected_roles = []; + for (var i = 0; i < role_list.length; i++) { + selected_roles.push(role_list[i] + ':' + role_list[i]); + } + return selected_roles; + }, + + prepareSelectBoxes: function(options){ + this.options = _.extend(this.options, options); + var fetched_permissions = this.options.fetched_permissions; + var self = this; + + var selected_add_item_roles = this._serializeRoles(fetched_permissions.add_library_item_role_list); + var selected_manage_folder_roles = this._serializeRoles(fetched_permissions.manage_folder_role_list); + var selected_modify_folder_roles = this._serializeRoles(fetched_permissions.modify_folder_role_list); + + self.addSelectObject = new mod_select.View(this._createSelectOptions(this, 'add_perm', selected_add_item_roles, false)); + self.manageSelectObject = new mod_select.View(this._createSelectOptions(this, 'manage_perm', selected_manage_folder_roles, false)); + self.modifySelectObject = new mod_select.View(this._createSelectOptions(this, 'modify_perm', selected_modify_folder_roles, false)); + }, + + _createSelectOptions: function(self, id, init_data){ + var select_options = { + minimumInputLength: 0, + css: id, + multiple:true, + placeholder: 'Click to select a role', + container: self.$el.find('#' + id), + ajax: { + url: "/api/folders/" + self.id + "/permissions?scope=available", + dataType: 'json', + quietMillis: 100, + data: function (term, page) { // page is the one-based page number tracked by Select2 + return { + q: term, //search term + page_limit: 10, // page size + page: page // page number + }; + }, + results: function (data, page) { + var more = (page * 10) < data.total; // whether or not there are more results available + // notice we return the value of more so Select2 knows if more results can be loaded + return {results: data.roles, more: more}; + } + }, + formatResult : function roleFormatResult(role) { + return role.name + ' type: ' + role.type; + }, + + formatSelection: function roleFormatSelection(role) { + return role.name; + }, + initSelection: function(element, callback) { + // the input tag has a value attribute preloaded that points to a preselected role's id + // this function resolves that id attribute to an object that select2 can render + // using its formatResult renderer - that way the role name is shown preselected + var data = []; + $(element.val().split(",")).each(function() { + var item = this.split(':'); + data.push({ + id: item[1], + name: item[1] + }); + }); + callback(data); + }, + initialData: init_data.join(','), + dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller + }; + + return select_options; + }, + + comingSoon: function(){ + mod_toastr.warning('Feature coming soon'); + }, + + copyToClipboard: function(){ + var href = Backbone.history.location.href; + if (href.lastIndexOf('/permissions') !== -1){ + href = href.substr(0, href.lastIndexOf('/permissions')); + } + window.prompt("Copy to clipboard: Ctrl+C, Enter", href); + }, + + _extractIds: function(roles_list){ + ids_list = []; + for (var i = roles_list.length - 1; i >= 0; i--) { + ids_list.push(roles_list[i].id); + }; + return ids_list; + }, + savePermissions: function(event){ + var self = this; + + var add_ids = this._extractIds(this.addSelectObject.$el.select2('data')); + var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data')); + var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data')); + + $.post("/api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + .done(function(fetched_permissions){ + //fetch dataset again + self.showPermissions({fetched_permissions:fetched_permissions}) + mod_toastr.success('Permissions saved'); + }) + .fail(function(){ + mod_toastr.error('An error occurred while setting folder permissions :('); + }) + }, + + templateFolder : function(){ + var tmpl_array = []; + // CONTAINER START + tmpl_array.push('<div class="library_style_container">'); + + tmpl_array.push(' <div id="library_toolbar">'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>'); + tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); + tmpl_array.push(' </div>'); + + // tmpl_array.push('<% if (item.get("is_unrestricted")) { %>'); + tmpl_array.push(' <p>'); + tmpl_array.push(' This dataset is unrestricted so everybody can access it. Just share the URL of this page. '); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> '); + tmpl_array.push(' </p>'); + // tmpl_array.push('<% } %>'); + + tmpl_array.push('<div class="dataset_table">'); + + tmpl_array.push(' <table class="grid table table-striped table-condensed">'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); + tmpl_array.push(' </tr>'); + + tmpl_array.push(' <% if (item.get("data_type")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data type</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' </table>'); + tmpl_array.push('</div>'); + + // CONTAINER END + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + }, + + templateFolderPermissions : function(){ + var tmpl_array = []; + // CONTAINER START + tmpl_array.push('<div class="library_style_container">'); + + + tmpl_array.push(' <div id="library_toolbar">'); + tmpl_array.push(' <a href="#/folders/<%= folder.get("id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the folder contents" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Parent folder</span></button></a>'); + tmpl_array.push(' </div>'); + + tmpl_array.push('<h1>Folder: <%= _.escape(folder.get("name")) %></h1>'); + + tmpl_array.push('<div class="alert alert-warning">'); + tmpl_array.push('<% if (is_admin) { %>'); + tmpl_array.push('You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.'); + tmpl_array.push('<% } else { %>'); + tmpl_array.push('You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.'); + tmpl_array.push('<% }%>'); + tmpl_array.push('</div>'); + + tmpl_array.push('<div class="dataset_table">'); + + tmpl_array.push('<h2>Folder permissions</h2>'); + + tmpl_array.push('<h4>Roles that can manage permissions on this folder</h4>'); + tmpl_array.push('<div id="manage_perm" class="manage_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this folder.</div>'); + + tmpl_array.push('<h4>Roles that can add items to this folder</h4>'); + tmpl_array.push('<div id="add_perm" class="add_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).</div>'); + + tmpl_array.push('<h4>Roles that can modify this folder</h4>'); + tmpl_array.push('<div id="modify_perm" class="modify_perm roles-selection"></div>'); + tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this folder (name, etc.).</div>'); + + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); + + tmpl_array.push('</div>'); + + // CONTAINER END + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + } + +}); + +return { + FolderView: FolderView +}; + +}); diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -88,6 +88,7 @@ render: function (options) { this.options = _.defaults(this.options, options); var template = this.templateFolder(); + $(".tooltip").hide(); // TODO move to server // find the upper id in the full path @@ -116,7 +117,7 @@ var fetched_metadata = this.folderContainer.attributes.metadata; fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined'; Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata); - $('.dataset').hover(function() { + $('.library-row').hover(function() { $(this).find('.show_on_hover').show(); }, function () { $(this).find('.show_on_hover').hide(); @@ -156,7 +157,7 @@ * @param {Item or FolderAsModel} model of the view that will be rendered */ renderOne: function(model){ - if (model.get('data_type') !== 'folder'){ + if (model.get('type') !== 'folder'){ this.options.contains_file = true; // model.set('readable_size', this.size_to_string(model.get('file_size'))); } @@ -168,7 +169,7 @@ this.$el.find('#first_folder_item').after(rowView.el); - $('.dataset').hover(function() { + $('.library-row').hover(function() { $(this).find('.show_on_hover').show(); }, function () { $(this).find('.show_on_hover').hide(); diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/mvc/library/library-folderrow-view.js --- a/static/scripts/mvc/library/library-folderrow-view.js +++ b/static/scripts/mvc/library/library-folderrow-view.js @@ -82,7 +82,7 @@ templateRowFolder: function() { tmpl_array = []; - tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">'); + tmpl_array.push('<tr class="folder_row light library-row" id="<%- content_item.id %>">'); tmpl_array.push(' <td>'); tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>'); tmpl_array.push(' </td>'); @@ -93,7 +93,9 @@ tmpl_array.push(' <td>folder</td>'); tmpl_array.push(' <td></td>'); tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated - tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#/folders/<%- content_item.get("folder_id") %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-folder-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>'); + tmpl_array.push(' </td>'); tmpl_array.push('</tr>'); return _.template(tmpl_array.join('')); @@ -102,7 +104,7 @@ templateRowFile: function(){ tmpl_array = []; - tmpl_array.push('<tr class="dataset_row light dataset" id="<%- content_item.id %>">'); + tmpl_array.push('<tr class="dataset_row light library-row" id="<%- content_item.id %>">'); tmpl_array.push(' <td>'); tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>'); tmpl_array.push(' </td>'); @@ -125,7 +127,7 @@ templateRowDeletedFile: function(){ tmpl_array = []; - tmpl_array.push('<tr class="active deleted_dataset dataset" id="<%- content_item.id %>">'); + tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">'); tmpl_array.push(' <td>'); tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>'); tmpl_array.push(' </td>'); diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/mvc/library/library-library-view.js --- a/static/scripts/mvc/library/library-library-view.js +++ b/static/scripts/mvc/library/library-library-view.js @@ -52,19 +52,10 @@ }, render: function(options){ - // $(".tooltip").remove(); + $(".tooltip").remove(); this.options = _.extend(this.options, options); - var template = this.templateDataset(); + var template = this.templateLibrary(); this.$el.html(template({item: this.model})); - $(".peek").html(this.model.get("peek")); - $("#center [data-toggle]").tooltip(); - }, - - enableModification: function(){ - $(".tooltip").remove(); - var template = this.templateModifyDataset(); - this.$el.html(template({item: this.model})); - $(".peek").html(this.model.get("peek")); $("#center [data-toggle]").tooltip(); }, @@ -78,17 +69,21 @@ showPermissions: function(options){ this.options = _.extend(this.options, options); - // $(".tooltip").remove(); + $(".tooltip").remove(); if (this.options.fetched_permissions !== undefined){ - if (this.options.fetched_permissions.access_dataset_roles.length === 0){ + if (this.options.fetched_permissions.access_library_role_list.length === 0){ this.model.set({is_unrestricted:true}); } else{ this.model.set({is_unrestricted:false}); } } + var is_admin = false; + if (Galaxy.currUser){ + is_admin = Galaxy.currUser.isAdmin(); + } var template = this.templateLibraryPermissions(); - this.$el.html(template({library: this.model})); + this.$el.html(template({library: this.model, is_admin:is_admin})); var self = this; if (this.options.fetched_permissions === undefined){ @@ -124,13 +119,14 @@ var selected_manage_library_roles = this._serializeRoles(fetched_permissions.manage_library_role_list); var selected_modify_library_roles = this._serializeRoles(fetched_permissions.modify_library_role_list); - self.accessSelectObject = new mod_select.View(this._createSelectOptions(this, 'access_perm', selected_access_library_roles)); - self.addSelectObject = new mod_select.View(this._createSelectOptions(this, 'add_perm', selected_add_item_roles)); - self.manageSelectObject = new mod_select.View(this._createSelectOptions(this, 'manage_perm', selected_manage_library_roles)); - self.modifySelectObject = new mod_select.View(this._createSelectOptions(this, 'modify_perm', selected_modify_library_roles)); + self.accessSelectObject = new mod_select.View(this._createSelectOptions(this, 'access_perm', selected_access_library_roles, true)); + self.addSelectObject = new mod_select.View(this._createSelectOptions(this, 'add_perm', selected_add_item_roles, false)); + self.manageSelectObject = new mod_select.View(this._createSelectOptions(this, 'manage_perm', selected_manage_library_roles, false)); + self.modifySelectObject = new mod_select.View(this._createSelectOptions(this, 'modify_perm', selected_modify_library_roles, false)); }, - _createSelectOptions: function(self, id, init_data){ + _createSelectOptions: function(self, id, init_data, is_library_access){ + is_library_access = is_library_access === true ? is_library_access : false; var select_options = { minimumInputLength: 0, css: id, @@ -138,7 +134,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#' + id), ajax: { - url: "/api/libraries/" + self.id + "/permissions?scope=available", + url: "/api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access, dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -290,15 +286,20 @@ var tmpl_array = []; // CONTAINER START tmpl_array.push('<div class="library_style_container">'); + tmpl_array.push(' <div id="library_toolbar">'); tmpl_array.push(' <a href="#"><button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Libraries</span></button></a>'); tmpl_array.push(' </div>'); - tmpl_array.push('<h1>Permissions: <%= _.escape(library.get("name")) %></h1>'); + tmpl_array.push('<h1>Library: <%= _.escape(library.get("name")) %></h1>'); tmpl_array.push('<div class="alert alert-warning">'); + tmpl_array.push('<% if (is_admin) { %>'); + tmpl_array.push('You are logged in as an <strong>administrator</strong> therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.'); + tmpl_array.push('<% } else { %>'); tmpl_array.push('You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.'); + tmpl_array.push('<% }%>'); tmpl_array.push('</div>'); tmpl_array.push('<div class="dataset_table">'); diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/mvc/library/library-librarylist-view.js --- a/static/scripts/mvc/library/library-librarylist-view.js +++ b/static/scripts/mvc/library/library-librarylist-view.js @@ -53,6 +53,11 @@ * or from a given array of library models, * or renders an empty list in case no data is given. */ render: function (options) { + /** + * need to hide manually because of the element removal + * bug in tooltip + */ + $(".tooltip").hide(); var template = this.templateLibraryList(); var libraries_to_render = null; var include_deleted = Galaxy.libraries.preferences.get('with_deleted'); diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view"],function(f,c,h,l,i,a,g,e,j,d){var m=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/download/:format":"download"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var k=l.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new k({id:"global-lib-prefs"});this.library_router=new m();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new e.LibraryToolbarView();Galaxy.libraries.libraryListView=new g.LibraryListView()});this.library_router.on("route:folder_content",function(n){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new j.FolderToolbarView({id:n});Galaxy.libraries.folderListView=new a.FolderListView({id:n})});this.library_router.on("route:download",function(n,o){if($("#folder_list_body").find(":checked").length===0){h.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+n,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(n,o);Galaxy.libraries.library_router.navigate("folders/"+n,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(o,n){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new d.LibraryDatasetView({id:n})});this.library_router.on("route:dataset_permissions",function(o,n){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new d.LibraryDatasetView({id:n,show_permissions:true})});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view","mvc/library/library-library-view","mvc/library/library-folder-view"],function(h,e,j,n,k,c,i,g,l,f,b,a){var o=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","library/:library_id/permissions":"library_permissions","folders/:folder_id/permissions":"folder_permissions","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/download/:format":"download"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var m=n.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var d=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,libraryView:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new m({id:"global-lib-prefs"});this.library_router=new o();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView()});this.library_router.on("route:folder_content",function(p){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p})});this.library_router.on("route:download",function(p,q){if($("#folder_list_body").find(":checked").length===0){j.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(p,q);Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p})});this.library_router.on("route:dataset_permissions",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,show_permissions:true})});this.library_router.on("route:library_permissions",function(p){if(Galaxy.libraries.libraryView){Galaxy.libraries.libraryView.$el.unbind("click")}Galaxy.libraries.libraryView=new b.LibraryView({id:p,show_permissions:true})});this.library_router.on("route:folder_permissions",function(p){if(Galaxy.libraries.folderView){Galaxy.libraries.folderView.$el.unbind("click")}Galaxy.libraries.folderView=new a.FolderView({id:p,show_permissions:true})});Backbone.history.start({pushState:false})}});return{GalaxyApp:d}}); \ No newline at end of file diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/packed/mvc/library/library-dataset-view.js --- a/static/scripts/packed/mvc/library/library-dataset-view.js +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){f(e)},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var g=new c.HistoryItem();g.url=g.urlRoot+f+"/contents";var e="/api/histories/"+f+"/set_as_current";$.ajax({url:e,type:"PUT"});g.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(i,h){if(typeof h.responseJSON!=="undefined"){d.error("Dataset not imported. "+h.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while fetching dataset permissions. :(")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you")}).fail(function(){d.error("An error occurred while making dataset private :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted")}).fail(function(){d.error("An error occurred while making dataset unrestricted :(")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i})}).fail(function(){d.error("An error occurred while setting dataset permissions :(")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Permissions: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){f(e)},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var g=new c.HistoryItem();g.url=g.urlRoot+f+"/contents";var e="/api/histories/"+f+"/set_as_current";$.ajax({url:e,type:"PUT"});g.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(i,h){if(typeof h.responseJSON!=="undefined"){d.error("Dataset not imported. "+h.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while fetching dataset permissions. :(")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you")}).fail(function(){d.error("An error occurred while making dataset private :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted")}).fail(function(){d.error("An error occurred while making dataset unrestricted :(")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting dataset permissions :(")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(' <button data-toggle="tooltip" data-placement="top" title="Show previous versions" class="btn btn-default toolbtn-previous-versions primary-button" type="button"><span class="fa fa-clock-o"></span> Versions</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/packed/mvc/library/library-folder-view.js --- /dev/null +++ b/static/scripts/packed/mvc/library/library-folder-view.js @@ -0,0 +1,1 @@ +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchFolder()}},fetchFolder:function(e){this.options=_.extend(this.options,e);this.model=new c.FolderAsModel({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateFolder();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},shareFolder:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateFolderPermissions();this.$el.html(g({folder:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/folders/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while fetching folder permissions. :(")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f]+":"+g[f])}return e},prepareSelectBoxes:function(h){this.options=_.extend(this.options,h);var f=this.options.fetched_permissions;var g=this;var i=this._serializeRoles(f.add_library_item_role_list);var j=this._serializeRoles(f.manage_folder_role_list);var e=this._serializeRoles(f.modify_folder_role_list);g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",i,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",j,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",e,false))},_createSelectOptions:function(e,j,h){var i={minimumInputLength:0,css:j,multiple:true,placeholder:"Click to select a role",container:e.$el.find("#"+j),ajax:{url:"/api/folders/"+e.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(k,l){return{q:k,page_limit:10,page:l}},results:function(m,l){var k=(l*10)<m.total;return{results:m.roles,more:k}}},formatResult:function f(k){return k.name+" type: "+k.type},formatSelection:function g(k){return k.name},initSelection:function(k,m){var l=[];$(k.val().split(",")).each(function(){var n=this.split(":");l.push({id:n[1],name:n[1]})});m(l)},initialData:h.join(","),dropdownCssClass:"bigdrop"};return i},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var e=this._extractIds(this.addSelectObject.$el.select2("data"));var i=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post("/api/folders/"+g.id+"/permissions?action=set_permissions",{"add_ids[]":e,"manage_ids[]":i,"modify_ids[]":f,}).done(function(j){g.showPermissions({fetched_permissions:j});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting folder permissions :(")})},templateFolder:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateFolderPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#/folders/<%= folder.get("id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the folder contents" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Parent folder</span></button></a>');e.push(" </div>");e.push('<h1>Folder: <%= _.escape(folder.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Folder permissions</h2>");e.push("<h4>Roles that can manage permissions on this folder</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this folder.</div>');e.push("<h4>Roles that can add items to this folder</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).</div>');e.push("<h4>Roles that can modify this folder</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this folder (name, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{FolderView:b}}); \ No newline at end of file diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("data_type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el);$(".dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/packed/mvc/library/library-folderrow-view.js --- a/static/scripts/packed/mvc/library/library-folderrow-view.js +++ b/static/scripts/packed/mvc/library/library-folderrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(c,e,f,d,b){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(g){this.render(g)},render:function(g){var h=null;if(g.get("type")==="folder"){this.options.type="folder";h=this.templateRowFolder()}else{this.options.type="file";if(g.get("deleted")){h=this.templateRowDeletedFile()}else{h=this.templateRowFile()}}this.setElement(h({content_item:g}));this.$el.show();return this},showDatasetDetails:function(){Galaxy.libraries.datasetView=new b.LibraryDatasetView({id:this.id})},undelete_dataset:function(i){$(".tooltip").hide();var h=this;var g=$(i.target).closest("tr")[0].id;var j=Galaxy.libraries.folderListView.collection.get(g);j.url=j.urlRoot+j.id+"?undelete=true";j.destroy({success:function(l,k){Galaxy.libraries.folderListView.collection.remove(g);var m=new d.Item(k);Galaxy.libraries.folderListView.collection.add(m);f.success("Dataset undeleted. Click this to see it.","",{onclick:function(){h.showDatasetDetails()}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error("Dataset was not undeleted. "+k.responseJSON.err_msg)}else{f.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td>");tmpl_array.push(' <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');tmpl_array.push(' <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push(" </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))}});return{FolderRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(c,e,f,d,b){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(g){this.render(g)},render:function(g){var h=null;if(g.get("type")==="folder"){this.options.type="folder";h=this.templateRowFolder()}else{this.options.type="file";if(g.get("deleted")){h=this.templateRowDeletedFile()}else{h=this.templateRowFile()}}this.setElement(h({content_item:g}));this.$el.show();return this},showDatasetDetails:function(){Galaxy.libraries.datasetView=new b.LibraryDatasetView({id:this.id})},undelete_dataset:function(i){$(".tooltip").hide();var h=this;var g=$(i.target).closest("tr")[0].id;var j=Galaxy.libraries.folderListView.collection.get(g);j.url=j.urlRoot+j.id+"?undelete=true";j.destroy({success:function(l,k){Galaxy.libraries.folderListView.collection.remove(g);var m=new d.Item(k);Galaxy.libraries.folderListView.collection.add(m);f.success("Dataset undeleted. Click this to see it.","",{onclick:function(){h.showDatasetDetails()}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error("Dataset was not undeleted. "+k.responseJSON.err_msg)}else{f.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light library-row" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td>");tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#/folders/<%- content_item.get("folder_id") %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-folder-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push(" </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light library-row" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td>");tmpl_array.push(' <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');tmpl_array.push(' <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push(" </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))}});return{FolderRowView:a}}); \ No newline at end of file diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/packed/mvc/library/library-library-view.js --- /dev/null +++ b/static/scripts/packed/mvc/library/library-library-view.js @@ -0,0 +1,1 @@ +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchLibrary()}},fetchLibrary:function(e){this.options=_.extend(this.options,e);this.model=new c.Library({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateLibrary();this.$el.html(f({item:this.model}));$("#center [data-toggle]").tooltip()},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_library_role_list.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateLibraryPermissions();this.$el.html(g({library:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while fetching library permissions. :(")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f]+":"+g[f])}return e},prepareSelectBoxes:function(i){this.options=_.extend(this.options,i);var e=this.options.fetched_permissions;var g=this;var f=this._serializeRoles(e.access_library_role_list);var j=this._serializeRoles(e.add_library_item_role_list);var h=this._serializeRoles(e.manage_library_role_list);var k=this._serializeRoles(e.modify_library_role_list);g.accessSelectObject=new a.View(this._createSelectOptions(this,"access_perm",f,true));g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",j,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",h,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",k,false))},_createSelectOptions:function(f,k,i,e){e=e===true?e:false;var j={minimumInputLength:0,css:k,multiple:true,placeholder:"Click to select a role",container:f.$el.find("#"+k),ajax:{url:"/api/libraries/"+f.id+"/permissions?scope=available&is_library_access="+e,dataType:"json",quietMillis:100,data:function(l,m){return{q:l,page_limit:10,page:m}},results:function(n,m){var l=(m*10)<n.total;return{results:n.roles,more:l}}},formatResult:function g(l){return l.name+" type: "+l.type},formatSelection:function h(l){return l.name},initSelection:function(l,n){var m=[];$(l.val().split(",")).each(function(){var o=this.split(":");m.push({id:o[1],name:o[1]})});n(m)},initialData:i.join(","),dropdownCssClass:"bigdrop"};return j},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you")}).fail(function(){d.error("An error occurred while making dataset private :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted")}).fail(function(){d.error("An error occurred while making dataset unrestricted :(")})},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var i=this._extractIds(this.accessSelectObject.$el.select2("data"));var e=this._extractIds(this.addSelectObject.$el.select2("data"));var j=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post("/api/libraries/"+g.id+"/permissions?action=set_permissions",{"access_ids[]":i,"add_ids[]":e,"manage_ids[]":j,"modify_ids[]":f,}).done(function(k){g.showPermissions({fetched_permissions:k});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting library permissions :(")})},templateLibrary:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateLibraryPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#"><button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Libraries</span></button></a>');e.push(" </div>");e.push('<h1>Library: <%= _.escape(library.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library permissions</h2>");e.push("<h4>Roles that can access the library</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can access this library. If there are no access roles set on the library it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on this library</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this library (includes giving access).</div>');e.push("<h4>Roles that can add items to this library</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this library (folders and datasets).</div>');e.push("<h4>Roles that can modify this library</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this library (name, synopsis, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{LibraryView:b}}); \ No newline at end of file diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/packed/mvc/library/library-librarylist-view.js --- a/static/scripts/packed/mvc/library/library-librarylist-view.js +++ b/static/scripts/packed/mvc/library/library-librarylist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){h.render()},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);if(j.prepend){this.$el.find("#library_list_body").prepend(h.el)}else{this.$el.find("#library_list_body").append(h.el)}this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},});return{LibraryListView:f}}); \ No newline at end of file +define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){h.render()},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},render:function(i){$(".tooltip").hide();var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);if(j.prepend){this.$el.find("#library_list_body").prepend(h.el)}else{this.$el.find("#library_list_body").append(h.el)}this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},});return{LibraryListView:f}}); \ No newline at end of file diff -r 482de41429fce74a9aac990b992c42eb8ed109ed -r f521140aef303991b1ad07edec495d698275e24c static/scripts/packed/mvc/library/library-libraryrow-view.js --- a/static/scripts/packed/mvc/library/library-libraryrow-view.js +++ b/static/scripts/packed/mvc/library/library-libraryrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true;vis_config.undelete_library_btn=false}}this.element_visibility_config=vis_config},permissions_on_library:function(){d.info("Coming soon. Stay tuned.")},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){d.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){d.error(k.responseJSON.err_msg)}else{d.error("An error occured during updating the library :(")}}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured during deleting the library :(")}}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured while undeleting the library :(")}}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true;vis_config.undelete_library_btn=false}}this.element_visibility_config=vis_config},permissions_on_library:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove()},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){d.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){d.error(k.responseJSON.err_msg)}else{d.error("An error occured during updating the library :(")}}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured during deleting the library :(")}}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured while undeleting the library :(")}}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button></a>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/9f52741f8c34/ Changeset: 9f52741f8c34 User: martenson Date: 2014-08-05 18:24:13 Summary: Merge Affected #: 28 files diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -20,7 +20,7 @@ from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP, TWOBIT_MAGIC_SIZE -from galaxy.datatypes.metadata import MetadataElement +from galaxy.datatypes.metadata import MetadataElement,ListParameter,DictParameter from galaxy.datatypes import metadata from galaxy.datatypes.sniff import * import dataproviders @@ -550,8 +550,36 @@ @dataproviders.decorators.has_dataproviders class SQlite ( Binary ): + """Class describing a Sqlite database """ + MetadataElement( name="tables", default=[], param=ListParameter, desc="Database Tables", readonly=True, visible=True, no_value=[] ) + MetadataElement( name="table_columns", default={}, param=DictParameter, desc="Database Table Columns", readonly=True, visible=True, no_value={} ) + MetadataElement( name="table_row_count", default={}, param=DictParameter, desc="Database Table Row Count", readonly=True, visible=True, no_value={} ) file_ext = "sqlite" + def init_meta( self, dataset, copy_from=None ): + Binary.init_meta( self, dataset, copy_from=copy_from ) + + def set_meta( self, dataset, overwrite = True, **kwd ): + try: + tables = [] + columns = dict() + rowcounts = dict() + conn = sqlite3.connect(dataset.file_name) + c = conn.cursor() + tables_query = "SELECT name,sql FROM sqlite_master WHERE type='table' ORDER BY name" + rslt = c.execute(tables_query).fetchall() + for table,sql in rslt: + tables.append(table) + columns[table] = re.sub('^.*\((.*)\)$','\\1',sql).split(',') + for table in tables: + row_query = "SELECT count(*) FROM %s" % table + rowcounts[table] = c.execute(row_query).fetchone()[0] + dataset.metadata.tables = tables + dataset.metadata.table_columns = columns + dataset.metadata.table_row_count = rowcounts + except Exception, exc: + pass + # Connects and runs a query that should work on any real database # If the file is not sqlite, an exception will be thrown and the sniffer will return false def sniff( self, filename ): @@ -568,6 +596,14 @@ def set_peek( self, dataset, is_multi_byte=False ): if not dataset.dataset.purged: dataset.peek = "SQLite Database" + lines = ['SQLite Database'] + if dataset.metadata.tables: + for table in dataset.metadata.tables: + try: + lines.append('%s [%s]' % (table,dataset.metadata.table_row_count[table])) + except: + continue + dataset.peek = '\n'.join(lines) dataset.blurb = data.nice_size( dataset.get_size() ) else: dataset.peek = 'file does not exist' diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/galaxy/managers/api_keys.py --- /dev/null +++ b/lib/galaxy/managers/api_keys.py @@ -0,0 +1,26 @@ + + +class ApiKeyManager( object ): + + def __init__( self, app ): + self.app = app + + def create_api_key( self, user ): + guid = self.app.security.get_new_guid() + new_key = self.app.model.APIKeys() + new_key.user_id = user.id + new_key.key = guid + sa_session = self.app.model.context + sa_session.add( new_key ) + sa_session.flush() + return guid + + def get_or_create_api_key( self, user ): + # Logic Galaxy has always used - but it would appear to have a race + # condition. Worth fixing? Would kind of need a message queue to fix + # in multiple process mode. + if user.api_keys: + key = user.api_keys[0].key + else: + key = self.create_api_key( user ) + return key diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -69,7 +69,7 @@ from galaxy.model import Workflow from tool_shed.util import common_util from tool_shed.util import shed_util_common as suc -from .loader import load_tool, template_macro_params +from .loader import load_tool, template_macro_params, raw_tool_xml_tree, imported_macro_paths from .execute import execute as execute_job from .wrappers import ( ToolParameterValueWrapper, @@ -2989,6 +2989,23 @@ def get_default_history_by_trans( self, trans, create=False ): return trans.get_history( create=create ) + @classmethod + def get_externally_referenced_paths( self, path ): + """ Return relative paths to externally referenced files by the tool + described by file at `path`. External components should not assume things + about the structure of tool xml files (this is the tool's responsibility). + """ + tree = raw_tool_xml_tree(path) + root = tree.getroot() + external_paths = [] + for code_elem in root.findall( 'code' ): + external_path = code_elem.get( 'file' ) + if external_path: + external_paths.append( external_path ) + external_paths.extend( imported_macro_paths( root ) ) + # May also need to load external citation files as well at some point. + return external_paths + class OutputParameterJSONTool( Tool ): """ diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/galaxy/tools/loader.py --- a/lib/galaxy/tools/loader.py +++ b/lib/galaxy/tools/loader.py @@ -10,7 +10,7 @@ """ Loads tool from file system and preprocesses tool macros. """ - tree = parse_xml(path) + tree = raw_tool_xml_tree(path) root = tree.getroot() _import_macros(root, path) @@ -38,14 +38,31 @@ return param_dict +def raw_tool_xml_tree(path): + """ Load raw (no macro expansion) tree representation of tool represented + at the specified path. + """ + tree = parse_xml(path) + return tree + + +def imported_macro_paths(root): + macros_el = _macros_el(root) + return _imported_macro_paths_from_el(macros_el) + + def _import_macros(root, path): tool_dir = os.path.dirname(path) - macros_el = root.find('macros') + macros_el = _macros_el(root) if macros_el: macro_els = _load_macros(macros_el, tool_dir) _xml_set_children(macros_el, macro_els) +def _macros_el(root): + return root.find('macros') + + def _macros_of_type(root, type, el_func): macros_el = root.find('macros') macro_dict = {} @@ -159,6 +176,17 @@ def _load_imported_macros(macros_el, tool_dir): macros = [] + for tool_relative_import_path in _imported_macro_paths_from_el(macros_el): + import_path = \ + os.path.join(tool_dir, tool_relative_import_path) + file_macros = _load_macro_file(import_path, tool_dir) + macros.extend(file_macros) + + return macros + + +def _imported_macro_paths_from_el(macros_el): + imported_macro_paths = [] macro_import_els = [] if macros_el: macro_import_els = macros_el.findall("import") @@ -166,12 +194,8 @@ raw_import_path = macro_import_el.text tool_relative_import_path = \ os.path.basename(raw_import_path) # Sanitize this - import_path = \ - os.path.join(tool_dir, tool_relative_import_path) - file_macros = _load_macro_file(import_path, tool_dir) - macros.extend(file_macros) - - return macros + imported_macro_paths.append( tool_relative_import_path ) + return imported_macro_paths def _load_macro_file(path, tool_dir): diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/galaxy/util/topsort.py --- a/lib/galaxy/util/topsort.py +++ b/lib/galaxy/util/topsort.py @@ -12,12 +12,17 @@ topsort( [(1,2), (3,3)] ) -may return any of (but nothing other than) +Valid topological sorts would be any of (but nothing other than) [3, 1, 2] [1, 3, 2] [1, 2, 3] +... however this variant ensures that 'key' order (first element of +tuple) is preserved so the following will be result returned: + + [1, 3, 2] + because those are the permutations of the input elements that respect the "1 precedes 2" and "3 precedes 3" input constraints. Note that a constraint of the form (x, x) is really just a trick @@ -31,8 +36,9 @@ many methods to help analyze and break the cycles. This requires a good deal more code than topsort itself! """ +from galaxy.util.odict import odict as OrderedDict +from exceptions import Exception -from exceptions import Exception class CycleError(Exception): def __init__(self, sofar, numpreds, succs): @@ -83,7 +89,7 @@ def get_preds(self): if self.preds is not None: return self.preds - self.preds = preds = {} + self.preds = preds = OrderedDict() remaining_elts = self.get_elements() for x in remaining_elts: preds[x] = [] @@ -112,7 +118,7 @@ from random import choice x = choice(remaining_elts) answer = [] - index = {} + index = OrderedDict() in_answer = index.has_key while not in_answer(x): index[x] = len(answer) # index of x in answer @@ -124,8 +130,8 @@ return answer def topsort(pairlist): - numpreds = {} # elt -> # of predecessors - successors = {} # elt -> list of successors + numpreds = OrderedDict() # elt -> # of predecessors + successors = OrderedDict() # elt -> list of successors for first, second in pairlist: # make sure every elt is a key in numpreds if not numpreds.has_key(first): @@ -174,8 +180,8 @@ return answer def topsort_levels(pairlist): - numpreds = {} # elt -> # of predecessors - successors = {} # elt -> list of successors + numpreds = OrderedDict() # elt -> # of predecessors + successors = OrderedDict() # elt -> list of successors for first, second in pairlist: # make sure every elt is a key in numpreds if not numpreds.has_key(first): diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -13,6 +13,7 @@ from galaxy.web import url_for from galaxy.web.base import pluginframework +from galaxy.managers import api_keys import logging log = logging.getLogger( __name__ ) @@ -338,6 +339,19 @@ config = self.resource_parser.parse_config( trans, controller, param_confs, query_dict ) return config + def fill_template( self, trans, plugin, template_filename, **kwargs ): + # TODO: As part of a future note plugin registry effort - move this + # override and let VisualizationsRegistry just revert to using parent's + # fill_template. + if 'get_api_key' not in kwargs: + + def get_api_key(): + return api_keys.ApiKeyManager( trans.app ).get_or_create_api_key( trans.user ) + + kwargs[ 'get_api_key' ] = get_api_key + + return super( VisualizationsRegistry, self ).fill_template( trans, plugin, template_filename, **kwargs ) + # ------------------------------------------------------------------- parsing the config file class ParsingException( ValueError ): diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -37,6 +37,7 @@ from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation, HistoryDatasetAssociation +from galaxy.managers import api_keys from galaxy.datatypes.metadata import FileParameter from galaxy.tools.parameters import RuntimeValue, visit_input_values from galaxy.tools.parameters.basic import DataToolParameter @@ -286,16 +287,12 @@ class CreatesApiKeysMixin: """ Mixing centralizing logic for creating API keys for user objects. + + Deprecated - please use api_keys.ApiKeyManager for new development. """ def create_api_key( self, trans, user ): - guid = trans.app.security.get_new_guid() - new_key = trans.app.model.APIKeys() - new_key.user_id = user.id - new_key.key = guid - trans.sa_session.add( new_key ) - trans.sa_session.flush() - return guid + return api_keys.ApiKeyManager( trans.app ).create_api_key( user ) class SharableItemSecurityMixin: @@ -1693,8 +1690,18 @@ # the local Galaxy instance. Each tuple in the list of missing_tool_tups # will be ( tool_id, tool_name, tool_version ). missing_tool_tups = [] + supplied_steps = data[ 'steps' ] + # Try to iterate through imported workflow in such a way as to + # preserve step order. + step_indices = supplied_steps.keys() + try: + step_indices = sorted( step_indices, key=int ) + except ValueError: + # to defensive, were these ever or will they ever not be integers? + pass # First pass to build step objects and populate basic values - for step_dict in data[ 'steps' ].itervalues(): + for step_index in step_indices: + step_dict = supplied_steps[ step_index ] # Create the model class for the step step = model.WorkflowStep() steps.append( step ) diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/galaxy/web/base/pluginframework.py --- a/lib/galaxy/web/base/pluginframework.py +++ b/lib/galaxy/web/base/pluginframework.py @@ -588,6 +588,9 @@ ``plugin.template_path`` :returns: rendered template """ + if 'plugin_path' not in kwargs: + kwargs[ 'plugin_path'] = os.path.abspath( plugin.path ) + # defined here to be overridden return trans.fill_template( template_filename, template_lookup=plugin.template_lookup, **kwargs ) diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/galaxy/webapps/galaxy/api/authenticate.py --- a/lib/galaxy/webapps/galaxy/api/authenticate.py +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -15,14 +15,19 @@ from urllib import unquote from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy.managers import api_keys from galaxy import exceptions -from galaxy.web.base.controller import BaseAPIController, CreatesApiKeysMixin +from galaxy.web.base.controller import BaseAPIController import logging log = logging.getLogger( __name__ ) -class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ): +class AuthenticationController( BaseAPIController ): + + def __init__( self, app ): + super( AuthenticationController, self ).__init__( app ) + self.api_keys_manager = api_keys.ApiKeyManager( app ) @expose_api_anonymous def get_api_key( self, trans, **kwd ): @@ -47,10 +52,7 @@ user = user[0] is_valid_user = user.check_password( password ) if ( is_valid_user ): - if user.api_keys: - key = user.api_keys[0].key - else: - key = self.create_api_key( trans, user ) + key = self.api_keys_manager.get_or_create_api_key( user ) return dict( api_key=key ) else: raise exceptions.AuthenticationFailed() diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -53,6 +53,8 @@ self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "shed-tool-data" ), os.getcwd() ) self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) + self.integrated_tool_panel_config = resolve_path( kwargs.get( 'integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.root ) + self.builds_file_path = resolve_path( kwargs.get( "builds_file_path", os.path.join( self.tool_data_path, 'shared', 'ucsc', 'builds.txt') ), self.root ) self.len_file_path = resolve_path( kwargs.get( "len_file_path", os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ), self.root ) self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) # Install and test framework for testing tools contained in repositories. diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py @@ -5,6 +5,7 @@ from galaxy.model.orm import and_ from galaxy.util import listify from galaxy.tools.deps.resolvers import INDETERMINATE_DEPENDENCY +from tool_shed.util import basic_util from tool_shed.util import common_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util @@ -48,11 +49,12 @@ pass sa_session = app.install_model.context can_install_tool_dependency = False - tool_dependency = get_tool_dependency_by_name_version_type_repository( app, - tool_shed_repository, - tool_dependency_name, - tool_dependency_version, - tool_dependency_type ) + tool_dependency = \ + tool_dependency_util.get_tool_dependency_by_name_version_type_repository( app, + tool_shed_repository, + tool_dependency_name, + tool_dependency_version, + tool_dependency_type ) if tool_dependency.status == app.install_model.ToolDependency.installation_status.INSTALLING: # The tool dependency is in an Installing state, so we don't want to do anything to it. If the tool # dependency is being installed by someone else, we don't want to interfere with that. This assumes diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/tool_shed/galaxy_install/tools/data_manager.py --- a/lib/tool_shed/galaxy_install/tools/data_manager.py +++ b/lib/tool_shed/galaxy_install/tools/data_manager.py @@ -1,5 +1,6 @@ import logging import os +import threading from tool_shed.galaxy_install.tools import tool_panel_manager @@ -18,12 +19,19 @@ Persist the current in-memory list of config_elems to a file named by the value of config_filename. """ - fh = open( config_filename, 'wb' ) - fh.write( '<?xml version="1.0"?>\n<data_managers>\n' ) - for elem in config_elems: - fh.write( xml_util.xml_to_string( elem ) ) - fh.write( '</data_managers>\n' ) - fh.close() + lock = threading.Lock() + lock.acquire( True ) + try: + fh = open( config_filename, 'wb' ) + fh.write( '<?xml version="1.0"?>\n<data_managers>\n' ) + for elem in config_elems: + fh.write( xml_util.xml_to_string( elem ) ) + fh.write( '</data_managers>\n' ) + fh.close() + except Exception, e: + log.exception( "Exception in DataManagerHandler.data_manager_config_elems_to_xml_file: %s" % str( e ) ) + finally: + lock.release() def install_data_managers( self, shed_data_manager_conf_filename, metadata_dict, shed_config_dict, relative_install_dir, repository, repository_tools_tups ): diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/tool_shed/galaxy_install/tools/tool_panel_manager.py --- a/lib/tool_shed/galaxy_install/tools/tool_panel_manager.py +++ b/lib/tool_shed/galaxy_install/tools/tool_panel_manager.py @@ -1,7 +1,6 @@ import logging import os -import shutil -import tempfile +import threading import galaxy.tools from galaxy.tools.search import ToolBoxSearch @@ -90,15 +89,19 @@ Persist the current in-memory list of config_elems to a file named by the value of config_filename. """ - fd, filename = tempfile.mkstemp( prefix="tmp-toolshed-cetxf" ) - os.write( fd, '<?xml version="1.0"?>\n' ) - os.write( fd, '<toolbox tool_path="%s">\n' % str( tool_path ) ) - for elem in config_elems: - os.write( fd, '%s' % xml_util.xml_to_string( elem, use_indent=True ) ) - os.write( fd, '</toolbox>\n' ) - os.close( fd ) - shutil.move( filename, os.path.abspath( config_filename ) ) - os.chmod( config_filename, 0644 ) + lock = threading.Lock() + lock.acquire( True ) + try: + fh = open( config_filename, 'wb' ) + fh.write( '<?xml version="1.0"?>\n<toolbox tool_path="%s">\n' % str( tool_path ) ) + for elem in config_elems: + fh.write( xml_util.xml_to_string( elem, use_indent=True ) ) + fh.write( '</toolbox>\n' ) + fh.close() + except Exception, e: + log.exception( "Exception in ToolPanelManager.config_elems_to_xml_file: %s" % str( e ) ) + finally: + lock.release() def generate_tool_elem( self, tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ): diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -3,6 +3,7 @@ import os import tempfile +from galaxy.tools import Tool from galaxy.tools import parameters from galaxy.tools.parameters import dynamic_options @@ -311,15 +312,14 @@ message = '' tmp_tool_config = hg_util.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) if tmp_tool_config: - element_tree, error_message = xml_util.parse_xml( tmp_tool_config ) - if element_tree is None: + tool_element, error_message = xml_util.parse_xml( tmp_tool_config ) + if tool_element is None: return tool, message - element_tree_root = element_tree.getroot() - # Look for code files required by the tool config. + # Look for external files required by the tool config. tmp_code_files = [] - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) + external_paths = Tool.get_externally_referenced_paths( tmp_tool_config ) + for path in external_paths: + tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, path, work_dir ) if tmp_code_file_name: tmp_code_files.append( tmp_code_file_name ) tool, valid, message = self.load_tool_from_config( repository_id, tmp_tool_config ) diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var DrawResults=function(options){this.incomplete_features=options.incomplete_features;this.feature_mapper=options.feature_mapper};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=_.extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};_.extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords,incomplete_features=[];for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((this.mode==="Dense"||slot!==null)&&(feature_start<view_end&&feature_end>view_start)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1]);if(feature_start<view_start||feature_end>view_end){incomplete_features.push(feature)}}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return new DrawResults({incomplete_features:incomplete_features,feature_mapper:feature_mapper})},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};_.extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};_.extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.detail_block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),draw_height=(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),rect_y=y_start+1,paint_utils=new ReadPainterUtils(ctx,draw_height,w_scale,mode),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,rect_y,s_end-s_start,draw_height)}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,rect_y,Math.max(1,Math.round(w_scale)),draw_height)}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,rect_y,cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+9,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+9,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};_.extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};_.extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};_.extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);paint_utils.row_height=row_height;draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var DrawResults=function(options){this.incomplete_features=options.incomplete_features;this.feature_mapper=options.feature_mapper};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=_.extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.ceil((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};_.extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords,incomplete_features=[];for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((this.mode==="Dense"||slot!==null)&&(feature_start<view_end&&feature_end>view_start)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1]);if(feature_start<view_start||feature_end>view_end){incomplete_features.push(feature)}}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return new DrawResults({incomplete_features:incomplete_features,feature_mapper:feature_mapper})},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};_.extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};_.extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset},get_draw_coord=function(sequence_coord){return Math.floor(Math.max(0,(sequence_coord-tile_low-0.5)*w_scale))};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.detail_block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),draw_height=(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),rect_y=y_start+1,paint_utils=new ReadPainterUtils(ctx,draw_height,w_scale,mode),drawing_blocks=[],s_start,s_end;var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){s_start=get_draw_coord(feature_start+block[0]);s_end=get_draw_coord(feature_start+block[1]);if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,rect_y,s_end-s_start,draw_height)}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset;s_start=get_draw_coord(seq_start);s_end=get_draw_coord(seq_start+cig_len);if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,rect_y,Math.max(1,Math.round(w_scale)),draw_height)}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,rect_y,cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+9,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+9,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};_.extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};_.extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};_.extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);paint_utils.row_height=row_height;draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div();var ac=this;ad.config.on("change",function(){ac.changed()})},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.other_tiles_features_drawn={};this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*Q)),ak,am,ah,ai=[],ao=[];while((ac*Q*af)<ag){ak=Math.floor(ac*Q*af);am=new w.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(Q*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(av){var aw=ab.omit(ac,ab.map(av.incomplete_features,function(ay){return ay[0]}));aw=ab.omit(aw,ab.keys(av.other_tiles_features_drawn));if(ab.size(aw)!==0){var at={data:ab.values(aw)},au=ap.view.canvas_manager.new_canvas(),ar=au.getContext("2d");au.height=Math.max(av.canvas.height,ap.get_canvas_height(at,av.mode,av.w_scale,100));au.width=av.canvas.width;ar.drawImage(av.canvas,0,0);ar.translate(ah.left_offset,0);var ax=ap.draw_tile(at,ar,av.mode,av.region,av.w_scale,av.seq_data);$(av.canvas).replaceWith($(ax.canvas));av.canvas=au;ab.extend(av.other_tiles_features_drawn,ac)}})}if(ah.filters_manager){var ag=ah.filters_manager.filters,ak;for(ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<ao.length;ai++){if(ao[ai].data.length){al=ao[ai].data[0];for(ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(ao[0] instanceof M){var ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new b(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ad,ac,ae){c.call(this,ad,ac,ae);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var n=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div();var ac=this;ad.config.on("change",function(){ac.changed()})},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.other_tiles_features_drawn={};this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*Q)),ak=Math.floor(ac*Q*af),am,ah,ai=[],ao=[];while((ac*Q*af)<ag){am=new w.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(Q*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1;ak=am.get("end")}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=Math.round((ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah);if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(av){var aw=ab.omit(ac,ab.map(av.incomplete_features,function(ay){return ay[0]}));aw=ab.omit(aw,ab.keys(av.other_tiles_features_drawn));if(ab.size(aw)!==0){var at={data:ab.values(aw)},au=ap.view.canvas_manager.new_canvas(),ar=au.getContext("2d");au.height=Math.max(av.canvas.height,ap.get_canvas_height(at,av.mode,av.w_scale,100));au.width=av.canvas.width;ar.drawImage(av.canvas,0,0);ar.translate(ah.left_offset,0);var ax=ap.draw_tile(at,ar,av.mode,av.region,av.w_scale,av.seq_data);$(av.canvas).replaceWith($(ax.canvas));av.canvas=au;ab.extend(av.other_tiles_features_drawn,ac)}})}if(ah.filters_manager){var ag=ah.filters_manager.filters,ak;for(ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<ao.length;ai++){if(ao[ai].data.length){al=ao[ai].data[0];for(ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(ao[0] instanceof M){var ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary 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d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -196,7 +196,7 @@ ctx.fillStyle = ctx.strokeStyle = painter_color; top_overflow = bot_overflow = false; - x_scaled = Math.round((data[i][0] - view_start) * w_scale); + x_scaled = Math.ceil((data[i][0] - view_start) * w_scale); y = data[i][1]; // Process Y (scaler) value. @@ -771,6 +771,11 @@ offset += cig_len; } return offset; + }, + // Gets drawing coordinate for a sequence coordinate. Assumes closure variables w_scale and tile_low. + get_draw_coord = function(sequence_coord) { + // -0.5 to offset sequence between bases. + return Math.floor( Math.max(0, (sequence_coord - tile_low - 0.5) * w_scale) ); }; ctx.textAlign = "center"; @@ -784,7 +789,9 @@ draw_height = (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT), rect_y = y_start + 1, paint_utils = new ReadPainterUtils(ctx, draw_height, w_scale, mode), - drawing_blocks = []; + drawing_blocks = [], + s_start, + s_end; // Keep list of items that need to be drawn on top of initial drawing layer. var draw_last = []; @@ -799,10 +806,9 @@ var block = drawing_blocks[i]; if (is_overlap([feature_start + block[0], feature_start + block[1]], tile_region)) { - // -0.5 to offset sequence between bases. - var s_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start + block[0] - tile_low - 0.5) * w_scale) ), - s_end = Math.floor( Math.max(0, (feature_start + block[1] - tile_low - 0.5) * w_scale) ); - + s_start = get_draw_coord(feature_start + block[0]); + s_end = get_draw_coord(feature_start + block[1]); + // Make sure that block is drawn even if it too small to be rendered officially; in this case, // read is drawn at 1px. // TODO: need to ensure that s_start, s_end are calculated the same for both slotting @@ -823,11 +829,10 @@ cig_op = "MIDNSHP=X"[ cig[0] ], cig_len = cig[1]; - var seq_start = feature_start + base_offset, - // -0.5 to offset sequence between bases. - s_start = Math.floor( Math.max(-0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ), - s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low - 0.5) * w_scale) ); - + var seq_start = feature_start + base_offset; + s_start = get_draw_coord(seq_start); + s_end = get_draw_coord(seq_start + cig_len); + // Skip feature if it's not in tile. if (!is_overlap([seq_start, seq_start + cig_len], tile_region)) { // Update offsets. diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2758,7 +2758,8 @@ var // Index of first tile that overlaps visible region. tile_index = Math.floor( low / (resolution * TILE_SIZE) ), - tile_low, + // Base that first tile starts with. + tile_low = Math.floor(tile_index * TILE_SIZE * resolution), tile_region, tile_promise, tile_promises = [], @@ -2766,7 +2767,6 @@ // Draw tiles. while ( ( tile_index * TILE_SIZE * resolution ) < high ) { // Get tile region. - tile_low = Math.floor(tile_index * TILE_SIZE * resolution); tile_region = new visualization.GenomeRegion({ chrom: this.view.chrom, start: tile_low, @@ -2778,7 +2778,10 @@ $.when(tile_promise).then(function(tile) { tiles.push(tile); }); + + // Go to next tile. tile_index += 1; + tile_low = tile_region.get('end'); } // Step (c) for (re)moving tiles when clear_after is false. @@ -3081,12 +3084,12 @@ tile.predisplay_actions(); // Position tile element based on current viewport. - var left = ( tile.low - (this.is_overview? this.view.max_low : this.view.low) ) * w_scale; + var left = Math.round( ( tile.low - (this.is_overview? this.view.max_low : this.view.low) ) * w_scale ); if (this.left_offset) { left -= this.left_offset; } tile_element.css('left', left); - + if ( tile_element.hasClass("remove") ) { // Step (b) for (re)moving tiles. See _draw() function for description of algorithm // for removing tiles. diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 test/api/test_authenticate.py --- /dev/null +++ b/test/api/test_authenticate.py @@ -0,0 +1,29 @@ +import base64 + +from base.interactor import get_request +from base import api + + +TEST_USER_EMAIL = "auth_user_test@bx.psu.edu" +TEST_USER_PASSWORD = "testpassword1" + + +class AuthenticationApiTestCase( api.ApiTestCase ): + + def test_auth( self ): + self._setup_user( TEST_USER_EMAIL, TEST_USER_PASSWORD ) + baseauth_url = self._api_url( "authenticate/baseauth", use_key=False ) + unencoded_credentials = "%s:%s" % ( TEST_USER_EMAIL, TEST_USER_PASSWORD ) + authorization = base64.b64encode(unencoded_credentials) + headers = { + "Authorization": authorization, + } + auth_response = get_request( baseauth_url, headers=headers ) + self._assert_status_code_is( auth_response, 200 ) + auth_dict = auth_response.json() + self._assert_has_keys( auth_dict, "api_key" ) + + # Verify key... + random_api_url = self._api_url( "users", use_key=False ) + random_api_response = get_request( random_api_url, params=dict( key=auth_dict[ "api_key" ] ) ) + self._assert_status_code_is( random_api_response, 200 ) diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 test/api/test_users.py --- /dev/null +++ b/test/api/test_users.py @@ -0,0 +1,24 @@ +from base import api + +TEST_USER_EMAIL = "user_for_users_index_test@bx.psu.edu" + + +class UsersApiTestCase( api.ApiTestCase ): + + def test_index( self ): + self._setup_user( TEST_USER_EMAIL ) + all_users_response = self._get( "users", admin=True ) + self._assert_status_code_is( all_users_response, 200 ) + all_users = all_users_response.json() + # New user is in list + assert len( [ u for u in all_users if u[ "email" ] == TEST_USER_EMAIL ] ) == 1 + # Request made from admin user, so should at least self and this + # new user. + assert len( all_users ) > 1 + + def test_index_only_self_for_nonadmins( self ): + self._setup_user( TEST_USER_EMAIL ) + with self._different_user( ): + all_users_response = self._get( "users" ) + # Non admin users can only see themselves + assert len( all_users_response.json() ) == 1 diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 test/api/test_workflow_topoambigouity.ga --- /dev/null +++ b/test/api/test_workflow_topoambigouity.ga @@ -0,0 +1,471 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "topoambigouity", + "steps": { + "0": { + "annotation": "", + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "l" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 193.7604217529297, + "top": 156.00001525878906 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"l\"}", + "tool_version": null, + "type": "data_input", + 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"user_outputs": [] + }, + "10": { + "annotation": "", + "id": 10, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "e" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 683.3750462532043, + "top": 600.5972752571106 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"e\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "11": { + "annotation": "", + "id": 11, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "f" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 692.3854222297668, + "top": 694.5729222297668 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"f\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "12": { + "annotation": "", + "id": 12, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "g" + } + ], + "name": "Input dataset", + "outputs": [], + "position": { + "left": 681.5173802375793, + "top": 760.7014012336731 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"g\"}", + "tool_version": null, + "type": "data_input", + "user_outputs": [] + }, + "13": { + "annotation": "", + "id": 13, + "input_connections": { + "input1": { + "id": 3, + "output_name": "output" + }, + "queries_0|input2": { + "id": 4, + "output_name": "output" + }, + "queries_1|input2": { + "id": 5, + "output_name": "output" + }, + "queries_2|input2": { + "id": 6, + "output_name": "output" + } + }, + "inputs": [], + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 660.3368382453918, + "top": 404.57295274734497 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "cat1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}, {\\\"input2\\\": null, \\\"__index__\\\": 1}, {\\\"input2\\\": null, \\\"__index__\\\": 2}]\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "14": { + "annotation": "", + "id": 14, + "input_connections": { + "input1": { + "id": 13, + "output_name": "out_file1" + }, + "queries_0|input2": { + "id": 10, + "output_name": "output" + }, + "queries_1|input2": { + "id": 11, + "output_name": "output" + }, + "queries_2|input2": { + "id": 12, + "output_name": "output" + } + }, + "inputs": [], + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 915.5451512336731, + "top": 394.7639012336731 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "cat1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}, {\\\"input2\\\": null, \\\"__index__\\\": 1}, {\\\"input2\\\": null, \\\"__index__\\\": 2}]\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "15": { + "annotation": "", + "id": 15, + "input_connections": { + "input1": { + "id": 14, + "output_name": "out_file1" + }, + "queries_0|input2": { + "id": 8, + "output_name": "output" + }, + "queries_1|input2": { + "id": 9, + "output_name": "output" + }, + "queries_2|input2": { + "id": 7, + "output_name": "output" + } + }, + "inputs": [], + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 217.61113023757935, + "top": 760.8055882453918 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "cat1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}, {\\\"input2\\\": null, \\\"__index__\\\": 1}, {\\\"input2\\\": null, \\\"__index__\\\": 2}]\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "16": { + "annotation": "", + "id": 16, + "input_connections": { + "input1": { + "id": 0, + "output_name": "output" + }, + "queries_0|input2": { + "id": 1, + "output_name": "output" + }, + "queries_1|input2": { + "id": 2, + "output_name": "output" + }, + "queries_2|input2": { + "id": 15, + "output_name": "out_file1" + } + }, + "inputs": [], + "name": "Concatenate datasets", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 462.9583592414856, + "top": 194.15626573562622 + }, + "post_job_actions": {}, + "tool_errors": null, + "tool_id": "cat1", + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}, {\\\"input2\\\": null, \\\"__index__\\\": 1}, {\\\"input2\\\": null, \\\"__index__\\\": 2}]\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + } + } +} \ No newline at end of file diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -105,6 +105,31 @@ self.dataset_populator.wait_for_history( history_id, assert_ok=True ) self.assertEquals("1 2 3\n4 5 6\n7 8 9\n0 a b\n", self.dataset_populator.get_history_dataset_content( history_id ) ) + def test_workflow_stability( self ): + # Run this index stability test with following command: + # ./run_tests.sh test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_stability + from pkg_resources import resource_string + num_tests = 1 + for workflow_file in [ "test_workflow_topoambigouity.ga", "test_workflow_topoambigouity_auto_laidout.ga" ]: + workflow_str = resource_string( __name__, workflow_file ) + workflow = self.workflow_populator.load_workflow( "test1", content=workflow_str ) + last_step_map = self._step_map( workflow ) + for i in range(num_tests): + uploaded_workflow_id = self.workflow_populator.create_workflow( workflow ) + download_response = self._get( "workflows/%s/download" % uploaded_workflow_id ) + downloaded_workflow = download_response.json() + step_map = self._step_map(downloaded_workflow) + assert step_map == last_step_map + last_step_map = step_map + + def _step_map(self, workflow): + # Build dict mapping 'tep index to input name. + step_map = {} + for step_index, step in workflow["steps"].iteritems(): + if step[ "type" ] == "data_input": + step_map[step_index] = step["inputs"][0]["name"] + return step_map + @skip_without_tool( "cat1" ) def test_extract_from_history( self ): history_id = self.dataset_populator.new_history() diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 test/base/api.py --- a/test/base/api.py +++ b/test/base/api.py @@ -41,8 +41,8 @@ url = "%s?%s" % ( url, query ) return url - def _setup_user( self, email ): - self.galaxy_interactor.ensure_user_with_email(email) + def _setup_user( self, email, password=None ): + self.galaxy_interactor.ensure_user_with_email( email, password=password ) users = self._get( "users", admin=True ).json() user = [ user for user in users if user["email"] == email ][0] return user diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -325,16 +325,17 @@ ) return self._post( "tools", files=files, data=data ) - def ensure_user_with_email( self, email ): + def ensure_user_with_email( self, email, password=None ): admin_key = self.master_api_key all_users = self._get( 'users', key=admin_key ).json() try: test_user = [ user for user in all_users if user["email"] == email ][0] except IndexError: username = re.sub('[^a-z-]', '--', email.lower()) + password = password or 'testpass' data = dict( email=email, - password='testuser', + password=password, username=username, ) test_user = self._post( 'users', data, key=admin_key ).json() diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 test/unit/test_topsort.py --- /dev/null +++ b/test/unit/test_topsort.py @@ -0,0 +1,39 @@ +from galaxy.util import topsort + + +def test_topsort_level_stability(): + data = [ + (0, 2), + (1, 2), + (2, 3), + (2, 4), + (3, 4), + (3, 5), + (6, 2), + ] + assert topsort.topsort_levels( data )[ 0 ] == [ 0, 1, 6 ] + assert topsort.topsort( data ) == [ 0, 1, 6, 2, 3, 4, 5 ] + # Swap first two edges - so 1 appears first + swap( data, 0, 1 ) + assert topsort.topsort_levels( data )[ 0 ] == [ 1, 0, 6 ] + assert topsort.topsort( data ) == [ 1, 0, 6, 2, 3, 4, 5 ] + + # Shouldn't really affect sorting of 1 0 6 + swap( data, 3, 4 ) + assert topsort.topsort_levels( data )[ 0 ] == [ 1, 0, 6 ] + assert topsort.topsort( data ) == [ 1, 0, 6, 2, 3, 4, 5 ] + + # Place 0 before 6 in original list + swap( data, 1, 6 ) + assert topsort.topsort_levels( data )[ 0 ] == [ 1, 6, 0 ] + assert topsort.topsort( data ) == [ 1, 6, 0, 2, 3, 4, 5 ] + + +def test_topsort_doc(): + assert topsort.topsort([(1, 2), (3, 3)]) == [1, 3, 2] + + +def swap(lst, i, j): + tmp = lst[j] + lst[j] = lst[i] + lst[i] = tmp diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 test/unit/tools/test_tool_external_files.py --- /dev/null +++ b/test/unit/tools/test_tool_external_files.py @@ -0,0 +1,30 @@ +""" Unit test logic related to finding externally referenced files in tool +descriptions. +""" +import tempfile +import os +import shutil +from galaxy.tools import Tool + + +def test_finds_external_code_file(): + assert __external_files("""<tool><code file="foo.py" /></tool>""") == ["foo.py"] + + +def test_finds_skips_empty_code_file_attribute(): + assert __external_files("""<tool><code /></tool>""") == [] + + +def test_finds_external_macro_file(): + assert __external_files("""<tool><macros><import>cool_macros.xml</import></macros></tool>""") == ["cool_macros.xml"] + + +def __external_files(contents): + base_path = tempfile.mkdtemp() + try: + tool_path = os.path.join(base_path, "tool.xml") + with open(tool_path, "w") as f: + f.write(contents) + return Tool.get_externally_referenced_paths(tool_path) + finally: + shutil.rmtree(base_path) diff -r f521140aef303991b1ad07edec495d698275e24c -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 tool_shed_wsgi.ini.sample --- a/tool_shed_wsgi.ini.sample +++ b/tool_shed_wsgi.ini.sample @@ -36,6 +36,9 @@ # Temporary storage for additional datasets, this should be shared through the cluster new_file_path = database/tmp +# File containing old-style genome builds +#builds_file_path = tool-data/shared/ucsc/builds.txt + # Session support (beaker) use_beaker_session = True session_type = memory https://bitbucket.org/galaxy/galaxy-central/commits/e08ba0b8a7d8/ Changeset: e08ba0b8a7d8 User: martenson Date: 2014-08-05 20:37:18 Summary: bugfix showiong permissions of the upper folder insted of the selected one Affected #: 4 files diff -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 -r e08ba0b8a7d8a5fbb6d5460e7986c4c32264338f static/scripts/mvc/library/library-folder-view.js --- a/static/scripts/mvc/library/library-folder-view.js +++ b/static/scripts/mvc/library/library-folder-view.js @@ -255,7 +255,7 @@ tmpl_array.push(' <div id="library_toolbar">'); - tmpl_array.push(' <a href="#/folders/<%= folder.get("id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the folder contents" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Parent folder</span></button></a>'); + tmpl_array.push(' <a href="#/folders/<%= folder.get("parent_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Parent folder</span></button></a>'); tmpl_array.push(' </div>'); tmpl_array.push('<h1>Folder: <%= _.escape(folder.get("name")) %></h1>'); @@ -284,7 +284,7 @@ tmpl_array.push('<div id="modify_perm" class="modify_perm roles-selection"></div>'); tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this folder (name, etc.).</div>'); - tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); + tmpl_array.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>'); tmpl_array.push('</div>'); diff -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 -r e08ba0b8a7d8a5fbb6d5460e7986c4c32264338f static/scripts/mvc/library/library-folderrow-view.js --- a/static/scripts/mvc/library/library-folderrow-view.js +++ b/static/scripts/mvc/library/library-folderrow-view.js @@ -94,7 +94,7 @@ tmpl_array.push(' <td></td>'); tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated tmpl_array.push(' <td>'); - tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#/folders/<%- content_item.get("folder_id") %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-folder-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>'); + tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#/folders/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-folder-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>'); tmpl_array.push(' </td>'); tmpl_array.push('</tr>'); diff -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 -r e08ba0b8a7d8a5fbb6d5460e7986c4c32264338f static/scripts/packed/mvc/library/library-folder-view.js --- a/static/scripts/packed/mvc/library/library-folder-view.js +++ b/static/scripts/packed/mvc/library/library-folder-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchFolder()}},fetchFolder:function(e){this.options=_.extend(this.options,e);this.model=new c.FolderAsModel({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateFolder();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},shareFolder:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateFolderPermissions();this.$el.html(g({folder:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/folders/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while fetching folder permissions. :(")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f]+":"+g[f])}return e},prepareSelectBoxes:function(h){this.options=_.extend(this.options,h);var f=this.options.fetched_permissions;var g=this;var i=this._serializeRoles(f.add_library_item_role_list);var j=this._serializeRoles(f.manage_folder_role_list);var e=this._serializeRoles(f.modify_folder_role_list);g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",i,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",j,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",e,false))},_createSelectOptions:function(e,j,h){var i={minimumInputLength:0,css:j,multiple:true,placeholder:"Click to select a role",container:e.$el.find("#"+j),ajax:{url:"/api/folders/"+e.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(k,l){return{q:k,page_limit:10,page:l}},results:function(m,l){var k=(l*10)<m.total;return{results:m.roles,more:k}}},formatResult:function f(k){return k.name+" type: "+k.type},formatSelection:function g(k){return k.name},initSelection:function(k,m){var l=[];$(k.val().split(",")).each(function(){var n=this.split(":");l.push({id:n[1],name:n[1]})});m(l)},initialData:h.join(","),dropdownCssClass:"bigdrop"};return i},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var e=this._extractIds(this.addSelectObject.$el.select2("data"));var i=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post("/api/folders/"+g.id+"/permissions?action=set_permissions",{"add_ids[]":e,"manage_ids[]":i,"modify_ids[]":f,}).done(function(j){g.showPermissions({fetched_permissions:j});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting folder permissions :(")})},templateFolder:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateFolderPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#/folders/<%= folder.get("id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the folder contents" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Parent folder</span></button></a>');e.push(" </div>");e.push('<h1>Folder: <%= _.escape(folder.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Folder permissions</h2>");e.push("<h4>Roles that can manage permissions on this folder</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this folder.</div>');e.push("<h4>Roles that can add items to this folder</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).</div>');e.push("<h4>Roles that can modify this folder</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this folder (name, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{FolderView:b}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchFolder()}},fetchFolder:function(e){this.options=_.extend(this.options,e);this.model=new c.FolderAsModel({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateFolder();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},shareFolder:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateFolderPermissions();this.$el.html(g({folder:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/folders/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while fetching folder permissions. :(")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f]+":"+g[f])}return e},prepareSelectBoxes:function(h){this.options=_.extend(this.options,h);var f=this.options.fetched_permissions;var g=this;var i=this._serializeRoles(f.add_library_item_role_list);var j=this._serializeRoles(f.manage_folder_role_list);var e=this._serializeRoles(f.modify_folder_role_list);g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",i,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",j,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",e,false))},_createSelectOptions:function(e,j,h){var i={minimumInputLength:0,css:j,multiple:true,placeholder:"Click to select a role",container:e.$el.find("#"+j),ajax:{url:"/api/folders/"+e.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(k,l){return{q:k,page_limit:10,page:l}},results:function(m,l){var k=(l*10)<m.total;return{results:m.roles,more:k}}},formatResult:function f(k){return k.name+" type: "+k.type},formatSelection:function g(k){return k.name},initSelection:function(k,m){var l=[];$(k.val().split(",")).each(function(){var n=this.split(":");l.push({id:n[1],name:n[1]})});m(l)},initialData:h.join(","),dropdownCssClass:"bigdrop"};return i},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var e=this._extractIds(this.addSelectObject.$el.select2("data"));var i=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post("/api/folders/"+g.id+"/permissions?action=set_permissions",{"add_ids[]":e,"manage_ids[]":i,"modify_ids[]":f,}).done(function(j){g.showPermissions({fetched_permissions:j});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting folder permissions :(")})},templateFolder:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateFolderPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#/folders/<%= folder.get("parent_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Parent folder</span></button></a>');e.push(" </div>");e.push('<h1>Folder: <%= _.escape(folder.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Folder permissions</h2>");e.push("<h4>Roles that can manage permissions on this folder</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this folder.</div>');e.push("<h4>Roles that can add items to this folder</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).</div>');e.push("<h4>Roles that can modify this folder</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this folder (name, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{FolderView:b}}); \ No newline at end of file diff -r 9f52741f8c34c2dfcb2cdd74e54fc54d8ae4ff50 -r e08ba0b8a7d8a5fbb6d5460e7986c4c32264338f static/scripts/packed/mvc/library/library-folderrow-view.js --- a/static/scripts/packed/mvc/library/library-folderrow-view.js +++ b/static/scripts/packed/mvc/library/library-folderrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(c,e,f,d,b){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(g){this.render(g)},render:function(g){var h=null;if(g.get("type")==="folder"){this.options.type="folder";h=this.templateRowFolder()}else{this.options.type="file";if(g.get("deleted")){h=this.templateRowDeletedFile()}else{h=this.templateRowFile()}}this.setElement(h({content_item:g}));this.$el.show();return this},showDatasetDetails:function(){Galaxy.libraries.datasetView=new b.LibraryDatasetView({id:this.id})},undelete_dataset:function(i){$(".tooltip").hide();var h=this;var g=$(i.target).closest("tr")[0].id;var j=Galaxy.libraries.folderListView.collection.get(g);j.url=j.urlRoot+j.id+"?undelete=true";j.destroy({success:function(l,k){Galaxy.libraries.folderListView.collection.remove(g);var m=new d.Item(k);Galaxy.libraries.folderListView.collection.add(m);f.success("Dataset undeleted. Click this to see it.","",{onclick:function(){h.showDatasetDetails()}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error("Dataset was not undeleted. "+k.responseJSON.err_msg)}else{f.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light library-row" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td>");tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#/folders/<%- content_item.get("folder_id") %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-folder-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push(" </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light library-row" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td>");tmpl_array.push(' <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');tmpl_array.push(' <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push(" </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))}});return{FolderRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-dataset-view"],function(c,e,f,d,b){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(g){this.render(g)},render:function(g){var h=null;if(g.get("type")==="folder"){this.options.type="folder";h=this.templateRowFolder()}else{this.options.type="file";if(g.get("deleted")){h=this.templateRowDeletedFile()}else{h=this.templateRowFile()}}this.setElement(h({content_item:g}));this.$el.show();return this},showDatasetDetails:function(){Galaxy.libraries.datasetView=new b.LibraryDatasetView({id:this.id})},undelete_dataset:function(i){$(".tooltip").hide();var h=this;var g=$(i.target).closest("tr")[0].id;var j=Galaxy.libraries.folderListView.collection.get(g);j.url=j.urlRoot+j.id+"?undelete=true";j.destroy({success:function(l,k){Galaxy.libraries.folderListView.collection.remove(g);var m=new d.Item(k);Galaxy.libraries.folderListView.collection.add(m);f.success("Dataset undeleted. Click this to see it.","",{onclick:function(){h.showDatasetDetails()}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error("Dataset was not undeleted. "+k.responseJSON.err_msg)}else{f.error("An error occured! Dataset was not undeleted. Please try again.")}}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light library-row" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td>");tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#/folders/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-folder-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push(" </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light library-row" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td>");tmpl_array.push(' <% if (content_item.get("is_unrestricted")) { %><span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("is_private")) { %><span data-toggle="tooltip" data-placement="top" title="Private dataset" style="color:grey;" class="fa fa-key fa-lg"></span><% } %>');tmpl_array.push(' <% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %><span data-toggle="tooltip" data-placement="top" title="Restricted dataset" style="color:grey;" class="fa fa-shield fa-lg"></span><% } %>');tmpl_array.push(' <% if (content_item.get("can_manage")) { %><a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn show_on_hover" title="Manage permissions" style="display:none;"><span class="fa fa-group"></span></button></a><% } %>');tmpl_array.push(" </td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none; margin-left:1em;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))}});return{FolderRowView:a}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/461b62549cd9/ Changeset: 461b62549cd9 User: martenson Date: 2014-08-06 18:39:43 Summary: shortening of long desc/synopsis of libraries, button with library information available within folders Affected #: 6 files diff -r e08ba0b8a7d8a5fbb6d5460e7986c4c32264338f -r 461b62549cd9cf48965c004649634446d83883d1 static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -287,10 +287,6 @@ $row.find('.fa-file').removeClass('fa-file').addClass('fa-file-o'); }, -// MMMMMMMMMMMMMMMMMM -// === TEMPLATES ==== -// MMMMMMMMMMMMMMMMMM - templateFolder : function (){ var tmpl_array = []; @@ -330,7 +326,7 @@ tmpl_array.push(' </tbody>'); tmpl_array.push('</table>'); - tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>'); + tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>'); return _.template(tmpl_array.join('')); } diff -r e08ba0b8a7d8a5fbb6d5460e7986c4c32264338f -r 461b62549cd9cf48965c004649634446d83883d1 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -16,6 +16,7 @@ 'click #toolbtn_bulk_import' : 'modalBulkImport', 'click .toolbtn_add_files' : 'addFilesToFolderModal', 'click #include_deleted_datasets_chk' : 'checkIncludeDeleted', + 'click #toolbtn_show_libinfo' : 'showLibInfo', 'click #toolbtn_bulk_delete' : 'deleteSelectedDatasets' }, @@ -513,34 +514,59 @@ }); }, + showLibInfo: function(){ + var self = this; + var template = this.templateLibInfoInModal(); + this.modal = Galaxy.modal; + this.modal.show({ + closing_events : true, + title : 'Library Information', + body : template({library:library}), + buttons : { + 'Close' : function() {Galaxy.modal.hide();} + } + }); + }, + templateToolBar: function(){ tmpl_array = []; - // CONTAINER + // CONTAINER START tmpl_array.push('<div class="library_style_container">'); - // TOOLBAR - tmpl_array.push('<div id="library_toolbar">'); - tmpl_array.push('<span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>'); - tmpl_array.push('<div class="btn-group add-library-items" style="display:none;">'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>'); - tmpl_array.push('</div>'); + // TOOLBAR START + tmpl_array.push(' <div id="library_toolbar">'); + tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>'); + tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>'); + tmpl_array.push(' </div>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>'); tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">'); - tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); - tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>'); - tmpl_array.push(' </button>'); - tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); - tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); - tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); - tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); - tmpl_array.push(' </ul>'); + tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>'); + tmpl_array.push(' </button>'); + tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); + tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); + tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); + tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); + tmpl_array.push(' </ul>'); tmpl_array.push(' </div>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>'); - tmpl_array.push(' </div>'); - tmpl_array.push(' <div id="folder_items_element">'); - // library items will append here - tmpl_array.push(' </div>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>'); + tmpl_array.push(' </div>'); + // TOOLBAR END + tmpl_array.push(' <div id="folder_items_element">'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + // CONTAINER END + + return _.template(tmpl_array.join('')); + }, + + templateLibInfoInModal: function(){ + tmpl_array = []; + + tmpl_array.push('<div id="lif_info_modal">'); tmpl_array.push('</div>'); return _.template(tmpl_array.join('')); diff -r e08ba0b8a7d8a5fbb6d5460e7986c4c32264338f -r 461b62549cd9cf48965c004649634446d83883d1 static/scripts/mvc/library/library-libraryrow-view.js --- a/static/scripts/mvc/library/library-libraryrow-view.js +++ b/static/scripts/mvc/library/library-libraryrow-view.js @@ -118,7 +118,6 @@ /* User clicked the 'cancel' button so we render normal rowView */ cancel_library_modification: function(){ - mod_toastr.info('Modifications canceled'); this.edit_mode = false; this.repaint(); }, @@ -238,12 +237,31 @@ tmpl_array.push(' <% } else { %>'); tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>'); tmpl_array.push(' <% } %>'); - tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); - tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); + + tmpl_array.push(' <% if(library.get("description")) { %>'); + tmpl_array.push(' <% if( (library.get("description")).length> 80 ) { %>'); + tmpl_array.push(' <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("description")) %>"><%= _.escape(library.get("description")).substring(0, 80) + "..." %></td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td><%= _.escape(library.get("description"))%></td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if(library.get("synopsis")) { %>'); + tmpl_array.push(' <% if( (library.get("synopsis")).length> 120 ) { %>'); + tmpl_array.push(' <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("synopsis")) %>"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %></td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td><%= _.escape(library.get("synopsis"))%></td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% } else if(edit_mode){ %>'); - tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>'); - tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>'); - tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>'); + tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_name" placeholder="name" ><%- library.get("name") %></textarea></td>'); + tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_description" placeholder="description" ><%- library.get("description") %></textarea></td>'); + tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_synopsis" placeholder="synopsis" ><%- library.get("synopsis") %></textarea></td>'); tmpl_array.push(' <% } %>'); tmpl_array.push(' <td class="right-center">'); tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>'); diff -r e08ba0b8a7d8a5fbb6d5460e7986c4c32264338f -r 461b62549cd9cf48965c004649634446d83883d1 static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r e08ba0b8a7d8a5fbb6d5460e7986c4c32264338f -r 461b62549cd9cf48965c004649634446d83883d1 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=false;var f=true;if(Galaxy.currUser){i=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}var h=this.templateToolBar();this.$el.html(h({id:this.options.id,admin_user:i,anonym:f}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var f=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new c.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";f.push(m)}this.options.chain_call_control.total_number=f.length;var g="/api/histories/"+k+"/set_as_current";$.ajax({url:g,type:"PUT"});this.chainCall(f,n)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('<div id="library_toolbar">');tmpl_array.push('<span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>');tmpl_array.push('<div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("</div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=false;var f=true;if(Galaxy.currUser){i=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}var h=this.templateToolBar();this.$el.html(h({id:this.options.id,admin_user:i,anonym:f}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var f=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new c.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";f.push(m)}this.options.chain_call_control.total_number=f.length;var g="/api/histories/"+k+"/set_as_current";$.ajax({url:g,type:"PUT"});this.chainCall(f,n)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},showLibInfo:function(){var f=this;var g=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:g({library:library}),buttons:{Close:function(){Galaxy.modal.hide()}}})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>');tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file diff -r e08ba0b8a7d8a5fbb6d5460e7986c4c32264338f -r 461b62549cd9cf48965c004649634446d83883d1 static/scripts/packed/mvc/library/library-libraryrow-view.js --- a/static/scripts/packed/mvc/library/library-libraryrow-view.js +++ b/static/scripts/packed/mvc/library/library-libraryrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true;vis_config.undelete_library_btn=false}}this.element_visibility_config=vis_config},permissions_on_library:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove()},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){d.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){d.error(k.responseJSON.err_msg)}else{d.error("An error occured during updating the library :(")}}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured during deleting the library :(")}}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured while undeleting the library :(")}}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button></a>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true;vis_config.undelete_library_btn=false}}this.element_visibility_config=vis_config},permissions_on_library:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove()},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){d.error(k.responseJSON.err_msg)}else{d.error("An error occured during updating the library :(")}}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured during deleting the library :(")}}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured while undeleting the library :(")}}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <% if(library.get("description")) { %>');tmpl_array.push(' <% if( (library.get("description")).length> 80 ) { %>');tmpl_array.push(' <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("description")) %>"><%= _.escape(library.get("description")).substring(0, 80) + "..." %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><%= _.escape(library.get("description"))%></td>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(" <td></td>");tmpl_array.push(" <% } %>");tmpl_array.push(' <% if(library.get("synopsis")) { %>');tmpl_array.push(' <% if( (library.get("synopsis")).length> 120 ) { %>');tmpl_array.push(' <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("synopsis")) %>"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><%= _.escape(library.get("synopsis"))%></td>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(" <td></td>");tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_name" placeholder="name" ><%- library.get("name") %></textarea></td>');tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_description" placeholder="description" ><%- library.get("description") %></textarea></td>');tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_synopsis" placeholder="synopsis" ><%- library.get("synopsis") %></textarea></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button></a>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/2d977e8d79cd/ Changeset: 2d977e8d79cd User: martenson Date: 2014-08-06 18:40:17 Summary: Merge Affected #: 34 files diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c lib/galaxy/managers/citations.py --- a/lib/galaxy/managers/citations.py +++ b/lib/galaxy/managers/citations.py @@ -157,8 +157,8 @@ if self.raw_bibtex is DoiCitation.BIBTEX_UNSET: return """@MISC{%s, - DOI = '%s', - note = 'Failed to fetch BibTeX for DOI.' + DOI = {%s}, + note = {Failed to fetch BibTeX for DOI.} }""" % (self.__doi, self.__doi) else: return self.raw_bibtex diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -70,10 +70,18 @@ cfg = cloudman.CloudManConfig(key_id, secret, cluster_name, ami, instance_type, password, placement=zone) cml = cloudman.launch.CloudManLauncher(key_id, secret) - result = cml.launch(cluster_name, ami, instance_type, password, - cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, - cfg.security_groups, cfg.placement, - bucket_default=bucket_default) + # This should probably be handled better on the bioblend side, but until + # an egg update can be made, this needs to conditionally include the + # parameter or not, even if the value is None. + if bucket_default: + result = cml.launch(cluster_name, ami, instance_type, password, + cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, + cfg.security_groups, cfg.placement, + bucket_default=bucket_default) + else: + result = cml.launch(cluster_name, ami, instance_type, password, + cfg.kernel_id, cfg.ramdisk_id, cfg.key_name, + cfg.security_groups, cfg.placement) # result is a dict with sg_names, kp_name, kp_material, rs, and instance_id if not result['rs']: trans.response.status = 400 diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c static/scripts/mvc/citation/citation-model.js --- a/static/scripts/mvc/citation/citation-model.js +++ b/static/scripts/mvc/citation/citation-model.js @@ -37,7 +37,8 @@ var BaseCitationCollection = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend( { /** root api url */ urlRoot : galaxy_config.root + 'api', - model : Citation + partial : true, // Assume some tools in history/workflow may not be properly annotated yet. + model : Citation, } ); var HistoryCitationCollection = BaseCitationCollection.extend( { @@ -51,7 +52,8 @@ /** complete api url */ url : function() { return this.urlRoot + '/tools/' + this.tool_id + '/citations'; - } + }, + partial : false, // If a tool has citations, assume they are complete. } ); //============================================================================== diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c static/scripts/mvc/citation/citation-view.js --- a/static/scripts/mvc/citation/citation-view.js +++ b/static/scripts/mvc/citation/citation-view.js @@ -94,7 +94,7 @@ return info + "."; }, _asSentence: function(str) { - return str ? str + ". " : ""; + return (str && str.trim()) ? str + ". " : ""; } }); @@ -120,7 +120,7 @@ }, render: function() { - this.$el.html(this.citationsElement); + this.$el.html(this.citationsElement()); this.collection.each(function( item ){ this.renderCitation( item ); }, this); @@ -142,29 +142,40 @@ this.$(".citations-formatted").show(); }, - citationsElement: [ - '<div class="toolForm">', - '<div class="toolFormTitle">', - _l("Citations"), - ' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>', - ' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>', - '</div>', - '<div class="toolFormBody" style="padding:5px 10px">', - '<div style="padding:5px 10px">', - '<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate', - ' citations explicitly at this time. When writing up your analysis, please manually', - ' review your histories and find all references', - ' that should be cited in order to completely describe your work. Also, please remember to', - ' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.', - '</div>', - '<span class="citations-formatted"></span>', - '</div>', - '<div class="citations-bibtex toolFormBody" style="padding:5px 10px">', - '<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>', - '</div>', - '</div>' - ].join( '' ) + partialWarningElement: function() { + if( this.collection.partial ) { + return [ + '<div style="padding:5px 10px">', + '<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate', + ' citations explicitly at this time. When writing up your analysis, please manually', + ' review your histories and find all references', + ' that should be cited in order to completely describe your work. Also, please remember to', + ' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.', + '</div>', + ].join(''); + } else { + return ''; + } + }, + citationsElement: function() { + return [ + '<div class="toolForm">', + '<div class="toolFormTitle">', + _l("Citations"), + ' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>', + ' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>', + '</div>', + '<div class="toolFormBody" style="padding:5px 10px">', + this.partialWarningElement(), + '<span class="citations-formatted"></span>', + '</div>', + '<div class="citations-bibtex toolFormBody" style="padding:5px 10px">', + '<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>', + '</div>', + '</div>' + ].join( '' ); + } }); //============================================================================== diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c static/scripts/packed/mvc/citation/citation-model.js --- a/static/scripts/packed/mvc/citation/citation-model.js +++ b/static/scripts/packed/mvc/citation/citation-model.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.Model.extend(a.LoggableMixin).extend({initialize:function(){var g=this.attributes.content;var h=new BibtexParser(g).entries[0];this.entry=h},entryType:function(){return this.entry.EntryType},fields:function(){return this.entry.Fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",model:f});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"}});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file +define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.Model.extend(a.LoggableMixin).extend({initialize:function(){var g=this.attributes.content;var h=new BibtexParser(g).entries[0];this.entry=h},entryType:function(){return this.entry.EntryType},fields:function(){return this.entry.Fields}});var b=Backbone.Collection.extend(a.LoggableMixin).extend({urlRoot:galaxy_config.root+"api",partial:true,model:f,});var d=b.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}});var c=b.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:false,});return{Citation:f,HistoryCitationCollection:d,ToolCitationCollection:c}}); \ No newline at end of file diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c static/scripts/packed/mvc/citation/citation-view.js --- a/static/scripts/packed/mvc/citation/citation-view.js +++ b/static/scripts/packed/mvc/citation/citation-view.js @@ -1,1 +1,1 @@ -define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/"+k.DOI;g+='[<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return f?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement);this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},citationsElement:['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">','<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")});return{CitationView:b,CitationListView:e}}); \ No newline at end of file +define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var j=this.model;var i=j.entryType();var k=j.fields();var g="";var n=this._asSentence((k.author?k.author:"")+(k.year?(" ("+k.year+")"):""))+" ";var m=k.title||"";var h=k.pages?("pp. "+k.pages):"";var o=k.address;if(i=="article"){g=n+this._asSentence(m)+(k.journal?("In <em>"+k.journal+", "):"")+(k.volume?k.volume:"")+(k.number?("("+k.number+"), "):", ")+this._asSentence(h)+this._asSentence(k.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=n+this._asSentence(m)+(k.booktitle?("In <em>"+k.booktitle+", "):"")+(h?h:"")+(o?", "+o:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=n+this._asSentence(m)+(k.howpublished?k.howpublished+". ":"")+(k.note?k.note+".":"")}else{if(i=="techreport"){g=n+". "+this._asSentence(m)+this._asSentence(k.institution)+this._asSentence(k.number)+this._asSentence(k.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=this._asSentence(n)+" "+this._formatBookInfo(k)}else{g=this._asSentence(n)+" "+this._asSentence(m)+this._asSentence(k.howpublished)+this._asSentence(k.note)}}}}}var l="";if(k.DOI){l="http://dx.doi.org/"+k.DOI;g+='[<a href="'+l+'">doi:'+k.DOI+"</a>]"}var f=k.url||l;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}}); \ No newline at end of file diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div();var ac=this;ad.config.on("change",function(){ac.changed()})},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.other_tiles_features_drawn={};this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*Q)),ak=Math.floor(ac*Q*af),am,ah,ai=[],ao=[];while((ac*Q*af)<ag){am=new w.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(Q*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1;ak=am.get("end")}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=Math.round((ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah);if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(av){var aw=ab.omit(ac,ab.map(av.incomplete_features,function(ay){return ay[0]}));aw=ab.omit(aw,ab.keys(av.other_tiles_features_drawn));if(ab.size(aw)!==0){var at={data:ab.values(aw)},au=ap.view.canvas_manager.new_canvas(),ar=au.getContext("2d");au.height=Math.max(av.canvas.height,ap.get_canvas_height(at,av.mode,av.w_scale,100));au.width=av.canvas.width;ar.drawImage(av.canvas,0,0);ar.translate(ah.left_offset,0);var ax=ap.draw_tile(at,ar,av.mode,av.region,av.w_scale,av.seq_data);$(av.canvas).replaceWith($(ax.canvas));av.canvas=au;ab.extend(av.other_tiles_features_drawn,ac)}})}if(ah.filters_manager){var ag=ah.filters_manager.filters,ak;for(ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<ao.length;ai++){if(ao[ai].data.length){al=ao[ai].data[0];for(ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(ao[0] instanceof M){var ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new b(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ad,ac,ae){c.call(this,ad,ac,ae);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var n=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container);var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div();var ac=this;ad.config.on("change",function(){ac.changed()})},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.other_tiles_features_drawn={};this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ak=Math.floor(Q*af),ac=Math.floor(al/ak),am,ah,ai=[],ao=[];while((ac*ak)<ag){am=new w.GenomeRegion({chrom:this.view.chrom,start:ac*ak,end:Math.min((ac+1)*ak,this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=Math.round((ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah);if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(av){var aw=ab.omit(ac,ab.map(av.incomplete_features,function(ay){return ay[0]}));aw=ab.omit(aw,ab.keys(av.other_tiles_features_drawn));if(ab.size(aw)!==0){var at={data:ab.values(aw)},au=ap.view.canvas_manager.new_canvas(),ar=au.getContext("2d");au.height=Math.max(av.canvas.height,ap.get_canvas_height(at,av.mode,av.w_scale,100));au.width=av.canvas.width;ar.drawImage(av.canvas,0,0);ar.translate(ah.left_offset,0);var ax=ap.draw_tile(at,ar,av.mode,av.region,av.w_scale,av.seq_data);$(av.canvas).replaceWith($(ax.canvas));av.canvas=au;ab.extend(av.other_tiles_features_drawn,ac)}})}if(ah.filters_manager){var ag=ah.filters_manager.filters,ak;for(ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<ao.length;ai++){if(ao[ai].data.length){al=ao[ai].data[0];for(ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(ao[0] instanceof M){var ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new b(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ad,ac,ae){c.call(this,ad,ac,ae);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var n=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1021,7 +1021,7 @@ d.current_x = d.offsetX; var delta_chrom = Math.round(delta / view.viewport_container.width() * (view.high - view.low)); view.move_delta(delta_chrom); - }) + }); /* FIXME: Do not do this for now because it's too jittery. Some kind of gravity approach is needed here because moving left/right should be difficult. @@ -1600,7 +1600,7 @@ // Restore tool visibility from state; default to hidden. var hidden = true; if (options.tool_state !== undefined && options.tool_state.hidden !== undefined) { - hidden = options.tool_state.hidden + hidden = options.tool_state.hidden; } this.set('hidden', hidden); @@ -2756,22 +2756,22 @@ this.tiles_div.children().addClass("remove"); var + // Tile width in bases. + tile_width = Math.floor(TILE_SIZE * resolution), // Index of first tile that overlaps visible region. - tile_index = Math.floor( low / (resolution * TILE_SIZE) ), - // Base that first tile starts with. - tile_low = Math.floor(tile_index * TILE_SIZE * resolution), + tile_index = Math.floor(low / tile_width), tile_region, tile_promise, tile_promises = [], tiles = []; // Draw tiles. - while ( ( tile_index * TILE_SIZE * resolution ) < high ) { + while ( (tile_index * tile_width) < high ) { // Get tile region. tile_region = new visualization.GenomeRegion({ chrom: this.view.chrom, - start: tile_low, + start: tile_index * tile_width, // Tile high cannot be larger than view.max_high, which the chromosome length. - end: Math.min( tile_low + Math.ceil( TILE_SIZE * resolution ), this.view.max_high ) + end: Math.min( (tile_index + 1) * tile_width, this.view.max_high) }); tile_promise = this.draw_helper(tile_region, w_scale, options); tile_promises.push(tile_promise); @@ -2781,7 +2781,6 @@ // Go to next tile. tile_index += 1; - tile_low = tile_region.get('end'); } // Step (c) for (re)moving tiles when clear_after is false. diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/genebed_maf_to_fasta.xml --- a/tools/maf/genebed_maf_to_fasta.xml +++ b/tools/maf/genebed_maf_to_fasta.xml @@ -1,5 +1,8 @@ <tool id="GeneBed_Maf_Fasta2" name="Stitch Gene blocks" version="1.0.1"><description>given a set of coding exon intervals</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python"> #if $maf_source_type.maf_source == "user" #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} #else #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --mafSourceType=$maf_source_type.maf_source --geneBED --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} @@ -87,12 +90,7 @@ * stitches blocks together and resolves overlaps based on alignment score; * outputs alignments in FASTA format. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml +++ b/tools/maf/interval2maf.xml @@ -1,5 +1,8 @@ <tool id="Interval2Maf1" name="Extract MAF blocks" version="1.0.1"><description>given a set of genomic intervals</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python"> #if $maf_source_type.maf_source == "user" #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --mafIndex=$maf_source_type.mafFile.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species #else #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species @@ -283,12 +286,7 @@ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/interval2maf_pairwise.xml --- a/tools/maf/interval2maf_pairwise.xml +++ b/tools/maf/interval2maf_pairwise.xml @@ -1,5 +1,8 @@ <tool id="Interval2Maf_pairwise1" name="Extract Pairwise MAF blocks" version="1.0.1"><description>given a set of genomic intervals</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$mafType --interval_file=$input1 --output_file=$out_file1 --indexLocation=${GALAXY_DATA_INDEX_DIR}/maf_pairwise.loc</command><inputs><param name="input1" type="data" format="interval" label="Interval File"> @@ -39,12 +42,7 @@ .. image:: ${static_path}/images/maf_icons/interval2maf.png ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/interval_maf_to_merged_fasta.xml --- a/tools/maf/interval_maf_to_merged_fasta.xml +++ b/tools/maf/interval_maf_to_merged_fasta.xml @@ -1,5 +1,8 @@ <tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks" version="1.0.1"><description>given a set of genomic intervals</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python"> #if $maf_source_type.maf_source == "user" #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} #else #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} @@ -103,12 +106,7 @@ .. image:: ${static_path}/images/maf_icons/stitchMaf.png ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/macros.xml --- /dev/null +++ b/tools/maf/macros.xml @@ -0,0 +1,16 @@ +<macros> + <token name="@HELP_CITATIONS@"> +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btr398</citation> + </citations> + </xml> +</macros> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_by_block_number.xml --- a/tools/maf/maf_by_block_number.xml +++ b/tools/maf/maf_by_block_number.xml @@ -1,5 +1,8 @@ <tool id="maf_by_block_number1" name="Extract MAF by block number" version="1.0.1"><description>given a set of block numbers and a MAF file</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_by_block_number.py $input1 $input2 $out_file1 $block_col $species</command><inputs><param format="txt" name="input1" type="data" label="Block Numbers"/> @@ -29,12 +32,7 @@ This tool takes a list of block numbers, one per line, and extracts the corresponding MAF blocks from the provided file. Block numbers start at 0. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_filter.xml --- a/tools/maf/maf_filter.xml +++ b/tools/maf/maf_filter.xml @@ -1,5 +1,8 @@ <tool id="MAF_filter" name="Filter MAF" version="1.0.1"><description>by specified attributes</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_filter.py $maf_filter_file $input1 $out_file1 $out_file1.files_path $species $min_size $max_size $min_species_per_block $exclude_incomplete_blocks ${input1.metadata.species}</command><inputs><page> @@ -191,12 +194,7 @@ You can also provide a size range and limit your output to the MAF blocks which fall within the specified range. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - -</help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_limit_size.xml --- a/tools/maf/maf_limit_size.xml +++ b/tools/maf/maf_limit_size.xml @@ -1,5 +1,8 @@ <tool id="maf_limit_size1" name="Filter MAF blocks" version="1.0.1"><description>by Size</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_limit_size.py $input1 $out_file1 $min_size $max_size</command><inputs><page> @@ -25,12 +28,7 @@ This tool takes a MAF file and a size range and extracts the MAF blocks which fall within the specified range. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_limit_to_species.xml --- a/tools/maf/maf_limit_to_species.xml +++ b/tools/maf/maf_limit_to_species.xml @@ -1,5 +1,8 @@ <tool id="MAF_Limit_To_Species1" name="Filter MAF blocks"><description>by Species</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_limit_to_species.py $species $input1 $out_file1 $allow_partial $min_species</command><inputs><param name="input1" type="data" format="maf" label="MAF file"/> @@ -39,13 +42,8 @@ * **Exclude blocks with have only one species** - if this option is set to **YES** all single sequence alignment blocks WILL NOT be returned. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_reverse_complement.xml --- a/tools/maf/maf_reverse_complement.xml +++ b/tools/maf/maf_reverse_complement.xml @@ -1,5 +1,8 @@ <tool id="MAF_Reverse_Complement_1" name="Reverse Complement" version="1.0.1"><description>a MAF file</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_reverse_complement.py $input1 $out_file1 $species</command><inputs><page> @@ -42,12 +45,7 @@ s panTro1.chr6 31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT s mm5.chr6 120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_split_by_species.xml --- a/tools/maf/maf_split_by_species.xml +++ b/tools/maf/maf_split_by_species.xml @@ -1,5 +1,8 @@ <tool id="MAF_split_blocks_by_species1" name="Split MAF blocks" version="1.0.0"><description>by Species</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_split_by_species.py $input1 $out_file1 $collapse_columns</command><inputs><param format="maf" name="input1" type="data" label="MAF file to split"/> @@ -211,13 +214,8 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - +@HELP_CITATIONS@ </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_stats.xml --- a/tools/maf/maf_stats.xml +++ b/tools/maf/maf_stats.xml @@ -1,5 +1,8 @@ <tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1"><description>Alignment coverage information</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python"> maf_stats.py #if $maf_source_type.maf_source == "user": @@ -109,12 +112,7 @@ where **coverage** is the number of nucleotides divided by the total length of the provided intervals. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_thread_for_species.xml --- a/tools/maf/maf_thread_for_species.xml +++ b/tools/maf/maf_thread_for_species.xml @@ -1,5 +1,8 @@ <tool id="MAF_Thread_For_Species1" name="Join MAF blocks"><description>by Species</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_thread_for_species.py $input1 $out_file1 $species</command><inputs><param format="maf" name="input1" type="data" label="MAF file"/> @@ -48,13 +51,9 @@ s hg17.chr7 127471195 389 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG s panTro1.chr6 129885076 389 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG ------- +@HELP_CITATIONS@ + </help> + <expand macro="citations" /> -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_to_bed.xml --- a/tools/maf/maf_to_bed.xml +++ b/tools/maf/maf_to_bed.xml @@ -1,5 +1,8 @@ <tool id="MAF_To_BED1" name="MAF to BED" force_history_refresh="True"><description>Converts a MAF formatted file to the BED format</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_to_bed.py "${ input1 }" "${ out_file1 }" "${ species }" "${ complete_blocks }" "." "${ out_file1.id }"</command><inputs><param format="maf" name="input1" type="data" label="MAF file to convert"/> @@ -123,14 +126,9 @@ 5. score - A score between 0 and 1000. 6. strand - Defines the strand - either '+' or '-'. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - +@HELP_CITATIONS@ </help> + <expand macro="citations" /><code file="maf_to_bed_code.py"/></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_to_fasta.xml --- a/tools/maf/maf_to_fasta.xml +++ b/tools/maf/maf_to_fasta.xml @@ -1,5 +1,8 @@ <tool id="MAF_To_Fasta1" name="MAF to FASTA" version="1.0.1"><description>Converts a MAF formatted file to FASTA format</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python"> #if $fasta_target_type.fasta_type == "multiple" #maf_to_fasta_multiple_sets.py $input1 $out_file1 $fasta_target_type.species $fasta_target_type.complete_blocks #else #maf_to_fasta_concat.py $fasta_target_type.species $input1 $out_file1 @@ -188,12 +191,7 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - - </help> +@HELP_CITATIONS@ + </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/maf_to_interval.xml --- a/tools/maf/maf_to_interval.xml +++ b/tools/maf/maf_to_interval.xml @@ -1,5 +1,8 @@ <tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True"><description>Converts a MAF formatted file to the Interval format</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">maf_to_interval.py "${ input1 }" "${ out_file1 }" "${ out_file1.id }" "." "${ input1.dbkey }" "${ species }" "${ input1.metadata.species }" "${ complete_blocks }" "${ remove_gaps }"</command><inputs><param format="maf" name="input1" type="data" label="MAF file to convert"/> @@ -121,13 +124,8 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - - +@HELP_CITATIONS@ </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/maf/vcf_to_maf_customtrack.xml --- a/tools/maf/vcf_to_maf_customtrack.xml +++ b/tools/maf/vcf_to_maf_customtrack.xml @@ -1,5 +1,8 @@ <tool id="vcf_to_maf_customtrack1" name="VCF to MAF Custom Track"><description>for display at UCSC</description> + <macros> + <import>macros.xml</import> + </macros><command interpreter="python">vcf_to_maf_customtrack.py '$out_file1' #if $vcf_source_type.vcf_file '${vcf_source_type.vcf_file[0].vcf_input.dbkey}' @@ -121,12 +124,8 @@ s CHB+JPT_1.5 0 1 + 1 *------ s CHB+JPT_2.5 0 7 + 7 *GGA*** ------- - -**Citation** - -If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ - +@HELP_CITATIONS@ </help> + <expand macro="citations" /></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/phenotype_association/beam.xml --- a/tools/phenotype_association/beam.xml +++ b/tools/phenotype_association/beam.xml @@ -134,4 +134,8 @@ Submitted. </help> + <citations> + <citation type="doi">10.1038/ng2110</citation> + <citation type="doi">10.1214/11-AOAS469</citation> + </citations></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/phenotype_association/gpass.xml --- a/tools/phenotype_association/gpass.xml +++ b/tools/phenotype_association/gpass.xml @@ -109,4 +109,7 @@ Submitted. </help> + <citations> + <citation type="doi">10.1198/jasa.2011.ap10657</citation> + </citations></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/phenotype_association/ldtools.xml --- a/tools/phenotype_association/ldtools.xml +++ b/tools/phenotype_association/ldtools.xml @@ -108,4 +108,7 @@ Am J Hum Genet. 74(1):106-20. Epub 2003 Dec 15. </help> + <citations> + <citation type="doi">10.1086/381000</citation> + </citations></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/phenotype_association/linkToDavid.xml --- a/tools/phenotype_association/linkToDavid.xml +++ b/tools/phenotype_association/linkToDavid.xml @@ -107,4 +107,8 @@ Genome Biol. 4(5):P3. Epub 2003 Apr 3. </help> + <citations> + <citation type="doi">10.1038/nprot.2008.211</citation> + <citation type="doi">10.1186/gb-2003-4-5-p3</citation> + </citations></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/phenotype_association/linkToGProfile.xml --- a/tools/phenotype_association/linkToGProfile.xml +++ b/tools/phenotype_association/linkToGProfile.xml @@ -87,4 +87,7 @@ Nucleic Acids Res. 35(Web Server issue):W193-200. Epub 2007 May 3. </help> + <citations> + <citation type="doi">10.1093/nar/gkm226</citation> + </citations></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/phenotype_association/lps.xml --- a/tools/phenotype_association/lps.xml +++ b/tools/phenotype_association/lps.xml @@ -301,4 +301,19 @@ --></help> + <citations> + <citation type="bibtex">@ARTICLE{Kim07aninterior-point, + author = {Seung-jean Kim and Kwangmoo Koh and Michael Lustig and Stephen Boyd and Dimitry Gorinevsky}, + title = {An interior-point method for large-scale l1-regularized logistic regression}, + journal = {Journal of Machine Learning Research}, + year = {2007}, + volume = {8}, + pages = {1519-1555}, +}</citation> + <citation type="bibtex">@MISC{Shi08lasso-patternsearchalgorithm, + author = {Weiliang Shi and Grace Wahba and Stephen Wright and Kristine Lee and Ronald Klein and Barbara Klein}, + title = { LASSO-Patternsearch Algorithm with Application to Ophthalmology and Genomic Data}, + year = {2008} +}</citation> + </citations></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/phenotype_association/pass.xml --- a/tools/phenotype_association/pass.xml +++ b/tools/phenotype_association/pass.xml @@ -123,4 +123,8 @@ Submitted. </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btn549</citation> + <citation type="doi">10.1093/bioinformatics/btq379</citation> + </citations></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/phenotype_association/sift.xml --- a/tools/phenotype_association/sift.xml +++ b/tools/phenotype_association/sift.xml @@ -171,4 +171,10 @@ Nat Protoc. 4(7):1073-81. Epub 2009 Jun 25. </help> + <citations> + <citation type="doi">10.1101/gr.176601</citation> + <citation type="doi">10.1101/gr.212802</citation> + <citation type="doi">10.1093/nar/gkg509</citation> + <citation type="doi">10.1038/nprot.2009.86</citation> + </citations></tool> diff -r 461b62549cd9cf48965c004649634446d83883d1 -r 2d977e8d79cd2a1545f385116bc583f3bae5419c tools/plotting/boxplot.xml --- a/tools/plotting/boxplot.xml +++ b/tools/plotting/boxplot.xml @@ -105,4 +105,7 @@ </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq281</citation> + </citations></tool> https://bitbucket.org/galaxy/galaxy-central/commits/ab0b32ff32ee/ Changeset: ab0b32ff32ee User: martenson Date: 2014-08-06 21:22:19 Summary: fix for library row staying in edit mode after being deleted if the 'include_deleted' was unchecked Affected #: 2 files diff -r 2d977e8d79cd2a1545f385116bc583f3bae5419c -r ab0b32ff32eee7b76689d846b021c27ba5ff340d static/scripts/mvc/library/library-libraryrow-view.js --- a/static/scripts/mvc/library/library-libraryrow-view.js +++ b/static/scripts/mvc/library/library-libraryrow-view.js @@ -118,6 +118,7 @@ /* User clicked the 'cancel' button so we render normal rowView */ cancel_library_modification: function(){ + // mod_toastr.info('Modifications canceled'); this.edit_mode = false; this.repaint(); }, @@ -185,6 +186,7 @@ row_view.edit_mode = false; if (Galaxy.libraries.preferences.get('with_deleted') === false){ $('.tooltip').hide(); + row_view.repaint(library); row_view.$el.remove(); } else if (Galaxy.libraries.preferences.get('with_deleted') === true){ row_view.repaint(library); diff -r 2d977e8d79cd2a1545f385116bc583f3bae5419c -r ab0b32ff32eee7b76689d846b021c27ba5ff340d static/scripts/packed/mvc/library/library-libraryrow-view.js --- a/static/scripts/packed/mvc/library/library-libraryrow-view.js +++ b/static/scripts/packed/mvc/library/library-libraryrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true;vis_config.undelete_library_btn=false}}this.element_visibility_config=vis_config},permissions_on_library:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove()},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){d.error(k.responseJSON.err_msg)}else{d.error("An error occured during updating the library :(")}}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured during deleting the library :(")}}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured while undeleting the library :(")}}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <% if(library.get("description")) { %>');tmpl_array.push(' <% if( (library.get("description")).length> 80 ) { %>');tmpl_array.push(' <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("description")) %>"><%= _.escape(library.get("description")).substring(0, 80) + "..." %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><%= _.escape(library.get("description"))%></td>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(" <td></td>");tmpl_array.push(" <% } %>");tmpl_array.push(' <% if(library.get("synopsis")) { %>');tmpl_array.push(' <% if( (library.get("synopsis")).length> 120 ) { %>');tmpl_array.push(' <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("synopsis")) %>"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><%= _.escape(library.get("synopsis"))%></td>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(" <td></td>");tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_name" placeholder="name" ><%- library.get("name") %></textarea></td>');tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_description" placeholder="description" ><%- library.get("description") %></textarea></td>');tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_synopsis" placeholder="synopsis" ><%- library.get("synopsis") %></textarea></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button></a>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true;vis_config.undelete_library_btn=false}}this.element_visibility_config=vis_config},permissions_on_library:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove()},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){d.error(k.responseJSON.err_msg)}else{d.error("An error occured during updating the library :(")}}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.repaint(g);e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured during deleting the library :(")}}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error occured while undeleting the library :(")}}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <% if(library.get("description")) { %>');tmpl_array.push(' <% if( (library.get("description")).length> 80 ) { %>');tmpl_array.push(' <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("description")) %>"><%= _.escape(library.get("description")).substring(0, 80) + "..." %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><%= _.escape(library.get("description"))%></td>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(" <td></td>");tmpl_array.push(" <% } %>");tmpl_array.push(' <% if(library.get("synopsis")) { %>');tmpl_array.push(' <% if( (library.get("synopsis")).length> 120 ) { %>');tmpl_array.push(' <td data-toggle="tooltip" data-placement="bottom" title="<%= _.escape(library.get("synopsis")) %>"><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><%= _.escape(library.get("synopsis"))%></td>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(" <td></td>");tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_name" placeholder="name" ><%- library.get("name") %></textarea></td>');tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_description" placeholder="description" ><%- library.get("description") %></textarea></td>');tmpl_array.push(' <td><textarea rows="4" class="form-control input_library_synopsis" placeholder="synopsis" ><%- library.get("synopsis") %></textarea></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button></a>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/1ac8394ca93e/ Changeset: 1ac8394ca93e User: martenson Date: 2014-08-06 21:22:51 Summary: Merge Affected #: 1 file diff -r ab0b32ff32eee7b76689d846b021c27ba5ff340d -r 1ac8394ca93ec7bef323b98b39797c61971b706f tools/phenotype_association/lps.xml --- a/tools/phenotype_association/lps.xml +++ b/tools/phenotype_association/lps.xml @@ -308,12 +308,16 @@ journal = {Journal of Machine Learning Research}, year = {2007}, volume = {8}, - pages = {1519-1555}, + pages = {1519--1555}, }</citation> - <citation type="bibtex">@MISC{Shi08lasso-patternsearchalgorithm, + <citation type="bibtex">@ARTICLE{Shi08lasso-patternsearchalgorithm, author = {Weiliang Shi and Grace Wahba and Stephen Wright and Kristine Lee and Ronald Klein and Barbara Klein}, - title = { LASSO-Patternsearch Algorithm with Application to Ophthalmology and Genomic Data}, - year = {2008} + title = {LASSO-Patternsearch Algorithm with Application to Ophthalmology and Genomic Data}, + journal= {Stat Interface}, + year = {2008}, + volume = {1}, + number = {1}, + pages = {137--153} }</citation></citations></tool> https://bitbucket.org/galaxy/galaxy-central/commits/446d299ab100/ Changeset: 446d299ab100 User: martenson Date: 2014-08-06 23:20:59 Summary: fix for bug that removed the empty folder message when sort was clicked Affected #: 3 files diff -r 1ac8394ca93ec7bef323b98b39797c61971b706f -r 446d299ab1007901976b550bc418451992c83087 static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -34,7 +34,7 @@ events: { 'click #select-all-checkboxes' : 'selectAll', 'click .dataset_row' : 'selectClickedRow', - 'click .sort-folder-link' : 'sort_clicked' + 'click .sort-folder-link' : 'sortColumnClicked' }, // cache of rendered views @@ -194,7 +194,7 @@ }, /** User clicked the table heading = he wants to sort stuff */ - sort_clicked : function(event){ + sortColumnClicked : function(event){ event.preventDefault(); if (this.sort === 'asc'){ this.sortFolder('name','desc'); @@ -205,6 +205,7 @@ } this.render(); this.renderAll(); + this.checkEmptiness(); }, /** diff -r 1ac8394ca93ec7bef323b98b39797c61971b706f -r 446d299ab1007901976b550bc418451992c83087 static/scripts/mvc/library/library-folderrow-view.js --- a/static/scripts/mvc/library/library-folderrow-view.js +++ b/static/scripts/mvc/library/library-folderrow-view.js @@ -53,10 +53,6 @@ * Undeletes the dataset on server and renders it again. */ undelete_dataset : function(event){ - /** - * need to hide manually because of the element removal - * bug in tooltip - */ $(".tooltip").hide(); var that = this; var dataset_id = $(event.target).closest('tr')[0].id; diff -r 1ac8394ca93ec7bef323b98b39797c61971b706f -r 446d299ab1007901976b550bc418451992c83087 static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sortColumnClicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sortColumnClicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll();this.checkEmptiness()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/03add18a83ba/ Changeset: 03add18a83ba User: martenson Date: 2014-08-11 20:38:06 Summary: initial implementation of library dataset versioning API and UI Affected #: 10 files diff -r 446d299ab1007901976b550bc418451992c83087 -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -59,16 +59,20 @@ full_path.insert(0, dataset_item) full_path = full_path[ ::-1 ] - nice_size = util.nice_size( int( library_dataset.library_dataset_dataset_association.get_size() ) ) - - date_uploaded = library_dataset.library_dataset_dataset_association.create_time.strftime( "%Y-%m-%d %I:%M %p" ) + # Find expired versions of the library dataset + expired_ldda_versions = [] + for expired_ldda in library_dataset.expired_datasets: + expired_ldda_versions.append( ( trans.security.encode_id( expired_ldda.id ), expired_ldda.name ) ) rval = trans.security.encode_all_ids( library_dataset.to_dict() ) + if len(expired_ldda_versions) > 0: + rval[ 'has_versions' ] = True + rval[ 'expired_versions' ] = expired_ldda_versions rval[ 'deleted' ] = library_dataset.deleted rval[ 'folder_id' ] = 'F' + rval[ 'folder_id' ] rval[ 'full_path' ] = full_path - rval[ 'file_size' ] = nice_size - rval[ 'date_uploaded' ] = date_uploaded + rval[ 'file_size' ] = util.nice_size( int( library_dataset.library_dataset_dataset_association.get_size() ) ) + rval[ 'date_uploaded' ] = library_dataset.library_dataset_dataset_association.create_time.strftime( "%Y-%m-%d %I:%M %p" ) rval[ 'can_user_modify' ] = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset) or trans.user_is_admin() rval[ 'is_unrestricted' ] = trans.app.security_agent.dataset_is_public( library_dataset.library_dataset_dataset_association.dataset ) @@ -77,6 +81,38 @@ return rval @expose_api + def show_version( self, trans, encoded_dataset_id, encoded_ldda_id, **kwd ): + """ + show_version( self, trans, encoded_dataset_id, encoded_ldda_id, **kwd ): + * GET /api/libraries/datasets/:encoded_dataset_id/versions/:encoded_ldda_id + Displays information about specific version of the library_dataset (i.e. ldda). + + :param encoded_dataset_id: the encoded id of the dataset to query + :type encoded_dataset_id: an encoded id string + + :param encoded_ldda_id: the encoded id of the ldda to query + :type encoded_ldda_id: an encoded id string + + :rtype: dictionary + :returns: dict of ldda's details + """ + try: + library_dataset = self.get_library_dataset( trans, id=encoded_dataset_id, check_ownership=False, check_accessible=True ) + except Exception: + raise exceptions.ObjectNotFound( 'Requested library_dataset was not found.' ) + + try: + ldda = self.get_library_dataset_dataset_association( trans, id=encoded_ldda_id, check_ownership=False, check_accessible=False ) + except Exception, e: + raise exceptions.ObjectNotFound( 'Requested version of library dataset was not found.' + str(e) ) + + if ldda not in library_dataset.expired_datasets: + raise exceptions.ObjectNotFound( 'Given library dataset does not have the requested version.' ) + + rval = trans.security.encode_all_ids( ldda.to_dict() ) + return rval + + @expose_api def show_roles( self, trans, encoded_dataset_id, **kwd ): """ show_roles( self, trans, id, **kwd ): @@ -93,7 +129,6 @@ :rtype: dictionary :returns: either dict of current roles for all permission types or dict of available roles to choose from (is the same for any permission type) - """ current_user_roles = trans.get_current_user_roles() diff -r 446d299ab1007901976b550bc418451992c83087 -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -255,12 +255,18 @@ action='set_permissions', conditions=dict( method=[ "POST" ] ) ) - webapp.mapper.connect( 'show_lda_item', + webapp.mapper.connect( 'show_ld_item', '/api/libraries/datasets/:id', controller='lda_datasets', action='show', conditions=dict( method=[ "GET" ] ) ) + webapp.mapper.connect( 'show_version_of_ld_item', + '/api/libraries/datasets/:encoded_dataset_id/versions/:encoded_ldda_id', + controller='lda_datasets', + action='show_version', + conditions=dict( method=[ "GET" ] ) ) + webapp.mapper.connect( 'show_legitimate_lda_roles', '/api/libraries/datasets/:encoded_dataset_id/permissions', controller='lda_datasets', diff -r 446d299ab1007901976b550bc418451992c83087 -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -40,13 +40,14 @@ }, routes: { - "" : "libraries", - "library/:library_id/permissions" : "library_permissions", - "folders/:folder_id/permissions" : "folder_permissions", - "folders/:id" : "folder_content", - "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", - "folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions", - "folders/:folder_id/download/:format" : "download" + "" : "libraries", + "library/:library_id/permissions" : "library_permissions", + "folders/:folder_id/permissions" : "folder_permissions", + "folders/:id" : "folder_content", + "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", + "folders/:folder_id/datasets/:dataset_id/permissions" : "dataset_permissions", + "folders/:folder_id/datasets/:dataset_id/versions/:ldda_id" : "dataset_version", + "folders/:folder_id/download/:format" : "download" }, back: function() { @@ -119,6 +120,12 @@ } Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}); }); + this.library_router.on('route:dataset_version', function(folder_id, dataset_id, ldda_id){ + if (Galaxy.libraries.datasetView){ + Galaxy.libraries.datasetView.$el.unbind('click'); + } + Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, ldda_id: ldda_id, show_version: true}); + }); this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ if (Galaxy.libraries.datasetView){ diff -r 446d299ab1007901976b550bc418451992c83087 -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -44,12 +44,15 @@ fetchDataset: function(options){ this.options = _.extend(this.options, options); + this.model = new mod_library_model.Item({id:this.options.id}); var that = this; this.model.fetch({ success: function() { if (that.options.show_permissions){ that.showPermissions(); + } else if (that.options.show_version) { + that.fetchVersion(); } else { that.render(); } @@ -65,14 +68,38 @@ }, render: function(options){ + this.options = _.extend(this.options, options); $(".tooltip").remove(); - this.options = _.extend(this.options, options); var template = this.templateDataset(); this.$el.html(template({item: this.model})); $(".peek").html(this.model.get("peek")); $("#center [data-toggle]").tooltip(); }, + fetchVersion: function(options){ + this.options = _.extend(this.options, options); + that = this; + if (!this.options.ldda_id){ + this.render(); + mod_toastr.error('Library dataset version requested but no id provided.'); + } else { + this.ldda = new mod_library_model.Ldda({id:this.options.ldda_id}); + this.ldda.url = this.ldda.urlRoot + this.model.id + '/versions/' + this.ldda.id; + this.ldda.fetch({ + success: function(){ + that.renderVersion(); + } + }); + } + }, + + renderVersion: function(){ + $(".tooltip").remove(); + var template = this.templateVersion(); + this.$el.html(template({item: this.model, ldda: this.ldda})); + $(".peek").html(this.ldda.get("peek")); + }, + enableModification: function(){ $(".tooltip").remove(); var template = this.templateModifyDataset(); @@ -473,9 +500,6 @@ tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>'); tmpl_array.push(' <% } %>'); - // tmpl_array.push(' <% if (item.get("has_versions")) { %>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Show previous versions" class="btn btn-default toolbtn-previous-versions primary-button" type="button"><span class="fa fa-clock-o"></span> Versions</span></button>'); - // tmpl_array.push(' <% } %>'); tmpl_array.push(' </div>'); @@ -492,10 +516,10 @@ tmpl_array.push('</ol>'); tmpl_array.push('<% if (item.get("is_unrestricted")) { %>'); - tmpl_array.push(' <p>'); + tmpl_array.push(' <div class="alert alert-info">'); tmpl_array.push(' This dataset is unrestricted so everybody can access it. Just share the URL of this page. '); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> '); - tmpl_array.push(' </p>'); + tmpl_array.push(' </div>'); tmpl_array.push('<% } %>'); tmpl_array.push('<div class="dataset_table">'); @@ -595,6 +619,147 @@ tmpl_array.push(' <pre class="peek">'); tmpl_array.push(' </pre>'); tmpl_array.push(' </div>'); + + tmpl_array.push(' <% if (item.get("has_versions")) { %>'); + tmpl_array.push(' <div>'); + tmpl_array.push(' <h3>Expired versions:</h3>'); + tmpl_array.push(' <ul>'); + tmpl_array.push(' <% _.each(item.get("expired_versions"), function(version) { %>'); + tmpl_array.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>'); + tmpl_array.push(' <% }) %>'); + tmpl_array.push(' <ul>'); + tmpl_array.push(' </div>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push('</div>'); + + // CONTAINER END + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + }, + + templateVersion : function(){ + var tmpl_array = []; + // CONTAINER START + tmpl_array.push('<div class="library_style_container">'); + + tmpl_array.push(' <div id="library_toolbar">'); + tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to current dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Latest dataset</span></button><a>'); + tmpl_array.push(' </div>'); + + // BREADCRUMBS + tmpl_array.push('<ol class="breadcrumb">'); + tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>'); + tmpl_array.push(' <% _.each(item.get("full_path"), function(path_item) { %>'); + tmpl_array.push(' <% if (path_item[0] != item.id) { %>'); + tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> '); + tmpl_array.push( '<% } else { %>'); + tmpl_array.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</ol>'); + + tmpl_array.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>'); + + tmpl_array.push('<div class="dataset_table">'); + + tmpl_array.push(' <table class="grid table table-striped table-condensed">'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>'); + tmpl_array.push(' <td><%= _.escape(ldda.get("name")) %></td>'); + tmpl_array.push(' </tr>'); + + tmpl_array.push(' <% if (ldda.get("data_type")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data type</th>'); + tmpl_array.push(' <td><%= _.escape(ldda.get("data_type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("genome_build")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Genome build</th>'); + tmpl_array.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("file_size")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Size</th>'); + tmpl_array.push(' <td><%= _.escape(ldda.get("file_size")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("date_uploaded")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>'); + tmpl_array.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("uploaded_by")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Uploaded by</th>'); + tmpl_array.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("metadata_data_lines")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("metadata_comment_lines")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Comment Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("metadata_columns")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Number of Columns</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("metadata_column_types")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Column Types</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("message")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Message</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("misc_blurb")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous blurb</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (ldda.get("misc_info")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' </table>'); + tmpl_array.push(' <div>'); + tmpl_array.push(' <pre class="peek">'); + tmpl_array.push(' </pre>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); // CONTAINER END diff -r 446d299ab1007901976b550bc418451992c83087 -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -314,9 +314,10 @@ this.refreshUserHistoriesList(function(self){ self.modal = Galaxy.modal; var template_modal = self.templateAddFilesInModal(); + var folder_name = self.options.full_path[self.options.full_path.length - 1][1] self.modal.show({ closing_events : true, - title : 'Add datasets from history to ' + self.options.folder_name, + title : 'Add datasets from history to ' + folder_name, body : template_modal({histories: self.histories.models}), buttons : { 'Add' : function() {self.addAllDatasetsFromHistory();}, diff -r 446d299ab1007901976b550bc418451992c83087 -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 static/scripts/mvc/library/library-model.js --- a/static/scripts/mvc/library/library-model.js +++ b/static/scripts/mvc/library/library-model.js @@ -84,7 +84,11 @@ // FOLDER RELATED MODELS var Item = Backbone.Model.extend({ - urlRoot : '/api/libraries/datasets/' + urlRoot : '/api/libraries/datasets/' + }); + + var Ldda = Backbone.Model.extend({ + urlRoot : '/api/libraries/datasets/' }); var FolderAsModel = Backbone.Model.extend({ @@ -193,6 +197,7 @@ FolderAsModel : FolderAsModel, Libraries : Libraries, Item : Item, + Ldda : Ldda, Folder : Folder, FolderContainer : FolderContainer, HistoryItem : HistoryItem, diff -r 446d299ab1007901976b550bc418451992c83087 -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view","mvc/library/library-library-view","mvc/library/library-folder-view"],function(h,e,j,n,k,c,i,g,l,f,b,a){var o=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","library/:library_id/permissions":"library_permissions","folders/:folder_id/permissions":"folder_permissions","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/download/:format":"download"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var m=n.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var d=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,libraryView:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new m({id:"global-lib-prefs"});this.library_router=new o();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView()});this.library_router.on("route:folder_content",function(p){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p})});this.library_router.on("route:download",function(p,q){if($("#folder_list_body").find(":checked").length===0){j.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(p,q);Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p})});this.library_router.on("route:dataset_permissions",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,show_permissions:true})});this.library_router.on("route:library_permissions",function(p){if(Galaxy.libraries.libraryView){Galaxy.libraries.libraryView.$el.unbind("click")}Galaxy.libraries.libraryView=new b.LibraryView({id:p,show_permissions:true})});this.library_router.on("route:folder_permissions",function(p){if(Galaxy.libraries.folderView){Galaxy.libraries.folderView.$el.unbind("click")}Galaxy.libraries.folderView=new a.FolderView({id:p,show_permissions:true})});Backbone.history.start({pushState:false})}});return{GalaxyApp:d}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view","mvc/library/library-dataset-view","mvc/library/library-library-view","mvc/library/library-folder-view"],function(h,e,j,n,k,c,i,g,l,f,b,a){var o=Backbone.Router.extend({initialize:function(){this.routesHit=0;Backbone.history.on("route",function(){this.routesHit++},this)},routes:{"":"libraries","library/:library_id/permissions":"library_permissions","folders/:folder_id/permissions":"folder_permissions","folders/:id":"folder_content","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/datasets/:dataset_id/versions/:ldda_id":"dataset_version","folders/:folder_id/download/:format":"download"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var m=n.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var d=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,libraryView:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new m({id:"global-lib-prefs"});this.library_router=new o();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new g.LibraryToolbarView();Galaxy.libraries.libraryListView=new i.LibraryListView()});this.library_router.on("route:folder_content",function(p){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new l.FolderToolbarView({id:p});Galaxy.libraries.folderListView=new c.FolderListView({id:p})});this.library_router.on("route:download",function(p,q){if($("#folder_list_body").find(":checked").length===0){j.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(p,q);Galaxy.libraries.library_router.navigate("folders/"+p,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p})});this.library_router.on("route:dataset_version",function(q,p,r){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,ldda_id:r,show_version:true})});this.library_router.on("route:dataset_permissions",function(q,p){if(Galaxy.libraries.datasetView){Galaxy.libraries.datasetView.$el.unbind("click")}Galaxy.libraries.datasetView=new f.LibraryDatasetView({id:p,show_permissions:true})});this.library_router.on("route:library_permissions",function(p){if(Galaxy.libraries.libraryView){Galaxy.libraries.libraryView.$el.unbind("click")}Galaxy.libraries.libraryView=new b.LibraryView({id:p,show_permissions:true})});this.library_router.on("route:folder_permissions",function(p){if(Galaxy.libraries.folderView){Galaxy.libraries.folderView.$el.unbind("click")}Galaxy.libraries.folderView=new a.FolderView({id:p,show_permissions:true})});Backbone.history.start({pushState:false})}});return{GalaxyApp:d}}); \ No newline at end of file diff -r 446d299ab1007901976b550bc418451992c83087 -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 static/scripts/packed/mvc/library/library-dataset-view.js --- a/static/scripts/packed/mvc/library/library-dataset-view.js +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){f(e)},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var g=new c.HistoryItem();g.url=g.urlRoot+f+"/contents";var e="/api/histories/"+f+"/set_as_current";$.ajax({url:e,type:"PUT"});g.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(i,h){if(typeof h.responseJSON!=="undefined"){d.error("Dataset not imported. "+h.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while fetching dataset permissions. :(")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you")}).fail(function(){d.error("An error occurred while making dataset private :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted")}).fail(function(){d.error("An error occurred while making dataset unrestricted :(")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting dataset permissions :(")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(' <button data-toggle="tooltip" data-placement="top" title="Show previous versions" class="btn btn-default toolbtn-previous-versions primary-button" type="button"><span class="fa fa-clock-o"></span> Versions</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){f(e)},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var g=new c.HistoryItem();g.url=g.urlRoot+f+"/contents";var e="/api/histories/"+f+"/set_as_current";$.ajax({url:e,type:"PUT"});g.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(i,h){if(typeof h.responseJSON!=="undefined"){d.error("Dataset not imported. "+h.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while fetching dataset permissions. :(")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you")}).fail(function(){d.error("An error occurred while making dataset private :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted")}).fail(function(){d.error("An error occurred while making dataset unrestricted :(")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting dataset permissions :(")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to current dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 446d299ab1007901976b550bc418451992c83087 -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=false;var f=true;if(Galaxy.currUser){i=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}var h=this.templateToolBar();this.$el.html(h({id:this.options.id,admin_user:i,anonym:f}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var f=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new c.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";f.push(m)}this.options.chain_call_control.total_number=f.length;var g="/api/histories/"+k+"/set_as_current";$.ajax({url:g,type:"PUT"});this.chainCall(f,n)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},showLibInfo:function(){var f=this;var g=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:g({library:library}),buttons:{Close:function(){Galaxy.modal.hide()}}})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>');tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=false;var f=true;if(Galaxy.currUser){i=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}var h=this.templateToolBar();this.$el.html(h({id:this.options.id,admin_user:i,anonym:f}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var f=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new c.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";f.push(m)}this.options.chain_call_control.total_number=f.length;var g="/api/histories/"+k+"/set_as_current";$.ajax({url:g,type:"PUT"});this.chainCall(f,n)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();var h=f.options.full_path[f.options.full_path.length-1][1];f.modal.show({closing_events:true,title:"Add datasets from history to "+h,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(i){f.fetchAndDisplayHistoryContents(i.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},showLibInfo:function(){var f=this;var g=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:g({library:library}),buttons:{Close:function(){Galaxy.modal.hide()}}})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>');tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file diff -r 446d299ab1007901976b550bc418451992c83087 -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 static/scripts/packed/mvc/library/library-model.js --- a/static/scripts/packed/mvc/library/library-model.js +++ b/static/scripts/packed/mvc/library/library-model.js @@ -1,1 +1,1 @@ -define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(l){var k=true;if((!l)&&(this.get("deleted"))){k=false}return k}});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(k){k=k||{}},getVisible:function(l,m){m=m||[];var k=new i(this.filter(function(n){return n.isVisible(l)}));return k},sortByNameAsc:function(){this.comparator=function(l,k){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}return 0};this.sort();return this},sortByNameDesc:function(){this.comparator=function(l,k){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}return 0};this.sort();return this}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var c=Backbone.Collection.extend({model:g,sortByNameAsc:function(){this.comparator=function(l,k){if(l.get("type")===k.get("type")){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return 1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}return 0}else{if(l.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this},sortByNameDesc:function(){this.comparator=function(l,k){if(l.get("type")===k.get("type")){if(l.get("name").toLowerCase()>k.get("name").toLowerCase()){return -1}if(k.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}return 0}else{if(l.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this}});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(k){this.get("folder").reset(k.folder_contents);return k}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(k){this.id=k.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Collection.extend({url:"/api/histories",model:h});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:j}}); \ No newline at end of file +define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(m){var l=true;if((!m)&&(this.get("deleted"))){l=false}return l}});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(l){l=l||{}},getVisible:function(m,n){n=n||[];var l=new i(this.filter(function(o){return o.isVisible(m)}));return l},sortByNameAsc:function(){this.comparator=function(m,l){if(m.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}if(l.get("name").toLowerCase()>m.get("name").toLowerCase()){return -1}return 0};this.sort();return this},sortByNameDesc:function(){this.comparator=function(m,l){if(m.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}if(l.get("name").toLowerCase()>m.get("name").toLowerCase()){return 1}return 0};this.sort();return this}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var k=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var c=Backbone.Collection.extend({model:g,sortByNameAsc:function(){this.comparator=function(m,l){if(m.get("type")===l.get("type")){if(m.get("name").toLowerCase()>l.get("name").toLowerCase()){return 1}if(l.get("name").toLowerCase()>m.get("name").toLowerCase()){return -1}return 0}else{if(m.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this},sortByNameDesc:function(){this.comparator=function(m,l){if(m.get("type")===l.get("type")){if(m.get("name").toLowerCase()>l.get("name").toLowerCase()){return -1}if(l.get("name").toLowerCase()>m.get("name").toLowerCase()){return 1}return 0}else{if(m.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this}});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(l){this.get("folder").reset(l.folder_contents);return l}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(l){this.id=l.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Collection.extend({url:"/api/histories",model:h});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Ldda:k,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:j}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/8b087dace61b/ Changeset: 8b087dace61b User: martenson Date: 2014-08-11 20:38:22 Summary: Merge Affected #: 77 files diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/dataset_collections/__init__.py --- a/lib/galaxy/dataset_collections/__init__.py +++ b/lib/galaxy/dataset_collections/__init__.py @@ -1,7 +1,6 @@ from .registry import DatasetCollectionTypesRegistry from .matching import MatchingCollections from .type_description import CollectionTypeDescriptionFactory -from .util import validate_input_element_identifiers from galaxy import model @@ -14,7 +13,7 @@ UsesTagsMixin, ) from galaxy.managers import hdas # TODO: Refactor all mixin use into managers. - +from galaxy.managers.collections_util import validate_input_element_identifiers from galaxy.util import validation from galaxy.util import odict diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/dataset_collections/util.py --- a/lib/galaxy/dataset_collections/util.py +++ /dev/null @@ -1,95 +0,0 @@ -from galaxy import exceptions -from galaxy import web -from galaxy import model - -import logging -log = logging.getLogger( __name__ ) - -ERROR_MESSAGE_UNKNOWN_SRC = "Unknown dataset source (src) %s." -ERROR_MESSAGE_NO_NESTED_IDENTIFIERS = "Dataset source new_collection requires nested element_identifiers for new collection." -ERROR_MESSAGE_NO_NAME = "Cannot load invalid dataset identifier - missing name - %s" -ERROR_MESSAGE_NO_COLLECTION_TYPE = "No collection_type define for nested collection %s." -ERROR_MESSAGE_INVALID_PARAMETER_FOUND = "Found invalid parameter %s in element identifier description %s." -ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND = "Found duplicated element identifier name %s." - - -def api_payload_to_create_params( payload ): - """ - Cleanup API payload to pass into dataset_collections. - """ - required_parameters = [ "collection_type", "element_identifiers" ] - missing_parameters = [ p for p in required_parameters if p not in payload ] - if missing_parameters: - message = "Missing required parameters %s" % missing_parameters - raise exceptions.ObjectAttributeMissingException( message ) - - params = dict( - collection_type=payload.get( "collection_type" ), - element_identifiers=payload.get( "element_identifiers" ), - name=payload.get( "name", None ), - ) - - return params - - -def validate_input_element_identifiers( element_identifiers ): - """ Scan through the list of element identifiers supplied by the API consumer - and verify the structure is valid. - """ - log.debug( "Validating %d element identifiers for collection creation." % len( element_identifiers ) ) - identifier_names = set() - for element_identifier in element_identifiers: - if "__object__" in element_identifier: - message = ERROR_MESSAGE_INVALID_PARAMETER_FOUND % ( "__model_object__", element_identifier ) - raise exceptions.RequestParameterInvalidException( message ) - if "name" not in element_identifier: - message = ERROR_MESSAGE_NO_NAME % element_identifier - raise exceptions.RequestParameterInvalidException( message ) - name = element_identifier[ "name" ] - if name in identifier_names: - message = ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND % name - raise exceptions.RequestParameterInvalidException( message ) - else: - identifier_names.add( name ) - src = element_identifier.get( "src", "hda" ) - if src not in [ "hda", "hdca", "ldda", "new_collection" ]: - message = ERROR_MESSAGE_UNKNOWN_SRC % src - raise exceptions.RequestParameterInvalidException( message ) - if src == "new_collection": - if "element_identifiers" not in element_identifier: - message = ERROR_MESSAGE_NO_NESTED_IDENTIFIERS - raise exceptions.RequestParameterInvalidException( ERROR_MESSAGE_NO_NESTED_IDENTIFIERS ) - if "collection_type" not in element_identifier: - message = ERROR_MESSAGE_NO_COLLECTION_TYPE % element_identifier - raise exceptions.RequestParameterInvalidException( message ) - validate_input_element_identifiers( element_identifier[ "element_identifiers" ] ) - - -def dictify_dataset_collection_instance( dataset_colleciton_instance, parent, security, view="element" ): - dict_value = dataset_colleciton_instance.to_dict( view=view ) - encoded_id = security.encode_id( dataset_colleciton_instance.id ) - if isinstance( parent, model.History ): - encoded_history_id = security.encode_id( parent.id ) - dict_value[ 'url' ] = web.url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset_collection" ) - elif isinstance( parent, model.LibraryFolder ): - encoded_library_id = security.encode_id( parent.library.id ) - encoded_folder_id = security.encode_id( parent.id ) - # TODO: Work in progress - this end-point is not right yet... - dict_value[ 'url' ] = web.url_for( 'library_content', library_id=encoded_library_id, id=encoded_id, folder_id=encoded_folder_id ) - if view == "element": - dict_value[ 'elements' ] = map( dictify_element, dataset_colleciton_instance.collection.elements ) - security.encode_all_ids( dict_value, recursive=True ) # TODO: Use Kyle's recusrive formulation of this. - return dict_value - - -def dictify_element( element ): - dictified = element.to_dict( view="element" ) - object_detials = element.element_object.to_dict() - if element.child_collection: - # Recursively yield elements for each nested collection... - object_detials[ "elements" ] = map( dictify_element, element.child_collection.elements ) - - dictified[ "object" ] = object_detials - return dictified - -__all__ = [ api_payload_to_create_params, dictify_dataset_collection_instance ] diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -85,7 +85,7 @@ if not dataset.dbkey: dataset.dbkey = 'hg18' # punt! if dataset.has_data(): - for site_name, site_url in app.build_sites.get_ucsc_by_build(dataset.dbkey): + for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): if site_name in app.config.ucsc_display_sites: site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs internal_url = "%s" % url_for( controller='dataset', diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -234,7 +234,7 @@ # Filter UCSC sites to only those that are supported by this build and # enabled. valid_sites = [ ( name, url ) - for name, url in app.build_sites.get_ucsc_by_build( dataset.dbkey ) + for name, url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ) if name in app.config.ucsc_display_sites ] if not valid_sites: return [] @@ -750,7 +750,7 @@ ret_val = [] seqid, start, stop = self.get_estimated_display_viewport( dataset ) if seqid is not None: - for site_name, site_url in app.build_sites.get_ucsc_by_build( dataset.dbkey ): + for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): if site_name in app.config.ucsc_display_sites: redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % @@ -1103,7 +1103,7 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport( dataset ) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_by_build( dataset.dbkey ): + for site_name, site_url in app.build_sites.get_ucsc_sites_by_build( dataset.dbkey ): if site_name in app.config.ucsc_display_sites: redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % ( site_url, dataset.dbkey, chrom, start, stop ) ) link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) @@ -1285,7 +1285,7 @@ ret_val = [] chrom, start, stop = self.get_estimated_display_viewport(dataset) if chrom is not None: - for site_name, site_url in app.build_sites.get_ucsc_by_build(dataset.dbkey): + for site_name, site_url in app.build_sites.get_ucsc_sites_by_build(dataset.dbkey): if site_name in app.config.ucsc_display_sites: internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/managers/citations.py --- a/lib/galaxy/managers/citations.py +++ b/lib/galaxy/managers/citations.py @@ -49,7 +49,7 @@ def _raw_get_bibtex( self, doi ): dx_url = "http://dx.doi.org/" + doi - headers = {'Accept': "text/bibliography; style=bibtex" } + headers = {'Accept': 'text/bibliography; style=bibtex, application/x-bibtex'} req = urllib2.Request(dx_url, data="", headers=headers) response = urllib2.urlopen(req) bibtex = response.read() diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/managers/collections.py --- /dev/null +++ b/lib/galaxy/managers/collections.py @@ -0,0 +1,1 @@ +""" Future home of dataset collections managers. """ diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/managers/collections_util.py --- /dev/null +++ b/lib/galaxy/managers/collections_util.py @@ -0,0 +1,95 @@ +from galaxy import exceptions +from galaxy import web +from galaxy import model + +import logging +log = logging.getLogger( __name__ ) + +ERROR_MESSAGE_UNKNOWN_SRC = "Unknown dataset source (src) %s." +ERROR_MESSAGE_NO_NESTED_IDENTIFIERS = "Dataset source new_collection requires nested element_identifiers for new collection." +ERROR_MESSAGE_NO_NAME = "Cannot load invalid dataset identifier - missing name - %s" +ERROR_MESSAGE_NO_COLLECTION_TYPE = "No collection_type define for nested collection %s." +ERROR_MESSAGE_INVALID_PARAMETER_FOUND = "Found invalid parameter %s in element identifier description %s." +ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND = "Found duplicated element identifier name %s." + + +def api_payload_to_create_params( payload ): + """ + Cleanup API payload to pass into dataset_collections. + """ + required_parameters = [ "collection_type", "element_identifiers" ] + missing_parameters = [ p for p in required_parameters if p not in payload ] + if missing_parameters: + message = "Missing required parameters %s" % missing_parameters + raise exceptions.ObjectAttributeMissingException( message ) + + params = dict( + collection_type=payload.get( "collection_type" ), + element_identifiers=payload.get( "element_identifiers" ), + name=payload.get( "name", None ), + ) + + return params + + +def validate_input_element_identifiers( element_identifiers ): + """ Scan through the list of element identifiers supplied by the API consumer + and verify the structure is valid. + """ + log.debug( "Validating %d element identifiers for collection creation." % len( element_identifiers ) ) + identifier_names = set() + for element_identifier in element_identifiers: + if "__object__" in element_identifier: + message = ERROR_MESSAGE_INVALID_PARAMETER_FOUND % ( "__model_object__", element_identifier ) + raise exceptions.RequestParameterInvalidException( message ) + if "name" not in element_identifier: + message = ERROR_MESSAGE_NO_NAME % element_identifier + raise exceptions.RequestParameterInvalidException( message ) + name = element_identifier[ "name" ] + if name in identifier_names: + message = ERROR_MESSAGE_DUPLICATED_IDENTIFIER_FOUND % name + raise exceptions.RequestParameterInvalidException( message ) + else: + identifier_names.add( name ) + src = element_identifier.get( "src", "hda" ) + if src not in [ "hda", "hdca", "ldda", "new_collection" ]: + message = ERROR_MESSAGE_UNKNOWN_SRC % src + raise exceptions.RequestParameterInvalidException( message ) + if src == "new_collection": + if "element_identifiers" not in element_identifier: + message = ERROR_MESSAGE_NO_NESTED_IDENTIFIERS + raise exceptions.RequestParameterInvalidException( ERROR_MESSAGE_NO_NESTED_IDENTIFIERS ) + if "collection_type" not in element_identifier: + message = ERROR_MESSAGE_NO_COLLECTION_TYPE % element_identifier + raise exceptions.RequestParameterInvalidException( message ) + validate_input_element_identifiers( element_identifier[ "element_identifiers" ] ) + + +def dictify_dataset_collection_instance( dataset_colleciton_instance, parent, security, view="element" ): + dict_value = dataset_colleciton_instance.to_dict( view=view ) + encoded_id = security.encode_id( dataset_colleciton_instance.id ) + if isinstance( parent, model.History ): + encoded_history_id = security.encode_id( parent.id ) + dict_value[ 'url' ] = web.url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset_collection" ) + elif isinstance( parent, model.LibraryFolder ): + encoded_library_id = security.encode_id( parent.library.id ) + encoded_folder_id = security.encode_id( parent.id ) + # TODO: Work in progress - this end-point is not right yet... + dict_value[ 'url' ] = web.url_for( 'library_content', library_id=encoded_library_id, id=encoded_id, folder_id=encoded_folder_id ) + if view == "element": + dict_value[ 'elements' ] = map( dictify_element, dataset_colleciton_instance.collection.elements ) + security.encode_all_ids( dict_value, recursive=True ) # TODO: Use Kyle's recusrive formulation of this. + return dict_value + + +def dictify_element( element ): + dictified = element.to_dict( view="element" ) + object_detials = element.element_object.to_dict() + if element.child_collection: + # Recursively yield elements for each nested collection... + object_detials[ "elements" ] = map( dictify_element, element.child_collection.elements ) + + dictified[ "object" ] = object_detials + return dictified + +__all__ = [ api_payload_to_create_params, dictify_dataset_collection_instance ] diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -9,10 +9,9 @@ from galaxy.model import orm from galaxy.managers import base as manager_base -import galaxy.managers.hdas +import galaxy.managers.collections_util import galaxy.web -import galaxy.dataset_collections.util import logging log = logging.getLogger( __name__ ) @@ -140,8 +139,10 @@ Returns a dictionary containing ``history`` and ``contents``, serialized history and an array of serialized history contents respectively. """ + # import here prevents problems related to circular dependecy between histories and hdas managers. + import galaxy.managers.hdas hda_mgr = galaxy.managers.hdas.HDAManager() - collection_dictifier = galaxy.dataset_collections.util.dictify_dataset_collection_instance + collection_dictifier = galaxy.managers.collections_util.dictify_dataset_collection_instance history_dictionary = {} contents_dictionaries = [] diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/util/build_sites.py --- a/lib/galaxy/util/build_sites.py +++ b/lib/galaxy/util/build_sites.py @@ -38,7 +38,7 @@ self._build_sites['ucsc'] = self.read_build_sites( self._app.config.ucsc_build_sites ) self._build_sites['gbrowse'] = self.read_build_sites( self._app.config.gbrowse_build_sites ) - def get_site_by_build( self, site_type, build ): + def _get_site_by_build( self, site_type, build ): sites = [] for site in self._build_sites[site_type]: if build in site['builds']: diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1664,7 +1664,7 @@ session.flush() return imported_stored - def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False ): + def _workflow_from_dict( self, trans, data, source=None, add_to_menu=False, publish=False ): """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ @@ -1752,6 +1752,7 @@ workflow.stored_workflow = stored stored.latest_workflow = workflow stored.user = trans.user + stored.published = publish if data[ 'annotation' ]: self.add_item_annotation( trans.sa_session, stored.user, stored, data[ 'annotation' ] ) diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/webapps/galaxy/api/dataset_collections.py --- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py +++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py @@ -4,8 +4,7 @@ from galaxy.web.base.controller import UsesHistoryMixin from galaxy.web.base.controller import UsesLibraryMixinItems -from galaxy.dataset_collections.util import api_payload_to_create_params -from galaxy.dataset_collections.util import dictify_dataset_collection_instance +from galaxy.managers.collections_util import api_payload_to_create_params, dictify_dataset_collection_instance from logging import getLogger log = getLogger( __name__ ) diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -16,12 +16,9 @@ from galaxy.web.base.controller import UsesLibraryMixinItems from galaxy.web.base.controller import UsesTagsMixin -from galaxy.dataset_collections.util import api_payload_to_create_params -from galaxy.dataset_collections.util import dictify_dataset_collection_instance - - from galaxy.managers import histories from galaxy.managers import hdas +from galaxy.managers.collections_util import api_payload_to_create_params, dictify_dataset_collection_instance import logging log = logging.getLogger( __name__ ) diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -5,11 +5,10 @@ from galaxy import web from galaxy import exceptions from galaxy.web import _future_expose_api as expose_api -from galaxy.dataset_collections.util import api_payload_to_create_params -from galaxy.dataset_collections.util import dictify_dataset_collection_instance from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin from galaxy.web.base.controller import HTTPBadRequest, url_for +from galaxy.managers.collections_util import api_payload_to_create_params, dictify_dataset_collection_instance from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex from sqlalchemy.orm.exc import MultipleResultsFound from sqlalchemy.orm.exc import NoResultFound diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -9,7 +9,8 @@ from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import to_json_string from galaxy.visualization.data_providers.genome import * -from galaxy.dataset_collections.util import dictify_dataset_collection_instance + +from galaxy.managers.collections_util import dictify_dataset_collection_instance import logging log = logging.getLogger( __name__ ) diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -6,21 +6,27 @@ import logging from sqlalchemy import desc, or_ -from galaxy import exceptions, util, web +from galaxy import exceptions, util from galaxy.model.item_attrs import UsesAnnotations +from galaxy.managers import histories from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.web.base.controller import UsesHistoryMixin +from galaxy.web.base.controller import SharableMixin from galaxy.workflow.extract import extract_workflow from galaxy.workflow.run import invoke -from galaxy.workflow.run import WorkflowRunConfig +from galaxy.workflow.run_request import build_workflow_run_config log = logging.getLogger(__name__) -class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin, UsesAnnotations, SharableMixin): - @web.expose_api + def __init__( self, app ): + super( BaseAPIController, self ).__init__( app ) + self.history_manager = histories.HistoryManager() + + @expose_api def index(self, trans, **kwd): """ GET /api/workflows @@ -54,30 +60,21 @@ rval.append(item) return rval - @web.expose_api + @expose_api def show(self, trans, id, **kwd): """ GET /api/workflows/{encoded_workflow_id} Displays information needed to run a workflow from the command line. """ - workflow_id = id - try: - decoded_workflow_id = trans.security.decode_id(workflow_id) - except TypeError: - trans.response.status = 400 - return "Malformed workflow id ( %s ) specified, unable to decode." % str(workflow_id) - try: - stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).get(decoded_workflow_id) - if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is neither importable, nor owned by or shared with current user") - except: - trans.response.status = 400 - return "That workflow does not exist." + stored_workflow = self.__get_stored_workflow( trans, id ) + if stored_workflow.importable is False and stored_workflow.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: + message = "Workflow is neither importable, nor owned by or shared with current user" + raise exceptions.ItemAccessibilityException( message ) + item = stored_workflow.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) - item['url'] = url_for('workflow', id=workflow_id) + item['url'] = url_for('workflow', id=id) item['owner'] = stored_workflow.user.username latest_workflow = stored_workflow.latest_workflow inputs = {} @@ -114,7 +111,7 @@ item['steps'] = steps return item - @web.expose_api + @expose_api def create(self, trans, payload, **kwd): """ POST /api/workflows @@ -161,10 +158,20 @@ :param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history :type workflow_name: str """ + ways_to_create = set( [ + 'workflow_id', + 'installed_repository_file', + 'from_history_id', + 'shared_workflow_id', + 'workflow', + ] ).intersection( payload ) + if len( ways_to_create ) == 0: + message = "One parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterMissingException( message ) - if len( set( ['workflow_id', 'installed_repository_file', 'from_history_id'] ).intersection( payload ) ) > 1: - trans.response.status = 403 - return "Only one among 'workflow_id', 'installed_repository_file', 'from_history_id' must be specified" + if len( ways_to_create ) > 1: + message = "Only one parameter among - %s - must be specified" % ", ".join( ways_to_create ) + raise exceptions.RequestParameterInvalidException( message ) if 'installed_repository_file' in payload: workflow_controller = trans.webapp.controllers[ 'workflow' ] @@ -193,121 +200,27 @@ item[ 'url' ] = url_for( 'workflow', id=item[ 'id' ] ) return item + if 'shared_workflow_id' in payload: + workflow_id = payload[ 'shared_workflow_id' ] + return self.__api_import_shared_workflow( trans, workflow_id, payload ) + + if 'workflow' in payload: + return self.__api_import_new_workflow( trans, payload, **kwd ) + workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: - trans.response.status = 403 - return "Either workflow_id, installed_repository_file or from_history_id must be specified" - - # Pull other parameters out of payload. - param_map = payload.get( 'parameters', {} ) - inputs = payload.get( 'inputs', None ) - inputs_by = payload.get( 'inputs_by', None ) - if inputs is None: - # Default to legacy behavior - read ds_map and reference steps - # by unencoded step id (a raw database id). - inputs = payload.get( 'ds_map', {} ) - inputs_by = inputs_by or 'step_id' - else: - inputs = inputs or {} - # New default is to reference steps by index of workflow step - # which is intrinsic to the workflow and independent of the state - # of Galaxy at the time of workflow import. - inputs_by = inputs_by or 'step_index' - - valid_inputs_by = [ 'step_id', 'step_index', 'name' ] - if inputs_by not in valid_inputs_by: - trans.response.status = 403 - error_message_template = "Invalid inputs_by specified '%s' must be one of %s" - error_message = error_message_template % ( inputs_by, valid_inputs_by ) - raise ValueError( error_message ) - - add_to_history = 'no_add_to_history' not in payload - history_param = payload.get('history', '') + message = "Invalid workflow_id specified." + raise exceptions.RequestParameterInvalidException( message ) # Get workflow + accessibility check. - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) workflow = stored_workflow.latest_workflow - # Sanity checks. - if not workflow: - trans.response.status = 400 - return "Workflow not found." - if len( workflow.steps ) == 0: - trans.response.status = 400 - return "Workflow cannot be run because it does not have any steps" - if workflow.has_cycles: - trans.response.status = 400 - return "Workflow cannot be run because it contains cycles" - if workflow.has_errors: - trans.response.status = 400 - return "Workflow cannot be run because of validation errors in some steps" + run_config = build_workflow_run_config( trans, workflow, payload ) + history = run_config.target_history - # Get target history. - if history_param.startswith('hist_id='): - # Passing an existing history to use. - history = trans.sa_session.query(self.app.model.History).get(trans.security.decode_id(history_param[8:])) - if history.user != trans.user and not trans.user_is_admin(): - trans.response.status = 400 - return "Invalid History specified." - else: - # Send workflow outputs to new history. - history = self.app.model.History(name=history_param, user=trans.user) - trans.sa_session.add(history) - trans.sa_session.flush() - - # Set workflow inputs. - for k in inputs: - try: - if inputs[k]['src'] == 'ldda': - ldda = trans.sa_session.query(self.app.model.LibraryDatasetDatasetAssociation).get( - trans.security.decode_id(inputs[k]['id'])) - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) - content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - elif inputs[k]['src'] == 'ld': - ldda = trans.sa_session.query(self.app.model.LibraryDataset).get( - trans.security.decode_id(inputs[k]['id'])).library_dataset_dataset_association - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) - content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - elif inputs[k]['src'] == 'hda': - # Get dataset handle, add to dict and history if necessary - content = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get( - trans.security.decode_id(inputs[k]['id'])) - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) - elif inputs[k]['src'] == 'hdca': - content = self.app.dataset_collections_service.get_dataset_collection_instance( - trans, - 'history', - inputs[k]['id'] - ) - else: - trans.response.status = 400 - return "Unknown dataset source '%s' specified." % inputs[k]['src'] - if add_to_history and content.history != history: - content = content.copy() - if isinstance( content, self.app.model.HistoryDatasetAssociation ): - history.add_dataset( content ) - else: - history.add_dataset_collection( content ) - inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly - except AssertionError: - trans.response.status = 400 - return "Invalid Dataset '%s' Specified" % inputs[k]['id'] - - # Run each step, connecting outputs to inputs - replacement_dict = payload.get('replacement_params', {}) - - run_config = WorkflowRunConfig( - target_history=history, - replacement_dict=replacement_dict, - inputs=inputs, - inputs_by=inputs_by, - param_map=param_map, - ) - + # invoke may throw MessageExceptions on tool erors, failure + # to match up inputs, etc... outputs = invoke( trans=trans, workflow=workflow, @@ -327,30 +240,22 @@ return rval - @web.expose_api + @expose_api def workflow_dict( self, trans, workflow_id, **kwd ): """ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow as a json dictionary. """ - try: - stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - except Exception, e: - return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e )) - # check to see if user has permissions to selected workflow - if stored_workflow.user != trans.user and not trans.user_is_admin(): - if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: - trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) ret_dict = self._workflow_to_dict( trans, stored_workflow ) if not ret_dict: # This workflow has a tool that's missing from the distribution - trans.response.status = 400 - return "Workflow cannot be exported due to missing tools." + message = "Workflow cannot be exported due to missing tools." + raise exceptions.MessageException( message ) return ret_dict - @web.expose_api + @expose_api def delete( self, trans, id, **kwd ): """ DELETE /api/workflows/{encoded_workflow_id} @@ -379,19 +284,39 @@ # TODO: Unsure of response message to let api know that a workflow was successfully deleted return ( "Workflow '%s' successfully deleted" % stored_workflow.name ) - @web.expose_api - def import_new_workflow(self, trans, payload, **kwd): + @expose_api + def import_new_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated workflow id. Author: rpark # currently assumes payload['workflow'] is a json representation of a workflow to be inserted into the database + + Deprecated in favor to POST /api/workflows with encoded 'workflow' in + payload the same way. """ + return self.__api_import_new_workflow( trans, payload, **kwd ) + def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] - workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="API" ) + publish = util.string_as_bool( payload.get( "publish", False ) ) + # If 'publish' set, default to importable. + importable = util.string_as_bool( payload.get( "importable", publish ) ) + + if publish and not importable: + raise exceptions.RequestParameterInvalidException( "Published workflow must be importable." ) + + from_dict_kwds = dict( + source="API", + publish=publish, + ) + workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds ) + + if importable: + self._make_item_accessible( trans.sa_session, workflow ) + trans.sa_session.flush() # galaxy workflow newly created id workflow_id = workflow.id @@ -409,7 +334,7 @@ return item @expose_api - def import_shared_workflow(self, trans, payload, **kwd): + def import_shared_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/import Import a workflow shared by other users. @@ -423,14 +348,17 @@ workflow_id = payload.get('workflow_id', None) if workflow_id is None: raise exceptions.ObjectAttributeMissingException( "Missing required parameter 'workflow_id'." ) + self.__api_import_shared_workflow( trans, workflow_id, payload ) + + def __api_import_shared_workflow( self, trans, workflow_id, payload, **kwd ): try: stored_workflow = self.get_stored_workflow( trans, workflow_id, check_ownership=False ) except: raise exceptions.ObjectNotFound( "Malformed workflow id ( %s ) specified." % workflow_id ) if stored_workflow.importable is False: - raise exceptions.MessageException( 'The owner of this workflow has disabled imports via this link.' ) + raise exceptions.ItemAccessibilityException( 'The owner of this workflow has disabled imports via this link.' ) elif stored_workflow.deleted: - raise exceptions.MessageException( "You can't import this workflow because it has been deleted." ) + raise exceptions.ItemDeletionException( "You can't import this workflow because it has been deleted." ) imported_workflow = self._import_shared_workflow( trans, stored_workflow ) item = imported_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(imported_workflow.id) @@ -491,3 +419,32 @@ if out is not None: return self.encode_all_ids( trans, out.to_dict('element'), True) return None + + def __get_stored_accessible_workflow( self, trans, workflow_id ): + stored_workflow = self.__get_stored_workflow( trans, workflow_id ) + + # check to see if user has permissions to selected workflow + if stored_workflow.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: + message = "Workflow is not owned by or shared with current user" + raise exceptions.ItemAccessibilityException( message ) + + return stored_workflow + + def __get_stored_workflow( self, trans, workflow_id ): + workflow_id = self.__decode_id( trans, workflow_id ) + try: + query = trans.sa_session.query( trans.app.model.StoredWorkflow ) + stored_workflow = query.get( workflow_id ) + except Exception: + raise exceptions.ObjectNotFound( "No such workflow found - invalid workflow identifier." ) + if stored_workflow is None: + raise exceptions.ObjectNotFound( "No such workflow found." ) + return stored_workflow + + def __decode_id( self, trans, workflow_id, model_type="workflow" ): + try: + return trans.security.decode_id( workflow_id ) + except Exception: + message = "Malformed %s id ( %s ) specified, unable to decode" % ( model_type, workflow_id ) + raise exceptions.MalformedId( message ) diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -213,13 +213,13 @@ webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) - # "POST /api/workflows/import" => ``workflows.import_workflow()``. - # Defines a named route "import_workflow". - webapp.mapper.connect( 'import_workflow', '/api/workflows/upload', controller='workflows', action='import_new_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with 'workflow' in payload. + webapp.mapper.connect( 'import_workflow_deprecated', '/api/workflows/upload', controller='workflows', action='import_new_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) - webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_workflow', conditions=dict( method=['POST'] ) ) + # Deprecated in favor of POST /api/workflows with shared_workflow_id in payload. + webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) ) webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET'])) webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET'])) diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -51,7 +51,7 @@ use_panels = True title = "Saved Workflows" model_class = model.StoredWorkflow - default_filter = { "name" : "All", "tags": "All" } + default_filter = { "name": "All", "tags": "All" } default_sort_key = "-update_time" columns = [ grids.TextColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), @@ -62,10 +62,11 @@ ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", visible=False, filterable="standard" ) - ) + "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", visible=False, filterable="standard" + ) + ) operations = [ grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Run", condition=( lambda item: not item.deleted ), async_compatible=False ), @@ -95,19 +96,24 @@ ] columns.append( grids.MulticolFilterColumn( - "Search name, annotation, owner, and tags", - cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], - key="free-text-search", visible=False, filterable="standard" ) - ) + "Search name, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], + key="free-text-search", visible=False, filterable="standard" + ) + ) operations = [ - grids.GridOperation( "Import", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="imp" ) ), - grids.GridOperation( "Save as File", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="export_to_file" ) ), + grids.GridOperation( + "Import", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="imp") + ), + grids.GridOperation( + "Save as File", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="export_to_file" ) + ), ] def build_initial_query( self, trans, **kwargs ): @@ -275,7 +281,7 @@ user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, stored_workflow ) return trans.fill_template_mako( "workflow/display.mako", item=stored_workflow, item_data=stored_workflow.latest_workflow.steps, - user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) + user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) @web.expose def get_item_content_async( self, trans, id ): @@ -390,7 +396,7 @@ # Do import. stored = self.get_stored_workflow( trans, id, check_ownership=False ) - if stored.importable == False: + if stored.importable is False: return trans.show_error_message( "The owner of this workflow has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True ) elif stored.deleted: return trans.show_error_message( "You can't import this workflow because it has been deleted.<br>You can %s" % referer_message, use_panels=True ) @@ -415,7 +421,7 @@ if 'annotation' in kwargs: # Set workflow annotation; sanitize annotation before adding it. annotation = sanitize_html( kwargs[ 'annotation' ], 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), stored, annotation ) + self.add_item_annotation( trans.sa_session, trans.get_user(), stored, annotation ) trans.sa_session.flush() return trans.fill_template( 'workflow/edit_attributes.mako', stored=stored, @@ -511,7 +517,7 @@ """ Returns workflow's name and link. """ stored = self.get_stored_workflow( trans, id ) - return_dict = { "name" : stored.name, "link" : url_for(controller='workflow', action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } + return_dict = { "name": stored.name, "link": url_for(controller='workflow', action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } return return_dict @web.expose @@ -583,8 +589,8 @@ return self.editor( trans, id=trans.security.encode_id(stored_workflow.id )) else: return form( url_for(controller="workflow", action="create"), "Create New Workflow", submit_text="Create", use_panels=True ) \ - .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ - .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) + .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ + .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) @web.expose def delete( self, trans, id=None ): @@ -665,7 +671,7 @@ module = module_factory.new( trans, type, **kwargs ) return { 'type': module.type, - 'name': module.get_name(), + 'name': module.get_name(), 'tool_id': module.get_tool_id(), 'tool_state': module.get_state(), 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), @@ -750,9 +756,9 @@ 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), 'form_html': module.get_config_form(), - 'annotation' : annotation_str, - 'post_job_actions' : {}, - 'workflow_outputs' : [] + 'annotation': annotation_str, + 'post_job_actions': {}, + 'workflow_outputs': [] } # Connections input_connections = step.input_connections @@ -838,8 +844,8 @@ errors.append("Step %s requires tool '%s'." % (step_dict['id'], step_dict['tool_id'])) if errors: return dict( name=workflow.name, - message="This workflow includes missing or invalid tools. It cannot be saved until the following steps are removed or the missing tools are enabled.", - errors=errors) + message="This workflow includes missing or invalid tools. It cannot be saved until the following steps are removed or the missing tools are enabled.", + errors=errors ) # First pass to build step objects and populate basic values for key, step_dict in data['steps'].iteritems(): # Create the model class for the step @@ -932,18 +938,19 @@ workflow_content = json.dumps( workflow_dict, indent=4, sort_keys=True ) # Create myExperiment request. - request_raw = trans.fill_template( "workflow/myexp_export.mako", \ - workflow_name=workflow_dict['name'], \ - workflow_description=workflow_dict['annotation'], \ - workflow_content=workflow_content, \ - workflow_svg=self._workflow_to_svg_canvas( trans, stored ).standalone_xml() - ) + request_raw = trans.fill_template( + "workflow/myexp_export.mako", + workflow_name=workflow_dict['name'], + workflow_description=workflow_dict['annotation'], + workflow_content=workflow_content, + workflow_svg=self._workflow_to_svg_canvas( trans, stored ).standalone_xml() + ) # strip() b/c myExperiment XML parser doesn't allow white space before XML; utf-8 handles unicode characters. request = unicode( request_raw.strip(), 'utf-8' ) # Do request and get result. auth_header = base64.b64encode( '%s:%s' % ( myexp_username, myexp_password )) - headers = { "Content-type": "text/xml", "Accept": "text/xml", "Authorization" : "Basic %s" % auth_header } + headers = { "Content-type": "text/xml", "Accept": "text/xml", "Authorization": "Basic %s" % auth_header } myexp_url = trans.app.config.get( "myexperiment_url", self.__myexp_url ) conn = httplib.HTTPConnection( myexp_url ) # NOTE: blocks web thread. @@ -958,14 +965,14 @@ myexp_workflow_id = parser.tag_content workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( controller='workflow', action='list' ) if myexp_workflow_id: - return trans.show_message( \ + return trans.show_message( """Workflow '%s' successfully exported to myExperiment. <br/><a href="http://%s/workflows/%s">Click here to view the workflow on myExperiment</a> %s """ % ( stored.name, myexp_url, myexp_workflow_id, workflow_list_str ), use_panels=True ) else: - return trans.show_error_message( \ - "Workflow '%s' could not be exported to myExperiment. Error: %s %s" % \ + return trans.show_error_message( + "Workflow '%s' could not be exported to myExperiment. Error: %s %s" % ( stored.name, response_data, workflow_list_str ), use_panels=True ) @web.json_pretty @@ -1205,10 +1212,10 @@ jobs, warnings = summarize( trans ) # Render return trans.fill_template( - "workflow/build_from_current_history.mako", - jobs=jobs, - warnings=warnings, - history=history + "workflow/build_from_current_history.mako", + jobs=jobs, + warnings=warnings, + history=history ) else: stored_workflow = extract_workflow( @@ -1223,10 +1230,10 @@ workflow_id = trans.security.encode_id( stored_workflow.id ) return trans.show_message( 'Workflow "%s" created from current history. You can <a href="%s" target="_parent">edit</a> or <a href="%s">run</a> the workflow.' % ( workflow_name, url_for( controller='workflow', action='editor', id=workflow_id ), - url_for( controller='workflow', action='run', id=workflow_id ) ) ) + url_for( controller='workflow', action='run', id=workflow_id ) ) ) @web.expose - def run( self, trans, id, history_id=None, multiple_input_mode="product", hide_fixed_params=False, **kwargs ): + def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) user = trans.get_user() if stored.user != user: @@ -1269,7 +1276,7 @@ # been POSTed # List to gather values for the template invocations = [] - for (kwargs, multi_input_keys) in _expand_multiple_inputs(kwargs, mode=multiple_input_mode): + for (kwargs, multi_input_keys) in _expand_multiple_inputs(kwargs): for step in workflow.steps: step.upgrade_messages = {} # Connections by input name @@ -1350,8 +1357,8 @@ trans.sa_session.flush() if invocations: return trans.fill_template( "workflow/run_complete.mako", - workflow=stored, - invocations=invocations ) + workflow=stored, + invocations=invocations ) else: # Prepare each step missing_tools = [] @@ -1388,24 +1395,27 @@ step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) if missing_tools: stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) - return trans.fill_template("workflow/run.mako", - steps=[], - workflow=stored, - hide_fixed_params=hide_fixed_params, - missing_tools=missing_tools) + return trans.fill_template( + "workflow/run.mako", + steps=[], + workflow=stored, + hide_fixed_params=hide_fixed_params, + missing_tools=missing_tools + ) # Render the form stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) return trans.fill_template( - "workflow/run.mako", - steps=workflow.steps, - workflow=stored, - has_upgrade_messages=has_upgrade_messages, - step_version_changes=step_version_changes, - errors=errors, - incoming=kwargs, - history_id=history_id, - hide_fixed_params=hide_fixed_params, - enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults) + "workflow/run.mako", + steps=workflow.steps, + workflow=stored, + has_upgrade_messages=has_upgrade_messages, + step_version_changes=step_version_changes, + errors=errors, + incoming=kwargs, + history_id=history_id, + hide_fixed_params=hide_fixed_params, + enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults + ) finally: # restore the active history if saved_history is not None: @@ -1484,12 +1494,12 @@ step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) # Render the form return trans.fill_template( - "workflow/tag_outputs.mako", - steps=workflow.steps, - workflow=stored, - has_upgrade_messages=has_upgrade_messages, - errors=errors, - incoming=kwargs + "workflow/tag_outputs.mako", + steps=workflow.steps, + workflow=stored, + has_upgrade_messages=has_upgrade_messages, + errors=errors, + incoming=kwargs ) @web.expose @@ -1539,7 +1549,7 @@ shared_by_others=shared_by_others, ids_in_menu=ids_in_menu, message=message, - refresh_frames=['tools'] ) + refresh_frames=refresh_frames ) def _workflow_to_svg_canvas( self, trans, stored ): workflow = stored.latest_workflow @@ -1619,17 +1629,17 @@ if len(step_dict['data_inputs']) > 0: box_height += 15 sep_y = y + len(step_dict['data_inputs']) * line_px + 40 - text.append( svgfig.Line(x-margin, sep_y, x+width-margin, sep_y).SVG() ) # + text.append( svgfig.Line(x - margin, sep_y, x + width - margin, sep_y).SVG() ) # input/output box - boxes.append( svgfig.Rect(x-margin, y+30, x+width-margin, y+30+box_height, fill="#ffffff").SVG() ) + boxes.append( svgfig.Rect(x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff").SVG() ) for conn, output_dict in step_dict['input_connections'].iteritems(): in_coords = in_pos[step_dict['id']][conn] out_conn_pos = out_pos[output_dict['id']][output_dict['output_name']] adjusted = (out_conn_pos[0] + widths[output_dict['id']], out_conn_pos[1]) - text.append( svgfig.SVG("circle", cx=out_conn_pos[0]+widths[output_dict['id']]-margin, cy=out_conn_pos[1]-margin, r=5, fill="#ffffff" ) ) - connectors.append( svgfig.Line(adjusted[0], adjusted[1]-margin, in_coords[0]-10, in_coords[1], arrow_end="true" ).SVG() ) + text.append( svgfig.SVG("circle", cx=out_conn_pos[0] + widths[output_dict['id']] - margin, cy=out_conn_pos[1] - margin, r=5, fill="#ffffff" ) ) + connectors.append( svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true" ).SVG() ) canvas.append(connectors) canvas.append(boxes) @@ -1653,17 +1663,15 @@ return " on %s and %s" % (", ".join(instance_ds_names[0:-1]), instance_ds_names[-1]) -def _expand_multiple_inputs(kwargs, mode): - (single_inputs, matched_multi_inputs, multiplied_multi_inputs) = \ - _split_inputs(kwargs, mode) +def _expand_multiple_inputs(kwargs): + (single_inputs, matched_multi_inputs, multiplied_multi_inputs) = _split_inputs(kwargs) # Build up every combination of inputs to be run together. input_combos = _extend_with_matched_combos(single_inputs, matched_multi_inputs) input_combos = _extend_with_multiplied_combos(input_combos, multiplied_multi_inputs) # Input name that are multiply specified - multi_input_keys = \ - matched_multi_inputs.keys() + multiplied_multi_inputs.keys() + multi_input_keys = matched_multi_inputs.keys() + multiplied_multi_inputs.keys() for input_combo in input_combos: for key, value in input_combo.iteritems(): @@ -1714,7 +1722,7 @@ return new_inputs -def _split_inputs(kwargs, mode): +def _split_inputs(kwargs): """ """ input_keys = filter(lambda a: a.endswith('|input'), kwargs) diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -13,48 +13,12 @@ from galaxy.tools.execute import execute from galaxy.util.odict import odict from galaxy.workflow import modules +from galaxy.workflow.run_request import WorkflowRunConfig import logging log = logging.getLogger( __name__ ) -class WorkflowRunConfig( object ): - """ Wrapper around all the ways a workflow execution can be parameterized. - - :param target_history: History to execute workflow in. - :type target_history: galaxy.model.History. - - :param replacement_dict: Workflow level parameters used for renaming post - job actions. - :type replacement_dict: dict - - :param copy_inputs_to_history: Should input data parameters be copied to - target_history. (Defaults to False) - :type copy_inputs_to_history: bool - - :param inputs: Map from step ids to dict's containing HDA for these steps. - :type inputs: dict - - :param inputs_by: How inputs maps to inputs (datasets/collections) to workflows - steps - by unencoded database id ('step_id'), index in workflow - 'step_index' (independent of database), or by input name for - that step ('name'). - :type inputs_by: str - - :param param_map: Override tool and/or step parameters (see documentation on - _update_step_parameters below). - :type param_map: - """ - - def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, inputs_by='step_id', param_map={} ): - self.target_history = target_history - self.replacement_dict = replacement_dict - self.copy_inputs_to_history = copy_inputs_to_history - self.inputs = inputs - self.inputs_by = inputs_by - self.param_map = param_map - - def invoke( trans, workflow, workflow_run_config ): """ Run the supplied workflow in the supplied target_history. """ @@ -73,9 +37,7 @@ self.target_history = workflow_run_config.target_history self.replacement_dict = workflow_run_config.replacement_dict self.copy_inputs_to_history = workflow_run_config.copy_inputs_to_history - self.inputs = workflow_run_config.inputs - self.inputs_by = workflow_run_config.inputs_by - self.inputs_by_step_id = {} + self.inputs_by_step_id = workflow_run_config.inputs self.param_map = workflow_run_config.param_map self.outputs = odict() @@ -223,8 +185,8 @@ outputs[ step.id ][ 'input_ds_copy' ] = new_hdca else: raise Exception("Unknown history content encountered") - if self.inputs: - outputs[ step.id ][ 'output' ] = self.inputs_by_step_id[ step.id ][ 'hda' ] + if self.inputs_by_step_id: + outputs[ step.id ][ 'output' ] = self.inputs_by_step_id[ step.id ] return job @@ -289,51 +251,10 @@ step.module = modules.module_factory.from_workflow_step( self.trans, step ) step.state = step.module.get_runtime_state() - # This is an input step. Make sure we have an available input. - if step.type in [ 'data_input', 'data_collection_input' ]: - if self.inputs_by == "step_id": - key = str( step.id ) - elif self.inputs_by == "name": - key = step.tool_inputs.get( 'name', None ) - else: - key = str( step.order_index ) - if key not in self.inputs: - message = "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id - raise exceptions.MessageException( message ) - else: - self.inputs_by_step_id[ step.id ] = self.inputs[ key ] - -def _update_step_parameters(step, param_map): - """ - Update ``step`` parameters based on the user-provided ``param_map`` dict. - - ``param_map`` should be structured as follows:: - - PARAM_MAP = {STEP_ID: PARAM_DICT, ...} - PARAM_DICT = {NAME: VALUE, ...} - - For backwards compatibility, the following (deprecated) format is - also supported for ``param_map``:: - - PARAM_MAP = {TOOL_ID: PARAM_DICT, ...} - - in which case PARAM_DICT affects all steps with the given tool id. - If both by-tool-id and by-step-id specifications are used, the - latter takes precedence. - - Finally (again, for backwards compatibility), PARAM_DICT can also - be specified as:: - - PARAM_DICT = {'param': NAME, 'value': VALUE} - - Note that this format allows only one parameter to be set per step. - """ - param_dict = param_map.get(step.tool_id, {}).copy() - param_dict.update(param_map.get(str(step.id), {})) +def _update_step_parameters(step, normalized_param_map): + param_dict = normalized_param_map.get(step.id, {}) if param_dict: - if 'param' in param_dict and 'value' in param_dict: - param_dict[param_dict['param']] = param_dict['value'] step.state.inputs.update(param_dict) diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f lib/galaxy/workflow/run_request.py --- /dev/null +++ b/lib/galaxy/workflow/run_request.py @@ -0,0 +1,230 @@ +from galaxy import exceptions + +from galaxy.managers import histories + +INPUT_STEP_TYPES = [ 'data_input', 'data_collection_input' ] + + +class WorkflowRunConfig( object ): + """ Wrapper around all the ways a workflow execution can be parameterized. + + :param target_history: History to execute workflow in. + :type target_history: galaxy.model.History. + + :param replacement_dict: Workflow level parameters used for renaming post + job actions. + :type replacement_dict: dict + + :param copy_inputs_to_history: Should input data parameters be copied to + target_history. (Defaults to False) + :type copy_inputs_to_history: bool + + :param inputs: Map from step ids to dict's containing HDA for these steps. + :type inputs: dict + + :param inputs_by: How inputs maps to inputs (datasets/collections) to workflows + steps - by unencoded database id ('step_id'), index in workflow + 'step_index' (independent of database), or by input name for + that step ('name'). + :type inputs_by: str + + :param param_map: Override step parameters - should be dict with step id keys and + tool param name-value dicts as values. + :type param_map: dict + """ + + def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, param_map={} ): + self.target_history = target_history + self.replacement_dict = replacement_dict + self.copy_inputs_to_history = copy_inputs_to_history + self.inputs = inputs + self.param_map = param_map + + +def normalize_inputs(steps, inputs, inputs_by): + normalized_inputs = {} + for step in steps: + if step.type not in INPUT_STEP_TYPES: + continue + + if inputs_by == "step_id": + inputs_key = str( step.id ) + elif inputs_by == "step_index": + inputs_key = str( step.order_index ) + elif inputs_by == "name": + inputs_key = step.tool_inputs.get( 'name', None ) + else: + message = "Workflow cannot be run because unexpected inputs_by value specified." + raise exceptions.MessageException( message ) + if inputs_key not in inputs: + message = "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id + raise exceptions.MessageException( message ) + + normalized_inputs[ step.id ] = inputs[ inputs_key ][ 'content' ] + + return normalized_inputs + + +def normalize_step_parameters(steps, param_map): + """ Take a complex param_map that can reference parameters by + step_id in the new flexible way or in the old one-parameter + per tep fashion or by tool id and normalize the parameters so + everything is referenced by a numeric step id. + """ + normalized_param_map = {} + for step in steps: + param_dict = _step_parameters(step, param_map) + if param_dict: + normalized_param_map[step.id] = param_dict + return normalized_param_map + + +def _step_parameters(step, param_map): + """ + Update ``step`` parameters based on the user-provided ``param_map`` dict. + + ``param_map`` should be structured as follows:: + + PARAM_MAP = {STEP_ID: PARAM_DICT, ...} + PARAM_DICT = {NAME: VALUE, ...} + + For backwards compatibility, the following (deprecated) format is + also supported for ``param_map``:: + + PARAM_MAP = {TOOL_ID: PARAM_DICT, ...} + + in which case PARAM_DICT affects all steps with the given tool id. + If both by-tool-id and by-step-id specifications are used, the + latter takes precedence. + + Finally (again, for backwards compatibility), PARAM_DICT can also + be specified as:: + + PARAM_DICT = {'param': NAME, 'value': VALUE} + + Note that this format allows only one parameter to be set per step. + """ + param_dict = param_map.get(step.tool_id, {}).copy() + param_dict.update(param_map.get(str(step.id), {})) + if param_dict: + if 'param' in param_dict and 'value' in param_dict: + param_dict[param_dict['param']] = param_dict['value'] + del param_dict[ 'param' ] + del param_dict[ 'value' ] + return param_dict + + +def build_workflow_run_config( trans, workflow, payload ): + app = trans.app + history_manager = histories.HistoryManager() + + # Pull other parameters out of payload. + param_map = payload.get( 'parameters', {} ) + param_map = normalize_step_parameters( workflow.steps, param_map ) + inputs = payload.get( 'inputs', None ) + inputs_by = payload.get( 'inputs_by', None ) + if inputs is None: + # Default to legacy behavior - read ds_map and reference steps + # by unencoded step id (a raw database id). + inputs = payload.get( 'ds_map', {} ) + inputs_by = inputs_by or 'step_id' + else: + inputs = inputs or {} + # New default is to reference steps by index of workflow step + # which is intrinsic to the workflow and independent of the state + # of Galaxy at the time of workflow import. + inputs_by = inputs_by or 'step_index' + + add_to_history = 'no_add_to_history' not in payload + history_param = payload.get('history', '') + + # Sanity checks. + if len( workflow.steps ) == 0: + raise exceptions.MessageException( "Workflow cannot be run because it does not have any steps" ) + if workflow.has_cycles: + raise exceptions.MessageException( "Workflow cannot be run because it contains cycles" ) + if workflow.has_errors: + message = "Workflow cannot be run because of validation errors in some steps" + raise exceptions.MessageException( message ) + + # Get target history. + if history_param.startswith('hist_id='): + # Passing an existing history to use. + encoded_history_id = history_param[ 8: ] + history_id = __decode_id( trans, encoded_history_id, model_type="history" ) + history = history_manager.get( trans, history_id, check_ownership=True ) + else: + # Send workflow outputs to new history. + history = app.model.History(name=history_param, user=trans.user) + trans.sa_session.add(history) + trans.sa_session.flush() + + # Set workflow inputs. + for input_dict in inputs.itervalues(): + if 'src' not in input_dict: + message = "Not input source type defined for input '%s'." % input_dict + raise exceptions.RequestParameterInvalidException( message ) + if 'id' not in input_dict: + message = "Not input id defined for input '%s'." % input_dict + raise exceptions.RequestParameterInvalidException( message ) + if 'content' in input_dict: + message = "Input cannot specify explicit 'content' attribute %s'." % input_dict + raise exceptions.RequestParameterInvalidException( message ) + input_source = input_dict['src'] + input_id = input_dict['id'] + try: + if input_source == 'ldda': + ldda = trans.sa_session.query(app.model.LibraryDatasetDatasetAssociation).get( + trans.security.decode_id(input_id)) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) + content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) + elif input_source == 'ld': + ldda = trans.sa_session.query(app.model.LibraryDataset).get( + trans.security.decode_id(input_id)).library_dataset_dataset_association + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) + content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) + elif input_source == 'hda': + # Get dataset handle, add to dict and history if necessary + content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get( + trans.security.decode_id(input_id)) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) + elif input_source == 'hdca': + content = app.dataset_collections_service.get_dataset_collection_instance( + trans, + 'history', + input_id + ) + else: + message = "Unknown workflow input source '%s' specified." % input_source + raise exceptions.RequestParameterInvalidException( message ) + if add_to_history and content.history != history: + content = content.copy() + if isinstance( content, app.model.HistoryDatasetAssociation ): + history.add_dataset( content ) + else: + history.add_dataset_collection( content ) + input_dict['content'] = content + except AssertionError: + message = "Invalid workflow input '%s' specified" % input_id + raise exceptions.ItemAccessibilityException( message ) + + normalized_inputs = normalize_inputs( workflow.steps, inputs, inputs_by ) + + # Run each step, connecting outputs to inputs + replacement_dict = payload.get('replacement_params', {}) + + run_config = WorkflowRunConfig( + target_history=history, + replacement_dict=replacement_dict, + inputs=normalized_inputs, + param_map=param_map, + ) + return run_config + + +def __decode_id( trans, workflow_id, model_type="workflow" ): + try: + return trans.security.decode_id( workflow_id ) + except Exception: + message = "Malformed %s id ( %s ) specified, unable to decode" % ( model_type, workflow_id ) + raise exceptions.MalformedId( message ) diff -r 03add18a83bad26eef0b6227e5b5b065ba7a3e30 -r 8b087dace61bb1426656b5599b1b15be72d98b9f static/scripts/libs/bibtex.js --- a/static/scripts/libs/bibtex.js +++ b/static/scripts/libs/bibtex.js @@ -93,6 +93,7 @@ 'booklet' : 14, 'masterthesis' : 15, 'conference' : 16 + ,'data' : 999 // Galaxy MOD: Handle @data citations coming from figshare. } /** @private */ this.MACROS_ = { 'jan' : 'January', This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/7b6bb5037e77/ Changeset: 7b6bb5037e77 User: martenson Date: 2014-08-12 23:39:36 Summary: library tweaks, help buttons, refactoring, Affected #: 15 files diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -161,10 +161,13 @@ # Check whether user can modify the current folder can_modify_folder = is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, folder ) - + parent_library_id = None + if folder.parent_library is not None: + parent_library_id = trans.security.encode_id( folder.parent_library.id ) metadata = dict( full_path=full_path, can_add_library_item=can_add_library_item, - can_modify_folder=can_modify_folder ) + can_modify_folder=can_modify_folder, + parent_library_id=parent_library_id ) folder_container = dict( metadata=metadata, folder_contents=folder_contents ) return folder_container diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -80,7 +80,7 @@ rval[ 'can_user_manage' ] = trans.app.security_agent.can_manage_dataset( current_user_roles, library_dataset.library_dataset_dataset_association.dataset) or trans.user_is_admin() return rval - @expose_api + @expose_api_anonymous def show_version( self, trans, encoded_dataset_id, encoded_ldda_id, **kwd ): """ show_version( self, trans, encoded_dataset_id, encoded_ldda_id, **kwd ): diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -88,6 +88,13 @@ this.ldda.fetch({ success: function(){ that.renderVersion(); + }, + error: function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error(response.responseJSON.err_msg); + } else { + mod_toastr.error('An error ocurred :('); + } } }); } @@ -153,8 +160,12 @@ var self = this; this.histories = new mod_library_model.GalaxyHistories(); this.histories.fetch({ - success: function (){ - callback(self); + success: function (histories){ + if (histories.length === 0){ + mod_toastr.warning('You have to create history first. Click this to do so.', '', {onclick: function() {window.location='/';}}); + } else { + callback(self); + } }, error: function(model, response){ if (typeof response.responseJSON !== "undefined"){ @@ -645,7 +656,7 @@ tmpl_array.push('<div class="library_style_container">'); tmpl_array.push(' <div id="library_toolbar">'); - tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to current dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Latest dataset</span></button><a>'); + tmpl_array.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>'); tmpl_array.push(' </div>'); // BREADCRUMBS diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -100,7 +100,7 @@ upper_folder_id = path[path.length-2][0]; } - this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, id: this.options.id, upper_folder_id: upper_folder_id, order: this.sort})); + this.$el.html(template({ path: this.folderContainer.attributes.metadata.full_path, parent_library_id: this.folderContainer.attributes.metadata.parent_library_id, id: this.options.id, upper_folder_id: upper_folder_id, order: this.sort})); // initialize the library tooltips $("#center [data-toggle]").tooltip(); @@ -304,7 +304,7 @@ tmpl_array.push('</ol>'); // FOLDER CONTENT - tmpl_array.push('<table id="folder_table" class="grid table table-condensed">'); + tmpl_array.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">'); tmpl_array.push(' <thead>'); tmpl_array.push(' <th class="button_heading"></th>'); tmpl_array.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -346,8 +346,12 @@ self.histories.get(history_id).set({'contents' : history_contents}); self.modal.$el.find('#selected_history_content').html(history_contents_template({history_contents: history_contents.models.reverse()})); }, - error: function(){ - mod_toastr.error('An error ocurred :('); + error: function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error(response.responseJSON.err_msg); + } else { + mod_toastr.error('An error ocurred :('); + } } }); }, @@ -516,17 +520,36 @@ }, showLibInfo: function(){ - var self = this; - var template = this.templateLibInfoInModal(); - this.modal = Galaxy.modal; - this.modal.show({ - closing_events : true, - title : 'Library Information', - body : template({library:library}), - buttons : { - 'Close' : function() {Galaxy.modal.hide();} + var library_id = Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id; + var library = null; + var that = this; + if (Galaxy.libraries.libraryListView !== null){ + library = Galaxy.libraries.libraryListView.collection.get(library_id); + } else { + library = new mod_library_model.Library({id: library_id}); + library.fetch({ + success: function(){ + var template = that.templateLibInfoInModal(); + that.modal = Galaxy.modal; + that.modal.show({ + closing_events : true, + title : 'Library Information', + body : template({library:library}), + buttons : { + 'Close' : function() {Galaxy.modal.hide();} + } + }); + }, + error: function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error(response.responseJSON.err_msg); + } else { + mod_toastr.error('An error ocurred :('); + } } - }); + }) + } + }, templateToolBar: function(){ @@ -536,7 +559,8 @@ tmpl_array.push('<div class="library_style_container">'); // TOOLBAR START tmpl_array.push(' <div id="library_toolbar">'); - tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>'); + tmpl_array.push(' <span><strong>DATA LIBRARIES</strong></span>'); + tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>'); tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>'); @@ -553,7 +577,9 @@ tmpl_array.push(' </ul>'); tmpl_array.push(' </div>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>'); + tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>'); + tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); + tmpl_array.push(' </div>'); // TOOLBAR END tmpl_array.push(' <div id="folder_items_element">'); @@ -568,6 +594,13 @@ tmpl_array = []; tmpl_array.push('<div id="lif_info_modal">'); + tmpl_array.push('<h2>Library name:</h2>'); + tmpl_array.push('<p><%- library.get("name") %></p>'); + tmpl_array.push('<h3>Library description:</h3>'); + tmpl_array.push('<p><%- library.get("description") %></p>'); + tmpl_array.push('<h3>Library synopsis:</h3>'); + tmpl_array.push('<p><%- library.get("synopsis") %></p>'); + tmpl_array.push('</div>'); return _.template(tmpl_array.join('')); diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/scripts/mvc/library/library-librarylist-view.js --- a/static/scripts/mvc/library/library-librarylist-view.js +++ b/static/scripts/mvc/library/library-librarylist-view.js @@ -29,15 +29,12 @@ initialize : function(options){ this.options = _.defaults(this.options || {}, options); - var viewContext = this; - + var that = this; this.rowViews = {}; - this.collection = new mod_library_model.Libraries(); - this.collection.fetch({ success: function(){ - viewContext.render(); + that.render(); }, error: function(model, response){ if (typeof response.responseJSON !== "undefined"){ @@ -53,10 +50,6 @@ * or from a given array of library models, * or renders an empty list in case no data is given. */ render: function (options) { - /** - * need to hide manually because of the element removal - * bug in tooltip - */ $(".tooltip").hide(); var template = this.templateLibraryList(); var libraries_to_render = null; diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/scripts/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/mvc/library/library-librarytoolbar-view.js @@ -116,12 +116,19 @@ tmpl_array.push('<div class="library_style_container">'); // TOOLBAR tmpl_array.push(' <div id="toolbar_form">'); - tmpl_array.push(' <% if(admin_user === true) { %>'); - tmpl_array.push(' <div id="library_toolbar">'); - tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>'); - tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>'); + tmpl_array.push(' <div id="library_toolbar">'); + tmpl_array.push(' <span><strong>DATA LIBRARIES</strong></span>'); + tmpl_array.push(' <% if(admin_user === true) { %>'); + tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"> | <input id="include_deleted_chk" style="margin: 0;" type="checkbox"> include deleted |</input></span>'); + tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>'); tmpl_array.push(' </div>'); - tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <div>'); + tmpl_array.push(' '); + tmpl_array.push(' </div>'); + tmpl_array.push(' </div>'); tmpl_array.push(' <div id="libraries_element">'); // table with libraries will append here diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/scripts/packed/mvc/library/library-dataset-view.js --- a/static/scripts/packed/mvc/library/library-dataset-view.js +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){f(e)},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var g=new c.HistoryItem();g.url=g.urlRoot+f+"/contents";var e="/api/histories/"+f+"/set_as_current";$.ajax({url:e,type:"PUT"});g.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(i,h){if(typeof h.responseJSON!=="undefined"){d.error("Dataset not imported. "+h.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while fetching dataset permissions. :(")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you")}).fail(function(){d.error("An error occurred while making dataset private :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted")}).fail(function(){d.error("An error occurred while making dataset unrestricted :(")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting dataset permissions :(")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to current dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred :(")}}})},importCurrentIntoHistory:function(){var f=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var g=new c.HistoryItem();g.url=g.urlRoot+f+"/contents";var e="/api/histories/"+f+"/set_as_current";$.ajax({url:e,type:"PUT"});g.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(i,h){if(typeof h.responseJSON!=="undefined"){d.error("Dataset not imported. "+h.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while fetching dataset permissions. :(")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while fetching data with permissions. :(")})}},comingSoon:function(){d.warning("Feature coming soon")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you")}).fail(function(){d.error("An error occurred while making dataset private :(")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted")}).fail(function(){d.error("An error occurred while making dataset unrestricted :(")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved")}).fail(function(){d.error("An error occurred while setting dataset permissions :(")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("data_type")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("data_type")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("data_type")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sortColumnClicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sortColumnClicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll();this.checkEmptiness()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view","mvc/library/library-dataset-view"],function(d,f,g,e,a,c){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sortColumnClicked"},rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);this.fetchFolder()},fetchFolder:function(h){var h=h||{};this.options.include_deleted=h.include_deleted;var i=this;this.collection=new e.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new e.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(j){i.folder_container=j;i.render();i.addAll(j.get("folder").models);if(i.options.dataset_id){row=_.findWhere(i.rowViews,{id:i.options.dataset_id});if(row){row.showDatasetDetails()}else{g.error("Dataset not found. Showing folder instead.")}}},error:function(k,j){if(typeof j.responseJSON!=="undefined"){g.error(j.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{g.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(h){this.options=_.defaults(this.options,h);var i=this.templateFolder();$(".tooltip").hide();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:k,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var h=this.folderContainer.attributes.metadata;h.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(h);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(h){_.each(h.reverse(),function(i){Galaxy.libraries.folderListView.collection.add(i)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var h=this;_.each(this.collection.models.reverse(),function(i){h.renderOne(i)});this.postRender()},renderOne:function(i){if(i.get("type")!=="folder"){this.options.contains_file=true}i.set("folder_id",this.id);var h=new a.FolderRowView(i);this.rowViews[i.get("id")]=h;this.$el.find("#first_folder_item").after(h.el);$(".library-row").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(h){this.$el.find("#"+h.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sortColumnClicked:function(h){h.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll();this.checkEmptiness()},sortFolder:function(i,h){if(i==="name"){if(h==="asc"){return this.collection.sortByNameAsc()}else{if(h==="desc"){return this.collection.sortByNameDesc()}}}},selectAll:function(i){var h=i.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=h;$row=$(this.parentElement.parentElement);if(h){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(i){var k="";var h;var j;if(i.target.localName==="input"){k=i.target;h=$(i.target.parentElement.parentElement);j="input"}else{if(i.target.localName==="td"){k=$("#"+i.target.parentElement.id).find(":checkbox")[0];h=$(i.target.parentElement);j="td"}}if(k.checked){if(j==="td"){k.checked="";this.makeWhiteRow(h)}else{if(j==="input"){this.makeDarkRow(h)}}}else{if(j==="td"){k.checked="selected";this.makeDarkRow(h)}else{if(j==="input"){this.makeWhiteRow(h)}}}},makeDarkRow:function(h){h.removeClass("light").addClass("dark");h.find("a").removeClass("light").addClass("dark");h.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(h){h.removeClass("dark").addClass("light");h.find("a").removeClass("dark").addClass("light");h.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var h=[];h.push('<ol class="breadcrumb">');h.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');h.push(" <% _.each(path, function(path_item) { %>");h.push(" <% if (path_item[0] != id) { %>");h.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');h.push("<% } else { %>");h.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');h.push(" <% } %>");h.push(" <% }); %>");h.push("</ol>");h.push('<table data-library-id="<%- parent_library_id %>" id="folder_table" class="grid table table-condensed">');h.push(" <thead>");h.push(' <th class="button_heading"></th>');h.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');h.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');h.push(' <th style="width:5%;">data type</th>');h.push(' <th style="width:10%;">size</th>');h.push(' <th style="width:160px;">time updated (UTC)</th>');h.push(' <th style="width:10%;"></th> ');h.push(" </thead>");h.push(' <tbody id="folder_list_body">');h.push(' <tr id="first_folder_item">');h.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" <td></td>");h.push(" </tr>");h.push(" </tbody>");h.push("</table>");h.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.</div>');return _.template(h.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=false;var f=true;if(Galaxy.currUser){i=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}var h=this.templateToolBar();this.$el.html(h({id:this.options.id,admin_user:i,anonym:f}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var f=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new c.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";f.push(m)}this.options.chain_call_control.total_number=f.length;var g="/api/histories/"+k+"/set_as_current";$.ajax({url:g,type:"PUT"});this.chainCall(f,n)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();var h=f.options.full_path[f.options.full_path.length-1][1];f.modal.show({closing_events:true,title:"Add datasets from history to "+h,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(i){f.fetchAndDisplayHistoryContents(i.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},showLibInfo:function(){var f=this;var g=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:g({library:library}),buttons:{Close:function(){Galaxy.modal.hide()}}})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>');tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(g){this.options=_.extend(this.options,g);var i=false;var f=true;if(Galaxy.currUser){i=Galaxy.currUser.isAdmin();f=Galaxy.currUser.isAnonymous()}var h=this.templateToolBar();this.$el.html(h({id:this.options.id,admin_user:i,anonym:f}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var k=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=k;var n=$("select[name=dataset_import_bulk] option:selected").text();var p=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){p.push(this.parentElement.parentElement.id)}});var o=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(o({history_name:n}));var l=100/p.length;this.initProgress(l);var f=[];for(var h=p.length-1;h>=0;h--){var j=p[h];var m=new c.HistoryItem();m.url=m.urlRoot+k+"/contents";m.content=j;m.source="library";f.push(m)}this.options.chain_call_control.total_number=f.length;var g="/api/histories/"+k+"/set_as_current";$.ajax({url:g,type:"PUT"});this.chainCall(f,n)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();var h=f.options.full_path[f.options.full_path.length-1][1];f.modal.show({closing_events:true,title:"Add datasets from history to "+h,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(i){f.fetchAndDisplayHistoryContents(i.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy());i.done(function(k){Galaxy.libraries.folderListView.collection.remove(h.id);f.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var j=new c.Item(k);Galaxy.libraries.folderListView.collection.add(j)}f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},showLibInfo:function(){var g=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var f=null;var h=this;if(Galaxy.libraries.libraryListView!==null){f=Galaxy.libraries.libraryListView.collection.get(g)}else{f=new c.Library({id:g});f.fetch({success:function(){var i=h.templateLibInfoInModal();h.modal=Galaxy.modal;h.modal.show({closing_events:true,title:"Library Information",body:i({library:f}),buttons:{Close:function(){Galaxy.modal.hide()}}})},error:function(j,i){if(typeof i.responseJSON!=="undefined"){e.error(i.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/scripts/packed/mvc/library/library-librarylist-view.js --- a/static/scripts/packed/mvc/library/library-librarylist-view.js +++ b/static/scripts/packed/mvc/library/library-librarylist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){h.render()},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},render:function(i){$(".tooltip").hide();var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);if(j.prepend){this.$el.find("#library_list_body").prepend(h.el)}else{this.$el.find("#library_list_body").append(h.el)}this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},});return{LibraryListView:f}}); \ No newline at end of file +define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(h){this.options=_.defaults(this.options||{},h);var i=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){i.render()},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},render:function(i){$(".tooltip").hide();var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);if(j.prepend){this.$el.find("#library_list_body").prepend(h.el)}else{this.$el.find("#library_list_body").append(h.el)}this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a> or visit the <a href="https://biostar.usegalaxy.org/">Galaxy support site</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},});return{LibraryListView:f}}); \ No newline at end of file diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/scripts/packed/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/packed/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-librarytoolbar-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},show_library_modal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.create_new_library_event()},Close:function(){d.modal.hide()}}})},create_new_library_event:function(){var f=this.serialize_new_library();if(this.validate_new_library(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clear_library_modal();Galaxy.libraries.libraryListView.render();b.success("Library created")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured :(")}}})}else{b.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(d){return d.name!==""},check_include_deleted:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form">');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"> include deleted</input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');tmpl_array.push(" </div>");tmpl_array.push(" <% } %>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=true;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},show_library_modal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.create_new_library_event()},Close:function(){d.modal.hide()}}})},create_new_library_event:function(){var f=this.serialize_new_library();if(this.validate_new_library(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clear_library_modal();Galaxy.libraries.libraryListView.render();b.success("Library created")},error:function(h,g){if(typeof g.responseJSON!=="undefined"){b.error(g.responseJSON.err_msg)}else{b.error("An error occured :(")}}})}else{b.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(d){return d.name!==""},check_include_deleted:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"> | <input id="include_deleted_chk" style="margin: 0;" type="checkbox"> include deleted |</input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button></span>');tmpl_array.push(" <% } %>");tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(" <div>");tmpl_array.push(" ");tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")}});return{LibraryToolbarView:c}}); \ No newline at end of file diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1329,6 +1329,7 @@ .libraryTitle th{text-align:left} pre.peek{background:white;color:black;overflow:auto} pre.peek th{color:white;background:#ebd9b2} +.help-button{float:right} span.expandLink{padding-left:12px;display:inline-block;vertical-align:middle;background:url(../images/silk/resultset_next.png) no-repeat} .folderRow.expanded span.expandLink{background:url(../images/silk/resultset_bottom.png) no-repeat} .folderRow span.rowIcon{float:left;margin-right:5px;width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png)} diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -32,6 +32,7 @@ .libraryTitle th{text-align:left} pre.peek{background:white;color:black;overflow:auto} pre.peek th{color:white;background:#ebd9b2} +.help-button{float:right} span.expandLink{padding-left:12px;display:inline-block;vertical-align:middle;background:url(../images/silk/resultset_next.png) no-repeat} .folderRow.expanded span.expandLink{background:url(../images/silk/resultset_bottom.png) no-repeat} .folderRow span.rowIcon{float:left;margin-right:5px;width:16px;height:16px;display:inline-block;vertical-align:middle;background:url(../images/silk/folder.png)} diff -r 8b087dace61bb1426656b5599b1b15be72d98b9f -r 7b6bb5037e778c05f04e414539966874169cc3e5 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -151,6 +151,10 @@ background: @table-heading-bg; } +.help-button { + float: right; +} + span.expandLink { padding-left: 12px; display: inline-block; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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