galaxy-commits May 2014

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commit/galaxy-central: martenson: data libraries: first take on api for requesting roles(assigned and assignable) for permissions; do not use - needs to be tested on test
by commits-noreply＠bitbucket.org 14 May '14

14 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/23bb24573f13/ Changeset: 23bb24573f13 User: martenson Date: 2014-05-14 19:53:01 Summary: data libraries: first take on api for requesting roles(assigned and assignable) for permissions; do not use - needs to be tested on test changes to UI, removed modal for dataset details, dissasembled into separate backbone view Affected #: 20 files diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -986,8 +986,8 @@ def dataset_is_private_to_user( self, trans, dataset ): """ - If the dataset object has exactly one access role and that is the - current user's private role then we consider the dataset private. + If the LibraryDataset object has exactly one access role and that is + the current user's private role then we consider the dataset private. """ private_role = self.get_private_user_role( trans.user ) access_roles = dataset.library_dataset_dataset_association.get_access_roles( trans ) diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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 @@ -68,53 +68,39 @@ raise exceptions.InternalServerError( 'Error loading from the database.' ) current_user_roles = trans.get_current_user_roles() - can_add_library_item = trans.user_is_admin() or trans.app.security_agent.can_add_library_item( current_user_roles, folder ) - if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): - if folder.parent_id is None: - try: - library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.root_folder_id == decoded_folder_id ).one() - except Exception: - raise exceptions.InternalServerError( 'Error loading from the database.' ) - if trans.app.security_agent.library_is_unrestricted( library ): - pass - else: - if trans.user: - log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) - else: - log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) ) - raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + # Special level of security on top of libraries. + if trans.app.security_agent.can_access_library( current_user_roles, folder.parent_library ): + pass + else: + if trans.user: + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) else: - if trans.user: - log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) - else: - log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) ) - raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + log.warning( "SECURITY: Anonymous user is trying to load restricted folder with ID of %s" % ( decoded_folder_id ) ) + raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) - def build_path( folder ): - """ - Search the path upwards recursively and load the whole route of - names and ids for breadcrumb building purposes. - - :param folder: current folder for navigating up - :param type: Galaxy LibraryFolder - - :returns: list consisting of full path to the library - :type: list - """ - path_to_root = [] - # We are almost in root - if folder.parent_id is None: - path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) - else: - # We add the current folder and traverse up one folder. - path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) - upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) - path_to_root.extend( build_path( upper_folder ) ) - return path_to_root - - # Return the reversed path so it starts with the library node. - full_path = build_path( folder )[::-1] + # if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + # log.debug('folder parent id: ' + str(folder.parent_id)) + # if folder.parent_id is None: + # try: + # library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.root_folder_id == decoded_folder_id ).one() + # except Exception: + # raise exceptions.InternalServerError( 'Error loading from the database.' ) + # if trans.app.security_agent.library_is_unrestricted( library ): + # pass + # else: + # if trans.user: + # log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) + # else: + # log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) ) + # raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) + # else: + # if trans.user: + # log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) ) + # else: + # log.debug('PARENT ID IS NOT NONE') + # log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) ) + # raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) ) folder_contents = [] update_time = '' @@ -128,17 +114,42 @@ 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 ) ) 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 + if trans.app.security_agent.dataset_is_public( content_item.library_dataset_dataset_association.dataset ): + is_unrestricted = True + else: + is_unrestricted = False + if trans.user: + is_private = trans.app.security_agent.dataset_is_private_to_user( trans, content_item ) + + # 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 ) + + nice_size = util.nice_size( int( content_item.library_dataset_dataset_association.get_size() ) ) + library_dataset_dict = content_item.to_dict() - library_dataset_dict[ 'is_unrestricted' ] = trans.app.security_agent.dataset_is_public( content_item.library_dataset_dataset_association.dataset ) - library_dataset_dict[ 'is_private' ] = trans.app.security_agent.dataset_is_private_to_user( trans, content_item ) - return_item.update( dict( data_type=library_dataset_dict[ 'data_type' ], - file_size=library_dataset_dict[ 'file_size' ], date_uploaded=library_dataset_dict[ 'date_uploaded' ], - is_unrestricted=library_dataset_dict[ 'is_unrestricted' ], - is_private=library_dataset_dict[ 'is_private' ] ) ) + is_unrestricted=is_unrestricted, + is_private=is_private, + can_manage=can_manage, + file_size=nice_size ) ) # For every item include the default meta-data return_item.update( dict( id=encoded_id, @@ -150,7 +161,42 @@ ) ) folder_contents.append( return_item ) - return { 'metadata': { 'full_path': full_path, 'can_add_library_item': can_add_library_item, 'folder_name': folder.name }, 'folder_contents': folder_contents } + # Return the reversed path so it starts with the library node. + 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 ) + + # Check whether user can modify current folder + can_modify_folder = 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, + can_modify_folder=can_modify_folder ) + folder_container = dict( metadata=metadata, folder_contents=folder_contents ) + return folder_container + + def build_path( self, trans, folder ): + """ + Search the path upwards recursively and load the whole route of + names and ids for breadcrumb building purposes. + + :param folder: current folder for navigating up + :param type: Galaxy LibraryFolder + + :returns: list consisting of full path to the library + :type: list + """ + path_to_root = [] + # We are almost in root + if folder.parent_id is None: + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + else: + # We add the current folder and traverse up one folder. + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + path_to_root.extend( self.build_path( trans, upper_folder ) ) + return path_to_root def _load_folder_contents( self, trans, folder, include_deleted ): """ @@ -291,14 +337,13 @@ :param encoded_folder_id: encoded id of Galaxy LibraryFolder :type encoded_folder_id: encoded string - :returns: last 16 chars of the encoded id in case it was Folder - (had 'F' prepended) + :returns: encoded id of Folder (had 'F' prepended) :type: string :raises: MalformedId """ - if ( len( encoded_folder_id ) == 17 and encoded_folder_id.startswith( 'F' )): - return encoded_folder_id[1:] + if ( ( len( encoded_folder_id ) % 16 == 1 ) and encoded_folder_id.startswith( 'F' ) ): + return encoded_folder_id[ 1: ] else: raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) ) @@ -307,11 +352,11 @@ """ GET /api/folders/{encoded_folder_id}/ """ - raise exceptions.NotImplemented( 'Showing the library folder content is not implemented.' ) + raise exceptions.NotImplemented( 'Showing the library folder content is not implemented here.' ) @web.expose_api def update( self, trans, id, library_id, payload, **kwd ): """ PUT /api/folders/{encoded_folder_id}/contents """ - raise exceptions.NotImplemented( 'Updating the library folder content is not implemented.' ) + raise exceptions.NotImplemented( 'Updating the library folder content is not implemented here.' ) diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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 @@ -47,12 +47,68 @@ dataset = self.get_library_dataset( trans, id=id, check_ownership=False, check_accessible=True ) except Exception: raise exceptions.ObjectNotFound( 'Requested dataset was not found.' ) + + # 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.insert(0, dataset_item) + full_path = full_path[ ::-1 ] + + nice_size = util.nice_size( int( dataset.library_dataset_dataset_association.get_size() ) ) + + date_uploaded = 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[ 'folder_id' ] = 'F' + rval[ 'folder_id' ] + rval[ 'full_path' ] = full_path + rval[ 'file_size' ] = nice_size + rval[ 'date_uploaded' ] = date_uploaded return rval @expose_api + def show_roles( self, trans, encoded_dataset_id, **kwd ): + """ + show_roles( self, trans, id, **kwd ): + GET /api/libraries/datasets/{encoded_dataset_id}/permissions: + Displays information about current and available roles + for a given dataset permission. + """ + current_user_roles = trans.get_current_user_roles() + page = int( kwd.get( 'page', None ) ) + page_limit = int( kwd.get( 'page_limit', None ) ) + 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.' ) + + cntrller = 'standard_user' + if trans.user_is_admin(): + cntrller = 'library_admin' + + roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) + 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 delete( self, trans, encoded_dataset_id, **kwd ): """ delete( self, trans, encoded_dataset_id, **kwd ): @@ -107,7 +163,9 @@ :raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound """ lddas = [] - datasets_to_download = kwd[ 'ldda_ids%5B%5D' ] + datasets_to_download = kwd.get( 'ldda_ids%5B%5D', None ) + if datasets_to_download is None: + datasets_to_download = kwd.get( 'ldda_ids', None ) if ( datasets_to_download is not None ): datasets_to_download = util.listify( datasets_to_download ) @@ -121,6 +179,8 @@ raise exceptions.InternalServerError( 'Internal error. ' + str( e.err_msg ) ) except Exception, e: raise exceptions.InternalServerError( 'Unknown error. ' + str( e ) ) + else: + raise exceptions.RequestParameterMissingException( 'Request has to contain a list of dataset ids to download.' ) if format in [ 'zip', 'tgz', 'tbz' ]: # error = False @@ -262,3 +322,25 @@ raise exceptions.InternalServerError( "This dataset contains no content." ) else: raise exceptions.RequestParameterInvalidException( "Wrong format parameter specified" ) + + def _build_path( self, trans, folder ): + """ + Search the path upwards recursively and load the whole route of + names and ids for breadcrumb building purposes. + + :param folder: current folder for navigating up + :param type: Galaxy LibraryFolder + + :returns: list consisting of full path to the library + :type: list + """ + path_to_root = [] + # We are almost in root + if folder.parent_id is None: + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + else: + # We add the current folder and traverse up one folder. + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + path_to_root.extend( self._build_path( trans, upper_folder ) ) + return path_to_root diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -218,6 +218,12 @@ action='show', conditions=dict( method=[ "GET" ] ) ) + webapp.mapper.connect( 'show_legitimate_lda_roles', + '/api/libraries/datasets/:encoded_dataset_id/permissions', + controller='lda_datasets', + action='show_roles', + conditions=dict( method=[ "GET" ] ) ) + webapp.mapper.connect( 'delete_lda_item', '/api/libraries/datasets/:encoded_dataset_id', controller='lda_datasets', diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -11,7 +11,8 @@ "mvc/library/library-folderlist-view", "mvc/library/library-librarylist-view", "mvc/library/library-librarytoolbar-view", - "mvc/library/library-foldertoolbar-view" + "mvc/library/library-foldertoolbar-view", + "mvc/library/library-dataset-view" ], function(mod_masthead, mod_utils, @@ -21,7 +22,8 @@ mod_folderlist_view, mod_librarylist_view, mod_librarytoolbar_view, - mod_foldertoolbar_view + mod_foldertoolbar_view, + mod_library_dataset_view ) { // ============================================================================ @@ -34,10 +36,11 @@ }, routes: { - "" : "libraries", - "folders/:id" : "folder_content", - "folders/:folder_id/datasets/:dataset_id" : "dataset_detail", - "folders/:folder_id/download/:format" : "download" + "" : "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() { @@ -80,14 +83,11 @@ this.library_router = new LibraryRouter(); this.library_router.on('route:libraries', function() { - // initialize and render the toolbar first Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView(); - // initialize and render libraries second Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView(); }); this.library_router.on('route:folder_content', function(id) { - // TODO maybe caching somewhere here, sessionstorage/localstorage? if (Galaxy.libraries.folderToolbarView){ Galaxy.libraries.folderToolbarView.$el.unbind('click'); } @@ -106,12 +106,10 @@ }); this.library_router.on('route:dataset_detail', function(folder_id, dataset_id){ - // if (Galaxy.libraries.folderToolbarView){ - // Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id, dataset_id: dataset_id}); - // } else { - Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: folder_id}); - Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: folder_id, dataset_id: dataset_id}); - // } + new mod_library_dataset_view.LibraryDatasetView({id: dataset_id}) + }); + this.library_router.on('route:dataset_permissions', function(folder_id, dataset_id){ + new mod_library_dataset_view.LibraryDatasetView({id: dataset_id, show_permissions: true}) }); Backbone.history.start({pushState: false}); diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 static/scripts/mvc/library/library-dataset-view.js --- /dev/null +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -0,0 +1,556 @@ +define([ + "libs/toastr", + "mvc/library/library-model", + 'mvc/ui/ui-select' + ], +function(mod_toastr, + mod_library_model, + mod_select + ) { + +var LibraryDatasetView = Backbone.View.extend({ + el: '#center', + + model: null, + + options: { + + }, + + events: { + "click .toolbtn_modify_dataset" : "enableModification", + "click .toolbtn_cancel_modifications" : "render", + "click .toolbtn_change_permissions" : "showPermissions", + "click .toolbtn-download-dataset" : "downloadDataset", + "click .toolbtn-import-dataset" : "importIntoHistory", + "click .toolbtn-share-dataset" : "shareDataset" + + }, + + initialize: function(options){ + this.options = _.extend(this.options, options); + if (this.options.id){ + this.fetchDataset(); + } + }, + + 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 { + 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(); + }, + + downloadDataset: function(){ + var url = '/api/libraries/datasets/download/uncompressed'; + var data = {'ldda_ids' : this.id}; + this.processDownload(url, data); + }, + + processDownload: function(url, data, method){ + //url and data options required + if( url && data ){ + //data can be string of parameters or array/object + data = typeof data == 'string' ? data : $.param(data); + //split params into form inputs + var inputs = ''; + $.each(data.split('&'), function(){ + var pair = this.split('='); + inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; + }); + //send request + $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') + .appendTo('body').submit().remove(); + + mod_toastr.info('Your download will begin soon'); + } + }, + + importIntoHistory: function(){ + this.refreshUserHistoriesList(function(self){ + var template = self.templateBulkImportInModal(); + self.modal = Galaxy.modal; + self.modal.show({ + closing_events : true, + title : 'Import into History', + body : template({histories : self.histories.models}), + buttons : { + 'Import' : function() {self.importCurrentIntoHistory();}, + 'Close' : function() {Galaxy.modal.hide();} + } + }); + }); + }, + + refreshUserHistoriesList: function(callback){ + var self = this; + this.histories = new mod_library_model.GalaxyHistories(); + this.histories.fetch({ + success: function (){ + callback(self); + }, + error: function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error(response.responseJSON.err_msg); + } else { + mod_toastr.error('An error ocurred :('); + } + } + }); + }, + + importCurrentIntoHistory: function(){ + var self = this; + var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); + var historyItem = new mod_library_model.HistoryItem(); + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + + // set the used history as current so user will see the last one + // that he imported into in the history panel on the 'analysis' page + var set_current_url = '/api/histories/' + history_id + '/set_as_current'; + $.ajax({ + url: set_current_url, + type: 'PUT' + }); + + // save the dataset into selected history + historyItem.save({ content : this.id, source : 'library' }, { + success : function(){ + Galaxy.modal.hide(); + mod_toastr.success('Dataset imported. Click this to start analysing it.', '', {onclick: function() {window.location='/';}}); + }, + error : function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error('Dataset not imported. ' + response.responseJSON.err_msg); + } else { + mod_toastr.error('An error occured! Dataset not imported. Please try again.'); + } + } + }); + }, + + shareDataset: function(){ + mod_toastr.info('Feature coming soon.'); + }, + + showPermissions: function(){ + $(".tooltip").remove(); + var template = this.templateDatasetPermissions(); + this.$el.html(template({item: this.model})); + + var self = this; + + this.access_perm = new mod_select.View({ + css: 'access_perm', + multiple:true, + placeholder: 'Click to select a role', + container: self.$el.find('#access_perm'), + ajax: { + url: "/api/libraries/datasets/5969b1f7201f12ae/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; + }, + + 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 = []; + $(element.val().split(",")).each(function(i) { + var item = this.split(':'); + data.push({ + id: item[1], + name: item[1] + }); + }); + callback(data); + }, + initialData: 'marten@bx.psu.edu:marten@bx.psu.edu', + dropdownCssClass: "bigdrop" // apply css that makes the dropdown taller + }); + // this.access_perm.$el.append($('<option>', {value:"NEWVAL", text: "New Option Text"})); + + // this.modify_perm = new mod_select.View({ + // css: 'modify_perm', + // placeholder: 'Select a role', + // // onchange : function() { + // // self.model.set('access_perm', self.select_genome.value()); + // // }, + // data: [{id:'test',text:'testik'}, {id:'dududu', text:'dadada'}], + // container: self.$el.find('#modify_perm'), + // multiple: true + // // value: self.model.get('access_perm') + // }); + // this.modify_perm.$el.append($('<option>', {value:"NEWVAL", text: "New Option Text"})); + + // this.manage_perm = new mod_select.View({ + // css: 'manage_perm', + // placeholder: 'Select a role', + // // onchange : function() { + // // self.model.set('access_perm', self.select_genome.value()); + // // }, + // data: [{id:'test',text:'testik'}, {id:'dududu', text:'dadada'}], + // container: self.$el.find('#manage_perm'), + // multiple: true + // // value: self.model.get('access_perm') + // }); + // this.manage_perm.$el.append($('<option>', {value:"NEWVAL", text: "New Option Text"})); + + $("#center [data-toggle]").tooltip(); + }, + + + templateDataset : 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="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(' <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>'); + 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>'); + + // 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="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(' <% if (item.get("genome_build")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Genome build</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("file_size")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Size</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("file_size")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("date_uploaded")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("uploaded_by")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Uploaded by</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("metadata_data_lines")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("metadata_comment_lines")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Comment Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("metadata_columns")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Number of Columns</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("metadata_column_types")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Column Types</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("message")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Message</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("misc_blurb")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous blurb</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% } %>'); + + tmpl_array.push(' <% if (item.get("misc_info")) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.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 + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + }, + + templateModifyDataset : 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="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>'); + 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>'); + + // 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="dataset_table">'); + tmpl_array.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>'); + 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><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>'); + tmpl_array.push(' </tr>'); + 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(' <tr>'); + tmpl_array.push(' <th scope="row">Genome build</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Size</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("file_size")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Uploaded by</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr scope="row">'); + tmpl_array.push(' <th scope="row">Data Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Comment Lines</th>'); + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td scope="row">unknown</td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Number of Columns</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Column Types</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Message</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous blurb</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); + tmpl_array.push(' </tr>'); + 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 + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + }, + + templateDatasetPermissions : 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="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>'); + 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>'); + + // 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('<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('<div class="dataset_table">'); + + tmpl_array.push('<h2>Basic permissions</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('</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('</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 permissions:</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('<div id="access_perm" class="access_perm roles-selection"></div>'); + 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('</div>'); + + // CONTAINER END + tmpl_array.push('</div>'); + + return _.template(tmpl_array.join('')); + }, + +templateBulkImportInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return _.template(tmpl_array.join('')); + } + +}); + +return { + LibraryDatasetView: LibraryDatasetView +}; + +}); diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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 @@ -4,12 +4,16 @@ "utils/utils", "libs/toastr", "mvc/library/library-model", - "mvc/library/library-folderrow-view"], + "mvc/library/library-folderrow-view", + "mvc/library/library-dataset-view" + ], function(mod_masthead, mod_utils, mod_toastr, mod_library_model, - mod_library_folderrow_view) { + mod_library_folderrow_view, + mod_library_dataset_view + ) { var FolderListView = Backbone.View.extend({ el : '#folder_items_element', @@ -42,16 +46,14 @@ }, fetchFolder: function(options){ - // this.options = _.defaults(this.options, options); var options = options || {}; this.options.include_deleted = options.include_deleted; var that = this; this.collection = new mod_library_model.Folder(); - // start to listen if someone adds a model to the collection + // start to listen if someone modifies collection this.listenTo(this.collection, 'add', this.renderOne); - this.listenTo(this.collection, 'remove', this.removeOne); this.folderContainer = new mod_library_model.FolderContainer({id: this.options.id}); @@ -65,7 +67,12 @@ that.render(); that.addAll(folder_container.get('folder').models); if (that.options.dataset_id){ - _.findWhere(that.rowViews, {id: that.options.dataset_id}).showDatasetDetails(); + row = _.findWhere(that.rowViews, {id: that.options.dataset_id}); + if (row) { + row.showDatasetDetails(); + } else { + mod_toastr.error('Dataset not found. Showing folder instead.'); + } } }, error: function(model, response){ @@ -109,7 +116,7 @@ var fetched_metadata = this.folderContainer.attributes.metadata; fetched_metadata.contains_file = typeof this.collection.findWhere({type: 'file'}) !== 'undefined'; Galaxy.libraries.folderToolbarView.configureElements(fetched_metadata); - $('.deleted_dataset').hover(function() { + $('.dataset').hover(function() { $(this).find('.show_on_hover').show(); }, function () { $(this).find('.show_on_hover').hide(); @@ -151,7 +158,7 @@ renderOne: function(model){ if (model.get('data_type') !== 'folder'){ this.options.contains_file = true; - model.set('readable_size', this.size_to_string(model.get('file_size'))); + // model.set('readable_size', this.size_to_string(model.get('file_size'))); } model.set('folder_id', this.id); var rowView = new mod_library_folderrow_view.FolderRowView(model); @@ -161,7 +168,7 @@ this.$el.find('#first_folder_item').after(rowView.el); - $('.deleted_dataset').hover(function() { + $('.dataset').hover(function() { $(this).find('.show_on_hover').show(); }, function () { $(this).find('.show_on_hover').hide(); @@ -213,21 +220,6 @@ } }, - /** - * convert size to nice string - * @param {int} size - * @return {string} readable representation of size with units - */ - size_to_string : function (size){ - var unit = ""; - if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else - if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else - if (size >= 100000) { size = size / 100000; unit = "MB"; } else - if (size >= 100) { size = size / 100; unit = "KB"; } else - { size = size * 10; unit = "b"; } - return (Math.round(size) / 10) + unit; - }, - /** * User clicked the checkbox in the table heading * @param {context} event @@ -320,7 +312,7 @@ 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>'); tmpl_array.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>'); tmpl_array.push(' <th style="width:5%;">data type</th>'); - tmpl_array.push(' <th style="width:5%;">size</th>'); + tmpl_array.push(' <th style="width:10%;">size</th>'); tmpl_array.push(' <th style="width:160px;">time updated (UTC)</th>'); tmpl_array.push(' <th style="width:10%;"></th> '); tmpl_array.push(' </thead>'); diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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 @@ -1,13 +1,14 @@ -// dependencies define([ "galaxy.masthead", "utils/utils", "libs/toastr", - "mvc/library/library-model"], + "mvc/library/library-model", + "mvc/library/library-dataset-view"], function(mod_masthead, mod_utils, mod_toastr, - mod_library_model) { + mod_library_model, + mod_library_dataset_view) { // galaxy library row view var FolderRowView = Backbone.View.extend({ @@ -15,7 +16,7 @@ lastSelectedHistory: '', events: { - 'click .undelete_dataset_btn' : 'undelete_dataset' + 'click .undelete_dataset_btn' : 'undelete_dataset' }, options: { @@ -27,9 +28,6 @@ }, render: function(folder_item){ - // if (typeof folder_item === 'undefined'){ - // folder_item = Galaxy.libraries.libraryFolderView.collection.get(this.$el.data('id')); - // } var template = null; if (folder_item.get('type') === 'folder'){ this.options.type = 'folder'; @@ -47,172 +45,8 @@ return this; }, - //show modal with current dataset info showDatasetDetails : function(){ - var id = this.id; - - //create new item - var item = new mod_library_model.Item(); - var histories = new mod_library_model.GalaxyHistories(); - item.id = id; - var self = this; - - //fetch the dataset info - item.fetch({ - success: function (item) { - // TODO can start rendering here already - //fetch user histories for import purposes - histories.fetch({ - success: function (histories){ - self.renderModalAfterFetch(item, histories); - }, - error: function(model, response){ - if (typeof response.responseJSON !== "undefined"){ - mod_toastr.error(response.responseJSON.err_msg); - } else { - mod_toastr.error('An error occured during fetching histories:('); - } - self.renderModalAfterFetch(item); - } - }); - }, - error: function(model, response){ - if (typeof response.responseJSON !== "undefined"){ - mod_toastr.error(response.responseJSON.err_msg); - } else { - mod_toastr.error('An error occured during loading dataset details :('); - } - } - }); -}, - - // show the current dataset in a modal - renderModalAfterFetch : function(item, histories){ - var size = this.size_to_string(item.get('file_size')); - var template = _.template(this.templateDatasetModal(), { item : item, size : size }); - // make modal - var self = this; - this.modal = Galaxy.modal; - this.modal.show({ - closing_events : true, - title : item.get('name'), - body : template, - buttons : { - 'Import' : function() { self.importCurrentIntoHistory(); }, - 'Download' : function() { self.downloadCurrent(); }, - 'Close' : function() { self.modal.hide(); } - }, - closing_callback : function(){ - var path_to_folder = Backbone.history.fragment.split('/datasets')[0]; - Galaxy.libraries.library_router.navigate('#' + path_to_folder, {trigger:true, replace:true}); - } - }); - - $(".peek").html(item.get("peek")); - - // show the import-into-history footer only if the request for histories succeeded - if (typeof history.models !== undefined){ - var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); - $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); - // preset last selected history if we know it - if (self.lastSelectedHistory.length > 0) { - $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); - } - } - }, - - // TODO this is dup func, unify - // convert size to nice string - size_to_string : function (size){ - // identify unit - var unit = ""; - if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else - if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else - if (size >= 100000) { size = size / 100000; unit = "MB"; } else - if (size >= 100) { size = size / 100; unit = "KB"; } else - { size = size * 10; unit = "b"; } - // return formatted string - return (Math.round(size) / 10) + unit; - }, - - // download dataset shown currently in modal - downloadCurrent : function(){ - //disable the buttons - this.modal.disableButton('Import'); - this.modal.disableButton('Download'); - - var library_dataset_id = []; - library_dataset_id.push($('#id_row').attr('data-id')); - var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : library_dataset_id}; - - this.processDownload(url, data); - this.modal.enableButton('Import'); - this.modal.enableButton('Download'); - }, - - // TODO this is dup func, unify - // create hidden form and submit through POST to initialize download - processDownload: function(url, data, method){ - //url and data options required - if( url && data ){ - //data can be string of parameters or array/object - data = typeof data == 'string' ? data : $.param(data); - //split params into form inputs - var inputs = ''; - $.each(data.split('&'), function(){ - var pair = this.split('='); - inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; - }); - //send request - $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') - .appendTo('body').submit().remove(); - - mod_toastr.info('Your download will begin soon'); - } - }, - - // import dataset shown currently in modal into selected history - importCurrentIntoHistory : function(){ - //disable the buttons - this.modal.disableButton('Import'); - this.modal.disableButton('Download'); - - var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); - this.lastSelectedHistory = history_id; //save selected history for further use - - var library_dataset_id = $('#id_row').attr('data-id'); - var historyItem = new mod_library_model.HistoryItem(); - var self = this; - historyItem.url = historyItem.urlRoot + history_id + '/contents'; - - // set the used history as current so user will see the last one - // that he imported into in the history panel on the 'analysis' page - var set_current_url = '/api/histories/' + history_id + '/set_as_current'; - $.ajax({ - url: set_current_url, - type: 'PUT' - }); - - // save the dataset into selected history - historyItem.save({ content : library_dataset_id, source : 'library' }, { - success : function(){ - mod_toastr.success('Dataset imported. Click this to start analysing it.', '', {onclick: function() {window.location='/'}}); - //enable the buttons - self.modal.enableButton('Import'); - self.modal.enableButton('Download'); - }, - error : function(model, response){ - if (typeof response.responseJSON !== "undefined"){ - mod_toastr.error('Dataset not imported. ' + response.responseJSON.err_msg); - } else { - mod_toastr.error('An error occured! Dataset not imported. Please try again.'); - } - //enable the buttons - self.modal.enableButton('Import'); - self.modal.enableButton('Download'); - } - }); + this.dataset_view = new mod_library_dataset_view.LibraryDatasetView({id: this.id}); }, /** @@ -232,8 +66,8 @@ success : function(model, response){ Galaxy.libraries.folderListView.collection.remove(dataset_id); var updated_dataset = new mod_library_model.Item(response); - Galaxy.libraries.folderListView.collection.add(updated_dataset) - mod_toastr.success('Dataset undeleted. Click this to see it.', '', {onclick: function() {that.showDatasetDetails()}}); + Galaxy.libraries.folderListView.collection.add(updated_dataset); + mod_toastr.success('Dataset undeleted. Click this to see it.', '', {onclick: function() {that.showDatasetDetails();}}); }, error : function(model, response){ if (typeof response.responseJSON !== "undefined"){ @@ -255,14 +89,9 @@ 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(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder - // tmpl_array.push(' <span>(empty folder)</span>'); - // tmpl_array.push(' <% } %>'); tmpl_array.push(' </td>'); tmpl_array.push(' <td>folder</td>'); tmpl_array.push(' <td></td>'); - // print item count only if it is given - // tmpl_array.push(' <td><% if (typeof content_item.get("item_count") !== "undefined") { _.escape(content_item.get("item_count")); print("item(s)") } %></td>'); tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated tmpl_array.push(' <td></td>'); tmpl_array.push('</tr>'); @@ -273,20 +102,20 @@ templateRowFile: function(){ tmpl_array = []; - tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">'); + 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>'); // dataset tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type - tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size + tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>'); // size tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated 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-group fa-lg"></span>'); - tmpl_array.push(' <% } %>'); + 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>'); @@ -296,94 +125,20 @@ templateRowDeletedFile: function(){ tmpl_array = []; - tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">'); + 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>'); // dataset tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type - tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size + tmpl_array.push(' <td><%= _.escape(content_item.get("file_size")) %></td>'); // size tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated 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('')); - }, - -templateDatasetModal : function(){ - var tmpl_array = []; - - tmpl_array.push('<div class="modal_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(' <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(' <tr>'); - tmpl_array.push(' <th scope="row">Genome build</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <th scope="row">Size</th>'); - tmpl_array.push(' <td><%= _.escape(size) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Uploaded by</th>'); - tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr scope="row">'); - tmpl_array.push(' <th scope="row">Data Lines</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <th scope="row">Comment Lines</th>'); - tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); - tmpl_array.push(' <% } else { %>'); - tmpl_array.push(' <td scope="row">unknown</td>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Number of Columns</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Column Types</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); - tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' </table>'); - tmpl_array.push(' <pre class="peek">'); - tmpl_array.push(' </pre>'); - tmpl_array.push('</div>'); - - return tmpl_array.join(''); -}, - -templateHistorySelectInModal : function(){ - var tmpl_array = []; - - tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">'); - tmpl_array.push('Select history: '); - tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> '); - tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box - tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push('</select>'); - tmpl_array.push('</span>'); - - return tmpl_array.join(''); -} + } }); diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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 @@ -519,16 +519,16 @@ // CONTAINER tmpl_array.push('<div class="library_style_container">'); // TOOLBAR - tmpl_array.push('<div id="library_folder_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"><span class="fa fa-trash-o fa-lg"></span></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(' <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(' <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>'); @@ -536,7 +536,7 @@ 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="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 diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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 @@ -115,7 +115,7 @@ tmpl_array.push('<div class="library_style_container">'); // TOOLBAR - tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">'); + 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"><span class="fa fa-trash-o fa-lg"></span></input></span>'); diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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"],function(e,c,g,k,h,a,f,d,i){var l=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/download/:format":"download"},back:function(){if(this.routesHit>1){window.history.back()}else{this.navigate("#",{trigger:true,replace:true})}}});var j=k.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,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#folder_list_body").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});this.library_router.on("route:dataset_detail",function(n,m){Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:n});Galaxy.libraries.folderListView=new a.FolderListView({id:n,dataset_id:m})});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"],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,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){new d.LibraryDatasetView({id:n})});this.library_router.on("route:dataset_permissions",function(o,n){new d.LibraryDatasetView({id:n,show_permissions:true})});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 static/scripts/packed/mvc/library/library-dataset-view.js --- /dev/null +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -0,0 +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_change_permissions":"showPermissions","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset"},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;var g=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var h=new c.HistoryItem();h.url=h.urlRoot+g+"/contents";var e="/api/histories/"+g+"/set_as_current";$.ajax({url:e,type:"PUT"});h.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(j,i){if(typeof i.responseJSON!=="undefined"){d.error("Dataset not imported. "+i.responseJSON.err_msg)}else{d.error("An error occured! Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},showPermissions:function(){$(".tooltip").remove();var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model}));var e=this;this.access_perm=new b.View({css:"access_perm",multiple:true,placeholder:"Click to select a role",container:e.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/5969b1f7201f12ae/permissions",dataType:"json",quietMillis:100,data:function(i,j){return{q:i,page_limit:10,page:j}},results:function(k,j){var i=(j*10)<k.total;return{results:k.roles,more:i}}},formatResult:function f(i){return i.name},formatSelection:function h(i){return i.name},initSelection:function(i,k){var j=[];$(i.val().split(",")).each(function(l){var m=this.split(":");j.push({id:m[1],name:m[1]})});k(j)},initialData:"marten@bx.psu.edu:marten@bx.psu.edu",dropdownCssClass:"bigdrop"});$("#center [data-toggle]").tooltip()},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(' <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>');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(' <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('<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("<h2>Advanced permissions</h2>");e.push("<p>You can assign any number of roles to any of the following three dataset permissions:</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("<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(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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"],function(c,e,f,d,a){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(g){this.options=_.defaults(this.options||{},g);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.listenTo(this.collection,"remove",this.removeOne);this.folderContainer=new d.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(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models);if(h.options.dataset_id){_.findWhere(h.rowViews,{id:h.options.dataset_id}).showDatasetDetails()}},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{f.error("An error ocurred :(. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(g){this.options=_.defaults(this.options,g);var h=this.templateFolder();var i=this.folderContainer.attributes.metadata.full_path;var j;if(i.length===1){j=0}else{j=i[i.length-2][0]}this.$el.html(h({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:j,order:this.sort}));$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},postRender:function(){var g=this.folderContainer.attributes.metadata;g.contains_file=typeof this.collection.findWhere({type:"file"})!=="undefined";Galaxy.libraries.folderToolbarView.configureElements(g);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness();this.postRender()},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)});this.postRender()},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}h.set("folder_id",this.id);var g=new a.FolderRowView(h);this.rowViews[h.get("id")]=g;this.$el.find("#first_folder_item").after(g.el);$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},removeOne:function(g){this.$el.find("#"+g.id).remove()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light").addClass("dark");g.find("a").removeClass("light").addClass("dark");g.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark").addClass("light");g.find("a").removeClass("dark").addClass("light");g.find(".fa-file").removeClass("fa-file").addClass("fa-file-o")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.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>');g.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>');g.push(' <th style="width:5%;">data type</th>');g.push(' <th style="width:5%;">size</th>');g.push(' <th style="width:160px;">time updated (UTC)</th>');g.push(' <th style="width:10%;"></th> ');g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.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>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");g.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(g.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();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 diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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"],function(b,d,e,c){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(f){this.render(f)},render:function(f){var g=null;if(f.get("type")==="folder"){this.options.type="folder";g=this.templateRowFolder()}else{this.options.type="file";if(f.get("deleted")){g=this.templateRowDeletedFile()}else{g=this.templateRowFile()}}this.setElement(g({content_item:f}));this.$el.show();return this},showDatasetDetails:function(){var i=this.id;var h=new c.Item();var g=new c.GalaxyHistories();h.id=i;var f=this;h.fetch({success:function(j){g.fetch({success:function(k){f.renderModalAfterFetch(j,k)},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error(k.responseJSON.err_msg)}else{e.error("An error occured during fetching histories:(")}f.renderModalAfterFetch(j)}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error(j.responseJSON.err_msg)}else{e.error("An error occured during loading dataset details :(")}}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:k.get("name"),body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}},closing_callback:function(){var l=Backbone.history.fragment.split("/datasets")[0];Galaxy.libraries.library_router.navigate("#"+l,{trigger:true,replace:true})}});$(".peek").html(k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};this.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},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]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var i=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=i;var g=$("#id_row").attr("data-id");var j=new c.HistoryItem();var h=this;j.url=j.urlRoot+i+"/contents";var f="/api/histories/"+i+"/set_as_current";$.ajax({url:f,type:"PUT"});j.save({content:g,source:"library"},{success:function(){e.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}});h.modal.enableButton("Import");h.modal.enableButton("Download")},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error("Dataset not imported. "+k.responseJSON.err_msg)}else{e.error("An error occured! Dataset not imported. Please try again.")}h.modal.enableButton("Import");h.modal.enableButton("Download")}})},undelete_dataset:function(h){$(".tooltip").hide();var g=this;var f=$(h.target).closest("tr")[0].id;var i=Galaxy.libraries.folderListView.collection.get(f);i.url=i.urlRoot+i.id+"?undelete=true";i.destroy({success:function(k,j){Galaxy.libraries.folderListView.collection.remove(f);var l=new c.Item(j);Galaxy.libraries.folderListView.collection.add(l);e.success("Dataset undeleted. Click this to see it.","",{onclick:function(){g.showDatasetDetails()}})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){e.error("Dataset was not undeleted. "+j.responseJSON.err_msg)}else{e.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" 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("readable_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-group fa-lg"></span>');tmpl_array.push(" <% } %>");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("readable_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(""))},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; 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 f.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.$el.show();return this},showDatasetDetails:function(){this.dataset_view=new b.LibraryDatasetView({id:this.id})},undelete_dataset:function(i){$(".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 diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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_folder_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"><span class="fa fa-trash-o fa-lg"></span></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_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"><span class="fa fa-trash-o fa-lg"></span></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 diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 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" margin-top:0.5em; ">');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"><span class="fa fa-trash-o fa-lg"></span></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(" <% 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"><span class="fa fa-trash-o fa-lg"></span></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 diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1305,18 +1305,21 @@ tr.dark td{background-color:#d6b161;color:white} tr.dark:hover td{background-color:#ebd4a4;color:white} a.dark{color:white} -.modal_table tr{border-bottom:1px solid #5f6990 !important} -.modal_table th{border:none !important} -.modal_table td{border:none !important} +.dataset_table tr{border-bottom:1px solid #5f6990 !important} +.dataset_table th{border:none !important} +.dataset_table td{border:none !important} th.button_heading{width:2em} -#library_folder_toolbar{margin-bottom:1em}#library_folder_toolbar span{margin-right:0.2em} +.bigdrop.select2-container .select2-results{max-height:300px} +.bigdrop .select2-results{max-height:300px} +.select2-container-multi{width:100%} +.roles-selection{width:66%} #library_toolbar{margin-bottom:1em}#library_toolbar span{margin-right:0.2em} img.expanderIcon{padding-right:4px} input.datasetCheckbox,li,ul{padding:0;margin:0} .rowTitle{padding:2px} ul{list-style:none} .libraryTitle th{text-align:left} -pre.peek{background:white;color:black;width:100%;overflow:auto} +pre.peek{background:white;color:black;overflow:auto} pre.peek th{color:white;background:#ebd9b2} 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} diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -16,18 +16,21 @@ tr.dark td{background-color:#d6b161;color:white} tr.dark:hover td{background-color:#ebd4a4;color:white} a.dark{color:white} -.modal_table tr{border-bottom:1px solid #5f6990 !important} -.modal_table th{border:none !important} -.modal_table td{border:none !important} +.dataset_table tr{border-bottom:1px solid #5f6990 !important} +.dataset_table th{border:none !important} +.dataset_table td{border:none !important} th.button_heading{width:2em} -#library_folder_toolbar{margin-bottom:1em}#library_folder_toolbar span{margin-right:0.2em} +.bigdrop.select2-container .select2-results{max-height:300px} +.bigdrop .select2-results{max-height:300px} +.select2-container-multi{width:100%} +.roles-selection{width:66%} #library_toolbar{margin-bottom:1em}#library_toolbar span{margin-right:0.2em} img.expanderIcon{padding-right:4px} input.datasetCheckbox,li,ul{padding:0;margin:0} .rowTitle{padding:2px} ul{list-style:none} .libraryTitle th{text-align:left} -pre.peek{background:white;color:black;width:100%;overflow:auto} +pre.peek{background:white;color:black;overflow:auto} pre.peek th{color:white;background:#ebd9b2} 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} diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -80,7 +80,7 @@ color: white; } -.modal_table{ +.dataset_table{ tr { border-bottom: 1px solid #5f6990 !important; } @@ -97,12 +97,19 @@ width: 2em; } -#library_folder_toolbar { - margin-bottom: 1em; - span { - margin-right: 0.2em; - } +.bigdrop.select2-container .select2-results { + max-height: 300px; } +.bigdrop .select2-results { + max-height: 300px; +} +.select2-container-multi{ + width: 100%; +} +.roles-selection { + width: 66%; +} + #library_toolbar { margin-bottom: 1em; span { @@ -135,7 +142,7 @@ pre.peek { background: white; color: black; - width: 100%; + // width: 100%; overflow: auto; } diff -r b027397c99c639d5b200b88649c6e7ca75a292f8 -r 23bb24573f1370b4f6322651d471d11ff5352447 templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -31,6 +31,7 @@ ${h.js( 'libs/jquery/jquery', 'libs/jquery/jquery-ui', + "libs/jquery/select2", 'libs/bootstrap', 'libs/underscore', 'libs/backbone/backbone', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: extended ui-select module to support multiple inputs and on-demand ajax loading of paginated data
by commits-noreply＠bitbucket.org 14 May '14

14 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b027397c99c6/ Changeset: b027397c99c6 User: martenson Date: 2014-05-14 19:50:15 Summary: extended ui-select module to support multiple inputs and on-demand ajax loading of paginated data Affected #: 2 files diff -r 882f51a4d9dced2ce731c5b4afa5bed9623933c2 -r b027397c99c639d5b200b88649c6e7ca75a292f8 static/scripts/mvc/ui/ui-select.js --- a/static/scripts/mvc/ui/ui-select.js +++ b/static/scripts/mvc/ui/ui-select.js @@ -11,10 +11,13 @@ { // options optionsDefault: { - css : '', - placeholder : 'No data available', - data : [], - value : null + css : '', + placeholder : 'No data available', + data : [], + value : null, + multiple : false, + minimumInputLength : 0, + initialData : '' }, // initialize @@ -40,17 +43,19 @@ // refresh this._refresh(); - // initial value - if (this.options.value) { - this._setValue(this.options.value); - } - - // add change event - var self = this; - if (this.options.onchange) { - this.$el.on('change', function() { - self.options.onchange(self.value()); - }); + if (!this.options.multiple){ + // initial value + if (this.options.value) { + this._setValue(this.options.value); + } + + // add change event + var self = this; + if (this.options.onchange) { + this.$el.on('change', function() { + self.options.onchange(self.value()); + }); + } } }, @@ -142,18 +147,33 @@ // refresh _refresh: function() { - // selected - var selected = this._getValue(); - - // add select2 data - this.$el.select2({ - data : this.select_data, - containerCssClass : this.options.css, - placeholder : this.options.placeholder - }); - - // select previous value (if exists) - this._setValue(selected); + // add select2 data based on type of input + if (!this.options.multiple){ + var selected = this._getValue(); + var select_opt = { + data : this.select_data, + containerCssClass : this.options.css, + placeholder : this.options.placeholder, + }; + this.$el.select2(select_opt); + // select previous value (if exists) + this._setValue(selected); + } else { + var select_opt = { + multiple : this.options.multiple, + containerCssClass : this.options.css, + placeholder : this.options.placeholder, + minimumInputLength : this.options.minimumInputLength, + ajax : this.options.ajax, + dropdownCssClass : this.options.dropdownCssClass, + escapeMarkup : this.options.escapeMarkup, + formatResult : this.options.formatResult, + formatSelection : this.options.formatSelection, + initSelection : this.options.initSelection, + initialData : this.options.initialData + }; + this.$el.select2(select_opt); + } }, // get index @@ -186,8 +206,8 @@ }, // element - _template: function() { - return '<input type="hidden"/>'; + _template: function(options) { + return '<input type="hidden" value="' + this.options.initialData + '"/>'; } }); diff -r 882f51a4d9dced2ce731c5b4afa5bed9623933c2 -r b027397c99c639d5b200b88649c6e7ca75a292f8 static/scripts/packed/mvc/ui/ui-select.js --- a/static/scripts/packed/mvc/ui/ui-select.js +++ b/static/scripts/packed/mvc/ui/ui-select.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var c=this._getValue();this.$el.select2({data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder});this._setValue(c)},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(){return'<input type="hidden"/>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:false,minimumInputLength:0,initialData:""},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));if(!this.options.container){console.log("ui-select::initialize() : container not specified.");return}this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(!this.options.multiple){if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){if(!this.options.multiple){var d=this._getValue();var c={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,};this.$el.select2(c);this._setValue(d)}else{var c={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(c)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden" value="'+this.options.initialData+'"/>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for when hours_between_check is defined in ini.
by commits-noreply＠bitbucket.org 14 May '14

14 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/882f51a4d9dc/ Changeset: 882f51a4d9dc User: dan Date: 2014-05-14 18:04:47 Summary: Fix for when hours_between_check is defined in ini. Affected #: 1 file diff -r 8b8b08da7231d3ea2bf7ccb6585a20f7e0c64cad -r 882f51a4d9dced2ce731c5b4afa5bed9623933c2 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -108,6 +108,8 @@ self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', False ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) + if isinstance( self.hours_between_check, basestring ): + self.hours_between_check = float( self.hours_between_check ) try: if isinstance( self.hours_between_check, int ): if self.hours_between_check < 1 or self.hours_between_check > 24: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Allow for an arbitrary number of tool_data_table_config_path files to be defined in ini file. Values are comma separated.
by commits-noreply＠bitbucket.org 14 May '14

14 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8b8b08da7231/ Changeset: 8b8b08da7231 User: dan Date: 2014-05-14 17:52:20 Summary: Allow for an arbitrary number of tool_data_table_config_path files to be defined in ini file. Values are comma separated. Affected #: 2 files diff -r 6b86b4186c455317cba726c7ad6579a030922421 -r 8b8b08da7231d3ea2bf7ccb6585a20f7e0c64cad lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -102,7 +102,7 @@ self.shed_tool_data_path = resolve_path( self.shed_tool_data_path, self.root ) else: self.shed_tool_data_path = self.tool_data_path - self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) + self.tool_data_table_config_path = [ resolve_path( x, self.root ) for x in kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ).split( ',' ) ] self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', False ) ) diff -r 6b86b4186c455317cba726c7ad6579a030922421 -r 8b8b08da7231d3ea2bf7ccb6585a20f7e0c64cad lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -56,19 +56,22 @@ 3. When a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local Galaxy instance. In this case, we have 2 entry types to handle, files whose root tag is <tables>, for example: """ - tree = util.parse_xml( config_filename ) - root = tree.getroot() table_elems = [] - for table_elem in root.findall( 'table' ): - table = ToolDataTable.from_elem( table_elem, tool_data_path, from_shed_config ) - table_elems.append( table_elem ) - if table.name not in self.data_tables: - self.data_tables[ table.name ] = table - log.debug( "Loaded tool data table '%s'", table.name ) - else: - log.debug( "Loading another instance of data table '%s', attempting to merge content.", table.name ) - self.data_tables[ table.name ].merge_tool_data_table( table, allow_duplicates=False ) #only merge content, do not persist to disk, do not allow duplicate rows when merging - # FIXME: This does not account for an entry with the same unique build ID, but a different path. + if not isinstance( config_filename, list ): + config_filename = [ config_filename ] + for filename in config_filename: + tree = util.parse_xml( filename ) + root = tree.getroot() + for table_elem in root.findall( 'table' ): + table = ToolDataTable.from_elem( table_elem, tool_data_path, from_shed_config ) + table_elems.append( table_elem ) + if table.name not in self.data_tables: + self.data_tables[ table.name ] = table + log.debug( "Loaded tool data table '%s'", table.name ) + else: + log.debug( "Loading another instance of data table '%s', attempting to merge content.", table.name ) + self.data_tables[ table.name ].merge_tool_data_table( table, allow_duplicates=False ) #only merge content, do not persist to disk, do not allow duplicate rows when merging + # FIXME: This does not account for an entry with the same unique build ID, but a different path. return table_elems def add_new_entries_from_config_file( self, config_filename, tool_data_path, shed_tool_data_table_config, persist=False ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Bugfix for updating history dataset collection name.
by commits-noreply＠bitbucket.org 14 May '14

14 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b86b4186c45/ Changeset: 6b86b4186c45 User: jmchilton Date: 2014-05-14 12:26:21 Summary: Bugfix for updating history dataset collection name. Thanks to Bjoern for the bug report. This attribute had been DatasetCollection in earlier versions of this code and the update code was only partially cut-over to use the new location for name (on HistoryDatasetCollectionAssociation). Affected #: 2 files diff -r e0d69ca8be55cd8cfd863ad7f128e95a42eabfd3 -r 6b86b4186c455317cba726c7ad6579a030922421 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2636,20 +2636,8 @@ return new_collection def set_from_dict( self, new_data ): - editable_keys = ( 'name' ) - changed = {} - - # unknown keys are ignored here - for key in [ k for k in new_data.keys() if k in editable_keys ]: - new_val = new_data[ key ] - old_val = self.__getattribute__( key ) - if new_val == old_val: - continue - - self.__setattr__( key, new_val ) - changed[ key ] = new_val - - return changed + # Nothing currently editable in this class. + return {} class DatasetCollectionInstance( object, HasName ): diff -r e0d69ca8be55cd8cfd863ad7f128e95a42eabfd3 -r 6b86b4186c455317cba726c7ad6579a030922421 test/api/test_history_contents.py --- a/test/api/test_history_contents.py +++ b/test/api/test_history_contents.py @@ -128,12 +128,28 @@ dataset_collection = show_response.json() assert dataset_collection[ "deleted" ] - def __show( self, hda ): - show_response = self._get( "histories/%s/contents/%s" % ( self.history_id, hda[ "id" ] ) ) + def test_update_dataset_collection( self ): + payload = self.dataset_collection_populator.create_pair_payload( + self.history_id, + type="dataset_collection" + ) + dataset_collection_response = self._post( "histories/%s/contents" % self.history_id, payload ) + self._assert_status_code_is( dataset_collection_response, 200 ) + hdca = dataset_collection_response.json() + update_url = self._api_url( "histories/%s/contents/dataset_collections/%s" % ( self.history_id, hdca[ "id" ] ), use_key=True ) + # Awkward json.dumps required here because of https://trello.com/c/CQwmCeG6 + body = json.dumps( dict( name="newnameforpair" ) ) + update_response = put_request( update_url, data=body ) + self._assert_status_code_is( update_response, 200 ) + show_response = self.__show( hdca ) + assert str( show_response.json()[ "name" ] ) == "newnameforpair" + + def __show( self, contents ): + show_response = self._get( "histories/%s/contents/%ss/%s" % ( self.history_id, contents["history_content_type"], contents[ "id" ] ) ) return show_response def __count_contents( self, history_id=None, **kwds ): - if history_id == None: + if history_id is None: history_id = self.history_id contents_response = self._get( "histories/%s/contents" % history_id, kwds ) return len( contents_response.json() ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fix duplicated names in on_text when using multiple data inputs.
by commits-noreply＠bitbucket.org 14 May '14

14 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e0d69ca8be55/ Changeset: e0d69ca8be55 User: jmchilton Date: 2014-05-14 00:47:57 Summary: Fix duplicated names in on_text when using multiple data inputs. Unit tests verifing the fixed, correct behavior included. Bug introduced in e8c84dd715782e7c1d709d8068e6033b835f7f39 as an unintended consequence of duplicating the first dataset in the dictionary of input datasets generated by the tool action code. Fixes https://trello.com/c/LCEKxImR. Affected #: 2 files diff -r c1873e4d23fa2c496990e5bdef83300e929ae40c -r e0d69ca8be55cd8cfd863ad7f128e95a42eabfd3 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -472,6 +472,15 @@ def on_text_for_names( input_names ): + # input_names may contain duplicates... this is because the first value in + # multiple input dataset parameters will appear twice once as param_name + # and once as param_name1. + unique_names = [] + for name in input_names: + if name not in unique_names: + unique_names.append( name ) + input_names = unique_names + # Build name for output datasets based on tool name and input names if len( input_names ) == 1: on_text = input_names[0] diff -r c1873e4d23fa2c496990e5bdef83300e929ae40c -r e0d69ca8be55cd8cfd863ad7f128e95a42eabfd3 test/unit/tools/test_actions.py --- a/test/unit/tools/test_actions.py +++ b/test/unit/tools/test_actions.py @@ -2,6 +2,7 @@ from galaxy import model from galaxy.tools.actions import DefaultToolAction +from galaxy.tools.actions import on_text_for_names import tools_support @@ -25,6 +26,19 @@ ''' +def test_on_text_for_names(): + def assert_on_text_is( expected, *names ): + on_text = on_text_for_names( names ) + assert on_text == expected, "Wrong on text value %s, expected %s" % ( on_text, expected ) + + assert_on_text_is( "data 1", "data 1" ) + assert_on_text_is( "data 1 and data 2", "data 1", "data 2" ) + assert_on_text_is( "data 1, data 2, and data 3", "data 1", "data 2", "data 3" ) + assert_on_text_is( "data 1, data 2, and others", "data 1", "data 2", "data 3", "data 4" ) + + assert_on_text_is( "data 1 and data 2", "data 1", "data 1", "data 2" ) + + class DefaultToolActionTestCase( unittest.TestCase, tools_support.UsesApp, tools_support.UsesTools ): def setUp( self ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merge from stable.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c1873e4d23fa/ Changeset: c1873e4d23fa User: dannon Date: 2014-05-13 23:39:55 Summary: Merge from stable. Affected #: 1 file diff -r b4680b54994ad6c62f05d354a2af5743344152e8 -r c1873e4d23fa2c496990e5bdef83300e929ae40c lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -177,10 +177,16 @@ while external_job_id is None and trynum < 5: try: external_job_id = self.ds.runJob(jt) - except drmaa.InternalException, e: + break + except ( drmaa.InternalException, drmaa.DeniedByDrmException ), e: trynum += 1 log.warning( '(%s) drmaa.Session.runJob() failed, will retry: %s', galaxy_id_tag, e ) time.sleep( 5 ) + else: + log.error( "(%s) All attempts to submit job failed" % galaxy_id_tag ) + job_wrapper.fail( "Unable to run this job due to a cluster error, please retry it later" ) + self.ds.deleteJobTemplate( jt ) + return else: job_wrapper.change_ownership_for_run() log.debug( '(%s) submitting with credentials: %s [uid: %s]' % ( galaxy_id_tag, job_wrapper.user_system_pwent[0], job_wrapper.user_system_pwent[2] ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fixes for DRMAA submission failures.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cc0fe62e54dc/ Changeset: cc0fe62e54dc Branch: stable User: jmchilton Date: 2014-05-12 20:32:34 Summary: Fixes for DRMAA submission failures. Mark job as failed once Galaxy is done attempting to submit the job, catch and retry drmaa.DeniedByDrmException like drmaa.InternalException. Affected #: 1 file diff -r 3534f67acd2a4f84899335326ac2cc8bcf05201d -r cc0fe62e54dc59607c26cd9152ef1ea7c85af625 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -177,10 +177,16 @@ while external_job_id is None and trynum < 5: try: external_job_id = self.ds.runJob(jt) - except drmaa.InternalException, e: + break + except ( drmaa.InternalException, drmaa.DeniedByDrmException ), e: trynum += 1 log.warning( '(%s) drmaa.Session.runJob() failed, will retry: %s', galaxy_id_tag, e ) time.sleep( 5 ) + else: + log.error( "(%s) All attempts to submit job failed" % galaxy_id_tag ) + job_wrapper.fail( "Unable to run this job due to a cluster error, please retry it later" ) + self.ds.deleteJobTemplate( jt ) + return else: job_wrapper.change_ownership_for_run() log.debug( '(%s) submitting with credentials: %s [uid: %s]' % ( galaxy_id_tag, job_wrapper.user_system_pwent[0], job_wrapper.user_system_pwent[2] ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Merged in natefoo/galaxy-central (pull request #392)
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b4680b54994a/ Changeset: b4680b54994a User: jmchilton Date: 2014-05-13 22:38:04 Summary: Merged in natefoo/galaxy-central (pull request #392) SSL client certificate support for LWR AMQP connections Affected #: 5 files diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -41,6 +41,16 @@  +  +  +  +  + </plugin><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -40,13 +40,17 @@ """ runner_name = "LWRRunner" - def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL ): + def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL, **kwds ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers ) self.async_status_updates = dict() self._init_monitor_thread() self._init_worker_threads() - client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url} + amqp_connect_ssl_args = {} + for kwd in kwds.keys(): + if kwd.startswith('amqp_connect_ssl_'): + amqp_connect_ssl_args[kwd] = kwds[kwd] + client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url, 'amqp_connect_ssl_args': amqp_connect_ssl_args or None} self.galaxy_url = galaxy_url self.client_manager = build_client_manager(**client_manager_kwargs) diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -30,13 +30,14 @@ name _default_. """ - def __init__(self, url, manager_name, timeout=DEFAULT_TIMEOUT): + def __init__(self, url, manager_name, connect_ssl=None, timeout=DEFAULT_TIMEOUT): """ """ if not kombu: raise Exception(KOMBU_UNAVAILABLE) self.__url = url self.__manager_name = manager_name + self.__connect_ssl = connect_ssl self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) self.__timeout = timeout @@ -46,7 +47,7 @@ def consume(self, queue_name, callback, check=True, connection_kwargs={}): queue = self.__queue(queue_name) - with self.connection(self.__url, **connection_kwargs) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl, **connection_kwargs) as connection: with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): while check: try: @@ -55,7 +56,7 @@ pass def publish(self, name, payload): - with self.connection(self.__url) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl) as connection: with pools.producers[connection].acquire() as producer: key = self.__queue_name(name) producer.publish( diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -13,6 +13,7 @@ from .object_client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager +from .util import parse_amqp_connect_ssl_params from .destination import url_to_destination_params from .amqp_exchange import LwrExchange @@ -76,7 +77,8 @@ def __init__(self, **kwds): self.url = kwds.get('url') self.manager_name = kwds.get("manager", "_default_") - self.exchange = LwrExchange(self.url, self.manager_name) + self.connect_ssl = parse_amqp_connect_ssl_params(kwds.get('amqp_connect_ssl_args', None)) + self.exchange = LwrExchange(self.url, self.manager_name, self.connect_ssl) self.status_cache = {} self.callback_lock = threading.Lock() self.callback_thread = None diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -62,6 +62,21 @@ contents.append(name) return contents +def parse_amqp_connect_ssl_params(params): + ssl = None + rval = None + ssl_options = filter(lambda x: x.startswith('amqp_connect_ssl_'), params.keys()) + if ssl_options: + ssl = __import__('ssl') + rval = {} + for option in ssl_options: + value = params.get(option) + option = option.replace('amqp_connect_ssl_', '', 1) + if option == 'cert_reqs': + value = getattr(ssl, value.upper()) + rval[option] = value + return rval + def filter_destination_params(destination_params, prefix): destination_params = destination_params or {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0405422ab342/ Changeset: 0405422ab342 User: natefoo Date: 2014-05-13 22:22:03 Summary: Allow specification of SSL client authentication parameters to the kombu connection. This is done via the `amqp_connect_ssl_*` options in `server.ini`. Affected #: 5 files diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r 0405422ab3422f1b1373c0b00398885a4d8423f6 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -41,6 +41,16 @@  +  +  +  +  + </plugin><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r 0405422ab3422f1b1373c0b00398885a4d8423f6 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -40,13 +40,17 @@ """ runner_name = "LWRRunner" - def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL ): + def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL, **kwds ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers ) self.async_status_updates = dict() self._init_monitor_thread() self._init_worker_threads() - client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url} + amqp_connect_ssl_args = {} + for kwd in kwds.keys(): + if kwd.startswith('amqp_connect_ssl_'): + amqp_connect_ssl_args[kwd] = kwds[kwd] + client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url, 'amqp_connect_ssl_args': amqp_connect_ssl_args or None} self.galaxy_url = galaxy_url self.client_manager = build_client_manager(**client_manager_kwargs) diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r 0405422ab3422f1b1373c0b00398885a4d8423f6 lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -30,13 +30,14 @@ name _default_. """ - def __init__(self, url, manager_name, timeout=DEFAULT_TIMEOUT): + def __init__(self, url, manager_name, connect_ssl=None, timeout=DEFAULT_TIMEOUT): """ """ if not kombu: raise Exception(KOMBU_UNAVAILABLE) self.__url = url self.__manager_name = manager_name + self.__connect_ssl = connect_ssl self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) self.__timeout = timeout @@ -46,7 +47,7 @@ def consume(self, queue_name, callback, check=True, connection_kwargs={}): queue = self.__queue(queue_name) - with self.connection(self.__url, **connection_kwargs) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl, **connection_kwargs) as connection: with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): while check: try: @@ -55,7 +56,7 @@ pass def publish(self, name, payload): - with self.connection(self.__url) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl) as connection: with pools.producers[connection].acquire() as producer: key = self.__queue_name(name) producer.publish( diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r 0405422ab3422f1b1373c0b00398885a4d8423f6 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -13,6 +13,7 @@ from .object_client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager +from .util import parse_amqp_connect_ssl_params from .destination import url_to_destination_params from .amqp_exchange import LwrExchange @@ -76,7 +77,8 @@ def __init__(self, **kwds): self.url = kwds.get('url') self.manager_name = kwds.get("manager", "_default_") - self.exchange = LwrExchange(self.url, self.manager_name) + self.connect_ssl = parse_amqp_connect_ssl_params(kwds.get('amqp_connect_ssl_args', None)) + self.exchange = LwrExchange(self.url, self.manager_name, self.connect_ssl) self.status_cache = {} self.callback_lock = threading.Lock() self.callback_thread = None diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r 0405422ab3422f1b1373c0b00398885a4d8423f6 lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -62,6 +62,21 @@ contents.append(name) return contents +def parse_amqp_connect_ssl_params(params): + ssl = None + rval = None + ssl_options = filter(lambda x: x.startswith('amqp_connect_ssl_'), params.keys()) + if ssl_options: + ssl = __import__('ssl') + rval = {} + for option in ssl_options: + value = params.get(option) + option = option.replace('amqp_connect_ssl_', '', 1) + if option == 'cert_reqs': + value = getattr(ssl, value.upper()) + rval[option] = value + return rval + def filter_destination_params(destination_params, prefix): destination_params = destination_params or {} https://bitbucket.org/galaxy/galaxy-central/commits/b4680b54994a/ Changeset: b4680b54994a User: jmchilton Date: 2014-05-13 22:38:04 Summary: Merged in natefoo/galaxy-central (pull request #392) SSL client certificate support for LWR AMQP connections Affected #: 5 files diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -41,6 +41,16 @@  +  +  +  +  + </plugin><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -40,13 +40,17 @@ """ runner_name = "LWRRunner" - def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL ): + def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL, **kwds ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers ) self.async_status_updates = dict() self._init_monitor_thread() self._init_worker_threads() - client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url} + amqp_connect_ssl_args = {} + for kwd in kwds.keys(): + if kwd.startswith('amqp_connect_ssl_'): + amqp_connect_ssl_args[kwd] = kwds[kwd] + client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url, 'amqp_connect_ssl_args': amqp_connect_ssl_args or None} self.galaxy_url = galaxy_url self.client_manager = build_client_manager(**client_manager_kwargs) diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -30,13 +30,14 @@ name _default_. """ - def __init__(self, url, manager_name, timeout=DEFAULT_TIMEOUT): + def __init__(self, url, manager_name, connect_ssl=None, timeout=DEFAULT_TIMEOUT): """ """ if not kombu: raise Exception(KOMBU_UNAVAILABLE) self.__url = url self.__manager_name = manager_name + self.__connect_ssl = connect_ssl self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) self.__timeout = timeout @@ -46,7 +47,7 @@ def consume(self, queue_name, callback, check=True, connection_kwargs={}): queue = self.__queue(queue_name) - with self.connection(self.__url, **connection_kwargs) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl, **connection_kwargs) as connection: with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): while check: try: @@ -55,7 +56,7 @@ pass def publish(self, name, payload): - with self.connection(self.__url) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl) as connection: with pools.producers[connection].acquire() as producer: key = self.__queue_name(name) producer.publish( diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -13,6 +13,7 @@ from .object_client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager +from .util import parse_amqp_connect_ssl_params from .destination import url_to_destination_params from .amqp_exchange import LwrExchange @@ -76,7 +77,8 @@ def __init__(self, **kwds): self.url = kwds.get('url') self.manager_name = kwds.get("manager", "_default_") - self.exchange = LwrExchange(self.url, self.manager_name) + self.connect_ssl = parse_amqp_connect_ssl_params(kwds.get('amqp_connect_ssl_args', None)) + self.exchange = LwrExchange(self.url, self.manager_name, self.connect_ssl) self.status_cache = {} self.callback_lock = threading.Lock() self.callback_thread = None diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -62,6 +62,21 @@ contents.append(name) return contents +def parse_amqp_connect_ssl_params(params): + ssl = None + rval = None + ssl_options = filter(lambda x: x.startswith('amqp_connect_ssl_'), params.keys()) + if ssl_options: + ssl = __import__('ssl') + rval = {} + for option in ssl_options: + value = params.get(option) + option = option.replace('amqp_connect_ssl_', '', 1) + if option == 'cert_reqs': + value = getattr(ssl, value.upper()) + rval[option] = value + return rval + def filter_destination_params(destination_params, prefix): destination_params = destination_params or {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits May 2014