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galaxy-dist commit dbe6ab1eaa7c: merge
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289568820 18000 # Node ID dbe6ab1eaa7ca7f9754c22bb2f6edd3fc26e3432 # Parent b5b6b92a71e960691bb514af32ba2e21a731bd4e # Parent ba34d996fff5669eca98ff98c6035a68ac93bd34 merge

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galaxy-dist commit fc1f67023d86: Fixes for building target library and folder SelectFields for transferring sample datasets. All folders are now present in the target folder SelectField. Move security-related methods from the model's User class to the security agent where they belong.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289574787 18000 # Node ID fc1f67023d86a69ea7229501b093d61748630f4c # Parent dc4af741ffc455c4737aff67c7d7de48c8628392 Fixes for building target library and folder SelectFields for transferring sample datasets. All folders are now present in the target folder SelectField. Move security-related methods from the model's User class to the security agent where they belong. --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -52,40 +52,6 @@ class User( object ): if role not in roles: roles.append( role ) return roles - def accessible_libraries( self, trans, actions ): - # TODO: eliminate this method - instead use - # trans.app.security_agent.get_accessible_libraries(). - # Get all permitted libraries for this user - all_libraries = trans.sa_session.query( trans.app.model.Library ) \ - .filter( trans.app.model.Library.table.c.deleted == False ) \ - .order_by( trans.app.model.Library.name ) - roles = self.all_roles() - actions_to_check = actions - # The libraries dictionary looks like: { library : '1,2' }, library : '3' } - # Its keys are the libraries that should be displayed for the current user and whose values are a - # string of comma-separated folder ids, of the associated folders the should NOT be displayed. - # The folders that should not be displayed may not be a complete list, but it is ultimately passed - # to the calling method to keep from re-checking the same folders when the library / folder - # select lists are rendered. - libraries = {} - for library in all_libraries: - can_show, hidden_folder_ids = trans.app.security_agent.show_library_item( self, roles, library, actions_to_check ) - if can_show: - libraries[ library ] = hidden_folder_ids - return libraries - def accessible_request_types( self, trans ): - active_request_types = trans.sa_session.query( trans.app.model.RequestType ) \ - .filter( trans.app.model.RequestType.table.c.deleted == False ) \ - .order_by( trans.app.model.RequestType.name ) - # Filter active_request_types to those that can be accessed by this user - role_ids = [ r.id for r in self.all_roles() ] - accessible_request_types = set() - for request_type in active_request_types: - for permission in request_type.actions: - if permission.role.id in role_ids: - accessible_request_types.add( request_type ) - accessible_request_types = [ request_type for request_type in accessible_request_types ] - return accessible_request_types class Job( object ): """ --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -77,7 +77,8 @@ class Requests( BaseController ): kwd[ 'message' ] = message # Allow the user to create a new request only if they have permission to access a # (sequencer configuration) request type. - if len( trans.user.accessible_request_types( trans ) ): + accessible_request_types = trans.app.security_agent.get_accessible_request_types( trans, trans.user ) + if accessible_request_types: self.request_grid.global_actions = [ grids.GridAction( "Create new request", dict( controller='requests_common', action='create_request', cntrller='requests' ) ) ] --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -414,7 +414,7 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, id=request_id, editing_samples=editing_samples ) ) - libraries = self.__get_accessible_libraries( trans, request.user ) + libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) # Build a list of sample widgets (based on the attributes of each sample) for display. displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) @@ -815,7 +815,7 @@ class RequestsCommon( BaseController, Us else: sample_index = len( displayable_sample_widgets ) if params.get( 'add_sample_button', False ): - libraries = self.__get_accessible_libraries( trans, request.user ) + libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) num_samples_to_add = int( params.get( 'num_sample_to_copy', 1 ) ) # See if the user has selected a sample to copy. copy_sample_index = int( params.get( 'copy_sample_index', -1 ) ) @@ -1214,20 +1214,14 @@ class RequestsCommon( BaseController, Us else: folder = None return library, folder + def __get_active_folders( self, library ): + """Return all of the active folders for the received library""" + root_folder = library.root_folder + active_folders = [ root_folder ] + for folder in root_folder.active_folders: + active_folders.append( folder ) + return active_folders # ===== Methods for handling form definition widgets ===== - def __get_accessible_libraries( self, trans, user ): - # Return a dictionary whose keys are libraries that user can - # access and whose values are empty string ''. This is because - # methods expect the dictionary instead of a simple list because - # this method replaces the deprecated model.User.accessible_libraries() - # method. TODO: fix methods that call this method to expect the list - # returne dby trans.app.securoty_agent.get_accessible_libraries() and - # then eliminate this method. - accessible_libraries = trans.app.security_agent.get_accessible_libraries( trans, user ) - accessible_libraries_dict = odict() - for library in accessible_libraries: - accessible_libraries_dict[ library ] = '' - return accessible_libraries_dict def __get_request_widgets( self, trans, id ): """Get the widgets for the request""" request = trans.sa_session.query( trans.model.Request ).get( id ) @@ -1275,7 +1269,7 @@ class RequestsCommon( BaseController, Us # Build the list of widgets which will be used to render each sample row on the request page if not request: return sample_widgets - libraries = self.__get_accessible_libraries( trans, request.user ) + libraries = trans.app.security_agent.get_accessible_libraries( trans, request.user ) # Build the list if sample widgets, populating the values from kwd. for index, sample in enumerate( samples ): id_index = index + 1 @@ -1361,7 +1355,7 @@ class RequestsCommon( BaseController, Us copy_sample_index_select_field.add_option( sample_dict[ 'name' ], index ) return copy_sample_index_select_field def __build_request_type_id_select_field( self, trans, selected_value='none' ): - accessible_request_types = trans.user.accessible_request_types( trans ) + accessible_request_types = trans.app.security_agent.get_accessible_request_types( trans, trans.user ) return build_select_field( trans, accessible_request_types, 'name', 'request_type_id', selected_value=selected_value, refresh_on_change=True ) def __build_user_id_select_field( self, trans, selected_value='none' ): active_users = trans.sa_session.query( trans.model.User ) \ @@ -1388,11 +1382,9 @@ class RequestsCommon( BaseController, Us def __build_library_and_folder_select_fields( self, trans, user, sample_index, libraries, sample=None, library_id=None, folder_id=None, **kwd ): # Create the library_id SelectField for a specific sample. The received libraries param is a list of all the libraries # accessible to the current user, and we add them as options to the library_select_field. If the user has selected an - # existing library then display all the accessible folders of the selected library in the folder_select_field. - # - # The libraries dictionary looks like: { library : '1,2' }, library : '3' }. Its keys are the libraries that - # should be displayed for the current user and its values are strings of comma-separated folder ids that should - # NOT be displayed. + # existing library then display all the folders of the selected library in the folder_select_field. Library folders do + # not have ACCESS permissions associated with them (only LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE), so all folders will + # be present in the folder_select_field for each library selected. params = util.Params( kwd ) library_select_field_name= "sample_%i_library_id" % sample_index folder_select_field_name = "sample_%i_folder_id" % sample_index @@ -1401,15 +1393,11 @@ class RequestsCommon( BaseController, Us if not folder_id: folder_id = params.get( folder_select_field_name, None ) selected_library = None - selected_hidden_folder_ids = [] - showable_folders = [] if library_id not in [ None, 'none' ]: - # If we have a selected library, get the list of it's folders that are not accessible to the current user - for library, hidden_folder_ids in libraries.items(): + for library in libraries: encoded_id = trans.security.encode_id( library.id ) if encoded_id == str( library_id ): selected_library = library - selected_hidden_folder_ids = hidden_folder_ids.split( ',' ) break elif sample and sample.library and library_id == 'none': # The user previously selected a library but is now resetting the selection to 'none' @@ -1417,21 +1405,17 @@ class RequestsCommon( BaseController, Us elif sample and sample.library: library_id = trans.security.encode_id( sample.library.id ) selected_library = sample.library - # sample_%i_library_id SelectField with refresh on change enabled + # Build the sample_%i_library_id SelectField with refresh on change enabled library_select_field = build_select_field( trans, - libraries.keys(), + libraries, 'name', library_select_field_name, initial_value='none', selected_value=str( library_id ).lower(), refresh_on_change=True ) - # Get all accessible folders for the selected library, if one is indeed selected + # Get all folders for the selected library, if one is indeed selected if selected_library: - showable_folders = trans.app.security_agent.get_showable_folders( user, - user.all_roles(), - selected_library, - [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ], - selected_hidden_folder_ids ) + folders = self.__get_active_folders( selected_library ) if folder_id: selected_folder_id = folder_id elif sample and sample.folder: @@ -1440,11 +1424,12 @@ class RequestsCommon( BaseController, Us selected_folder_id = trans.security.encode_id( selected_library.root_folder.id ) else: selected_folder_id = 'none' + folders = [] # TODO: Change the name of the library root folder to "Library root" to clarify to the # user that it is the root folder. We probably should just change this in the Library code, # and update the data in the db. folder_select_field = build_select_field( trans, - showable_folders, + folders, 'name', folder_select_field_name, initial_value='none', --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -84,7 +84,7 @@ [ 'Find Samples', h.url_for( controller='/requests', action='find_samples_index' ) ], [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] ] - tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.user.accessible_request_types( trans ) ) ) ) + tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) %> ## Visualization menu. --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -60,6 +60,8 @@ class RBACAgent: raise "Unimplemented Method" def get_private_user_role( self, user ): raise "Unimplemented Method" + def get_accessible_request_types( self, trans, user ): + raise "Unimplemented Method" def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False ): raise "Unimplemented Method" def history_set_default_permissions( self, history, permissions=None, dataset=False, bypass_manage_permission=False ): @@ -76,6 +78,8 @@ class RBACAgent: raise "Unimplemented Method" def get_accessible_libraries( self, trans, user ): raise "Unimplemented Method" + def get_permitted_libraries( self, trans, user, actions ): + raise "Unimplemented Method" def folder_is_public( self, library ): raise "Unimplemented Method" def make_folder_public( self, folder, count=0 ): @@ -247,7 +251,7 @@ class GalaxyRBACAgent( RBACAgent ): def can_access_library( self, roles, library ): return self.library_is_public( library ) or self.allow_action( roles, self.permitted_actions.LIBRARY_ACCESS, library ) def get_accessible_libraries( self, trans, user ): - """Return all data libraries that user can access""" + """Return all data libraries that the received user can access""" accessible_libraries = [] current_user_role_ids = [ role.id for role in user.all_roles() ] library_access_action = self.permitted_actions.LIBRARY_ACCESS.action @@ -499,6 +503,20 @@ class GalaxyRBACAgent( RBACAgent ): else: permissions[ action ] = [ item_permission.role ] return permissions + def get_accessible_request_types( self, trans, user ): + """Return all ReqquestTypes that the received user has permission to access.""" + active_request_types = trans.sa_session.query( trans.app.model.RequestType ) \ + .filter( trans.app.model.RequestType.table.c.deleted == False ) \ + .order_by( trans.app.model.RequestType.name ) + # Filter active_request_types to those that can be accessed by the received user + role_ids = [ r.id for r in user.all_roles() ] + accessible_request_types = set() + for request_type in active_request_types: + for permission in request_type.actions: + if permission.role.id in role_ids: + accessible_request_types.add( request_type ) + accessible_request_types = [ request_type for request_type in accessible_request_types ] + return accessible_request_types def copy_dataset_permissions( self, src, dst ): if not isinstance( src, self.model.Dataset ): src = src.dataset @@ -731,6 +749,34 @@ class GalaxyRBACAgent( RBACAgent ): else: raise 'Invalid class (%s) specified for target_library_item (%s)' % \ ( target_library_item.__class__, target_library_item.__class__.__name__ ) + def get_permitted_libraries( self, trans, user, actions ): + """ + This method is historical (it is not currently used), but may be useful again at some + point. It returns a dictionary whose keys are library objects and whose values are a + comma-separated string of folder ids. This method works with the show_library_item() + method below, and it returns libraries for which the received user has permission to + perform the received actions. Here is an example call to this method to return all + libraries for which the received user has LIBRARY_ADD permission: + libraries = trans.app.security_agent.get_permitted_libraries( trans, user, + [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + """ + all_libraries = trans.sa_session.query( trans.app.model.Library ) \ + .filter( trans.app.model.Library.table.c.deleted == False ) \ + .order_by( trans.app.model.Library.name ) + roles = user.all_roles() + actions_to_check = actions + # The libraries dictionary looks like: { library : '1,2' }, library : '3' } + # Its keys are the libraries that should be displayed for the current user and whose values are a + # string of comma-separated folder ids, of the associated folders the should NOT be displayed. + # The folders that should not be displayed may not be a complete list, but it is ultimately passed + # to the calling method to keep from re-checking the same folders when the library / folder + # select lists are rendered. + libraries = {} + for library in all_libraries: + can_show, hidden_folder_ids = self.show_library_item( self, roles, library, actions_to_check ) + if can_show: + libraries[ library ] = hidden_folder_ids + return libraries def show_library_item( self, user, roles, library_item, actions_to_check, hidden_folder_ids='' ): """ This method must be sent an instance of Library() or LibraryFolder(). Recursive execution produces a

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galaxy-dist commit caed55b53f5a: Allows the downloading of metadata files associated with datasets (such as bai indices for bam files). This is done by adding a dropdown menu to the Save icon of appropriate datasets. Could potentially be modified to access implicitly converted datatypes as well in the future. Closes #410
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1289525191 18000 # Node ID caed55b53f5a811226e0bfa1c177e7b3e57a909a # Parent ff7327f2946e9121139cefbf4a45dba2791b7162 Allows the downloading of metadata files associated with datasets (such as bai indices for bam files). This is done by adding a dropdown menu to the Save icon of appropriate datasets. Could potentially be modified to access implicitly converted datatypes as well in the future. Closes #410 --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -1,8 +1,10 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id <%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True )"> - <a name="${trans.security.encode_id( data.id )}"></a><% + dataset_id = trans.security.encode_id( data.id ) + from galaxy.datatypes.metadata import FileParameter + if data.state in ['no state','',None]: data_state = "queued" else: @@ -41,7 +43,6 @@ %endif %else: <% - dataset_id = trans.security.encode_id( data.id ) if for_editing: display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) else: @@ -117,10 +118,25 @@ %endif </div><div class="info">${_('Info: ')}${data.display_info()}</div> - <div> - <% dataset_id=trans.security.encode_id( data.id ) %> + <div> %if data.has_data(): + + ## Check for downloadable metadata files + <% meta_files = [ k for k in data.metadata.spec.keys() if isinstance( data.metadata.spec[k].param, FileParameter ) ] %> + %if meta_files: + <div popupmenu="dataset-${dataset_id}-popup"> + %for file_type in meta_files: + <a class="action-button" href="${h.url_for( controller='dataset', action='get_metadata_file', hda_id=dataset_id, metadata_type=file_type )}"> + Download ${file_type}</a> + %endfor + </div> + <div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"> + %endif <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Save" class="icon-button disk tooltip"></a> + %if meta_files: + </div> + %endif + %if for_editing: <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> %if app.config.get_bool( 'enable_tracks', False ) and data.ext in app.datatypes_registry.get_available_tracks(): --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -277,6 +277,7 @@ var updater_callback = function ( tracke // Keep going (if there are still any items to track) updater( tracked_datasets ); } + make_popup_menus(); }, error: function() { // Just retry, like the old method, should try to be smarter --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -305,7 +305,18 @@ class DatasetInterface( BaseController, return trans.show_error_message( msg ) - + @web.expose + def get_metadata_file(self, trans, hda_id, metadata_type): + """ Allows the downloading of metadata files associated with datasets (eg. bai index for bam files) """ + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( hda_id ) ) + if not data or not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ): + return trans.show_error_message( "You are not allowed to access this dataset" ) + + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150] + trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, metadata_type) + return open(data.metadata.get(metadata_type).file_name) + @web.expose def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd): """Catches the dataset id and displays file contents as directed""" @@ -323,8 +334,7 @@ class DatasetInterface( BaseController, data = None if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) - current_user_roles = trans.get_current_user_roles() - if not trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): + if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ): return trans.show_error_message( "You are not allowed to access this dataset" ) if data.state == trans.model.Dataset.states.UPLOAD: @@ -358,8 +368,7 @@ class DatasetInterface( BaseController, if not to_ext: to_ext = data.extension valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = data.name - fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] + fname = ''.join(c in valid_chars and c or '_' for c in data.name)[0:150] trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, to_ext) return open( data.file_name ) if not os.path.exists( data.file_name ):

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galaxy-dist commit 10d0ffe5b7e2: Include BLAST-XML to tabular in tool_conf.xml.sample
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286962559 -3600 # Node ID 10d0ffe5b7e22b2d122945ab5b7fa951a18c6e4a # Parent caed55b53f5a811226e0bfa1c177e7b3e57a909a Include BLAST-XML to tabular in tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -268,6 +268,7 @@ <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> + <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /><tool file="ncbi_blast_plus/blast_filter_fasta.xml" /></section><section name="NGS: Mapping" id="solexa_tools">

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galaxy-dist commit f2383b761f4e: Make sure samples have associated target libraries befoe enabling ability to transfer datasets, use better naming convention for request history code and templates, eliminate the ability to submit a request unless it has samples.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289507783 18000 # Node ID f2383b761f4e05442fd5ba6b1cde517732aa2c03 # Parent dfc848840870fa9936a69e62322446fcb940fb40 Make sure samples have associated target libraries befoe enabling ability to transfer datasets, use better naming convention for request history code and templates, eliminate the ability to submit a request unless it has samples. --- a/templates/requests/common/view_sample_datasets.mako +++ b/templates/requests/common/view_sample_datasets.mako @@ -7,14 +7,14 @@ is_complete = sample.request.is_complete is_submitted = sample.request.is_submitted can_select_datasets = is_admin and ( is_complete or is_submitted ) - can_transfer_datasets = is_admin and sample.untransferred_dataset_files + can_transfer_datasets = is_admin and sample.untransferred_dataset_files and sample.library and sample.folder %><br/><br/><ul class="manage-table-actions"> %if can_transfer_datasets: - <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li> + <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li> %endif <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=transfer_status )}">Refresh page</a></li><li><a class="action-button" id="sample-${sample.id}-popup" class="menubutton">Dataset Actions</a></li> --- a/templates/requests/common/edit_samples.mako +++ b/templates/requests/common/edit_samples.mako @@ -47,7 +47,7 @@ %if can_edit_request: <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -57,9 +57,9 @@ class Requests( BaseController ): action='undelete_request', cntrller='requests', **kwd ) ) - if operation == "request_events": + if operation == "view_request_history": return trans.response.send_redirect( web.url_for( controller='requests_common', - action='request_events', + action='view_request_history', cntrller='requests', **kwd ) ) --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -76,7 +76,7 @@ class RequestsGrid( grids.Grid ): StateColumn( "State", key='state', filterable="advanced", - link=( lambda item: iff( item.deleted, None, dict( operation="request_events", id=item.id ) ) ) + link=( lambda item: iff( item.deleted, None, dict( operation="view_request_history", id=item.id ) ) ) ) ] columns.append( grids.MulticolFilterColumn( "Search", @@ -579,8 +579,8 @@ class RequestsCommon( BaseController, Us status=status, message=message ) ) @web.expose - @web.require_login( "sequencing request events" ) - def request_events( self, trans, cntrller, **kwd ): + @web.require_login( "sequencing request history" ) + def view_request_history( self, trans, cntrller, **kwd ): params = util.Params( kwd ) request_id = params.get( 'id', None ) try: @@ -590,7 +590,7 @@ class RequestsCommon( BaseController, Us events_list = [] for event in request.events: events_list.append( ( event.state, time_ago( event.update_time ), event.comment ) ) - return trans.fill_template( '/requests/common/events.mako', + return trans.fill_template( '/requests/common/view_request_history.mako', cntrller=cntrller, events_list=events_list, request=request ) --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -72,7 +72,7 @@ <% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_transfer_datasets = is_admin and sample.untransferred_dataset_files + can_transfer_datasets = is_admin and sample.untransferred_dataset_files and sample.library and sample.folder %><br/><br/> @@ -85,8 +85,15 @@ </ul> %if not sample: + <br/><font color="red"><b><i>Select a sample before selecting datasets to transfer</i></b></font> - <br/><br/> + <br/> +%endif + +%if request.samples_without_library_destinations: + <br/> + <font color="red"><b><i>Select a target data library and folder for all samples before starting the sequence run</i></b></font> + <br/> %endif %if message: --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -175,9 +175,9 @@ class RequestsAdmin( BaseController, Use action='view_request', cntrller='requests_admin', **kwd ) ) - if operation == "request_events": + if operation == "view_request_history": return trans.response.send_redirect( web.url_for( controller='requests_common', - action='request_events', + action='view_request_history', cntrller='requests_admin', **kwd ) ) if operation == "reject": --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1517,7 +1517,7 @@ class TwillTestCase( unittest.TestCase ) for check_str in strings_not_displayed: self.check_string_not_in_page( check_str ) def view_request_history( self, cntrller, request_id, strings_displayed=[], strings_not_displayed=[] ): - self.visit_url( "%s/requests_common/request_events?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) + self.visit_url( "%s/requests_common/view_request_history?cntrller=%s&id=%s" % ( self.url, cntrller, request_id ) ) for check_str in strings_displayed: self.check_page_for_string( check_str ) for check_str in strings_not_displayed: --- a/templates/requests/common/events.mako +++ /dev/null @@ -1,53 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<% - is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_edit_request = ( is_admin and not request.is_complete ) or request.is_unsubmitted - can_reject_request = is_admin and request.is_submitted - can_add_samples = request.is_unsubmitted -%> - -<br/><br/> -<ul class="manage-table-actions"> - <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li> - <div popupmenu="request-${request.id}-popup"> - <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> - %if can_edit_request: - <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> - %endif - %if can_add_samples: - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> - %endif - %if can_reject_request: - <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> - %endif - </div> -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -<h2>History of Sequencing Request "${request.name}"</h2> - -<div class="toolForm"> - <table class="grid"> - <thead> - <tr> - <th>State</th> - <th>Last Update</th> - <th>Comments</th> - </tr> - </thead> - <tbody> - %for state, updated, comments in events_list: - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><b><a>${state}</a></b></td> - <td><a>${updated}</a></td> - <td><a>${comments}</a></td> - </tr> - %endfor - </tbody> - </table> -</div> --- a/templates/requests/common/edit_basic_request_info.mako +++ b/templates/requests/common/edit_basic_request_info.mako @@ -3,7 +3,13 @@ <% is_admin = cntrller == 'requests_admin' and trans.user_is_admin() - can_add_samples = request.is_unsubmitted + is_complete = request.is_complete + is_submitted = request.is_submitted + is_unsubmitted = request.is_unsubmitted + can_add_samples = is_unsubmitted + can_reject = is_admin and is_submitted + can_select_datasets = is_admin and ( is_complete or is_submitted ) + can_submit_request = request.samples and is_unsubmitted %><br/><br/> @@ -11,12 +17,14 @@ <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li><div popupmenu="request-${request.id}-popup"><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> - %if can_add_samples: + %if can_submit_request: <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> - %if is_admin and request.is_submitted: + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> + %endif + %if can_select_datasets: <a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ) )}">Select datasets to transfer</a> %endif </div> --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -8,7 +8,7 @@ <h2>Reject Sequencing Request "${request.name}"</h2><ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">View history</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">View history</a></li><li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id(request.id) )}">Browse this request</a> --- a/templates/requests/common/view_request.mako +++ b/templates/requests/common/view_request.mako @@ -44,7 +44,7 @@ %if can_edit_request: <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> %endif - <a class="action-button" href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">View history</a> %if can_reject: <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> %endif @@ -52,8 +52,15 @@ </ul> %if request.is_rejected: + <br/><font color="red"><b><i>Reason for rejection: </i></b></font><b>${request.last_comment}</b> - <br/><br/> + <br/> +%endif + +%if request.samples_without_library_destinations: + <br/> + <font color="red"><b><i>Select a target data library and folder for all samples before starting the sequence run</i></b></font> + <br/> %endif %if message: @@ -94,7 +101,7 @@ <div class="form-row"><label>${field_label}:</label> %if field_label == 'State': - <a href="${h.url_for( controller='requests_common', action='request_events', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a> + <a href="${h.url_for( controller='requests_common', action='view_request_history', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">${field_value}</a> %else: ${field_value} %endif @@ -154,6 +161,11 @@ render_buttons = can_edit_samples %> ${render_samples_grid( cntrller, request, displayable_sample_widgets=displayable_sample_widgets, action='view_request', editing_samples=False, encoded_selected_sample_ids=[], render_buttons=render_buttons, grid_header=grid_header )} + ## Render the other grids + <% trans.sa_session.refresh( request.type.sample_form ) %> + %for grid_index, grid_name in enumerate( request.type.sample_form.layout ): + ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=False )} + %endfor %else: There are no samples. %if can_add_samples: @@ -162,8 +174,3 @@ </ul> %endif %endif -## Render the other grids -<% trans.sa_session.refresh( request.type.sample_form ) %> -%for grid_index, grid_name in enumerate( request.type.sample_form.layout ): - ${render_request_type_sample_form_grids( grid_index, grid_name, request.type.sample_form.grid_fields( grid_index ), displayable_sample_widgets=displayable_sample_widgets, editing_samples=False )} -%endfor --- /dev/null +++ b/templates/requests/common/view_request_history.mako @@ -0,0 +1,58 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<% + is_admin = cntrller == 'requests_admin' and trans.user_is_admin() + is_complete = request.is_complete + is_submitted = request.is_submitted + is_unsubmitted = request.is_unsubmitted + can_add_samples = is_unsubmitted + can_edit_request = ( is_admin and not is_complete ) or is_unsubmitted + can_reject = is_admin and is_submitted + can_select_datasets = is_admin and ( is_complete or is_submitted ) + can_submit_request = request.samples and is_unsubmitted +%> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="request-${request.id}-popup" class="menubutton">Request Actions</a></li> + <div popupmenu="request-${request.id}-popup"> + <a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a> + %if can_edit_request: + <a class="action-button" href="${h.url_for( controller='requests_common', action='edit_basic_request_info', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Edit this request</a> + %endif + %if can_submit_request: + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_common', action='submit_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Submit this request</a> + %endif + %if can_reject: + <a class="action-button" href="${h.url_for( controller='requests_admin', action='reject_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Reject this request</a> + %endif + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<h2>History of sequencing request "${request.name}"</h2> + +<div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>State</th> + <th>Last Update</th> + <th>Comments</th> + </tr> + </thead> + <tbody> + %for state, updated, comments in events_list: + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td><b><a>${state}</a></b></td> + <td><a>${updated}</a></td> + <td><a>${comments}</a></td> + </tr> + %endfor + </tbody> + </table> +</div> --- a/templates/requests/common/common.mako +++ b/templates/requests/common/common.mako @@ -322,7 +322,7 @@ %if can_select_datasets: <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select datasets to transfer</a></li> %endif - %if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ): + %if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ) and sample.library and sample.folder: <li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li> %elif sample.datasets and len(sample.datasets ) == len( transferred_dataset_files ): <li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_sample_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ), transfer_status=trans.model.SampleDataset.transfer_status.COMPLETE )}">View transferred datasets</a></li>

1 0

galaxy-dist commit 5c212dfc6189: Fix a caption capitalisation
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286980710 -3600 # Node ID 5c212dfc6189bb41d334b0519411ca4f04fde9ec # Parent 122aaabe2c7eb48726f65233370926b838b6b444 Fix a caption capitalisation --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -62,7 +62,7 @@ blastn <option value="vecscreen">vecscreen</option> --></param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -57,7 +57,7 @@ blastp <option value="blastp">blastp</option><option value="blastp-short">blastp-short</option></param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -51,7 +51,7 @@ tblastx <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/></when></conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -52,7 +52,7 @@ blastx <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/></when></conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -52,7 +52,7 @@ tblastn <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/></when></conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /><param name="out_format" type="select" label="Output format"><option value="-outfmt 6" selected="True">Tabular</option><option value="-outfmt 5">BLAST XML</option>

1 0

galaxy-dist commit 082399b4681b: Remove broken blastn test
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1288001263 -3600 # Node ID 082399b4681b878d20a727150832ef30679b7e1c # Parent 0f6ace5c397b000993db8e491a33e42423cdc807 Remove broken blastn test --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -119,20 +119,6 @@ blastn <requirement type="binary">blastn</requirement></requirements><tests> - <test> - <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> -  - <param name="database" value="phiX" /> - <param name="blast_type" value="megablast" /> -  - <param name="evalue_cutoff" value="10.0" /> - <param name="filter_query" value="yes" /> - <param name="out_format" value="6" /> - <output name="output1" file="megablast_wrapper_test1.out"/> - </test></tests><help>

1 0

galaxy-dist commit d8184d91928c: Remove FASTA filter script from BLAST+ tools (I want to generalise it)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1287998919 -3600 # Node ID d8184d91928c83f0269bd0267be949bc5d676e8b # Parent 5c212dfc6189bb41d334b0519411ca4f04fde9ec Remove FASTA filter script from BLAST+ tools (I want to generalise it) --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -269,7 +269,6 @@ <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /><tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> - <tool file="ncbi_blast_plus/blast_filter_fasta.xml" /></section><section name="NGS: Mapping" id="solexa_tools"><tool file="sr_mapping/lastz_wrapper.xml" /> --- a/tools/ncbi_blast_plus/blast_filter_fasta.py +++ /dev/null @@ -1,38 +0,0 @@ -#!/usr/bin/env python -"""Filter a FASTA file using tabular output, e.g. from BLAST. - -Takes five command line options, tabular BLAST filename, ID column number -(using one based counting), input FASTA filename, and two output FASTA -filenames (for records with and without any BLAST hits). - -In the default NCBI BLAST+ tabular output, the query sequence ID is in column -one, and the ID of the match from the database is in column two. -""" -import sys -from galaxy_utils.sequence.fasta import fastaReader, fastaWriter - -#Parse Command Line -blast_file, blast_col, in_file, out_positive_file, out_negative_file = sys.argv[1:] -blast_col = int(blast_col)-1 -assert blast_col >= 0 - -#Read tabular BLAST file and record all queries with hit(s) -ids = set() -blast_handle = open(blast_file, "rU") -for line in blast_handle: - ids.add(line.split("\t")[blast_col]) -blast_handle.close() - -#Write filtered FASTA file based on IDs from BLAST file -reader = fastaReader(open(in_file, "rU")) -positive_writer = fastaWriter(open(out_positive_file, "w")) -negative_writer = fastaWriter(open(out_negative_file, "w")) -for record in reader: - #The [1:] is because the fastaReader leaves the > on the identifer. - if record.identifier and record.identifier.split()[0][1:] in ids: - positive_writer.write(record) - else: - negative_writer.write(record) -positive_writer.close() -negative_writer.close() -reader.close() --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ /dev/null @@ -1,37 +0,0 @@ -<tool id="blast_filter_fasta" name="Filter FASTA using BLAST output" version="0.0.1"> - <description>Divide a FASTA file based on BLAST hits</description> - <command interpreter="python"> - blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file - </command> - <inputs> - <param name="in_file" type="data" format="fasta" label="FASTA file to filter"/> - <param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> - <param name="blast_col" type="select" label="Column containing FASTA identifiers"> - <option value="1">Column 1 - BLAST query ID</option> - <option value="2">Column 2 - BLAST match ID</option> - </param> - </inputs> - <outputs> - <data name="out_positive_file" format="fasta" label="Sequences with BLAST hits" /> - <data name="out_negative_file" format="fasta" label="Sequences without BLAST hits" /> - </outputs> - <requirements> - </requirements> - <tests> - </tests> - <help> - -**What it does** - -Typical use would be to take a multi-sequence FASTA and the tabular output of -running BLAST on it, and divide the FASTA file in two: those sequence with a -BLAST hit, and those without. - -In the default NCBI BLAST+ tabular output, the query sequence ID is in column -one, and the ID of the match from the database is in column two. - -This allows you to filter the FASTA file for the subjects in the BLAST search, -rather than filtering the FASTA file for the queries in the BLAST search. - - </help> -</tool>

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galaxy-dist commit 0f6ace5c397b: Ignore backup files from some editors
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286965717 -3600 # Node ID 0f6ace5c397b000993db8e491a33e42423cdc807 # Parent d8184d91928c83f0269bd0267be949bc5d676e8b Ignore backup files from some editors --- a/.hgignore +++ b/.hgignore @@ -43,4 +43,4 @@ run_functional_tests.html *.orig .DS_Store *.rej - +*~

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galaxy-dist commit ff7327f2946e: When generating the list of target libraries for transferring sample datasets, use all libraries accessible to the request's user rather than all libraries for which that user has LIBRARY_ADD permission.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1289522279 18000 # Node ID ff7327f2946e9121139cefbf4a45dba2791b7162 # Parent f2383b761f4e05442fd5ba6b1cde517732aa2c03 When generating the list of target libraries for transferring sample datasets, use all libraries accessible to the request's user rather than all libraries for which that user has LIBRARY_ADD permission. --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -53,6 +53,8 @@ class User( object ): roles.append( role ) return roles def accessible_libraries( self, trans, actions ): + # TODO: eliminate this method - instead use + # trans.app.security_agent.get_accessible_libraries(). # Get all permitted libraries for this user all_libraries = trans.sa_session.query( trans.app.model.Library ) \ .filter( trans.app.model.Library.table.c.deleted == False ) \ --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -2,6 +2,7 @@ from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * from galaxy import model, util +from galaxy.util.odict import odict from galaxy.web.form_builder import * import logging, os, csv @@ -413,8 +414,7 @@ class RequestsCommon( BaseController, Us cntrller=cntrller, id=request_id, editing_samples=editing_samples ) ) - # Get all libraries for which the current user has permission to add items. - libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + libraries = self.__get_accessible_libraries( trans, request.user ) # Build a list of sample widgets (based on the attributes of each sample) for display. displayable_sample_widgets = self.__get_sample_widgets( trans, request, request.samples, **kwd ) encoded_selected_sample_ids = self.__get_encoded_selected_sample_ids( trans, request, **kwd ) @@ -815,8 +815,7 @@ class RequestsCommon( BaseController, Us else: sample_index = len( displayable_sample_widgets ) if params.get( 'add_sample_button', False ): - # Get all libraries for which the current user has permission to add items - libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + libraries = self.__get_accessible_libraries( trans, request.user ) num_samples_to_add = int( params.get( 'num_sample_to_copy', 1 ) ) # See if the user has selected a sample to copy. copy_sample_index = int( params.get( 'copy_sample_index', -1 ) ) @@ -1186,9 +1185,9 @@ class RequestsCommon( BaseController, Us # the first time a bar code was added to the sample, so change it's state # to the next associated SampleState. if sample.state.id == request.type.states[0].id: - event = trans.app.model.SampleEvent(sample, - request.type.states[1], - 'Bar code associated with the sample' ) + event = trans.model.SampleEvent( sample, + request.type.states[1], + 'Bar code associated with the sample' ) trans.sa_session.add( event ) trans.sa_session.flush() sample.bar_code = bar_code @@ -1216,6 +1215,19 @@ class RequestsCommon( BaseController, Us folder = None return library, folder # ===== Methods for handling form definition widgets ===== + def __get_accessible_libraries( self, trans, user ): + # Return a dictionary whose keys are libraries that user can + # access and whose values are empty string ''. This is because + # methods expect the dictionary instead of a simple list because + # this method replaces the deprecated model.User.accessible_libraries() + # method. TODO: fix methods that call this method to expect the list + # returne dby trans.app.securoty_agent.get_accessible_libraries() and + # then eliminate this method. + accessible_libraries = trans.app.security_agent.get_accessible_libraries( trans, user ) + accessible_libraries_dict = odict() + for library in accessible_libraries: + accessible_libraries_dict[ library ] = '' + return accessible_libraries_dict def __get_request_widgets( self, trans, id ): """Get the widgets for the request""" request = trans.sa_session.query( trans.model.Request ).get( id ) @@ -1263,8 +1275,7 @@ class RequestsCommon( BaseController, Us # Build the list of widgets which will be used to render each sample row on the request page if not request: return sample_widgets - # Get the list of libraries for which the current user has permission to add items. - libraries = request.user.accessible_libraries( trans, [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] ) + libraries = self.__get_accessible_libraries( trans, request.user ) # Build the list if sample widgets, populating the values from kwd. for index, sample in enumerate( samples ): id_index = index + 1 --- a/lib/galaxy/webapps/community/__init__.py +++ b/lib/galaxy/webapps/community/__init__.py @@ -1,3 +1,3 @@ -"""The Galaxy Reports application.""" +"""The Galaxy Tool Shed application.""" from galaxy.web.framework import expose, url_for --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -74,6 +74,8 @@ class RBACAgent: raise "Unimplemented Method" def make_library_public( self, library ): raise "Unimplemented Method" + def get_accessible_libraries( self, trans, user ): + raise "Unimplemented Method" def folder_is_public( self, library ): raise "Unimplemented Method" def make_folder_public( self, folder, count=0 ): @@ -244,6 +246,26 @@ class GalaxyRBACAgent( RBACAgent ): return self.allow_action( roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset ) def can_access_library( self, roles, library ): return self.library_is_public( library ) or self.allow_action( roles, self.permitted_actions.LIBRARY_ACCESS, library ) + def get_accessible_libraries( self, trans, user ): + """Return all data libraries that user can access""" + accessible_libraries = [] + current_user_role_ids = [ role.id for role in user.all_roles() ] + library_access_action = self.permitted_actions.LIBRARY_ACCESS.action + restricted_library_ids = [ lp.library_id for lp in trans.sa_session.query( trans.model.LibraryPermissions ) \ + .filter( trans.model.LibraryPermissions.table.c.action == library_access_action ) \ + .distinct() ] + accessible_restricted_library_ids = [ lp.library_id for lp in trans.sa_session.query( trans.model.LibraryPermissions ) \ + .filter( and_( trans.model.LibraryPermissions.table.c.action == library_access_action, + trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids ) ) ) ] + # Filter to get libraries accessible by the current user. Get both + # public libraries and restricted libraries accessible by the current user. + for library in trans.sa_session.query( trans.model.Library ) \ + .filter( and_( trans.model.Library.table.c.deleted == False, + ( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ), + trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) ) ) \ + .order_by( trans.app.model.Library.name ): + accessible_libraries.append( library ) + return accessible_libraries def can_access_library_item( self, roles, item, user ): if type( item ) == self.model.Library: return self.can_access_library( roles, item )

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