2 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/3b2acb89495b/ changeset: 3b2acb89495b user: dannon date: 2012-02-02 20:53:34 summary: Workflows: Add the ability to remove workflows that have been shared with you. affected #: 2 files

diff -r 50bf77aa34c3689a122187d7ba9b55deb348df92 -r 3b2acb89495bee2355f20fc3954baa174d486a3c lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -22,11 +22,11 @@ from galaxy.web.framework.helpers import to_unicode from galaxy.jobs.actions.post import ActionBox

-class StoredWorkflowListGrid( grids.Grid ): +class StoredWorkflowListGrid( grids.Grid ): class StepsColumn( grids.GridColumn ): def get_value(self, trans, grid, workflow): return len( workflow.latest_workflow.steps ) - + # Grid definition use_panels = True title = "Saved Workflows" @@ -40,10 +40,10 @@ grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] - columns.append( - grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1] ], + columns.append( + grids.MulticolFilterColumn( + "Search", + cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [ @@ -67,14 +67,14 @@ grids.PublicURLColumn( "Name", key="name", filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ), - grids.CommunityRatingColumn( "Community Rating", key="rating" ), + grids.CommunityRatingColumn( "Community Rating", key="rating" ), grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago ) ] - columns.append( - grids.MulticolFilterColumn( - "Search name, annotation, owner, and tags", - cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], + columns.append( + grids.MulticolFilterColumn( + "Search name, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [] @@ -84,20 +84,20 @@ def apply_query_filter( self, trans, query, **kwargs ): # A public workflow is published, has a slug, and is not deleted. return query.filter( self.model_class.published==True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False ) - + # Simple SGML parser to get all content in a single tag. class SingleTagContentsParser( sgmllib.SGMLParser ): - + def __init__( self, target_tag ): sgmllib.SGMLParser.__init__( self ) self.target_tag = target_tag self.cur_tag = None self.tag_content = "" - + def unknown_starttag( self, tag, attrs ): """ Called for each start tag. """ self.cur_tag = tag - + def handle_data( self, text ): """ Called for each block of plain text. """ if self.cur_tag == self.target_tag: @@ -106,13 +106,13 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAnnotations, UsesItemRatings ): stored_list_grid = StoredWorkflowListGrid() published_list_grid = StoredWorkflowAllPublishedGrid() - + __myexp_url = "www.myexperiment.org:80" - + @web.expose def index( self, trans ): return self.list( trans ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def list_grid( self, trans, **kwargs ): @@ -145,7 +145,7 @@ .filter( model.StoredWorkflow.deleted == False ) \ .order_by( desc( model.StoredWorkflow.update_time ) ) \ .all() - + # Legacy issue: all shared workflows must have slugs. slug_set = False for workflow_assoc in shared_by_others: @@ -157,7 +157,7 @@ return trans.fill_template( "workflow/list.mako", workflows = workflows, shared_by_others = shared_by_others ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def list_for_run( self, trans ): @@ -179,7 +179,7 @@ return trans.fill_template( "workflow/list_for_run.mako", workflows = workflows, shared_by_others = shared_by_others ) - + @web.expose def list_published( self, trans, **kwargs ): grid = self.published_list_grid( trans, **kwargs ) @@ -235,11 +235,11 @@ @web.expose def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ - + stored = self.get_stored_workflow( trans, id, False, True ) if stored is None: raise web.httpexceptions.HTTPNotFound() - + # Get data for workflow's steps. self.get_stored_workflow_steps( trans, stored ) # Get annotations. @@ -247,7 +247,7 @@ for step in stored.latest_workflow.steps: step.annotation = self.get_item_annotation_str( trans.sa_session, stored.user, step ) return trans.stream_template_mako( "/workflow/item_content.mako", item = stored, item_data = stored.latest_workflow.steps ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def share( self, trans, id, email="", use_panels=False ): @@ -285,45 +285,55 @@ item=stored, email=email, use_panels=use_panels ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def sharing( self, trans, id, **kwargs ): """ Handle workflow sharing. """ - - # Get session and workflow. + session = trans.sa_session - stored = self.get_stored_workflow( trans, id ) - session.add( stored ) - - # Do operation on workflow. - if 'make_accessible_via_link' in kwargs: - self._make_item_accessible( trans.sa_session, stored ) - elif 'make_accessible_and_publish' in kwargs: - self._make_item_accessible( trans.sa_session, stored ) - stored.published = True - elif 'publish' in kwargs: - stored.published = True - elif 'disable_link_access' in kwargs: - stored.importable = False - elif 'unpublish' in kwargs: - stored.published = False - elif 'disable_link_access_and_unpublish' in kwargs: - stored.importable = stored.published = False - elif 'unshare_user' in kwargs: - user = session.query( model.User ).get( trans.security.decode_id( kwargs['unshare_user' ] ) ) - if not user: - error( "User not found for provided id" ) + + if 'unshare_me' in kwargs: + # Remove self from shared associations with workflow. + stored = self.get_stored_workflow(trans, id, False, True) association = session.query( model.StoredWorkflowUserShareAssociation ) \ - .filter_by( user=user, stored_workflow=stored ).one() + .filter_by( user=trans.user, stored_workflow=stored ).one() session.delete( association ) - - # Legacy issue: workflows made accessible before recent updates may not have a slug. Create slug for any workflows that need them. - if stored.importable and not stored.slug: - self._make_item_accessible( trans.sa_session, stored ) - + session.flush() + return self.list( trans ) + else: + # Get session and workflow. + stored = self.get_stored_workflow( trans, id ) + session.add( stored ) + + # Do operation on workflow. + if 'make_accessible_via_link' in kwargs: + self._make_item_accessible( trans.sa_session, stored ) + elif 'make_accessible_and_publish' in kwargs: + self._make_item_accessible( trans.sa_session, stored ) + stored.published = True + elif 'publish' in kwargs: + stored.published = True + elif 'disable_link_access' in kwargs: + stored.importable = False + elif 'unpublish' in kwargs: + stored.published = False + elif 'disable_link_access_and_unpublish' in kwargs: + stored.importable = stored.published = False + elif 'unshare_user' in kwargs: + user = session.query( model.User ).get( trans.security.decode_id( kwargs['unshare_user' ] ) ) + if not user: + error( "User not found for provided id" ) + association = session.query( model.StoredWorkflowUserShareAssociation ) \ + .filter_by( user=user, stored_workflow=stored ).one() + session.delete( association ) + + # Legacy issue: workflows made accessible before recent updates may not have a slug. Create slug for any workflows that need them. + if stored.importable and not stored.slug: + self._make_item_accessible( trans.sa_session, stored ) + session.flush() - + return trans.fill_template( "/workflow/sharing.mako", use_panels=True, item=stored )

@web.expose @@ -335,7 +345,7 @@ referer_message = "<a href='%s'>return to the previous page</a>" % referer else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) - + # Do import. session = trans.sa_session stored = self.get_stored_workflow( trans, id, check_ownership=False ) @@ -353,19 +363,19 @@ session = trans.sa_session session.add( imported_stored ) session.flush() - + # Copy annotations. self.copy_item_annotation( session, stored.user, stored, imported_stored.user, imported_stored ) for order_index, step in enumerate( stored.latest_workflow.steps ): self.copy_item_annotation( session, stored.user, step, \ imported_stored.user, imported_stored.latest_workflow.steps[order_index] ) session.flush() - + # Redirect to load galaxy frames. return trans.show_ok_message( - message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s.""" + message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s.""" % ( stored.name, web.url_for( controller='workflow' ), referer_message ), use_panels=True ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def edit_attributes( self, trans, id, **kwargs ): @@ -382,11 +392,11 @@ annotation = sanitize_html( kwargs[ 'annotation' ], 'utf-8', 'text/html' ) self.add_item_annotation( trans.sa_session, trans.get_user(), stored, annotation ) trans.sa_session.flush() - return trans.fill_template( 'workflow/edit_attributes.mako', - stored=stored, - annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) + return trans.fill_template( 'workflow/edit_attributes.mako', + stored=stored, + annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def rename( self, trans, id, new_name=None, **kwargs ): @@ -403,10 +413,10 @@ #message = "Workflow renamed to '%s'." % new_name #return self.list_grid( trans, message=message, status='done' ) else: - return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), + return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename", use_panels=True ) \ .add_text( "new_name", "Workflow Name", value=to_unicode( stored.name ) ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def rename_async( self, trans, id, new_name=None, **kwargs ): @@ -417,7 +427,7 @@ stored.latest_workflow.name = san_new_name trans.sa_session.flush() return stored.name - + @web.expose @web.require_login( "use Galaxy workflows" ) def annotate_async( self, trans, id, new_annotation=None, **kwargs ): @@ -428,7 +438,7 @@ self.add_item_annotation( trans.sa_session, trans.get_user(), stored, new_annotation ) trans.sa_session.flush() return new_annotation - + @web.expose @web.require_login( "rate items" ) @web.json @@ -443,7 +453,7 @@ stored_rating = self.rate_item( trans.sa_session, trans.get_user(), stored, rating )

return self.get_ave_item_rating_data( trans.sa_session, stored ) - + @web.expose @web.require_login( "use Galaxy workflows" ) def set_accessible_async( self, trans, id=None, accessible=False ): @@ -459,7 +469,7 @@ stored.importable = importable trans.sa_session.flush() return - + @web.expose @web.require_login( "modify Galaxy items" ) def set_slug_async( self, trans, id, new_slug ): @@ -468,7 +478,7 @@ stored.slug = new_slug trans.sa_session.flush() return stored.slug - + @web.expose def get_embed_html_async( self, trans, id ): """ Returns HTML for embedding a workflow in a page. """ @@ -477,7 +487,7 @@ stored = self.get_stored_workflow( trans, id ) if stored: return "Embedded Workflow '%s'" % stored.name - + @web.expose @web.json @web.require_login( "use Galaxy workflows" ) @@ -489,33 +499,33 @@ trans.sa_session.flush() return_dict = { "name" : stored.name, "link" : url_for( action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } return return_dict - + @web.expose @web.require_login( "use Galaxy workflows" ) def gen_image( self, trans, id ): stored = self.get_stored_workflow( trans, id, check_ownership=True ) session = trans.sa_session - + workflow = stored.latest_workflow data = [] - + canvas = svgfig.canvas(style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left") text = svgfig.SVG("g") connectors = svgfig.SVG("g") boxes = svgfig.SVG("g") svgfig.Text.defaults["font-size"] = "10px" - + in_pos = {} out_pos = {} margin = 5 line_px = 16 # how much spacing between input/outputs widths = {} # store px width for boxes of each step max_width, max_x, max_y = 0, 0, 0 - + for step in workflow.steps: # Load from database representation module = module_factory.from_workflow_step( trans, step ) - + # Pack attributes into plain dictionary step_dict = { 'id': step.order_index, @@ -523,21 +533,21 @@ 'data_outputs': module.get_data_outputs(), 'position': step.position } - + input_conn_dict = {} for conn in step.input_connections: input_conn_dict[ conn.input_name ] = \ dict( id=conn.output_step.order_index, output_name=conn.output_name ) step_dict['input_connections'] = input_conn_dict - + data.append(step_dict) - + x, y = step.position['left'], step.position['top'] count = 0 - + max_len = len(module.get_name()) * 1.5 text.append( svgfig.Text(x, y + 20, module.get_name(), **{"font-size": "14px"} ).SVG() ) - + y += 45 for di in module.get_data_inputs(): cur_y = y+count*line_px @@ -547,11 +557,11 @@ text.append( svgfig.Text(x, cur_y, di['label']).SVG() ) count += 1 max_len = max(max_len, len(di['label'])) - - + + if len(module.get_data_inputs()) > 0: y += 15 - + for do in module.get_data_outputs(): cur_y = y+count*line_px if step.order_index not in out_pos: @@ -560,12 +570,12 @@ text.append( svgfig.Text(x, cur_y, do['name']).SVG() ) count += 1 max_len = max(max_len, len(do['name'])) - + widths[step.order_index] = max_len*5.5 max_x = max(max_x, step.position['left']) max_y = max(max_y, step.position['top']) max_width = max(max_width, widths[step.order_index]) - + for step_dict in data: width = widths[step_dict['id']] x, y = step_dict['position']['left'], step_dict['position']['top'] @@ -576,18 +586,18 @@ if len(step_dict['data_inputs']) > 0: box_height += 15 sep_y = y + len(step_dict['data_inputs']) * line_px + 40 - text.append( svgfig.Line(x-margin, sep_y, x+width-margin, sep_y).SVG() ) # - + text.append( svgfig.Line(x-margin, sep_y, x+width-margin, sep_y).SVG() ) # + # input/output box boxes.append( svgfig.Rect(x-margin, y+30, x+width-margin, y+30+box_height, fill="#ffffff").SVG() ) - + for conn, output_dict in step_dict['input_connections'].iteritems(): in_coords = in_pos[step_dict['id']][conn] out_conn_pos = out_pos[output_dict['id']][output_dict['output_name']] adjusted = (out_conn_pos[0] + widths[output_dict['id']], out_conn_pos[1]) text.append( svgfig.SVG("circle", cx=out_conn_pos[0]+widths[output_dict['id']]-margin, cy=out_conn_pos[1]-margin, r=5, fill="#ffffff" ) ) connectors.append( svgfig.Line(adjusted[0], adjusted[1]-margin, in_coords[0]-10, in_coords[1], arrow_end="true" ).SVG() ) - + canvas.append(connectors) canvas.append(boxes) canvas.append(text) @@ -597,8 +607,8 @@ canvas['viewBox'] = "0 0 %s %s" % (width, height) trans.response.set_content_type("image/svg+xml") return canvas.standalone_xml() - - + + @web.expose @web.require_login( "use Galaxy workflows" ) def clone( self, trans, id ): @@ -612,7 +622,7 @@ .filter_by( user=user, stored_workflow=stored ).count() == 0: error( "Workflow is not owned by or shared with current user" ) owner = False - + # Clone. new_stored = model.StoredWorkflow() new_stored.name = "Clone of '%s'" % stored.name @@ -629,7 +639,7 @@ new_swta.user_tname = swta.user_tname new_swta.user_value = swta.user_value new_swta.value = swta.value - new_stored.tags.append( new_swta ) + new_stored.tags.append( new_swta ) if not owner: new_stored.name += " shared by '%s'" % stored.user.email new_stored.user = user @@ -640,7 +650,7 @@ # Display the management page trans.set_message( 'Clone created with name "%s"' % new_stored.name ) return self.list( trans ) - + @web.expose @web.require_login( "create workflows" ) def create( self, trans, workflow_name=None, workflow_annotation="" ): @@ -672,12 +682,12 @@ return form( url_for(), "Create New Workflow", submit_text="Create", use_panels=True ) \ .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) - + @web.expose def delete( self, trans, id=None ): """ Mark a workflow as deleted - """ + """ # Load workflow from database stored = self.get_stored_workflow( trans, id ) # Marke as deleted and save @@ -687,7 +697,7 @@ # Display the management page trans.set_message( "Workflow '%s' deleted" % stored.name ) return self.list( trans ) - + @web.expose @web.require_login( "edit workflows" ) def editor( self, trans, id=None ): @@ -700,7 +710,7 @@ error( "Invalid workflow id" ) stored = self.get_stored_workflow( trans, id ) return trans.fill_template( "workflow/editor.mako", stored=stored, annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) ) - + @web.json def editor_form_post( self, trans, type='tool', tool_id=None, annotation=None, **incoming ): """ @@ -709,7 +719,7 @@ This is used for the form shown in the right pane when a node is selected. """ - + trans.workflow_building_mode = True module = module_factory.from_dict( trans, { 'type': type, @@ -717,7 +727,7 @@ 'tool_state': incoming.pop("tool_state") } ) module.update_state( incoming ) - + if type=='tool': return { 'tool_state': module.get_state(), @@ -737,7 +747,7 @@ 'form_html': module.get_config_form(), 'annotation': annotation } - + @web.json def get_new_module_info( self, trans, type, **kwargs ): """ @@ -855,7 +865,7 @@ # post_job_actions pja_dict = {} for pja in step.post_job_actions: - pja_dict[pja.action_type+pja.output_name] = dict(action_type = pja.action_type, + pja_dict[pja.action_type+pja.output_name] = dict(action_type = pja.action_type, output_name = pja.output_name, action_arguments = pja.action_arguments) step_dict['post_job_actions'] = pja_dict @@ -961,7 +971,7 @@ rval = dict( message="Workflow saved" ) rval['name'] = workflow.name return rval - + @web.expose @web.require_login( "use workflows" ) def export( self, trans, id=None, **kwd ): @@ -1014,27 +1024,27 @@ """ Exports a workflow to myExperiment website. """ - - # Load encoded workflow from database + + # Load encoded workflow from database user = trans.get_user() id = trans.security.decode_id( id ) trans.workflow_building_mode = True stored = trans.sa_session.query( model.StoredWorkflow ).get( id ) self.security_check( trans, stored, False, True ) - + # Convert workflow to dict. workflow_dict = self._workflow_to_dict( trans, stored ) - + # # Create and submit workflow myExperiment request. # - + # Create workflow content XML. workflow_dict_packed = simplejson.dumps( workflow_dict, indent=4, sort_keys=True ) workflow_content = trans.fill_template( "workflow/myexp_export_content.mako", \ workflow_dict_packed=workflow_dict_packed, \ workflow_steps=workflow_dict['steps'] ) - + # Create myExperiment request. request_raw = trans.fill_template( "workflow/myexp_export.mako", \ workflow_name=workflow_dict['name'], \ @@ -1043,7 +1053,7 @@ ) # strip() b/c myExperiment XML parser doesn't allow white space before XML; utf-8 handles unicode characters. request = unicode( request_raw.strip(), 'utf-8' ) - + # Do request and get result. auth_header = base64.b64encode( '%s:%s' % ( myexp_username, myexp_password )) headers = { "Content-type": "text/xml", "Accept": "text/xml", "Authorization" : "Basic %s" % auth_header } @@ -1053,7 +1063,7 @@ response = conn.getresponse() response_data = response.read() conn.close() - + # Do simple parse of response to see if export successful and provide user feedback. parser = SingleTagContentsParser( 'id' ) parser.feed( response_data ) @@ -1062,13 +1072,13 @@ if myexp_workflow_id: return trans.show_message( \ "Workflow '%s' successfully exported to myExperiment. %s" % \ - ( stored.name, workflow_list_str ), + ( stored.name, workflow_list_str ), use_panels=True ) else: return trans.show_error_message( \ "Workflow '%s' could not be exported to myExperiment. Error: %s. %s" % \ ( stored.name, response_data, workflow_list_str ), use_panels=True ) - + @web.json_pretty def for_direct_import( self, trans, id ): """ @@ -1087,15 +1097,15 @@ """ Get the latest Workflow for the StoredWorkflow identified by `id` and encode it as a json string that can be imported back into Galaxy - + This has slightly different information than the above. In particular, it does not attempt to decode forms and build UIs, it just stores the raw state. """ - + # Get workflow. stored = self.get_stored_workflow( trans, id, check_ownership=False, check_accessible=True ) - + # Stream workflow to file. stored_dict = self._workflow_to_dict( trans, stored ) valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' @@ -1146,7 +1156,7 @@ workflow_data = None if url: # Load workflow from external URL - # NOTE: blocks the web thread. + # NOTE: blocks the web thread. try: workflow_data = urllib2.urlopen( url ).read() except Exception, e: @@ -1204,9 +1214,9 @@ # A required tool is not available in the local Galaxy instance. # TODO: It would sure be nice to be able to redirect to a mako template here that displays a nice # page including the links to the configured tool sheds instead of this message, but trying - # to get the panels back is a nightmare since workflow eliminates the Galaxy panels. Someone + # to get the panels back is a nightmare since workflow eliminates the Galaxy panels. Someone # involved in workflow development needs to figure out what it will take to be able to switch - # back and forth between Galaxy (with panels ) and the workflow view (without panels ), having + # back and forth between Galaxy (with panels ) and the workflow view (without panels ), having # the Galaxy panels displayed whenever in Galaxy. message += "The workflow requires the following tools that are not available in this Galaxy instance." message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>" @@ -1222,7 +1232,7 @@ message += '<a href="%s">%s</a><br/>' % ( url, shed_name ) status = 'error' if installed_repository_file or tool_shed_url: - # Another Galaxy panels Hack: The request did not originate from the Galaxy + # Another Galaxy panels Hack: The request did not originate from the Galaxy # workflow view, so we don't need to render the Galaxy panels. action = 'center' else: @@ -1275,13 +1285,13 @@ if issubclass( base, Data ): types.add( base.__module__ + "." + base.__name__ ) visit_bases( types, base ) - for c in classes: + for c in classes: n = c.__module__ + "." + c.__name__ types = set( [ n ] ) visit_bases( types, c ) class_to_classes[ n ] = dict( ( t, True ) for t in types ) return dict( ext_to_class_name=ext_to_class_name, class_to_classes=class_to_classes ) - + @web.expose def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, workflow_name=None ): user = trans.get_user() @@ -1292,7 +1302,7 @@ jobs, warnings = get_job_dict( trans ) # Render return trans.fill_template( - "workflow/build_from_current_history.mako", + "workflow/build_from_current_history.mako", jobs=jobs, warnings=warnings, history=history ) @@ -1310,7 +1320,7 @@ job_ids = [ int( id ) for id in job_ids ] dataset_ids = [ int( id ) for id in dataset_ids ] # Find each job, for security we (implicately) check that they are - # associated witha job in the current history. + # associated witha job in the current history. jobs, warnings = get_job_dict( trans ) jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) steps = [] @@ -1351,7 +1361,7 @@ conn.output_step = other_step conn.output_name = other_name steps.append( step ) - steps_by_job_id[ job_id ] = step + steps_by_job_id[ job_id ] = step # Store created dataset hids for assoc in job.output_datasets: hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name ) @@ -1380,8 +1390,8 @@ # Index page with message return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) ## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>" - ## % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) ) - + ## % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) ) + @web.expose def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) @@ -1589,8 +1599,8 @@ trans.set_history(saved_history)

def get_item( self, trans, id ): - return self.get_stored_workflow( trans, id ) - + return self.get_stored_workflow( trans, id ) + @web.expose def tag_outputs( self, trans, id, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) @@ -1644,7 +1654,7 @@ has_upgrade_messages = True # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) - step.module.add_dummy_datasets( connections=step.input_connections ) + step.module.add_dummy_datasets( connections=step.input_connections ) # Store state with the step step.state = step.module.state # Error dict @@ -1665,7 +1675,7 @@ has_upgrade_messages=has_upgrade_messages, errors=errors, incoming=kwargs ) - + @web.expose def configure_menu( self, trans, workflow_ids=None ): user = trans.get_user() @@ -1693,7 +1703,7 @@ user.stored_workflow_menu_entries.append( m ) sess.flush() return trans.show_message( "Menu updated", refresh_frames=['tools'] ) - else: + else: user = trans.get_user() ids_in_menu = set( [ x.stored_workflow_id for x in user.stored_workflow_menu_entries ] ) workflows = trans.sa_session.query( model.StoredWorkflow ) \ @@ -1709,7 +1719,7 @@ workflows=workflows, shared_by_others=shared_by_others, ids_in_menu=ids_in_menu ) - + def _workflow_to_dict( self, trans, stored ): """ Converts a workflow to a dict of attributes suitable for exporting. @@ -1734,7 +1744,7 @@ step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) annotation_str = "" if step_annotation: - annotation_str = step_annotation.annotation + annotation_str = step_annotation.annotation # Step info step_dict = { 'id': step.order_index, @@ -1752,7 +1762,7 @@ if module.type == 'tool': pja_dict = {} for pja in step.post_job_actions: - pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, + pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, output_name = pja.output_name, action_arguments = pja.action_arguments ) step_dict[ 'post_job_actions' ] = pja_dict @@ -1868,8 +1878,8 @@ # Unpack and add post-job actions. post_job_actions = step_dict.get( 'post_job_actions', {} ) for name, pja_dict in post_job_actions.items(): - pja = PostJobAction( pja_dict[ 'action_type' ], - step, pja_dict[ 'output_name' ], + pja = PostJobAction( pja_dict[ 'action_type' ], + step, pja_dict[ 'output_name' ], pja_dict[ 'action_arguments' ] ) # Second pass to deal with connections between steps for step in steps: @@ -1894,7 +1904,7 @@ trans.sa_session.add( stored ) trans.sa_session.flush() return stored, missing_tool_tups - + ## ---- Utility methods -------------------------------------------------------

def attach_ordered_steps( workflow, steps ): @@ -1937,13 +1947,13 @@ return [ steps[i] for i in node_order ] except CycleError: return None - + def order_workflow_steps_with_levels( steps ): try: return topsort_levels( edgelist_for_workflow_steps( steps ) ) except CycleError: return None - + class FakeJob( object ): """ Fake job object for datasets that have no creating_job_associations, @@ -1952,7 +1962,7 @@ def __init__( self, dataset ): self.is_fake = True self.id = "fake_%s" % dataset.id - + def get_job_dict( trans ): """ Return a dictionary of Job -> [ Dataset ] mappings, for all finished @@ -1967,22 +1977,22 @@ if dataset.state in ( 'new', 'running', 'queued' ): warnings.add( "Some datasets still queued or running were ignored" ) continue - + #if this hda was copied from another, we need to find the job that created the origial hda job_hda = dataset while job_hda.copied_from_history_dataset_association: job_hda = job_hda.copied_from_history_dataset_association - + if not job_hda.creating_job_associations: jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] - + for assoc in job_hda.creating_job_associations: job = assoc.job if job in jobs: jobs[ job ].append( ( assoc.name, dataset ) ) else: jobs[ job ] = [ ( assoc.name, dataset ) ] - return jobs, warnings + return jobs, warnings

def cleanup_param_values( inputs, values ): """ @@ -2015,7 +2025,7 @@ key = prefix + key + "_" for k in root_values.keys(): if k.startswith( key ): - del root_values[k] + del root_values[k] elif isinstance( input, Repeat ): group_values = values[key] for i, rep_values in enumerate( group_values ): @@ -2029,4 +2039,4 @@ cleanup( prefix, input.cases[current_case].inputs, group_values ) cleanup( "", inputs, values ) return associations - +

diff -r 50bf77aa34c3689a122187d7ba9b55deb348df92 -r 3b2acb89495bee2355f20fc3954baa174d486a3c templates/workflow/list.mako --- a/templates/workflow/list.mako +++ b/templates/workflow/list.mako @@ -103,6 +103,7 @@ <a class="action-button" href="${h.url_for( controller='workflow', action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug )}" target="_top">View</a><a class="action-button" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">Run</a><a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a> + <a class="action-button" confirm="Are you sure you want to remove the shared workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='sharing', unshare_me=True, id=trans.security.encode_id( workflow.id ))}">Remove</a></div></td></tr>

https://bitbucket.org/galaxy/galaxy-central/changeset/0a001dea3613/ changeset: 0a001dea3613 user: dannon date: 2012-02-02 20:55:19 summary: Merge. affected #: 7 files

diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -96,7 +96,7 @@ self.retry_job_output_collection = int( kwargs.get( 'retry_job_output_collection', 0 ) ) self.job_walltime = kwargs.get( 'job_walltime', None ) self.admin_users = kwargs.get( "admin_users", "" ) - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu") + self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join@bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None )

diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -196,7 +196,6 @@ if job_wrapper.get_state() == model.Job.states.DELETED: log.debug( "Job %s deleted by user before it entered the queue" % job_wrapper.get_id_tag() ) if self.app.config.cleanup_job in ( "always", "onsuccess" ): - self.cleanup( ( ofile, efile, jt.remoteCommand ) ) job_wrapper.cleanup() return

@@ -334,25 +333,12 @@ except: log.exception("Job wrapper finish method failed")

- # clean up the drm files - if self.app.config.cleanup_job == "always" or ( not stderr and self.app.config.cleanup_job == "onsuccess" ): - self.cleanup( ( ofile, efile, job_file ) ) - def fail_job( self, drm_job_state ): """ Seperated out so we can use the worker threads for it. """ self.stop_job( self.sa_session.query( self.app.model.Job ).get( drm_job_state.job_wrapper.job_id ) ) drm_job_state.job_wrapper.fail( drm_job_state.fail_message ) - if self.app.config.cleanup_job == "always": - self.cleanup( ( drm_job_state.ofile, drm_job_state.efile, drm_job_state.job_file ) ) - - def cleanup( self, files ): - for file in files: - try: - os.unlink( file ) - except Exception, e: - log.warning( "Unable to cleanup: %s" % str( e ) )

def put( self, job_wrapper ): """Add a job to the queue (by job identifier)""" @@ -440,6 +426,6 @@ # The expected output is a single line containing a single numeric value: # the DRMAA job-ID. If not the case, will throw an error. jobId = stdoutdata - return jobId; + return jobId

diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -68,7 +68,7 @@ self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu") + self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join@bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None )

diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 lib/galaxy/webapps/demo_sequencer/config.py --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ b/lib/galaxy/webapps/demo_sequencer/config.py @@ -45,7 +45,7 @@ self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/demo_sequencer" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") - self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu") + self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join@bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )

diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -72,6 +72,8 @@ <% subscribe_check_box.checked = True %> %endif ${subscribe_check_box.get_html()} + <p>See <a href="http://galaxyproject.org/wiki/Mailing%20Lists" target="_blank"> + all Galaxy project mailing lists</a>.</p></div> %endif %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1:

diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 tools/variant_detection/freebayes.xml --- a/tools/variant_detection/freebayes.xml +++ b/tools/variant_detection/freebayes.xml @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="freebayes" name="FreeBayes" version="0.0.1"> +<tool id="freebayes" name="FreeBayes" version="0.0.2"><requirements><requirement type="package" version="0.9.4">freebayes</requirement><requirement type="package">samtools</requirement> @@ -29,11 +29,17 @@

##outputs --vcf "${output_vcf}" - --trace "${output_trace}" - --failed-alleles "${output_failed_alleles_bed}"

##advanced options #if str( $options_type.options_type_selector ) == "advanced": + ##additional outputs + #if $options_type.output_trace_option: + --trace "${output_trace}" + #end if + #if $options_type.output_failed_alleles_option: + --failed-alleles "${output_failed_alleles_bed}" + #end if + ##additional inputs #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file": --targets "${options_type.target_limit_type.input_target_bed}" @@ -186,8 +192,13 @@ <!-- Do nothing here --></when><when value="advanced"> - - <!-- input and output --> + + <!-- output --> + <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" /> + <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" /> + + + <!-- input --><conditional name="target_limit_type"><param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets"><option value="do_not_limit" selected="True">Do not limit</option> @@ -398,8 +409,12 @@ </inputs><outputs><data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> - <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)" /> - <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)" /> + <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)"> + <filter>options_type['options_type_selector'] == "advanced" and options_type['output_failed_alleles_option'] is True</filter> + </data> + <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)"> + <filter>options_type['options_type_selector'] == "advanced" and options_type['output_trace_option'] is True</filter> + </data></outputs><tests><test> @@ -408,8 +423,8 @@ <param name="input_bam" ftype="bam" value="gatk/fake_phiX_reads_1.bam"/><param name="options_type_selector" value="basic"/><output name="output_vcf" file="variant_detection/freebayes/freebayes_out_1.vcf.contains" compare="contains"/> - <output name="output_trace" file="variant_detection/freebayes/freebayes_out_1.output_trace" /> - <output name="output_failed_alleles_bed" file="empty_file.dat" /> + <!-- <output name="output_failed_alleles_bed" file="empty_file.dat" /> + <output name="output_trace" file="variant_detection/freebayes/freebayes_out_1.output_trace" /> --></test></tests><help>

diff -r 3b2acb89495bee2355f20fc3954baa174d486a3c -r 0a001dea361385d107989740582f855aa2b71dc4 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -205,7 +205,7 @@

# On the user registration form, users may choose to join the mailing list. # This is the address of the list they'll be subscribed to. -#mailing_join_addr = galaxy-user-join@bx.psu.edu +#mailing_join_addr = galaxy-announce-join@bx.psu.edu

# Datasets in an error state include a link to report the error. Those reports # will be sent to this address. Error reports are disabled if no address is set.

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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