[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d0133648ddb9/ Changeset: d0133648ddb9 User: jmchilton Date: 2014-08-08 17:42:20 Summary: Cleanup unused parameter left over in workflow controller. Affected #: 1 file diff -r 5f663734a26e8e2d1c462320741c86c9b5d9aef6 -r d0133648ddb96fc3e0c030c86802e0b6186b7f92 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1226,7 +1226,7 @@ url_for( controller='workflow', action='run', id=workflow_id ) ) ) @web.expose - def run( self, trans, id, history_id=None, multiple_input_mode="product", hide_fixed_params=False, **kwargs ): + def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) user = trans.get_user() if stored.user != user: @@ -1269,7 +1269,7 @@ # been POSTed # List to gather values for the template invocations = [] - for (kwargs, multi_input_keys) in _expand_multiple_inputs(kwargs, mode=multiple_input_mode): + for (kwargs, multi_input_keys) in _expand_multiple_inputs(kwargs): for step in workflow.steps: step.upgrade_messages = {} # Connections by input name @@ -1653,9 +1653,9 @@ return " on %s and %s" % (", ".join(instance_ds_names[0:-1]), instance_ds_names[-1]) -def _expand_multiple_inputs(kwargs, mode): +def _expand_multiple_inputs(kwargs): (single_inputs, matched_multi_inputs, multiplied_multi_inputs) = \ - _split_inputs(kwargs, mode) + _split_inputs(kwargs) # Build up every combination of inputs to be run together. input_combos = _extend_with_matched_combos(single_inputs, matched_multi_inputs) @@ -1714,7 +1714,7 @@ return new_inputs -def _split_inputs(kwargs, mode): +def _split_inputs(kwargs): """ """ input_keys = filter(lambda a: a.endswith('|input'), kwargs) https://bitbucket.org/galaxy/galaxy-central/commits/fcbd2849ebd1/ Changeset: fcbd2849ebd1 User: jmchilton Date: 2014-08-08 17:42:20 Summary: Some PEP-8 fixes for lib/galaxy/webapps/galaxy/controllers/workflow.py. Affected #: 1 file diff -r d0133648ddb96fc3e0c030c86802e0b6186b7f92 -r fcbd2849ebd17a80e66e0fbdac9df7bb37f88fa2 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -51,7 +51,7 @@ use_panels = True title = "Saved Workflows" model_class = model.StoredWorkflow - default_filter = { "name" : "All", "tags": "All" } + default_filter = { "name": "All", "tags": "All" } default_sort_key = "-update_time" columns = [ grids.TextColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), @@ -62,10 +62,11 @@ ] columns.append( grids.MulticolFilterColumn( - "Search", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", visible=False, filterable="standard" ) - ) + "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", visible=False, filterable="standard" + ) + ) operations = [ grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Run", condition=( lambda item: not item.deleted ), async_compatible=False ), @@ -95,19 +96,24 @@ ] columns.append( grids.MulticolFilterColumn( - "Search name, annotation, owner, and tags", - cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], - key="free-text-search", visible=False, filterable="standard" ) - ) + "Search name, annotation, owner, and tags", + cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ], + key="free-text-search", visible=False, filterable="standard" + ) + ) operations = [ - grids.GridOperation( "Import", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="imp" ) ), - grids.GridOperation( "Save as File", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="export_to_file" ) ), + grids.GridOperation( + "Import", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="imp") + ), + grids.GridOperation( + "Save as File", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="export_to_file" ) + ), ] def build_initial_query( self, trans, **kwargs ): @@ -275,7 +281,7 @@ user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, stored_workflow ) return trans.fill_template_mako( "workflow/display.mako", item=stored_workflow, item_data=stored_workflow.latest_workflow.steps, - user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) + user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) @web.expose def get_item_content_async( self, trans, id ): @@ -390,7 +396,7 @@ # Do import. stored = self.get_stored_workflow( trans, id, check_ownership=False ) - if stored.importable == False: + if stored.importable is False: return trans.show_error_message( "The owner of this workflow has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True ) elif stored.deleted: return trans.show_error_message( "You can't import this workflow because it has been deleted.<br>You can %s" % referer_message, use_panels=True ) @@ -415,7 +421,7 @@ if 'annotation' in kwargs: # Set workflow annotation; sanitize annotation before adding it. annotation = sanitize_html( kwargs[ 'annotation' ], 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), stored, annotation ) + self.add_item_annotation( trans.sa_session, trans.get_user(), stored, annotation ) trans.sa_session.flush() return trans.fill_template( 'workflow/edit_attributes.mako', stored=stored, @@ -511,7 +517,7 @@ """ Returns workflow's name and link. """ stored = self.get_stored_workflow( trans, id ) - return_dict = { "name" : stored.name, "link" : url_for(controller='workflow', action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } + return_dict = { "name": stored.name, "link": url_for(controller='workflow', action="display_by_username_and_slug", username=stored.user.username, slug=stored.slug ) } return return_dict @web.expose @@ -583,8 +589,8 @@ return self.editor( trans, id=trans.security.encode_id(stored_workflow.id )) else: return form( url_for(controller="workflow", action="create"), "Create New Workflow", submit_text="Create", use_panels=True ) \ - .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ - .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) + .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ + .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) @web.expose def delete( self, trans, id=None ): @@ -665,7 +671,7 @@ module = module_factory.new( trans, type, **kwargs ) return { 'type': module.type, - 'name': module.get_name(), + 'name': module.get_name(), 'tool_id': module.get_tool_id(), 'tool_state': module.get_state(), 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), @@ -750,9 +756,9 @@ 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), 'form_html': module.get_config_form(), - 'annotation' : annotation_str, - 'post_job_actions' : {}, - 'workflow_outputs' : [] + 'annotation': annotation_str, + 'post_job_actions': {}, + 'workflow_outputs': [] } # Connections input_connections = step.input_connections @@ -838,8 +844,8 @@ errors.append("Step %s requires tool '%s'." % (step_dict['id'], step_dict['tool_id'])) if errors: return dict( name=workflow.name, - message="This workflow includes missing or invalid tools. It cannot be saved until the following steps are removed or the missing tools are enabled.", - errors=errors) + message="This workflow includes missing or invalid tools. It cannot be saved until the following steps are removed or the missing tools are enabled.", + errors=errors ) # First pass to build step objects and populate basic values for key, step_dict in data['steps'].iteritems(): # Create the model class for the step @@ -932,18 +938,19 @@ workflow_content = json.dumps( workflow_dict, indent=4, sort_keys=True ) # Create myExperiment request. - request_raw = trans.fill_template( "workflow/myexp_export.mako", \ - workflow_name=workflow_dict['name'], \ - workflow_description=workflow_dict['annotation'], \ - workflow_content=workflow_content, \ - workflow_svg=self._workflow_to_svg_canvas( trans, stored ).standalone_xml() - ) + request_raw = trans.fill_template( + "workflow/myexp_export.mako", + workflow_name=workflow_dict['name'], + workflow_description=workflow_dict['annotation'], + workflow_content=workflow_content, + workflow_svg=self._workflow_to_svg_canvas( trans, stored ).standalone_xml() + ) # strip() b/c myExperiment XML parser doesn't allow white space before XML; utf-8 handles unicode characters. request = unicode( request_raw.strip(), 'utf-8' ) # Do request and get result. auth_header = base64.b64encode( '%s:%s' % ( myexp_username, myexp_password )) - headers = { "Content-type": "text/xml", "Accept": "text/xml", "Authorization" : "Basic %s" % auth_header } + headers = { "Content-type": "text/xml", "Accept": "text/xml", "Authorization": "Basic %s" % auth_header } myexp_url = trans.app.config.get( "myexperiment_url", self.__myexp_url ) conn = httplib.HTTPConnection( myexp_url ) # NOTE: blocks web thread. @@ -958,14 +965,14 @@ myexp_workflow_id = parser.tag_content workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( controller='workflow', action='list' ) if myexp_workflow_id: - return trans.show_message( \ + return trans.show_message( """Workflow '%s' successfully exported to myExperiment. <br/><a href="http://%s/workflows/%s">Click here to view the workflow on myExperiment</a> %s """ % ( stored.name, myexp_url, myexp_workflow_id, workflow_list_str ), use_panels=True ) else: - return trans.show_error_message( \ - "Workflow '%s' could not be exported to myExperiment. Error: %s %s" % \ + return trans.show_error_message( + "Workflow '%s' could not be exported to myExperiment. Error: %s %s" % ( stored.name, response_data, workflow_list_str ), use_panels=True ) @web.json_pretty @@ -1205,10 +1212,10 @@ jobs, warnings = summarize( trans ) # Render return trans.fill_template( - "workflow/build_from_current_history.mako", - jobs=jobs, - warnings=warnings, - history=history + "workflow/build_from_current_history.mako", + jobs=jobs, + warnings=warnings, + history=history ) else: stored_workflow = extract_workflow( @@ -1223,7 +1230,7 @@ workflow_id = trans.security.encode_id( stored_workflow.id ) return trans.show_message( 'Workflow "%s" created from current history. You can <a href="%s" target="_parent">edit</a> or <a href="%s">run</a> the workflow.' % ( workflow_name, url_for( controller='workflow', action='editor', id=workflow_id ), - url_for( controller='workflow', action='run', id=workflow_id ) ) ) + url_for( controller='workflow', action='run', id=workflow_id ) ) ) @web.expose def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ): @@ -1350,8 +1357,8 @@ trans.sa_session.flush() if invocations: return trans.fill_template( "workflow/run_complete.mako", - workflow=stored, - invocations=invocations ) + workflow=stored, + invocations=invocations ) else: # Prepare each step missing_tools = [] @@ -1388,24 +1395,27 @@ step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) if missing_tools: stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) - return trans.fill_template("workflow/run.mako", - steps=[], - workflow=stored, - hide_fixed_params=hide_fixed_params, - missing_tools=missing_tools) + return trans.fill_template( + "workflow/run.mako", + steps=[], + workflow=stored, + hide_fixed_params=hide_fixed_params, + missing_tools=missing_tools + ) # Render the form stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) return trans.fill_template( - "workflow/run.mako", - steps=workflow.steps, - workflow=stored, - has_upgrade_messages=has_upgrade_messages, - step_version_changes=step_version_changes, - errors=errors, - incoming=kwargs, - history_id=history_id, - hide_fixed_params=hide_fixed_params, - enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults) + "workflow/run.mako", + steps=workflow.steps, + workflow=stored, + has_upgrade_messages=has_upgrade_messages, + step_version_changes=step_version_changes, + errors=errors, + incoming=kwargs, + history_id=history_id, + hide_fixed_params=hide_fixed_params, + enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults + ) finally: # restore the active history if saved_history is not None: @@ -1484,12 +1494,12 @@ step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) # Render the form return trans.fill_template( - "workflow/tag_outputs.mako", - steps=workflow.steps, - workflow=stored, - has_upgrade_messages=has_upgrade_messages, - errors=errors, - incoming=kwargs + "workflow/tag_outputs.mako", + steps=workflow.steps, + workflow=stored, + has_upgrade_messages=has_upgrade_messages, + errors=errors, + incoming=kwargs ) @web.expose @@ -1539,7 +1549,7 @@ shared_by_others=shared_by_others, ids_in_menu=ids_in_menu, message=message, - refresh_frames=['tools'] ) + refresh_frames=refresh_frames ) def _workflow_to_svg_canvas( self, trans, stored ): workflow = stored.latest_workflow @@ -1619,17 +1629,17 @@ if len(step_dict['data_inputs']) > 0: box_height += 15 sep_y = y + len(step_dict['data_inputs']) * line_px + 40 - text.append( svgfig.Line(x-margin, sep_y, x+width-margin, sep_y).SVG() ) # + text.append( svgfig.Line(x - margin, sep_y, x + width - margin, sep_y).SVG() ) # input/output box - boxes.append( svgfig.Rect(x-margin, y+30, x+width-margin, y+30+box_height, fill="#ffffff").SVG() ) + boxes.append( svgfig.Rect(x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff").SVG() ) for conn, output_dict in step_dict['input_connections'].iteritems(): in_coords = in_pos[step_dict['id']][conn] out_conn_pos = out_pos[output_dict['id']][output_dict['output_name']] adjusted = (out_conn_pos[0] + widths[output_dict['id']], out_conn_pos[1]) - text.append( svgfig.SVG("circle", cx=out_conn_pos[0]+widths[output_dict['id']]-margin, cy=out_conn_pos[1]-margin, r=5, fill="#ffffff" ) ) - connectors.append( svgfig.Line(adjusted[0], adjusted[1]-margin, in_coords[0]-10, in_coords[1], arrow_end="true" ).SVG() ) + text.append( svgfig.SVG("circle", cx=out_conn_pos[0] + widths[output_dict['id']] - margin, cy=out_conn_pos[1] - margin, r=5, fill="#ffffff" ) ) + connectors.append( svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true" ).SVG() ) canvas.append(connectors) canvas.append(boxes) @@ -1654,16 +1664,14 @@ def _expand_multiple_inputs(kwargs): - (single_inputs, matched_multi_inputs, multiplied_multi_inputs) = \ - _split_inputs(kwargs) + (single_inputs, matched_multi_inputs, multiplied_multi_inputs) = _split_inputs(kwargs) # Build up every combination of inputs to be run together. input_combos = _extend_with_matched_combos(single_inputs, matched_multi_inputs) input_combos = _extend_with_multiplied_combos(input_combos, multiplied_multi_inputs) # Input name that are multiply specified - multi_input_keys = \ - matched_multi_inputs.keys() + multiplied_multi_inputs.keys() + multi_input_keys = matched_multi_inputs.keys() + multiplied_multi_inputs.keys() for input_combo in input_combos: for key, value in input_combo.iteritems(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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