1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/31f4f354b661/ Changeset: 31f4f354b661 User: jgoecks Date: 2013-12-23 01:24:37 Summary: Workflows API, running workflows: (a) improve code documentation and (b) add option to specify step_id when setting parameters so that parameters are set for a single step rather than all steps with a given tool id. Affected #: 1 file
diff -r 9264df2bd5f015e7d8c011683b4f89e6beeacb4a -r 31f4f354b66105d5c2bedc36d7fd80b37327b75e lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -104,15 +104,15 @@ However, we will import them if installed_repository_file is specified """
- # ------------------------------------------------------------------------------- # - ### RPARK: dictionary containing which workflows to change and edit ### - param_map = {}; - if (payload.has_key('parameters') ): - param_map = payload['parameters']; - # ------------------------------------------------------------------------------- # + # Pull parameters out of payload. + workflow_id = payload['workflow_id'] + param_map = payload.get('parameters', {}) + ds_map = payload['ds_map'] + add_to_history = 'no_add_to_history' not in payload + history_param = payload['history']
- - if 'workflow_id' not in payload: + # Get/create workflow. + if not workflow_id: # create new if 'installed_repository_file' in payload: workflow_controller = trans.webapp.controllers[ 'workflow' ] @@ -125,26 +125,31 @@ if 'installed_repository_file' in payload: trans.response.status = 403 return "installed_repository_file may not be specified with workflow_id" + + # Get workflow + accessibility check. stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get( - trans.security.decode_id(payload['workflow_id'])) + trans.security.decode_id(workflow_id)) if stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: trans.response.status = 400 return("Workflow is not owned by or shared with current user") workflow = stored_workflow.latest_workflow - if payload['history'].startswith('hist_id='): + + # Get target history. + if history_param.startswith('hist_id='): #Passing an existing history to use. history = trans.sa_session.query(self.app.model.History).get( - trans.security.decode_id(payload['history'][8:])) + trans.security.decode_id(history_param[8:])) if history.user != trans.user and not trans.user_is_admin(): trans.response.status = 400 return "Invalid History specified." else: - history = self.app.model.History(name=payload['history'], user=trans.user) + # Send workflow outputs to new history. + history = self.app.model.History(name=history_param, user=trans.user) trans.sa_session.add(history) trans.sa_session.flush() - ds_map = payload['ds_map'] - add_to_history = 'no_add_to_history' not in payload + + # Set workflow inputs. for k in ds_map: try: if ds_map[k]['src'] == 'ldda': @@ -172,6 +177,8 @@ except AssertionError: trans.response.status = 400 return "Invalid Dataset '%s' Specified" % ds_map[k]['id'] + + # Sanity checks. if not workflow: trans.response.status = 400 return "Workflow not found." @@ -184,6 +191,7 @@ if workflow.has_errors: trans.response.status = 400 return "Workflow cannot be run because of validation errors in some steps" + # Build the state for each step rval = {} for step in workflow.steps: @@ -197,16 +205,18 @@ step.module.add_dummy_datasets( connections=step.input_connections ) step.state = step.module.state
- #################################################### - #################################################### - # RPARK: IF TOOL_NAME IN PARAMETER MAP # + # Update step parameters as directed by payload's parameter mapping. if step.tool_id in param_map: + # Get parameter settings. change_param = param_map[step.tool_id]['param']; change_value = param_map[step.tool_id]['value']; - step.state.inputs[change_param] = change_value; - #################################################### - #################################################### + step_id = param_map[step.tool_id].get('step_id', '')
+ # Update step if there's no step id (i.e. all steps with tool are + # updated) or update if step ids match. + if not step_id or ( step_id and int( step_id ) == step.id ): + step.state.inputs[change_param] = change_value + if step.tool_errors: trans.response.status = 400 return "Workflow cannot be run because of validation errors in some steps: %s" % step_errors @@ -221,6 +231,7 @@ step.module = module_factory.from_workflow_step( trans, step ) step.state = step.module.get_runtime_state() step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) + # Run each step, connecting outputs to inputs workflow_invocation = self.app.model.WorkflowInvocation() workflow_invocation.workflow = workflow
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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