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Source code for galaxy.webapps.galaxy.api.workflows

"""
API operations for Workflows
"""
from __future__ import absolute_import

import logging

from six.moves.urllib.parse import unquote_plus
from sqlalchemy import desc, false, or_, true

from galaxy import (
    exceptions,
    model,
    util
)
from galaxy.managers import (
    histories,
    workflows
)
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.tools.parameters import populate_state
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import _future_expose_api as expose_api
from galaxy.web.base.controller import (
    BaseAPIController,
    SharableMixin,
    url_for,
    UsesStoredWorkflowMixin
)
from galaxy.workflow.extract import extract_workflow
from galaxy.workflow.modules import module_factory
from galaxy.workflow.run import invoke, queue_invoke
from galaxy.workflow.run_request import build_workflow_run_configs

log = logging.getLogger(__name__)


[docs]class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnnotations, SharableMixin):
[docs] def __init__( self, app ): super( WorkflowsAPIController, self ).__init__( app ) self.history_manager = histories.HistoryManager( app ) self.workflow_manager = workflows.WorkflowsManager( app ) self.workflow_contents_manager = workflows.WorkflowContentsManager( app )
[docs] @expose_api def index(self, trans, **kwd): """ GET /api/workflows Displays a collection of workflows. :param show_published: if True, show also published workflows :type show_published: boolean """ show_published = util.string_as_bool( kwd.get( 'show_published', 'False' ) ) rval = [] filter1 = ( trans.app.model.StoredWorkflow.user == trans.user ) if show_published: filter1 = or_( filter1, ( trans.app.model.StoredWorkflow.published == true() ) ) for wf in trans.sa_session.query( trans.app.model.StoredWorkflow ).filter( filter1, trans.app.model.StoredWorkflow.table.c.deleted == false() ).order_by( desc( trans.app.model.StoredWorkflow.table.c.update_time ) ).all(): item = wf.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(wf.id) item['url'] = url_for('workflow', id=encoded_id) item['owner'] = wf.user.username rval.append(item) for wf_sa in trans.sa_session.query( trans.app.model.StoredWorkflowUserShareAssociation ).filter_by( user=trans.user ).join( 'stored_workflow' ).filter( trans.app.model.StoredWorkflow.deleted == false() ).order_by( desc( trans.app.model.StoredWorkflow.update_time ) ).all(): item = wf_sa.stored_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id) item['url'] = url_for( 'workflow', id=encoded_id ) item['owner'] = wf_sa.stored_workflow.user.username rval.append(item) return rval
[docs] @expose_api def show(self, trans, id, **kwd): """ GET /api/workflows/{encoded_workflow_id} Displays information needed to run a workflow from the command line. """ stored_workflow = self.__get_stored_workflow( trans, id ) if stored_workflow.importable is False and 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: message = "Workflow is neither importable, nor owned by or shared with current user" raise exceptions.ItemAccessibilityException( message ) if kwd.get("legacy", False): style = "legacy" else: style = "instance" return self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style=style )
[docs] @expose_api def create(self, trans, payload, **kwd): """ POST /api/workflows Run or create workflows from the api. If installed_repository_file or from_history_id is specified a new workflow will be created for this user. Otherwise, workflow_id must be specified and this API method will cause a workflow to execute. :param installed_repository_file The path of a workflow to import. Either workflow_id, installed_repository_file or from_history_id must be specified :type installed_repository_file str :param workflow_id: An existing workflow id. Either workflow_id, installed_repository_file or from_history_id must be specified :type workflow_id: str :param parameters: If workflow_id is set - see _update_step_parameters() :type parameters: dict :param ds_map: If workflow_id is set - a dictionary mapping each input step id to a dictionary with 2 keys: 'src' (which can be 'ldda', 'ld' or 'hda') and 'id' (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively) :type ds_map: dict :param no_add_to_history: If workflow_id is set - if present in the payload with any value, the input datasets will not be added to the selected history :type no_add_to_history: str :param history: If workflow_id is set - optional history where to run the workflow, either the name of a new history or "hist_id=HIST_ID" where HIST_ID is the id of an existing history. If not specified, the workflow will be run a new unnamed history :type history: str :param replacement_params: If workflow_id is set - an optional dictionary used when renaming datasets :type replacement_params: dict :param from_history_id: Id of history to extract a workflow from. Either workflow_id, installed_repository_file or from_history_id must be specified :type from_history_id: str :param job_ids: If from_history_id is set - optional list of jobs to include when extracting a workflow from history :type job_ids: str :param dataset_ids: If from_history_id is set - optional list of HDA `hid`s corresponding to workflow inputs when extracting a workflow from history :type dataset_ids: str :param dataset_collection_ids: If from_history_id is set - optional list of HDCA `hid`s corresponding to workflow inputs when extracting a workflow from history :type dataset_collection_ids: str :param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history :type workflow_name: str :param allow_tool_state_corrections: If set to True, any Tool parameter changes will not prevent running workflow, defaults to False :type allow_tool_state_corrections: bool """ ways_to_create = set( [ 'workflow_id', 'installed_repository_file', 'from_history_id', 'shared_workflow_id', 'workflow', ] ) if len( ways_to_create.intersection( payload ) ) == 0: message = "One parameter among - %s - must be specified" % ", ".join( ways_to_create ) raise exceptions.RequestParameterMissingException( message ) if len( ways_to_create.intersection( payload ) ) > 1: message = "Only one parameter among - %s - must be specified" % ", ".join( ways_to_create ) raise exceptions.RequestParameterInvalidException( message ) if 'installed_repository_file' in payload: workflow_controller = trans.webapp.controllers[ 'workflow' ] result = workflow_controller.import_workflow( trans=trans, cntrller='api', **payload) return result if 'from_history_id' in payload: from_history_id = payload.get( 'from_history_id' ) from_history_id = self.decode_id( from_history_id ) history = self.history_manager.get_accessible( from_history_id, trans.user, current_history=trans.history ) job_ids = [ self.decode_id(_) for _ in payload.get( 'job_ids', [] ) ] dataset_ids = payload.get( 'dataset_ids', [] ) dataset_collection_ids = payload.get( 'dataset_collection_ids', [] ) workflow_name = payload[ 'workflow_name' ] stored_workflow = extract_workflow( trans=trans, user=trans.get_user(), history=history, job_ids=job_ids, dataset_ids=dataset_ids, dataset_collection_ids=dataset_collection_ids, workflow_name=workflow_name, ) item = stored_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } ) item[ 'url' ] = url_for( 'workflow', id=item[ 'id' ] ) return item if 'shared_workflow_id' in payload: workflow_id = payload[ 'shared_workflow_id' ] return self.__api_import_shared_workflow( trans, workflow_id, payload ) if 'workflow' in payload: return self.__api_import_new_workflow( trans, payload, **kwd ) workflow_id = payload.get( 'workflow_id', None ) if not workflow_id: message = "Invalid workflow_id specified." raise exceptions.RequestParameterInvalidException( message ) # Get workflow + accessibility check. stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) workflow = stored_workflow.latest_workflow run_configs = build_workflow_run_configs( trans, workflow, payload ) assert len(run_configs) == 1 run_config = run_configs[0] history = run_config.target_history # invoke may throw MessageExceptions on tool erors, failure # to match up inputs, etc... outputs, invocation = invoke( trans=trans, workflow=workflow, workflow_run_config=run_config, populate_state=True, ) trans.sa_session.flush() # Build legacy output - should probably include more information from # outputs. rval = {} rval['history'] = trans.security.encode_id( history.id ) rval['outputs'] = [] for step in workflow.steps: if step.type == 'tool' or step.type is None: for v in outputs[ step.id ].values(): rval[ 'outputs' ].append( trans.security.encode_id( v.id ) ) # Newer version of this API just returns the invocation as a dict, to # facilitate migration - produce the newer style response and blend in # the older information. invocation_response = self.__encode_invocation( trans, invocation, step_details=kwd.get('step_details', False) ) invocation_response.update( rval ) return invocation_response
[docs] @expose_api def workflow_dict( self, trans, workflow_id, **kwd ): """ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow as a json dictionary. """ stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id ) style = kwd.get("style", "export") ret_dict = self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style=style ) if not ret_dict: # This workflow has a tool that's missing from the distribution message = "Workflow cannot be exported due to missing tools." raise exceptions.MessageException( message ) return ret_dict
[docs] @expose_api def delete( self, trans, id, **kwd ): """ DELETE /api/workflows/{encoded_workflow_id} Deletes a specified workflow Author: rpark copied from galaxy.web.controllers.workflows.py (delete) """ workflow_id = id try: stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(self.decode_id(workflow_id)) except Exception as e: trans.response.status = 400 return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e )) # check to see if user has permissions to selected workflow if stored_workflow.user != trans.user and not trans.user_is_admin(): trans.response.status = 403 return("Workflow is not owned by current user") # Mark a workflow as deleted stored_workflow.deleted = True trans.sa_session.flush() # TODO: Unsure of response message to let api know that a workflow was successfully deleted return ( "Workflow '%s' successfully deleted" % stored_workflow.name )
[docs] @expose_api def import_new_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/upload Importing dynamic workflows from the api. Return newly generated workflow id. Author: rpark # currently assumes payload['workflow'] is a json representation of a workflow to be inserted into the database Deprecated in favor to POST /api/workflows with encoded 'workflow' in payload the same way. """ return self.__api_import_new_workflow( trans, payload, **kwd )
[docs] @expose_api def update( self, trans, id, payload, **kwds ): """ * PUT /api/workflows/{id} updates the workflow stored with ``id`` :type id: str :param id: the encoded id of the workflow to update :type payload: dict :param payload: a dictionary containing any or all the * workflow the json description of the workflow as would be produced by GET workflows/<id>/download or given to `POST workflows` The workflow contents will be updated to target this. * name optional string name for the workflow, if not present in payload, name defaults to existing name * annotation optional string annotation for the workflow, if not present in payload, annotation defaults to existing annotation * menu_entry optional boolean marking if the workflow should appear in the user's menu, if not present, workflow menu entries are not modified :rtype: dict :returns: serialized version of the workflow """ stored_workflow = self.__get_stored_workflow( trans, id ) if 'workflow' in payload: stored_workflow.name = sanitize_html(payload['name']) if ('name' in payload) else stored_workflow.name if 'annotation' in payload: newAnnotation = sanitize_html(payload['annotation']) self.add_item_annotation(trans.sa_session, trans.get_user(), stored_workflow, newAnnotation) if 'menu_entry' in payload: if payload['menu_entry']: menuEntry = model.StoredWorkflowMenuEntry() menuEntry.stored_workflow = stored_workflow trans.get_user().stored_workflow_menu_entries.append(menuEntry) else: # remove if in list entries = {x.stored_workflow_id: x for x in trans.get_user().stored_workflow_menu_entries} if (trans.security.decode_id(id) in entries): trans.get_user().stored_workflow_menu_entries.remove(entries[trans.security.decode_id(id)]) try: workflow, errors = self.workflow_contents_manager.update_workflow_from_dict( trans, stored_workflow, payload[ 'workflow' ], ) except workflows.MissingToolsException: raise exceptions.MessageException( "This workflow contains missing tools. It cannot be saved until they have been removed from the workflow or installed." ) else: message = "Updating workflow requires dictionary containing 'workflow' attribute with new JSON description." raise exceptions.RequestParameterInvalidException( message ) return self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style="instance" )
[docs] @expose_api def build_module( self, trans, payload={} ): """ POST /api/workflows/build_module Builds module models for the workflow editor. """ inputs = payload.get( 'inputs', {} ) module = module_factory.from_dict( trans, payload ) module_state = {} populate_state( trans, module.get_inputs(), inputs, module_state, check=False ) module.recover_state( module_state ) return { 'label' : inputs.get( '__label', '' ), 'annotation' : inputs.get( '__annotation', '' ), 'name' : module.get_name(), 'tool_state' : module.get_state(), 'data_inputs' : module.get_data_inputs(), 'data_outputs' : module.get_data_outputs(), 'config_form' : module.get_config_form(), 'post_job_actions' : module.get_post_job_actions( inputs ) }
# # -- Helper methods -- # def _get_tool( self, id, tool_version=None, user=None ): id = unquote_plus( id ) tool = self.app.toolbox.get_tool( id, tool_version ) if not tool or not tool.allow_user_access( user ): raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id) return tool def __api_import_new_workflow( self, trans, payload, **kwd ): data = payload['workflow'] publish = util.string_as_bool( payload.get( "publish", False ) ) # If 'publish' set, default to importable. importable = util.string_as_bool( payload.get( "importable", publish ) ) # Galaxy will try to upgrade tool versions that don't match exactly during import, # this prevents that. exact_tools = util.string_as_bool( payload.get( "exact_tools", False ) ) if publish and not importable: raise exceptions.RequestParameterInvalidException( "Published workflow must be importable." ) from_dict_kwds = dict( source="API", publish=publish, exact_tools=exact_tools, ) workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds ) if importable: self._make_item_accessible( trans.sa_session, workflow ) trans.sa_session.flush() # galaxy workflow newly created id workflow_id = workflow.id # api encoded, id encoded_id = trans.security.encode_id(workflow_id) # return list rval = [] item = workflow.to_dict(value_mapper={'id': trans.security.encode_id}) item['url'] = url_for('workflow', id=encoded_id) rval.append(item) return item
[docs] @expose_api def import_shared_workflow_deprecated(self, trans, payload, **kwd): """ POST /api/workflows/import Import a workflow shared by other users. :param workflow_id: the workflow id (required) :type workflow_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ # Pull parameters out of payload. workflow_id = payload.get('workflow_id', None) if workflow_id is None: raise exceptions.ObjectAttributeMissingException( "Missing required parameter 'workflow_id'." ) self.__api_import_shared_workflow( trans, workflow_id, payload )
def __api_import_shared_workflow( self, trans, workflow_id, payload, **kwd ): try: stored_workflow = self.get_stored_workflow( trans, workflow_id, check_ownership=False ) except: raise exceptions.ObjectNotFound( "Malformed workflow id ( %s ) specified." % workflow_id ) if stored_workflow.importable is False: raise exceptions.ItemAccessibilityException( 'The owner of this workflow has disabled imports via this link.' ) elif stored_workflow.deleted: raise exceptions.ItemDeletionException( "You can't import this workflow because it has been deleted." ) imported_workflow = self._import_shared_workflow( trans, stored_workflow ) item = imported_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } ) encoded_id = trans.security.encode_id(imported_workflow.id) item['url'] = url_for('workflow', id=encoded_id) return item
[docs] @expose_api def invoke( self, trans, workflow_id, payload, **kwd ): """ POST /api/workflows/{encoded_workflow_id}/invocations Schedule the workflow specified by `workflow_id` to run. """ # /usage is awkward in this context but is consistent with the rest of # this module. Would prefer to redo it all to use /invocation(s). # Get workflow + accessibility check. stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id) workflow = stored_workflow.latest_workflow run_configs = build_workflow_run_configs(trans, workflow, payload) is_batch = payload.get('batch') if not is_batch and len(run_configs) != 1: raise exceptions.RequestParameterInvalidException("Must specify 'batch' to use batch parameters.") invocations = [] for run_config in run_configs: workflow_scheduler_id = payload.get('scheduler', None) # TODO: workflow scheduler hints work_request_params = dict(scheduler=workflow_scheduler_id) workflow_invocation = queue_invoke( trans=trans, workflow=workflow, workflow_run_config=run_config, request_params=work_request_params ) invocation = self.encode_all_ids(trans, workflow_invocation.to_dict(), recursive=True) invocations.append(invocation) if is_batch: return invocations else: return invocations[0]
[docs] @expose_api def index_invocations(self, trans, workflow_id, **kwd): """ GET /api/workflows/{workflow_id}/invocations Get the list of the workflow invocations :param workflow_id: the workflow id (required) :type workflow_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ stored_workflow = self.__get_stored_workflow( trans, workflow_id ) results = self.workflow_manager.build_invocations_query( trans, stored_workflow.id ) out = [] for r in results: out.append( self.__encode_invocation( trans, r, view="collection" ) ) return out
[docs] @expose_api def show_invocation(self, trans, workflow_id, invocation_id, **kwd): """ GET /api/workflows/{workflow_id}/invocations/{invocation_id} Get detailed description of workflow invocation :param workflow_id: the workflow id (required) :type workflow_id: str :param invocation_id: the invocation id (required) :type invocation_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ decoded_workflow_invocation_id = self.decode_id( invocation_id ) workflow_invocation = self.workflow_manager.get_invocation( trans, decoded_workflow_invocation_id ) if workflow_invocation: return self.__encode_invocation( trans, workflow_invocation, step_details=kwd.get('step_details', False) ) return None
[docs] @expose_api def cancel_invocation(self, trans, workflow_id, invocation_id, **kwd): """ DELETE /api/workflows/{workflow_id}/invocations/{invocation_id} Cancel the specified workflow invocation. :param workflow_id: the workflow id (required) :type workflow_id: str :param invocation_id: the usage id (required) :type invocation_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ decoded_workflow_invocation_id = self.decode_id( invocation_id ) workflow_invocation = self.workflow_manager.cancel_invocation( trans, decoded_workflow_invocation_id ) return self.__encode_invocation( trans, workflow_invocation )
[docs] @expose_api def invocation_step(self, trans, workflow_id, invocation_id, step_id, **kwd): """ GET /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id} :param workflow_id: the workflow id (required) :type workflow_id: str :param invocation_id: the invocation id (required) :type invocation_id: str :param step_id: encoded id of the WorkflowInvocationStep (required) :type step_id: str :param payload: payload containing update action information for running workflow. :raises: exceptions.MessageException, exceptions.ObjectNotFound """ decoded_invocation_step_id = self.decode_id( step_id ) invocation_step = self.workflow_manager.get_invocation_step( trans, decoded_invocation_step_id ) return self.__encode_invocation_step( trans, invocation_step )
[docs] @expose_api def update_invocation_step(self, trans, workflow_id, invocation_id, step_id, payload, **kwd): """ PUT /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id} Update state of running workflow step invocation - still very nebulous but this would be for stuff like confirming paused steps can proceed etc.... :param workflow_id: the workflow id (required) :type workflow_id: str :param invocation_id: the usage id (required) :type invocation_id: str :param step_id: encoded id of the WorkflowInvocationStep (required) :type step_id: str :raises: exceptions.MessageException, exceptions.ObjectNotFound """ decoded_invocation_step_id = self.decode_id( step_id ) action = payload.get( "action", None ) invocation_step = self.workflow_manager.update_invocation_step( trans, decoded_invocation_step_id, action=action, ) return self.__encode_invocation_step( trans, invocation_step )
def __encode_invocation_step( self, trans, invocation_step ): return self.encode_all_ids( trans, invocation_step.to_dict( 'element' ), True ) def __get_stored_accessible_workflow( self, trans, workflow_id ): return self.workflow_manager.get_stored_accessible_workflow( trans, workflow_id ) def __get_stored_workflow( self, trans, workflow_id ): return self.workflow_manager.get_stored_workflow( trans, workflow_id ) def __encode_invocation( self, trans, invocation, view="element", step_details=False ): return self.encode_all_ids( trans, invocation.to_dict( view, step_details=step_details ), True )