This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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

API operations for Workflows

import hashlib
import json
import logging
import os

import requests
from gxformat2._yaml import ordered_dump
from markupsafe import escape
from sqlalchemy import desc, false, or_, true
from sqlalchemy.orm import joinedload

from galaxy import (
from galaxy.managers import (
from galaxy.managers.jobs import fetch_job_states, invocation_job_source_iter, summarize_job_metrics
from galaxy.managers.workflows import (
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
from galaxy.tools import recommendations
from galaxy.tools.parameters import populate_state
from galaxy.tools.parameters.basic import workflow_building_modes
from galaxy.util.sanitize_html import sanitize_html
from galaxy.version import VERSION
from galaxy.web import (
from galaxy.webapps.base.controller import (
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().__init__(app) self.history_manager = histories.HistoryManager(app) self.workflow_manager = app.workflow_manager self.workflow_contents_manager = app.workflow_contents_manager self.tool_recommendations = recommendations.ToolRecommendations()
def __get_full_shed_url(self, url): for shed_url in self.app.tool_shed_registry.tool_sheds.values(): if url in shed_url: return shed_url return None
[docs] @expose_api_anonymous_and_sessionless def index(self, trans, **kwd): """ GET /api/workflows """ return self.get_workflows_list(trans, **kwd)
[docs] @expose_api def get_workflow_menu(self, trans, **kwd): """ Get workflows present in the tools panel GET /api/workflows/menu """ user = trans.get_user() ids_in_menu = [x.stored_workflow_id for x in user.stored_workflow_menu_entries] return { 'ids_in_menu': ids_in_menu, 'workflows': self.get_workflows_list(trans, **kwd) }
[docs] @expose_api def set_workflow_menu(self, trans, **kwd): """ Save workflow menu to be shown in the tool panel PUT /api/workflows/menu """ payload = kwd.get('payload') user = trans.get_user() workflow_ids = payload.get('workflow_ids') if workflow_ids is None: workflow_ids = [] elif type(workflow_ids) != list: workflow_ids = [workflow_ids] workflow_ids_decoded = [] # Decode the encoded workflow ids for ids in workflow_ids: workflow_ids_decoded.append(trans.security.decode_id(ids)) sess = trans.sa_session # This explicit remove seems like a hack, need to figure out # how to make the association do it automatically. for m in user.stored_workflow_menu_entries: sess.delete(m) user.stored_workflow_menu_entries = [] q = sess.query(model.StoredWorkflow) # To ensure id list is unique seen_workflow_ids = set() for wf_id in workflow_ids_decoded: if wf_id in seen_workflow_ids: continue else: seen_workflow_ids.add(wf_id) m = model.StoredWorkflowMenuEntry() m.stored_workflow = q.get(wf_id) user.stored_workflow_menu_entries.append(m) sess.flush() message = "Menu updated." trans.set_message(message) return {'message': message, 'status': 'done'}
[docs] def get_workflows_list(self, trans, missing_tools=False, show_published=None, show_hidden=False, show_deleted=False, **kwd): """ Displays a collection of workflows. :param show_published: if True, show also published workflows :type show_published: boolean :param show_hidden: if True, show hidden workflows :type show_hidden: boolean :param show_deleted: if True, show deleted workflows :type show_deleted: boolean :param missing_tools: if True, include a list of missing tools per workflow :type missing_tools: boolean """ rval = [] filter1 = trans.app.model.StoredWorkflow.user == trans.user user = trans.get_user() if show_published or user is None and show_published is None: filter1 = or_(filter1, (trans.app.model.StoredWorkflow.published == true())) query = trans.sa_session.query(trans.app.model.StoredWorkflow).options( joinedload("annotations")).options( joinedload("latest_workflow").undefer("step_count").lazyload("steps")).options( joinedload("tags") ).filter(filter1) query = query.filter_by(hidden=true() if show_hidden else false(), deleted=true() if show_deleted else false()) for wf in query.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['annotations'] = [x.annotation for x in wf.annotations] item['url'] = url_for('workflow', id=encoded_id) item['owner'] = wf.user.username item['number_of_steps'] = wf.latest_workflow.step_count item['show_in_tool_panel'] = False if user is not None: item['show_in_tool_panel'] = wf.show_in_tool_panel(user_id=user.id) rval.append(item) for wf_sa in trans.sa_session.query(model.StoredWorkflowUserShareAssociation).join( model.StoredWorkflowUserShareAssociation.stored_workflow).options( joinedload("stored_workflow").joinedload("annotations")).options( joinedload("stored_workflow").joinedload("latest_workflow").undefer("step_count").lazyload("steps")).options( joinedload("stored_workflow").joinedload("user")).options( joinedload("stored_workflow").joinedload("tags")).filter(model.StoredWorkflowUserShareAssociation.user == trans.user).filter( model.StoredWorkflow.deleted == false()).order_by( desc(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['annotations'] = [x.annotation for x in wf_sa.stored_workflow.annotations] item['url'] = url_for('workflow', id=encoded_id) item['slug'] = wf_sa.stored_workflow.slug item['owner'] = wf_sa.stored_workflow.user.username item['number_of_steps'] = wf_sa.stored_workflow.latest_workflow.step_count item['show_in_tool_panel'] = False if user is not None: item['show_in_tool_panel'] = wf_sa.stored_workflow.show_in_tool_panel(user_id=user.id) rval.append(item) if missing_tools: workflows_missing_tools = [] workflows = [] workflows_by_toolshed = dict() for value in rval: tool_ids = [] workflow_details = self.workflow_contents_manager.workflow_to_dict(trans, self.__get_stored_workflow(trans, value['id']), style='instance') if 'steps' in workflow_details: for step in workflow_details['steps']: tool_id = workflow_details['steps'][step].get('tool_id') if tool_id and tool_id not in tool_ids and self.app.toolbox.is_missing_shed_tool(tool_id): tool_ids.append(tool_id) if len(tool_ids) > 0: value['missing_tools'] = tool_ids workflows_missing_tools.append(value) for workflow in workflows_missing_tools: for tool_id in workflow['missing_tools']: toolshed, _, owner, name, tool, version = tool_id.split('/') shed_url = self.__get_full_shed_url(toolshed) repo_identifier = '/'.join((toolshed, owner, name)) if repo_identifier not in workflows_by_toolshed: workflows_by_toolshed[repo_identifier] = dict(shed=shed_url.rstrip('/'), repository=name, owner=owner, tools=[tool_id], workflows=[workflow['name']]) else: if tool_id not in workflows_by_toolshed[repo_identifier]['tools']: workflows_by_toolshed[repo_identifier]['tools'].append(tool_id) if workflow['name'] not in workflows_by_toolshed[repo_identifier]['workflows']: workflows_by_toolshed[repo_identifier]['workflows'].append(workflow['name']) for repo_tag in workflows_by_toolshed: workflows.append(workflows_by_toolshed[repo_tag]) return workflows return rval
[docs] @expose_api_anonymous_and_sessionless def show(self, trans, id, **kwd): """ GET /api/workflows/{encoded_workflow_id} :param instance: true if fetch by Workflow ID instead of StoredWorkflow id, false by default. :type instance: boolean Displays information needed to run a workflow. """ stored_workflow = self.__get_stored_workflow(trans, id, **kwd) 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" version = kwd.get('version') if version is None and util.string_as_bool(kwd.get("instance", "false")): # A Workflow instance may not be the latest workflow version attached to StoredWorkflow. # This figures out the correct version so that we return the correct Workflow and version. workflow_id = self.decode_id(id) for version, workflow in enumerate(reversed(stored_workflow.workflows)): if workflow.id == workflow_id: break return self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style, version=version)
[docs] @expose_api def show_versions(self, trans, workflow_id, **kwds): """ GET /api/workflows/{encoded_workflow_id}/versions :param instance: true if fetch by Workflow ID instead of StoredWorkflow id, false by default. :type instance: boolean Lists all versions of this workflow. """ instance = util.string_as_bool(kwds.get("instance", "false")) stored_workflow = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_id, by_stored_id=not instance) return [{'version': i, 'update_time': str(w.update_time), 'steps': len(w.steps)} for i, w in enumerate(reversed(stored_workflow.workflows))]
[docs] @expose_api def create(self, trans, payload=None, **kwd): """ POST /api/workflows Run or create workflows from the api. .. tip:: When executing a workflow externally (e.g. from a script) it is recommended to use the :func:`galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController.invoke` method below instead. 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 _step_parameters() in lib/galaxy/workflow/run_request.py :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 :param use_cached_job: If set to True galaxy will attempt to find previously executed steps for all workflow steps with the exact same parameter combinations and will copy the outputs of the previously executed step. """ ways_to_create = { 'archive_source', 'workflow_id', 'installed_repository_file', 'from_history_id', 'from_path', 'shared_workflow_id', 'workflow', } if payload is None or 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: if not trans.user_is_admin: raise exceptions.AdminRequiredException() installed_repository_file = payload.get('installed_repository_file', '') if not os.path.exists(installed_repository_file): raise exceptions.RequestParameterInvalidException("Workflow file '%s' not found" % installed_repository_file) elif os.path.getsize(os.path.abspath(installed_repository_file)) > 0: with open(installed_repository_file, encoding='utf-8') as f: workflow_data = f.read() return self.__api_import_from_archive(trans, workflow_data, payload=payload) else: raise exceptions.MessageException("You attempted to open an empty file.") if 'archive_source' in payload: archive_source = payload['archive_source'] archive_file = payload.get('archive_file') archive_data = None if archive_source: if archive_source.startswith("file://"): if not trans.user_is_admin: raise exceptions.AdminRequiredException() workflow_src = {"src": "from_path", "path": archive_source[len("file://"):]} payload["workflow"] = workflow_src return self.__api_import_new_workflow(trans, payload, **kwd) elif archive_source == "trs_tool": trs_server = payload.get("trs_server") trs_tool_id = payload.get("trs_tool_id") trs_version_id = payload.get("trs_version_id") archive_data = self.app.trs_proxy.get_version_descriptor(trs_server, trs_tool_id, trs_version_id) else: try: archive_data = requests.get(archive_source).text except Exception: raise exceptions.MessageException("Failed to open URL '%s'." % escape(archive_source)) elif hasattr(archive_file, 'file'): uploaded_file = archive_file.file uploaded_file_name = uploaded_file.name if os.path.getsize(os.path.abspath(uploaded_file_name)) > 0: archive_data = util.unicodify(uploaded_file.read()) else: raise exceptions.MessageException("You attempted to upload an empty file.") else: raise exceptions.MessageException("Please provide a URL or file.") return self.__api_import_from_archive(trans, archive_data, "uploaded file", payload=payload) 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 'from_path' in payload: from_path = payload.get('from_path') object_id = payload.get("object_id") workflow_src = {"src": "from_path", "path": from_path} if object_id is not None: workflow_src["object_id"] = object_id payload["workflow"] = workflow_src return self.__api_import_new_workflow(trans, payload, **kwd) 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'] = [] if outputs: # Newer outputs don't necessarily fill 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(invocation, **kwd) invocation_response.update(rval) return invocation_response
[docs] @expose_api_raw_anonymous_and_sessionless def workflow_dict(self, trans, workflow_id, **kwd): """ GET /api/workflows/{encoded_workflow_id}/download Returns a selected workflow. :type style: str :param style: Style of export. The default is 'export', which is the meant to be used with workflow import endpoints. Other formats such as 'instance', 'editor', 'run' are more tied to the GUI and should not be considered stable APIs. The default format for 'export' is specified by the admin with the `default_workflow_export_format` config option. Style can be specified as either 'ga' or 'format2' directly to be explicit about which format to download. :param instance: true if fetch by Workflow ID instead of StoredWorkflow id, false by default. :type instance: boolean """ stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id, **kwd) style = kwd.get("style", "export") download_format = kwd.get('format') version = kwd.get('version') history_id = kwd.get('history_id') history = None if history_id: history = self.history_manager.get_accessible(self.decode_id(history_id), trans.user, current_history=trans.history) ret_dict = self.workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style, version=version, history=history) if download_format == 'json-download': sname = stored_workflow.name sname = ''.join(c in util.FILENAME_VALID_CHARS and c or '_' for c in sname)[0:150] if ret_dict.get("format-version", None) == "0.1": extension = "ga" else: extension = "gxwf.json" trans.response.headers["Content-Disposition"] = f'attachment; filename="Galaxy-Workflow-{sname}.{extension}"' trans.response.set_content_type('application/galaxy-archive') if style == "format2" and download_format != 'json-download': return ordered_dump(ret_dict) else: return format_return_as_json(ret_dict, pretty=True)
[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, util.unicodify(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} Update the workflow stored with ``id``. :type id: str :param id: the encoded id of the workflow to update :param instance: true if fetch by Workflow ID instead of StoredWorkflow id, false by default. :type instance: boolean :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 :tags: optional list containing list of tags to add to the workflow (overwriting existing tags), if not present, tags are not modified :from_tool_form: True iff encoded state coming in is encoded for the tool form. :rtype: dict :returns: serialized version of the workflow """ stored_workflow = self.__get_stored_workflow(trans, id, **kwds) workflow_dict = payload.get('workflow', {}) workflow_dict.update({k: v for k, v in payload.items() if k not in workflow_dict}) if workflow_dict: raw_workflow_description = self.__normalize_workflow(trans, workflow_dict) workflow_dict = raw_workflow_description.as_dict new_workflow_name = workflow_dict.get('name') old_workflow = stored_workflow.latest_workflow name_updated = (new_workflow_name and new_workflow_name != stored_workflow.name) steps_updated = 'steps' in workflow_dict if name_updated and not steps_updated: sanitized_name = sanitize_html(new_workflow_name or old_workflow.name) workflow = old_workflow.copy(user=trans.user) workflow.stored_workflow = stored_workflow workflow.name = sanitized_name stored_workflow.name = sanitized_name stored_workflow.latest_workflow = workflow trans.sa_session.add(workflow, stored_workflow) trans.sa_session.flush() if 'hidden' in workflow_dict and stored_workflow.hidden != workflow_dict['hidden']: stored_workflow.hidden = workflow_dict['hidden'] trans.sa_session.flush() if 'published' in workflow_dict and stored_workflow.published != workflow_dict['published']: stored_workflow.published = workflow_dict['published'] trans.sa_session.flush() if 'annotation' in workflow_dict and not steps_updated: newAnnotation = sanitize_html(workflow_dict['annotation']) self.add_item_annotation(trans.sa_session, trans.get_user(), stored_workflow, newAnnotation) trans.sa_session.flush() if 'menu_entry' in workflow_dict or 'show_in_tool_panel' in workflow_dict: if workflow_dict.get('menu_entry') or workflow_dict.get('show_in_tool_panel'): 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)]) # set tags if 'tags' in workflow_dict: trans.app.tag_handler.set_tags_from_list(user=trans.user, item=stored_workflow, new_tags_list=workflow_dict['tags']) if 'steps' in workflow_dict: try: workflow_update_options = WorkflowUpdateOptions(**payload) workflow, errors = self.workflow_contents_manager.update_workflow_from_raw_description( trans, stored_workflow, raw_workflow_description, workflow_update_options, ) except 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 refactor(self, trans, id, payload, **kwds): """ * PUT /api/workflows/{id}/refactor updates the workflow stored with ``id`` :type id: str :param id: the encoded id of the workflow to update :param instance: true if fetch by Workflow ID instead of StoredWorkflow id, false by default. :type instance: boolean :type payload: dict :param payload: a dictionary containing list of actions to apply. :rtype: dict :returns: serialized version of the workflow """ stored_workflow = self.__get_stored_workflow(trans, id, **kwds) refactor_request = RefactorRequest(**payload) return self.workflow_contents_manager.refactor( trans, stored_workflow, refactor_request )
[docs] @expose_api def build_module(self, trans, payload=None): """ POST /api/workflows/build_module Builds module models for the workflow editor. """ if payload is None: payload = {} inputs = payload.get('inputs', {}) trans.workflow_building_mode = workflow_building_modes.ENABLED module = module_factory.from_dict(trans, payload, from_tool_form=True) if 'tool_state' not in payload: module_state = {} populate_state(trans, module.get_inputs(), inputs, module_state, check=False) module.recover_state(module_state, from_tool_form=True) return { 'label' : inputs.get('__label', ''), 'annotation' : inputs.get('__annotation', ''), 'name' : module.get_name(), 'tool_state' : module.get_state(), 'inputs' : module.get_all_inputs(connectable_only=True), 'outputs' : module.get_all_outputs(), 'config_form' : module.get_config_form(), 'post_job_actions' : module.get_post_job_actions(inputs) }
[docs] @expose_api def get_tool_predictions(self, trans, payload, **kwd): """ POST /api/workflows/get_tool_predictions Fetch predicted tools for a workflow :type payload: dict :param payload: a dictionary containing two parameters 'tool_sequence' - comma separated sequence of tool ids 'remote_model_url' - (optional) path to the deep learning model """ remote_model_url = payload.get('remote_model_url', trans.app.config.tool_recommendation_model_path) tool_sequence = payload.get('tool_sequence', "") if 'tool_sequence' not in payload or remote_model_url is None: return tool_sequence, recommended_tools = self.tool_recommendations.get_predictions(trans, tool_sequence, remote_model_url) return { "current_tool": tool_sequence, "predicted_data": recommended_tools }
# # -- Helper methods -- # def __api_import_from_archive(self, trans, archive_data, source=None, payload=None): payload = payload or {} try: data = json.loads(archive_data) except Exception: if "GalaxyWorkflow" in archive_data: data = {"yaml_content": archive_data} else: raise exceptions.MessageException("The data content does not appear to be a valid workflow.") if not data: raise exceptions.MessageException("The data content is missing.") raw_workflow_description = self.__normalize_workflow(trans, data) workflow_create_options = WorkflowCreateOptions(**payload) workflow, missing_tool_tups = self._workflow_from_dict(trans, raw_workflow_description, workflow_create_options, source=source) workflow_id = workflow.id workflow = workflow.latest_workflow response = {"message": "Workflow '%s' imported successfully." % escape(workflow.name), "status": "success", "id": trans.security.encode_id(workflow_id)} if workflow.has_errors: response["message"] = "Imported, but some steps in this workflow have validation errors." response["status"] = "error" elif len(workflow.steps) == 0: response["message"] = "Imported, but this workflow has no steps." response["status"] = "error" elif workflow.has_cycles: response["message"] = "Imported, but this workflow contains cycles." response["status"] = "error" return response def __api_import_new_workflow(self, trans, payload, **kwd): data = payload['workflow'] raw_workflow_description = self.__normalize_workflow(trans, data) workflow_create_options = WorkflowCreateOptions(**payload) workflow, missing_tool_tups = self._workflow_from_dict( trans, raw_workflow_description, workflow_create_options, ) # galaxy workflow newly created id workflow_id = workflow.id # api encoded, id encoded_id = trans.security.encode_id(workflow_id) item = workflow.to_dict(value_mapper={'id': trans.security.encode_id}) item['annotations'] = [x.annotation for x in workflow.annotations] item['url'] = url_for('workflow', id=encoded_id) item['owner'] = workflow.user.username item['number_of_steps'] = len(workflow.latest_workflow.steps) return item def __normalize_workflow(self, trans, as_dict): return self.workflow_contents_manager.normalize_workflow_format(trans, as_dict)
[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 Exception: 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. .. note:: This method takes the same arguments as :func:`galaxy.webapps.galaxy.api.workflows.WorkflowsAPIController.create` above. """ # Get workflow + accessibility check. stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id, instance=kwd.get('instance', False)) 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, flush=False, ) invocations.append(workflow_invocation) trans.sa_session.flush() invocations = [self.encode_all_ids(trans, invocation.to_dict(), recursive=True) for invocation in invocations] if is_batch: return invocations else: return invocations[0]
[docs] @expose_api def index_invocations(self, trans, workflow_id=None, **kwd): """ GET /api/workflows/{workflow_id}/invocations GET /api/invocations Get the list of a user's workflow invocations. If workflow_id is supplied (either via URL or query parameter) it should be an encoded StoredWorkflow id and returned invocations will be restricted to that workflow. history_id (an encoded History id) can be used to further restrict the query. If neither a workflow_id or history_id is supplied, all the current user's workflow invocations will be indexed (as determined by the invocation being executed on one of the user's histories). :param workflow_id: an encoded stored workflow id to restrict query to :type workflow_id: str :param instance: true if fetch by Workflow ID instead of StoredWorkflow id, false by default. :type instance: boolean :param history_id: an encoded history id to restrict query to :type history_id: str :param user_id: an encoded user id to restrict query to, must be own id if not admin user :type user_id: str :param view: level of detail to return per invocation 'element' or 'collection'. :type view: str :param step_details: If 'view' is 'element', also include details on individual steps. :type step_details: bool :raises: exceptions.MessageException, exceptions.ObjectNotFound """ if workflow_id is not None: stored_workflow_id = self.__get_stored_workflow(trans, workflow_id, instance=kwd.get('instance', False)).id else: stored_workflow_id = None encoded_history_id = kwd.get("history_id", None) if encoded_history_id: history = self.history_manager.get_accessible(self.decode_id(encoded_history_id), trans.user, current_history=trans.history) history_id = history.id else: history_id = None encoded_user_id = kwd.get("user_id", None) if encoded_user_id: target_user_id = self.decode_id(encoded_user_id) else: target_user_id = None if not trans.user_is_admin: # We restrict the query to the current users' invocations user_id = trans.user.id if target_user_id and user_id != target_user_id: raise exceptions.AdminRequiredException("Only admins can index the invocations of others") else: # Get all invocation if user is admin user_id = target_user_id include_terminal = util.string_as_bool(kwd.get("include_terminal", True)) limit = kwd.get("limit", None) if limit is not None: limit = int(limit) invocations = self.workflow_manager.build_invocations_query( trans, stored_workflow_id=stored_workflow_id, history_id=history_id, user_id=user_id, include_terminal=include_terminal, limit=limit ) return self.workflow_manager.serialize_workflow_invocations(invocations, **kwd)
[docs] @expose_api def show_invocation(self, trans, invocation_id, **kwd): """ GET /api/workflows/{workflow_id}/invocations/{invocation_id} GET /api/invocations/{invocation_id} Get detailed description of workflow invocation :param invocation_id: the invocation id (required) :type invocation_id: str :param step_details: fetch details about individual invocation steps and populate a steps attribute in the resulting dictionary. Defaults to false. :type step_details: bool :param legacy_job_state: If step_details is true, and this is set to true populate the invocation step state with the job state instead of the invocation step state. This will also produce one step per job in mapping jobs to mimic the older behavior with respect to collections. Partially scheduled steps may provide incomplete information and the listed steps outputs are the mapped over step outputs but the individual job outputs when this is set - at least for now. :type legacy_job_state: bool :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, eager=True) if workflow_invocation: step_details = util.string_as_bool(kwd.pop('step_details', 'False')) legacy_job_state = util.string_as_bool(kwd.pop('legacy_job_state', 'False')) return self.__encode_invocation(workflow_invocation, step_details=step_details, legacy_job_state=legacy_job_state, **kwd) return None
[docs] @expose_api def cancel_invocation(self, trans, invocation_id, **kwd): """ DELETE /api/workflows/{workflow_id}/invocations/{invocation_id} DELETE /api/invocations/{invocation_id} Cancel the specified workflow invocation. :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(workflow_invocation, **kwd)
[docs] @expose_api def show_invocation_report(self, trans, invocation_id, **kwd): """ GET /api/workflows/{workflow_id}/invocations/{invocation_id}/report GET /api/invocations/{invocation_id}/report Get JSON summarizing invocation for reporting. """ kwd["format"] = "json" return self.workflow_manager.get_invocation_report(trans, invocation_id, **kwd)
[docs] @expose_api_raw def show_invocation_report_pdf(self, trans, invocation_id, **kwd): """ GET /api/workflows/{workflow_id}/invocations/{invocation_id}/report.pdf GET /api/invocations/{invocation_id}/report.pdf Get JSON summarizing invocation for reporting. """ kwd["format"] = "pdf" trans.response.set_content_type("application/pdf") return self.workflow_manager.get_invocation_report(trans, invocation_id, **kwd)
def _generate_invocation_bco(self, trans, invocation_id, **kwd): decoded_workflow_invocation_id = self.decode_id(invocation_id) workflow_invocation = self.workflow_manager.get_invocation(trans, decoded_workflow_invocation_id) history = workflow_invocation.history workflow = workflow_invocation.workflow stored_workflow = workflow.stored_workflow # pull in the user info from those who the history and workflow has been shared with contributing_users = [stored_workflow.user] # may want to extend this to have more reviewers. reviewing_users = [stored_workflow.user] encoded_workflow_id = trans.security.encode_id(stored_workflow.id) encoded_history_id = trans.security.encode_id(history.id) dict_workflow = json.loads(self.workflow_dict(trans, encoded_workflow_id)) spec_version = kwd.get('spec_version', 'https://w3id.org/ieee/ieee-2791-schema/2791object.json') for i, w in enumerate(reversed(stored_workflow.workflows)): if workflow == w: current_version = i contributors = [] for contributing_user in contributing_users: contributor = { 'orcid': kwd.get('xref', []), 'name': contributing_user.username, 'affiliation': "", 'contribution': ['authoredBy'], 'email': contributing_user.email, } contributors.append(contributor) reviewers = [] for reviewer in reviewing_users: reviewer = { 'status': 'approved', 'reviewer_comment': '', 'date': workflow_invocation.update_time.isoformat(), 'reviewer': { 'orcid': kwd.get('orcid', []), 'name': contributing_user.username, 'affiliation': "", 'contribution': 'curatedBy', 'email': contributing_user.email } } reviewers.append(reviewer) provenance_domain = { 'name': workflow.name, 'version': current_version, 'review': reviewers, 'derived_from': url_for('workflow', id=encoded_workflow_id, qualified=True), 'created': workflow_invocation.create_time.isoformat(), 'modified': workflow_invocation.update_time.isoformat(), 'contributors': contributors, 'license': 'https://spdx.org/licenses/CC-BY-4.0.html', } keywords = [] for tag in stored_workflow.tags: keywords.append(tag.user_tname) for tag in history.tags: if tag.user_tname not in keywords: keywords.append(tag.user_tname) metrics = {} tools, input_subdomain, output_subdomain, pipeline_steps, software_prerequisites = [], [], [], [], [] for step in workflow_invocation.steps: if step.workflow_step.type == 'tool': workflow_outputs_list , output_list, input_list = set(), [], [] for wo in step.workflow_step.workflow_outputs: workflow_outputs_list.add(wo.output_name) for job in step.jobs: metrics[i] = summarize_job_metrics(trans, job) for job_input in job.input_datasets: if hasattr(job_input.dataset, 'dataset_id'): encoded_dataset_id = trans.security.encode_id(job_input.dataset.dataset_id) input_obj = { # TODO: that should maybe be a step prefix + element identifier where appropriate. 'filename': job_input.dataset.name, 'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True), 'access_time': job_input.dataset.create_time.isoformat(), } input_list.append(input_obj) for job_output in job.output_datasets: if hasattr(job_output.dataset, 'dataset_id'): encoded_dataset_id = trans.security.encode_id(job_output.dataset.dataset_id) output_obj = { 'filename': job_output.dataset.name, 'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True), 'access_time': job_output.dataset.create_time.isoformat(), } output_list.append(output_obj) if job_output.name in workflow_outputs_list: output = { 'mediatype': job_output.dataset.extension, 'uri': { 'filename': job_output.dataset.name, 'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True), 'access_time': job_output.dataset.create_time.isoformat(), } } output_subdomain.append(output) workflow_step = step.workflow_step step_index = workflow_step.order_index current_step = dict_workflow['steps'][str(step_index)] pipeline_step = { 'step_number': step_index, 'name': current_step['name'], 'description': current_step['annotation'], 'version': current_step['tool_version'], 'prerequisite': kwd.get('prerequisite', []), 'input_list': input_list, 'output_list': output_list } pipeline_steps.append(pipeline_step) try: software_prerequisite = { 'name': current_step['content_id'], 'version': current_step['tool_version'], 'uri': { 'uri': current_step['content_id'], 'access_time': current_step['uuid'] } } if software_prerequisite['uri']['uri'] not in tools: software_prerequisites.append(software_prerequisite) tools.append(software_prerequisite['uri']['uri']) except Exception: continue if step.workflow_step.type == 'data_input' and step.output_datasets: for output_assoc in step.output_datasets: encoded_dataset_id = trans.security.encode_id(output_assoc.dataset_id) input_obj = { 'filename': step.workflow_step.label, 'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, qualified=True), 'access_time': step.workflow_step.update_time.isoformat(), } input_subdomain.append(input_obj) if step.workflow_step.type == 'data_collection_input' and step.output_dataset_collections: for output_dataset_collection_association in step.output_dataset_collections: encoded_dataset_id = trans.security.encode_id(output_dataset_collection_association.dataset_collection_id) input_obj = { 'filename': step.workflow_step.label, 'uri': url_for('history_content', history_id=encoded_history_id, id=encoded_dataset_id, type="dataset_collection", qualified=True), 'access_time': step.workflow_step.update_time.isoformat(), } input_subdomain.append(input_obj) usability_domain = [] for a in stored_workflow.annotations: usability_domain.append(a.annotation) for h in history.annotations: usability_domain.append(h.annotation) parametric_domain = [] for inv_step in workflow_invocation.steps: try: for k, v in inv_step.workflow_step.tool_inputs.items(): param, value, step = k, v, inv_step.workflow_step.order_index parametric_domain.append({'param': param, 'value': value, 'step': step}) except Exception: continue execution_domain = { 'script_access_type': 'a_galaxy_workflow', 'script': [url_for('workflows', encoded_workflow_id=encoded_workflow_id, qualified=True)], 'script_driver': 'Galaxy', 'software_prerequisites': software_prerequisites, 'external_data_endpoints': [ { 'name': 'Access to Galaxy', 'url': url_for('/', qualified=True) }, kwd.get('external_data_endpoints') ], 'environment_variables': kwd.get('environment_variables', {}) } extension = [ { 'extension_schema': 'https://raw.githubusercontent.com/biocompute-objects/extension_domain/6d2cd8482e6075746984662edcf78b57d3d38065/galaxy/galaxy_extension.json', 'galaxy_extension': { 'galaxy_url': url_for('/', qualified=True), 'galaxy_version': VERSION, # TODO: # 'aws_estimate': aws_estimate, # 'job_metrics': metrics } } ] error_domain = { 'empirical_error': kwd.get('empirical_error', []), 'algorithmic_error': kwd.get('algorithmic_error', []) } bco_dict = { 'provenance_domain': provenance_domain, 'usability_domain': usability_domain, 'extension_domain': extension, 'description_domain': { 'keywords': keywords, 'xref': kwd.get('xref', []), 'platform': ['Galaxy'], 'pipeline_steps': pipeline_steps, }, 'execution_domain': execution_domain, 'parametric_domain': parametric_domain, 'io_domain': { 'input_subdomain': input_subdomain, 'output_subdomain': output_subdomain, }, 'error_domain': error_domain, } # Generate etag from the BCO excluding object_id and spec_version, as # specified in https://github.com/biocompute-objects/BCO_Specification/blob/main/docs/top-level.md#203-etag-etag etag = hashlib.sha256(json.dumps(bco_dict, sort_keys=True).encode()).hexdigest() bco_dict.update({ 'object_id': url_for(controller="api/invocations/%s" % invocation_id, action='biocompute', qualified=True), 'spec_version': spec_version, 'etag': etag, }) return bco_dict
[docs] @expose_api def export_invocation_bco(self, trans, invocation_id, **kwd): ''' GET /api/invocations/{invocations_id}/biocompute Return a BioCompute Object for the workflow invocation. The BioCompute Object endpoints are in beta - important details such as how inputs and outputs are represented, how the workflow is encoded, and how author and version information is encoded, and how URLs are generated will very likely change in important ways over time. ''' return self._generate_invocation_bco(trans, invocation_id, **kwd)
[docs] @expose_api_raw def download_invocation_bco(self, trans, invocation_id, **kwd): """ GET /api/invocations/{invocations_id}/biocompute/download Returns a selected BioCompute Object as a file for download (HTTP headers configured with filename and such). The BioCompute Object endpoints are in beta - important details such as how inputs and outputs are represented, how the workflow is encoded, and how author and version information is encoded, and how URLs are generated will very likely change in important ways over time. """ ret_dict = self._generate_invocation_bco(trans, invocation_id, **kwd) trans.response.headers["Content-Disposition"] = 'attachment; filename="bco_%s.json"' % invocation_id trans.response.set_content_type("application/json") return format_return_as_json(ret_dict, pretty=True)
[docs] @expose_api def invocation_step(self, trans, invocation_id, step_id, **kwd): """ GET /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id} GET /api/invocations/{invocation_id}/steps/{step_id} :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_anonymous_and_sessionless def invocation_step_jobs_summary(self, trans, invocation_id, **kwd): """ GET /api/workflows/{workflow_id}/invocations/{invocation_id}/step_jobs_summary GET /api/invocations/{invocation_id}/step_jobs_summary return job state summary info aggregated across per step of the workflow invocation Warning: We allow anyone to fetch job state information about any object they can guess an encoded ID for - it isn't considered protected data. This keeps polling IDs as part of state calculation for large histories and collections as efficient as possible. :param invocation_id: the invocation id (required) :type invocation_id: str :rtype: dict[] :returns: an array of job summary object dictionaries for each step """ decoded_invocation_id = self.decode_id(invocation_id) ids = [] types = [] for (job_source_type, job_source_id, _) in invocation_job_source_iter(trans.sa_session, decoded_invocation_id): ids.append(job_source_id) types.append(job_source_type) return [self.encode_all_ids(trans, s) for s in fetch_job_states(trans.sa_session, ids, types)]
[docs] @expose_api_anonymous_and_sessionless def invocation_jobs_summary(self, trans, invocation_id, **kwd): """ GET /api/workflows/{workflow_id}/invocations/{invocation_id}/jobs_summary GET /api/invocations/{invocation_id}/jobs_summary return job state summary info aggregated across all current jobs of workflow invocation Warning: We allow anyone to fetch job state information about any object they can guess an encoded ID for - it isn't considered protected data. This keeps polling IDs as part of state calculation for large histories and collections as efficient as possible. :param invocation_id: the invocation id (required) :type invocation_id: str :rtype: dict :returns: a job summary object merged for all steps in workflow invocation """ ids = [self.decode_id(invocation_id)] types = ["WorkflowInvocation"] return [self.encode_all_ids(trans, s) for s in fetch_job_states(trans.sa_session, ids, types)][0]
[docs] @expose_api def update_invocation_step(self, trans, invocation_id, step_id, payload, **kwd): """ PUT /api/workflows/{workflow_id}/invocations/{invocation_id}/steps/{step_id} PUT /api/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 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 _workflow_from_dict(self, trans, data, workflow_create_options, source=None): """Creates a workflow from a dict. Created workflow is stored in the database and returned. """ publish = workflow_create_options.publish importable = workflow_create_options.is_importable if publish and not importable: raise exceptions.RequestParameterInvalidException("Published workflow must be importable.") workflow_contents_manager = self.app.workflow_contents_manager raw_workflow_description = workflow_contents_manager.ensure_raw_description(data) created_workflow = workflow_contents_manager.build_workflow_from_raw_description( trans, raw_workflow_description, workflow_create_options, source=source, ) if importable: self._make_item_accessible(trans.sa_session, created_workflow.stored_workflow) trans.sa_session.flush() self._import_tools_if_needed(trans, workflow_create_options, raw_workflow_description) return created_workflow.stored_workflow, created_workflow.missing_tools def _import_tools_if_needed(self, trans, workflow_create_options, raw_workflow_description): if not workflow_create_options.import_tools: return if not trans.user_is_admin: raise exceptions.AdminRequiredException() data = raw_workflow_description.as_dict tools = {} for key in data['steps']: item = data['steps'][key] if item is not None: if 'tool_shed_repository' in item: tool_shed_repository = item['tool_shed_repository'] if 'owner' in tool_shed_repository and 'changeset_revision' in tool_shed_repository and 'name' in tool_shed_repository and 'tool_shed' in tool_shed_repository: toolstr = tool_shed_repository['owner'] \ + tool_shed_repository['changeset_revision'] \ + tool_shed_repository['name'] \ + tool_shed_repository['tool_shed'] tools[toolstr] = tool_shed_repository irm = InstallRepositoryManager(self.app) install_options = workflow_create_options.install_options for k in tools: item = tools[k] tool_shed_url = 'https://' + item['tool_shed'] + '/' name = item['name'] owner = item['owner'] changeset_revision = item['changeset_revision'] irm.install(tool_shed_url, name, owner, changeset_revision, install_options) 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, **kwd): instance = util.string_as_bool(kwd.get("instance", "false")) return self.workflow_manager.get_stored_accessible_workflow(trans, workflow_id, by_stored_id=not instance) def __get_stored_workflow(self, trans, workflow_id, **kwd): instance = util.string_as_bool(kwd.get("instance", "false")) return self.workflow_manager.get_stored_workflow(trans, workflow_id, by_stored_id=not instance) def __encode_invocation(self, invocation, **kwd): return self.workflow_manager.serialize_workflow_invocation(invocation, **kwd)