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Source code for galaxy.webapps.galaxy.controllers.workflow

import logging

from markupsafe import escape
from sqlalchemy import desc
from sqlalchemy.orm import joinedload

from galaxy import (
from galaxy.managers.histories import HistoryManager
from galaxy.managers.sharable import SlugBuilder
from galaxy.model.item_attrs import UsesItemRatings
from galaxy.structured_app import StructuredApp
from galaxy.tools.parameters.workflow_utils import workflow_building_modes
from galaxy.util import FILENAME_VALID_CHARS
from galaxy.web import url_for
from galaxy.webapps.base.controller import (
from galaxy.workflow.extract import (
from galaxy.workflow.modules import load_module_sections
from ..api import depends

log = logging.getLogger(__name__)

[docs]class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesItemRatings): history_manager: HistoryManager = depends(HistoryManager) slug_builder = SlugBuilder()
[docs] def __init__(self, app: StructuredApp): super().__init__(app)
[docs] @web.expose def display_by_username_and_slug(self, trans, username, slug, format="html", **kwargs): """ Display workflow based on a username and slug. Format can be html, json, or json-download. """ # Get workflow by username and slug. Security is handled by the display methods below. session = trans.sa_session user = session.query(model.User).filter_by(username=username).first() if not user: raise web.httpexceptions.HTTPNotFound() stored_workflow = ( trans.sa_session.query(model.StoredWorkflow).filter_by(user=user, slug=slug, deleted=False).first() ) if not stored_workflow: raise web.httpexceptions.HTTPNotFound() encoded_id = trans.security.encode_id(stored_workflow.id) # Display workflow in requested format. if format == "html": return self._display(trans, stored_workflow) elif format == "json": return self.for_direct_import(trans, encoded_id) elif format == "json-download": return self.export_to_file(trans, encoded_id)
def _display(self, trans, stored_workflow): """Diplay workflow in client.""" if stored_workflow is None: raise web.httpexceptions.HTTPNotFound() # Security check raises error if user cannot access workflow. self.security_check(trans, stored_workflow, False, True) # Get data for workflow's steps. self.get_stored_workflow_steps(trans, stored_workflow) # Get annotations. stored_workflow.annotation = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, stored_workflow ) for step in stored_workflow.latest_workflow.steps: step.annotation = self.get_item_annotation_str(trans.sa_session, stored_workflow.user, step) # Encode page identifier. workflow_id = trans.security.encode_id(stored_workflow.id) # Redirect to client. return trans.response.send_redirect( web.url_for( controller="published", action="workflow", id=workflow_id, ) )
[docs] @web.expose @web.require_login("to import a workflow", use_panels=True) def imp(self, trans, id, **kwargs): """Imports a workflow shared by other users.""" # Set referer message. referer = trans.request.referer if referer and not referer.startswith(f"{trans.request.application_url}{url_for('/login')}"): referer_message = f"<a href='{escape(referer)}'>return to the previous page</a>" else: referer_message = f"<a href='{url_for('/')}'>go to Galaxy's start page</a>" # Do import. stored = self.get_stored_workflow(trans, id, check_ownership=False) if stored.importable is False: return trans.show_error_message( f"The owner of this workflow has disabled imports via this link.<br>You can {referer_message}", use_panels=True, ) elif stored.deleted: return trans.show_error_message( f"You can't import this workflow because it has been deleted.<br>You can {referer_message}", use_panels=True, ) self._import_shared_workflow(trans, stored) # Redirect to load galaxy frames. return trans.show_ok_message( message="""Workflow "{}" has been imported. <br>You can <a href="{}">start using this workflow</a> or {}.""".format( stored.name, web.url_for("/workflows/list"), referer_message ) )
[docs] @web.expose @web.require_login("use Galaxy workflows") def gen_image(self, trans, id, embed="false", version="", **kwargs): embed = util.asbool(embed) if version: version_int_or_none = int(version) else: version_int_or_none = None try: s = trans.app.workflow_manager.get_workflow_svg_from_id( trans, id, version=version_int_or_none, for_embed=embed ) trans.response.set_content_type("image/svg+xml") return s except Exception as e: log.exception("Failed to generate SVG image") error_message = str(e) return trans.show_error_message(error_message)
[docs] @web.expose @web.json @web.require_login("edit workflows") def editor(self, trans, id=None, workflow_id=None, version=None, **kwargs): """ Render the main workflow editor interface. The canvas is embedded as an iframe (necessary for scrolling to work properly), which is rendered by `editor_canvas`. """ new_workflow = False if not id: if workflow_id: stored_workflow = self.app.workflow_manager.get_stored_workflow(trans, workflow_id, by_stored_id=False) self.security_check(trans, stored_workflow, True, False) id = trans.security.encode_id(stored_workflow.id) else: new_workflow = True # The following query loads all user-owned workflows, # So that they can be copied or inserted in the workflow editor. workflows = ( trans.sa_session.query(model.StoredWorkflow) .filter_by(user=trans.user, deleted=False, hidden=False) .order_by(desc(model.StoredWorkflow.table.c.update_time)) .options(joinedload(model.StoredWorkflow.latest_workflow).joinedload(model.Workflow.steps)) .all() ) # create workflow module models module_sections = [] for module_section in load_module_sections(trans).values(): module_sections.append( { "title": module_section.get("title"), "name": module_section.get("name"), "elems": [ {"name": elem.get("name"), "title": elem.get("title"), "description": elem.get("description")} for elem in module_section.get("modules") ], } ) # create data manager tool models data_managers = [] if trans.user_is_admin and trans.app.data_managers.data_managers: for data_manager_val in trans.app.data_managers.data_managers.values(): tool = data_manager_val.tool if not tool.hidden: data_managers.append( { "id": tool.id, "name": tool.name, "hidden": tool.hidden, "description": tool.description, "is_workflow_compatible": tool.is_workflow_compatible, } ) stored = None if new_workflow is False: stored = self.get_stored_workflow(trans, id) if version is None: version = len(stored.workflows) - 1 else: version = int(version) # identify item tags item_tags = stored.make_tag_string_list() # create workflow models workflows = [ { "id": trans.security.encode_id(workflow.id), "latest_id": trans.security.encode_id(workflow.latest_workflow.id), "step_count": len(workflow.latest_workflow.steps), "name": workflow.name, } for workflow in workflows if new_workflow or workflow.id != stored.id ] # build workflow editor model editor_config = { "moduleSections": module_sections, "dataManagers": data_managers, "workflows": workflows, } # for existing workflow add its data to the model if new_workflow is False: editor_config.update( { "id": trans.security.encode_id(stored.id), "name": stored.name, "tags": item_tags, "initialVersion": version, "annotation": self.get_item_annotation_str(trans.sa_session, trans.user, stored), } ) # parse to mako return editor_config
[docs] @web.json def load_workflow(self, trans, id, version=None, **kwargs): """ Get the latest Workflow for the StoredWorkflow identified by `id` and encode it as a json string that can be read by the workflow editor web interface. """ trans.workflow_building_mode = workflow_building_modes.ENABLED stored = self.get_stored_workflow(trans, id, check_ownership=False, check_accessible=True) workflow_contents_manager = self.app.workflow_contents_manager return workflow_contents_manager.workflow_to_dict(trans, stored, style="editor", version=version)
[docs] @web.json_pretty def for_direct_import(self, trans, id, **kwargs): """ Get the latest Workflow for the StoredWorkflow identified by `id` and encode it as a json string that can be imported back into Galaxy This has slightly different information than the above. In particular, it does not attempt to decode forms and build UIs, it just stores the raw state. """ stored = self.get_stored_workflow(trans, id, check_ownership=False, check_accessible=True) return self._workflow_to_dict(trans, stored)
[docs] @web.json_pretty def export_to_file(self, trans, id): """ Get the latest Workflow for the StoredWorkflow identified by `id` and export it to a JSON file that can be imported back into Galaxy. This has slightly different information than the above. In particular, it does not attempt to decode forms and build UIs, it just stores the raw state. """ # Get workflow. stored = self.get_stored_workflow(trans, id, check_ownership=False, check_accessible=True) # Stream workflow to file. stored_dict = self._workflow_to_dict(trans, stored) if not stored_dict: # This workflow has a tool that's missing from the distribution trans.response.status = 400 return "Workflow cannot be exported due to missing tools." sname = stored.name sname = "".join(c in FILENAME_VALID_CHARS and c or "_" for c in sname)[0:150] trans.response.headers["Content-Disposition"] = f'attachment; filename="Galaxy-Workflow-{sname}.ga"' trans.response.set_content_type("application/galaxy-archive") return stored_dict
[docs] @web.expose def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None, dataset_names=None, dataset_collection_names=None, history_id=None, **kwargs, ): user = trans.get_user() history = trans.history if history_id: # Optionally target a different history than the current one. history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=history) if not user: return trans.show_error_message("Must be logged in to create workflows") if (job_ids is None and dataset_ids is None) or workflow_name is None: jobs, warnings = summarize(trans, history) # Render return trans.fill_template( "workflow/build_from_current_history.mako", jobs=jobs, warnings=warnings, history=history ) else: # If there is just one dataset name selected or one dataset collection, these # come through as string types instead of lists. xref #3247. dataset_names = util.listify(dataset_names) dataset_collection_names = util.listify(dataset_collection_names) stored_workflow = extract_workflow( trans, user=user, history=history, job_ids=job_ids, dataset_ids=dataset_ids, dataset_collection_ids=dataset_collection_ids, workflow_name=workflow_name, dataset_names=dataset_names, dataset_collection_names=dataset_collection_names, ) # Index page with message workflow_id = trans.security.encode_id(stored_workflow.id) edit_url = url_for(f"/workflows/edit?id={workflow_id}") run_url = url_for(f"/workflows/run?id={workflow_id}") return trans.show_message( f'Workflow "{escape(workflow_name)}" created from current history. ' f'You can <a href="{edit_url}" target="_parent">edit</a> or <a href="{run_url}" target="_parent">run</a> the workflow.' )