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

from __future__ import absolute_import

import base64
import json
import logging
import os
import sgmllib

import requests
from markupsafe import escape
from six.moves.http_client import HTTPConnection
from sqlalchemy import and_
from sqlalchemy.orm import eagerload, joinedload, lazyload, undefer
from sqlalchemy.sql import expression

from galaxy import (
from galaxy.managers import workflows
from galaxy.model.item_attrs import UsesItemRatings
from galaxy.model.mapping import desc
from galaxy.tools.parameters.basic import workflow_building_modes
from galaxy.util import (
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import error, url_for
from galaxy.web.base.controller import (
from galaxy.web.framework.helpers import (
from galaxy.workflow.extract import (
from galaxy.workflow.modules import (
from galaxy.workflow.render import (
from tool_shed.util import encoding_util

log = logging.getLogger(__name__)

[docs]class StoredWorkflowListGrid(grids.Grid):
[docs] class StepsColumn(grids.GridColumn):
[docs] def get_value(self, trans, grid, workflow): return len(workflow.latest_workflow.steps)
# Grid definition use_panels = True title = "Saved Workflows" model_class = model.StoredWorkflow default_filter = {"name": "All", "tags": "All"} default_sort_key = "-update_time" columns = [ grids.TextColumn("Name", key="name", attach_popup=True, filterable="advanced"), grids.IndividualTagsColumn("Tags", "tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid"), StepsColumn("Steps"), grids.GridColumn("Created", key="create_time", format=time_ago), grids.GridColumn("Last Updated", key="update_time", format=time_ago), ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[columns[0], columns[1]], key="free-text-search", visible=False, filterable="standard" ) ) operations = [ grids.GridOperation("Edit", allow_multiple=False, condition=(lambda item: not item.deleted), async_compatible=False), grids.GridOperation("Run", condition=(lambda item: not item.deleted), async_compatible=False), grids.GridOperation("Copy", condition=(lambda item: not item.deleted), async_compatible=False), grids.GridOperation("Rename", condition=(lambda item: not item.deleted), async_compatible=False), grids.GridOperation("Sharing", condition=(lambda item: not item.deleted), async_compatible=False), grids.GridOperation("Delete", condition=(lambda item: item.deleted), async_compatible=True), ]
[docs] def apply_query_filter(self, trans, query, **kwargs): return query.filter_by(user=trans.user, deleted=False)
[docs]class StoredWorkflowAllPublishedGrid(grids.Grid): title = "Published Workflows" model_class = model.StoredWorkflow default_sort_key = "update_time" default_filter = dict(public_url="All", username="All", tags="All") columns = [ grids.PublicURLColumn("Name", key="name", filterable="advanced", attach_popup=True), grids.OwnerAnnotationColumn("Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced"), grids.OwnerColumn("Owner", key="username", model_class=model.User, filterable="advanced"), grids.CommunityRatingColumn("Community Rating", key="rating"), grids.CommunityTagsColumn("Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid"), grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago) ] columns.append( grids.MulticolFilterColumn( "Search name, annotation, owner, and tags", cols_to_filter=[columns[0], columns[1], columns[2], columns[4]], key="free-text-search", visible=False, filterable="standard" ) ) operations = [ grids.GridOperation( "Import", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="imp") ), grids.GridOperation( "Save as File", condition=(lambda item: not item.deleted), allow_multiple=False, url_args=dict(action="export_to_file") ), ] num_rows_per_page = 50 use_paging = True
[docs] def build_initial_query(self, trans, **kwargs): # See optimization description comments and TODO for tags in matching public histories query. # In addition to that - be sure to lazyload the latest_workflow - it isn't needed and it causes all # of its steps to be eagerly loaded. return trans.sa_session.query(self.model_class).join("user").options(lazyload("latest_workflow"), eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
[docs] def apply_query_filter(self, trans, query, **kwargs): # A public workflow is published, has a slug, and is not deleted. return query.filter( self.model_class.published == expression.true()).filter( self.model_class.slug.isnot(None)).filter( self.model_class.deleted == expression.false())
# Simple SGML parser to get all content in a single tag.
[docs]class SingleTagContentsParser(sgmllib.SGMLParser):
[docs] def __init__(self, target_tag): sgmllib.SGMLParser.__init__(self) self.target_tag = target_tag self.cur_tag = None self.tag_content = ""
[docs] def unknown_starttag(self, tag, attrs): """ Called for each start tag. """ self.cur_tag = tag
[docs] def handle_data(self, text): """ Called for each block of plain text. """ if self.cur_tag == self.target_tag: self.tag_content += text
[docs]class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesItemRatings): stored_list_grid = StoredWorkflowListGrid() published_list_grid = StoredWorkflowAllPublishedGrid() __myexp_url = "www.myexperiment.org:80"
[docs] @web.expose @web.require_login("use Galaxy workflows") def list_grid(self, trans, **kwargs): """ List user's stored workflows. """ # status = message = None if 'operation' in kwargs: operation = kwargs['operation'].lower() if operation == "rename": return self.rename(trans, **kwargs) history_ids = util.listify(kwargs.get('id', [])) if operation == "sharing": return self.sharing(trans, id=history_ids) return self.stored_list_grid(trans, **kwargs)
[docs] @web.expose @web.require_login("use Galaxy workflows", use_panels=True) def list(self, trans): """ Render workflow main page (management of existing workflows) """ # Take care of proxy prefix in url as well redirect_url = url_for('/') + 'workflow' return trans.response.send_redirect(redirect_url)
[docs] @web.expose @web.json def list_published(self, trans, **kwargs): return self.published_list_grid(trans, **kwargs)
[docs] @web.expose def display_by_username_and_slug(self, trans, username, slug, format='html'): """ 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)
[docs] @web.expose def display_by_id(self, trans, id): """ Display workflow based on id. """ # Get workflow. stored_workflow = self.get_stored_workflow(trans, id) return self._display(trans, stored_workflow)
def _display(self, trans, stored_workflow): """ Diplay workflow as HTML page. """ 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) # Get rating data. user_item_rating = 0 if trans.get_user(): user_item_rating = self.get_user_item_rating(trans.sa_session, trans.get_user(), stored_workflow) if user_item_rating: user_item_rating = user_item_rating.rating else: user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data(trans.sa_session, stored_workflow) return trans.fill_template_mako("workflow/display.mako", item=stored_workflow, item_data=stored_workflow.latest_workflow.steps, user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings)
[docs] @web.expose def get_item_content_async(self, trans, id): """ Returns item content in HTML format. """ stored = self.get_stored_workflow(trans, id, False, True) if stored is None: raise web.httpexceptions.HTTPNotFound() # Get data for workflow's steps. self.get_stored_workflow_steps(trans, stored) # Get annotations. stored.annotation = self.get_item_annotation_str(trans.sa_session, stored.user, stored) for step in stored.latest_workflow.steps: step.annotation = self.get_item_annotation_str(trans.sa_session, stored.user, step) return trans.stream_template_mako("/workflow/item_content.mako", item=stored, item_data=stored.latest_workflow.steps)
[docs] @web.expose @web.require_login("use Galaxy workflows") def share(self, trans, id, email="", use_panels=False): msg = mtype = None # Load workflow from database stored = self.get_stored_workflow(trans, id) if email: other = trans.sa_session.query(model.User) \ .filter(and_(model.User.table.c.email == email, model.User.table.c.deleted == expression.false())) \ .first() if not other: mtype = "error" msg = ("User '%s' does not exist" % escape(email)) elif other == trans.get_user(): mtype = "error" msg = ("You cannot share a workflow with yourself") elif trans.sa_session.query(model.StoredWorkflowUserShareAssociation) \ .filter_by(user=other, stored_workflow=stored).count() > 0: mtype = "error" msg = ("Workflow already shared with '%s'" % escape(email)) else: share = model.StoredWorkflowUserShareAssociation() share.stored_workflow = stored share.user = other session = trans.sa_session session.add(share) session.flush() trans.set_message("Workflow '%s' shared with user '%s'" % (escape(stored.name), escape(other.email))) return trans.response.send_redirect(url_for(controller='workflow', action='sharing', id=id)) return trans.fill_template("/ind_share_base.mako", message=msg, messagetype=mtype, item=stored, email=email, use_panels=use_panels)
[docs] @web.expose @web.require_login("Share or export Galaxy workflows") def sharing(self, trans, id, **kwargs): """ Handle workflow sharing. """ session = trans.sa_session if 'unshare_me' in kwargs: # Remove self from shared associations with workflow. stored = self.get_stored_workflow(trans, id, False, True) association = session.query(model.StoredWorkflowUserShareAssociation) \ .filter_by(user=trans.user, stored_workflow=stored).one() session.delete(association) session.flush() return self.list(trans) else: # Get session and workflow. stored = self.get_stored_workflow(trans, id) session.add(stored) # Do operation on workflow. if 'make_accessible_via_link' in kwargs: self._make_item_accessible(trans.sa_session, stored) elif 'make_accessible_and_publish' in kwargs: self._make_item_accessible(trans.sa_session, stored) stored.published = True elif 'publish' in kwargs: stored.published = True elif 'disable_link_access' in kwargs: stored.importable = False elif 'unpublish' in kwargs: stored.published = False elif 'disable_link_access_and_unpublish' in kwargs: stored.importable = stored.published = False elif 'unshare_user' in kwargs: user = session.query(model.User).get(trans.security.decode_id(kwargs['unshare_user'])) if not user: error("User not found for provided id") association = session.query(model.StoredWorkflowUserShareAssociation) \ .filter_by(user=user, stored_workflow=stored).one() session.delete(association) # Legacy issue: workflows made accessible before recent updates may not have a slug. Create slug for any workflows that need them. if stored.importable and not stored.slug: self._make_item_accessible(trans.sa_session, stored) session.flush() return trans.fill_template("/workflow/sharing.mako", use_panels=True, item=stored)
[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: referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for('/') # Do import. stored = self.get_stored_workflow(trans, id, check_ownership=False) if stored.importable is False: return trans.show_error_message("The owner of this workflow has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True) elif stored.deleted: return trans.show_error_message("You can't import this workflow because it has been deleted.<br>You can %s" % referer_message, use_panels=True) self._import_shared_workflow(trans, stored) # Redirect to load galaxy frames. return trans.show_ok_message( message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s.""" % (stored.name, web.url_for('/workflows/list'), referer_message))
[docs] @web.expose @web.require_login("use Galaxy workflows") def rename_async(self, trans, id, new_name=None, **kwargs): stored = self.get_stored_workflow(trans, id) if new_name: san_new_name = sanitize_html(new_name) stored.name = san_new_name stored.latest_workflow.name = san_new_name trans.sa_session.flush() return stored.name
[docs] @web.expose @web.require_login("use Galaxy workflows") def annotate_async(self, trans, id, new_annotation=None, **kwargs): stored = self.get_stored_workflow(trans, id) if new_annotation: # Sanitize annotation before adding it. new_annotation = sanitize_html(new_annotation, 'utf-8', 'text/html') self.add_item_annotation(trans.sa_session, trans.get_user(), stored, new_annotation) trans.sa_session.flush() return new_annotation
[docs] @web.expose @web.require_login("rate items") @web.json def rate_async(self, trans, id, rating): """ Rate a workflow asynchronously and return updated community data. """ stored = self.get_stored_workflow(trans, id, check_ownership=False, check_accessible=True) if not stored: return trans.show_error_message("The specified workflow does not exist.") # Rate workflow. self.rate_item(trans.sa_session, trans.get_user(), stored, rating) return self.get_ave_item_rating_data(trans.sa_session, stored)
[docs] @web.expose @web.require_login("use Galaxy workflows") def set_accessible_async(self, trans, id=None, accessible=False): """ Set workflow's importable attribute and slug. """ stored = self.get_stored_workflow(trans, id) # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed. importable = accessible in ['True', 'true', 't', 'T'] if stored and stored.importable != importable: if importable: self._make_item_accessible(trans.sa_session, stored) else: stored.importable = importable trans.sa_session.flush() return
[docs] @web.expose def get_embed_html_async(self, trans, id): """ Returns HTML for embedding a workflow in a page. """ # TODO: user should be able to embed any item he has access to. see display_by_username_and_slug for security code. stored = self.get_stored_workflow(trans, id) if stored: return "Embedded Workflow '%s'" % stored.name
[docs] @web.expose @web.require_login("use Galaxy workflows") def gen_image(self, trans, id): stored = self.get_stored_workflow(trans, id, check_ownership=True) try: svg = self._workflow_to_svg_canvas(trans, stored) except Exception: status = 'error' message = 'Galaxy is unable to create the SVG image. Please check your workflow, there might be missing tools.' return trans.fill_template("/workflow/sharing.mako", use_panels=True, item=stored, status=status, message=message) trans.response.set_content_type("image/svg+xml") s = STANDALONE_SVG_TEMPLATE % svg.tostring() return s.encode('utf-8')
[docs] @web.expose @web.require_login("use Galaxy workflows") def copy(self, trans, id, save_as_name=None): # Get workflow to copy. stored = self.get_stored_workflow(trans, id, check_ownership=False) user = trans.get_user() if stored.user == user: owner = True else: if trans.sa_session.query(model.StoredWorkflowUserShareAssociation) \ .filter_by(user=user, stored_workflow=stored).count() == 0: error("Workflow is not owned by or shared with current user") owner = False # Copy. new_stored = model.StoredWorkflow() if (save_as_name): new_stored.name = '%s' % save_as_name else: new_stored.name = "Copy of %s" % stored.name new_stored.latest_workflow = stored.latest_workflow # Copy annotation. annotation_obj = self.get_item_annotation_obj(trans.sa_session, stored.user, stored) if annotation_obj: self.add_item_annotation(trans.sa_session, trans.get_user(), new_stored, annotation_obj.annotation) new_stored.copy_tags_from(trans.user, stored) if not owner: new_stored.name += " shared by %s" % stored.user.email new_stored.user = user # Persist session = trans.sa_session session.add(new_stored) session.flush() # Display the management page message = 'Created new workflow with name: %s' % escape(new_stored.name) trans.set_message(message) return_url = url_for('/') + 'workflow?status=done&message=%s' % escape(message) trans.response.send_redirect(return_url)
[docs] @web.expose_api def create(self, trans, payload=None, **kwd): if trans.request.method == 'GET': return { 'title' : 'Create Workflow', 'inputs' : [{ 'name' : 'workflow_name', 'label' : 'Name', 'value' : 'Unnamed workflow' }, { 'name' : 'workflow_annotation', 'label' : 'Annotation', 'help' : 'A description of the workflow; annotation is shown alongside shared or published workflows.' }]} else: user = trans.get_user() workflow_name = payload.get('workflow_name') workflow_annotation = payload.get('workflow_annotation') if not workflow_name: return self.message_exception(trans, 'Please provide a workflow name.') # Create the new stored workflow stored_workflow = model.StoredWorkflow() stored_workflow.name = workflow_name stored_workflow.user = user self.create_item_slug(trans.sa_session, stored_workflow) # And the first (empty) workflow revision workflow = model.Workflow() workflow.name = workflow_name workflow.stored_workflow = stored_workflow stored_workflow.latest_workflow = workflow # Add annotation. workflow_annotation = sanitize_html(workflow_annotation, 'utf-8', 'text/html') self.add_item_annotation(trans.sa_session, trans.get_user(), stored_workflow, workflow_annotation) # Persist session = trans.sa_session session.add(stored_workflow) session.flush() return {'id': trans.security.encode_id(stored_workflow.id), 'message': 'Workflow %s has been created.' % workflow_name}
[docs] @web.json def save_workflow_as(self, trans, workflow_name, workflow_data, workflow_annotation=""): """ Creates a new workflow based on Save As command. It is a new workflow, but is created with workflow_data already present. """ user = trans.get_user() if workflow_name is not None: workflow_contents_manager = workflows.WorkflowContentsManager(trans.app) stored_workflow = model.StoredWorkflow() stored_workflow.name = workflow_name stored_workflow.user = user self.create_item_slug(trans.sa_session, stored_workflow) workflow = model.Workflow() workflow.name = workflow_name workflow.stored_workflow = stored_workflow stored_workflow.latest_workflow = workflow # Add annotation. workflow_annotation = sanitize_html(workflow_annotation, 'utf-8', 'text/html') self.add_item_annotation(trans.sa_session, trans.get_user(), stored_workflow, workflow_annotation) # Persist session = trans.sa_session session.add(stored_workflow) session.flush() try: workflow, errors = workflow_contents_manager.update_workflow_from_dict( trans, stored_workflow, workflow_data, ) except workflows.MissingToolsException as e: return dict( name=e.workflow.name, message=("This workflow includes missing or invalid tools. " "It cannot be saved until the following steps are removed or the missing tools are enabled."), errors=e.errors, ) return (trans.security.encode_id(stored_workflow.id)) else: # This is an error state, 'save as' must have a workflow_name log.exception("Error in Save As workflow: no name.")
[docs] @web.expose def delete(self, trans, id=None): """ Mark a workflow as deleted """ # Load workflow from database stored = self.get_stored_workflow(trans, id) # Mark as deleted and save stored.deleted = True trans.user.stored_workflow_menu_entries = [entry for entry in trans.user.stored_workflow_menu_entries if entry.stored_workflow != stored] trans.sa_session.add(stored) trans.sa_session.flush() # Display the management page message = "Workflow deleted: %s" % escape(stored.name) trans.set_message(message) return trans.response.send_redirect(url_for('/') + 'workflow?status=done&message=%s' % escape(message))
[docs] @web.expose @web.require_login("edit workflows") def editor(self, trans, id=None): """ 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`. """ if not id: error("Invalid workflow id") stored = self.get_stored_workflow(trans, id) # 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) \ .order_by(desc(model.StoredWorkflow.table.c.update_time)) \ .options(joinedload('latest_workflow').joinedload('steps')) \ .all() return trans.fill_template("workflow/editor.mako", workflows=workflows, stored=stored, annotation=self.get_item_annotation_str(trans.sa_session, trans.user, stored))
[docs] @web.json def load_workflow(self, trans, id): """ 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=True, check_accessible=False) workflow_contents_manager = workflows.WorkflowContentsManager(trans.app) return workflow_contents_manager.workflow_to_dict(trans, stored, style="editor")
[docs] @web.expose @web.require_login("use workflows") def export_to_myexp(self, trans, id, myexp_username, myexp_password): """ Exports a workflow to myExperiment website. """ trans.workflow_building_mode = workflow_building_modes.ENABLED stored = self.get_stored_workflow(trans, id, check_ownership=False, check_accessible=True) # Convert workflow to dict. workflow_dict = self._workflow_to_dict(trans, stored) # # Create and submit workflow myExperiment request. # # Create workflow content JSON. workflow_content = json.dumps(workflow_dict, indent=4, sort_keys=True) # Create myExperiment request. request_raw = trans.fill_template( "workflow/myexp_export.mako", workflow_name=workflow_dict['name'], workflow_description=workflow_dict['annotation'], workflow_content=workflow_content, workflow_svg=self._workflow_to_svg_canvas(trans, stored).tostring() ) # strip() b/c myExperiment XML parser doesn't allow white space before XML; utf-8 handles unicode characters. request = unicodify(request_raw.strip(), 'utf-8') # Do request and get result. auth_header = base64.b64encode('%s:%s' % (myexp_username, myexp_password)) headers = {"Content-type": "text/xml", "Accept": "text/xml", "Authorization": "Basic %s" % auth_header} myexp_url = trans.app.config.get("myexperiment_url", self.__myexp_url) conn = HTTPConnection(myexp_url) # NOTE: blocks web thread. conn.request("POST", "/workflow.xml", request, headers) response = conn.getresponse() response_data = response.read() conn.close() # Do simple parse of response to see if export successful and provide user feedback. parser = SingleTagContentsParser('id') parser.feed(response_data) myexp_workflow_id = parser.tag_content workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for(controller='workflow', action='list') if myexp_workflow_id: return trans.show_message( """Workflow '%s' successfully exported to myExperiment. <br/> <a href="http://%s/workflows/%s">Click here to view the workflow on myExperiment</a> %s """ % (stored.name, myexp_url, myexp_workflow_id, workflow_list_str), use_panels=True) else: return trans.show_error_message( "Workflow '%s' could not be exported to myExperiment. Error: %s %s" % (stored.name, response_data, workflow_list_str), use_panels=True)
[docs] @web.json_pretty def for_direct_import(self, trans, id): """ 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 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. """ # 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"] = 'attachment; filename="Galaxy-Workflow-%s.ga"' % (sname) trans.response.set_content_type('application/galaxy-archive') return stored_dict
[docs] @web.expose @web.json def upload_import_workflow(self, trans, cntrller='workflow', **kwd): """ Import a workflow by reading an url, uploading a file, opening and reading the contents of a local file, or receiving the textual representation of a workflow via http. """ url = kwd.get('url', '') workflow_text = kwd.get('workflow_text', '') message = str(escape(kwd.get('message', ''))) status = kwd.get('status', 'done') import_button = kwd.get('import_button', False) # The special Galaxy integration landing page's URL on myExperiment myexperiment_target_url = 'http://%s/galaxy?galaxy_url=%s' % \ (trans.app.config.get("myexperiment_url", "www.myexperiment.org"), url_for('/', qualified=True)) # The source of the workflow, used by myExperiment to indicate the workflow came from there. workflow_source = kwd.get('workflow_source', 'uploaded file') # The following parameters will have values only if the workflow # id being imported from a Galaxy tool shed repository. tool_shed_url = kwd.get('tool_shed_url', '') repository_metadata_id = kwd.get('repository_metadata_id', '') add_to_menu = util.string_as_bool(kwd.get('add_to_menu', False)) # The workflow_name parameter is in the request only if the import originated # from a Galaxy tool shed, in which case the value was encoded. workflow_name = kwd.get('workflow_name', '') if workflow_name: workflow_name = encoding_util.tool_shed_decode(workflow_name) # The following parameters will have a value only if the import originated # from a tool shed repository installed locally or from the API. installed_repository_file = kwd.get('installed_repository_file', '') repository_id = kwd.get('repository_id', '') if installed_repository_file and not import_button: workflow_file = open(installed_repository_file, 'rb') workflow_text = workflow_file.read() workflow_file.close() import_button = True if tool_shed_url and not import_button: # Use urllib (send another request to the tool shed) to retrieve the workflow. params = dict(repository_metadata_id=repository_metadata_id, workflow_name=encoding_util.tool_shed_encode(workflow_name), open_for_url=True) pathspec = ['workflow', 'import_workflow'] workflow_text = util.url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) import_button = True if import_button: workflow_data = None if url: # Load workflow from external URL # NOTE: blocks the web thread. try: workflow_data = requests.get(url).text except Exception as e: message = "Failed to open URL: %s. Exception: %s" % (escape(url), escape(str(e))) status = 'error' elif workflow_text: # This case occurs when the workflow_text was sent via http from the tool shed. workflow_data = workflow_text else: # Load workflow from browsed file. file_data = kwd.get('file_data', '') if file_data in ('', None): message = 'No exported Galaxy workflow files were selected.' status = 'error' else: uploaded_file = file_data.file uploaded_file_name = uploaded_file.name # uploaded_file_filename = file_data.filename if os.path.getsize(os.path.abspath(uploaded_file_name)) > 0: # We're reading the file as text so we can re-use the existing code below. # This may not be ideal... workflow_data = uploaded_file.read() else: message = 'You attempted to upload an empty file.' status = 'error' if workflow_data: # Convert incoming workflow data from json try: data = json.loads(workflow_data) except Exception as e: data = None message = "The data content does not appear to be a Galaxy workflow." status = 'error' log.exception("Error importing workflow.") if data: # Create workflow if possible. If a required tool is not available in the local # Galaxy instance, the tool information will be available in the step_dict. src = None if cntrller != 'api': src = workflow_source workflow, missing_tool_tups = self._workflow_from_dict(trans, data, source=src, add_to_menu=add_to_menu) workflow = workflow.latest_workflow if workflow_name: workflow.name = workflow_name # Provide user feedback and show workflow list. if workflow.has_errors: message += "Imported, but some steps in this workflow have validation errors. " status = "error" if workflow.has_cycles: message += "Imported, but this workflow contains cycles. " status = "error" else: message += "Workflow %s imported successfully. " % escape(workflow.name) if missing_tool_tups: if trans.user_is_admin(): # A required tool is not available in the local Galaxy instance. # TODO: It would sure be nice to be able to redirect to a mako template here that displays a nice # page including the links to the configured tool sheds instead of this message, but trying # to get the panels back is a nightmare since workflow eliminates the Galaxy panels. Someone # involved in workflow development needs to figure out what it will take to be able to switch # back and forth between Galaxy (with panels ) and the workflow view (without panels ), having # the Galaxy panels displayed whenever in Galaxy. message += "The workflow requires the following tools that are not available in this Galaxy instance." message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/>" for missing_tool_tup in missing_tool_tups: missing_tool_id, missing_tool_name, missing_tool_version, step_id = missing_tool_tup message += "Tool name: %s, id: %s, version: %s." % ( escape(missing_tool_name), escape(missing_tool_id), escape(missing_tool_version)) message += "<br/>" for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): if shed_url.endswith('/'): shed_url = shed_url.rstrip('/') url = '%s/repository/find_tools?galaxy_url=%s' % (shed_url, url_for('/', qualified=True)) if missing_tool_tups: url += '&tool_id=' for missing_tool_tup in missing_tool_tups: missing_tool_id = missing_tool_tup[0] url += '%s,' % escape(missing_tool_id) message += 'url: %s, shed name: %s.' % (url, shed_name) status = 'error' if installed_repository_file or tool_shed_url: # Another Galaxy panels Hack: The request did not originate from the Galaxy # workflow view, so we don't need to render the Galaxy panels. action = 'center' else: # Another Galaxy panels hack: The request originated from the Galaxy # workflow view, so we need to render the Galaxy panels. action = 'index' return trans.response.send_redirect(web.url_for(controller='admin', action=action, message=message, status=status)) else: # TODO: Figure out what to do here... pass if tool_shed_url: # We've received the textual representation of a workflow from a Galaxy tool shed. message = "Workflow %s imported successfully." % escape(workflow.name) url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&message=%s' % \ (tool_shed_url, repository_metadata_id, encoding_util.tool_shed_encode(workflow_name), message) return trans.response.send_redirect(url) elif installed_repository_file: # The workflow was read from a file included with an installed tool shed repository. message = "Workflow %s imported successfully." % escape(workflow.name) if cntrller == 'api': return status, message return trans.response.send_redirect(web.url_for(controller='admin_toolshed', action='browse_repository', id=repository_id, message=message, status=status)) redirect_url = url_for('/') + 'workflows/list?status=' + status + '&message=%s' % escape(message) return trans.response.send_redirect(redirect_url) if cntrller == 'api': return status, message if status == 'error': redirect_url = url_for('/') + 'workflows/list?status=' + status + '&message=%s' % escape(message) return trans.response.send_redirect(redirect_url) else: return { 'url': url, 'message': message, 'status': status, 'myexperiment_target_url': myexperiment_target_url }
[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): user = trans.get_user() history = trans.get_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) # 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, 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) return trans.show_message('Workflow "%s" created from current history. ' 'You can <a href="%s" target="_parent">edit</a> or <a href="%s">run</a> the workflow.' % (escape(workflow_name), url_for(controller='workflow', action='editor', id=workflow_id), url_for(controller='workflow', action='run', id=workflow_id)))
[docs] def get_item(self, trans, id): return self.get_stored_workflow(trans, id)
[docs] @web.expose def tag_outputs(self, trans, id, **kwargs): stored = self.get_stored_workflow(trans, id, check_ownership=False) user = trans.get_user() if stored.user != user: if trans.sa_session.query(model.StoredWorkflowUserShareAssociation) \ .filter_by(user=user, stored_workflow=stored).count() == 0: error("Workflow is not owned by or shared with current user") # Get the latest revision workflow = stored.latest_workflow # It is possible for a workflow to have 0 steps if len(workflow.steps) == 0: error("Workflow cannot be tagged for outputs because it does not have any steps") if workflow.has_cycles: error("Workflow cannot be tagged for outputs because it contains cycles") if workflow.has_errors: error("Workflow cannot be tagged for outputs because of validation errors in some steps") # Build the state for each step errors = {} has_upgrade_messages = False # has_errors is never used # has_errors = False if kwargs: # If kwargs were provided, the states for each step should have # been POSTed for step in workflow.steps: if step.type == 'tool': # Extract just the output flags for this step. p = "%s|otag|" % step.id l = len(p) outputs = [k[l:] for (k, v) in kwargs.items() if k.startswith(p)] if step.workflow_outputs: for existing_output in step.workflow_outputs: if existing_output.output_name not in outputs: trans.sa_session.delete(existing_output) else: outputs.remove(existing_output.output_name) for outputname in outputs: m = model.WorkflowOutput(workflow_step_id=int(step.id), output_name=outputname) trans.sa_session.add(m) # Prepare each step trans.sa_session.flush() module_injector = WorkflowModuleInjector(trans) for step in workflow.steps: step.upgrade_messages = {} # Contruct modules module_injector.inject(step) if step.upgrade_messages: has_upgrade_messages = True if step.type == 'tool' or step.type is None: # Error dict if step.tool_errors: errors[step.id] = step.tool_errors # Render the form return trans.fill_template( "workflow/tag_outputs.mako", steps=workflow.steps, workflow=stored, has_upgrade_messages=has_upgrade_messages, errors=errors, incoming=kwargs )
def _workflow_to_svg_canvas(self, trans, stored): workflow = stored.latest_workflow workflow_canvas = WorkflowCanvas() for step in workflow.steps: # Load from database representation module = module_factory.from_workflow_step(trans, step) module_name = module.get_name() module_data_inputs = module.get_data_inputs() module_data_outputs = module.get_data_outputs() workflow_canvas.populate_data_for_step( step, module_name, module_data_inputs, module_data_outputs, ) workflow_canvas.add_steps() return workflow_canvas.finish()
def _build_workflow_on_str(instance_ds_names): # Returns suffix for new histories based on multi input iteration num_multi_inputs = len(instance_ds_names) if num_multi_inputs == 0: return "" elif num_multi_inputs == 1: return " on %s" % instance_ds_names[0] else: return " on %s and %s" % (", ".join(instance_ds_names[0:-1]), instance_ds_names[-1]) def _expand_multiple_inputs(kwargs): (single_inputs, matched_multi_inputs, multiplied_multi_inputs) = _split_inputs(kwargs) # Build up every combination of inputs to be run together. input_combos = _extend_with_matched_combos(single_inputs, matched_multi_inputs) input_combos = _extend_with_multiplied_combos(input_combos, multiplied_multi_inputs) # Input name that are multiply specified multi_input_keys = list(matched_multi_inputs.keys()) + list(multiplied_multi_inputs.keys()) for input_combo in input_combos: for key, value in input_combo.items(): kwargs[key] = value yield (kwargs, multi_input_keys) def _extend_with_matched_combos(single_inputs, multi_inputs): if len(multi_inputs) == 0: return [single_inputs] matched_multi_inputs = [] first_multi_input_key = next(iter(multi_inputs.keys())) first_multi_value = multi_inputs.get(first_multi_input_key) for value in first_multi_value: new_inputs = _copy_and_extend_inputs(single_inputs, first_multi_input_key, value) matched_multi_inputs.append(new_inputs) for multi_input_key, multi_input_values in multi_inputs.items(): if multi_input_key == first_multi_input_key: continue if len(multi_input_values) != len(first_multi_value): raise Exception("Failed to match up multi-select inputs, must select equal number of data files in each multiselect") for index, value in enumerate(multi_input_values): matched_multi_inputs[index][multi_input_key] = value return matched_multi_inputs def _extend_with_multiplied_combos(input_combos, multi_inputs): combos = input_combos for multi_input_key, multi_input_value in multi_inputs.items(): iter_combos = [] for combo in combos: for input_value in multi_input_value: iter_combos.append(_copy_and_extend_inputs(combo, multi_input_key, input_value)) combos = iter_combos return combos def _copy_and_extend_inputs(inputs, key, value): new_inputs = dict(inputs) new_inputs[key] = value return new_inputs def _split_inputs(kwargs): """ """ input_keys = [a for a in kwargs if a.endswith('|input')] single_inputs = {} matched_multi_inputs = {} multiplied_multi_inputs = {} for input_key in input_keys: input_val = kwargs[input_key] if isinstance(input_val, list): input_base = input_key[:-len("|input")] mode_key = "%s|multi_mode" % input_base mode = kwargs.get(mode_key, "matched") if mode == "matched": matched_multi_inputs[input_key] = input_val else: multiplied_multi_inputs[input_key] = input_val else: single_inputs[input_key] = input_val return (single_inputs, matched_multi_inputs, multiplied_multi_inputs)