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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 (
model,
util,
web,
)
from galaxy.managers.sharable import SlugBuilder
from galaxy.model.item_attrs import UsesItemRatings
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 (
BaseUIController,
SharableMixin,
UsesStoredWorkflowMixin,
)
from galaxy.workflow.extract import (
extract_workflow,
summarize,
)
from galaxy.workflow.modules import load_module_sections
log = logging.getLogger(__name__)
[docs]class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesItemRatings):
slug_builder = SlugBuilder()
[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,
**kwargs,
):
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)
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.'
)