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This document is for an in-development version 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.managers.workflows
import json
import logging
import os
import uuid
from typing import (
Any,
cast,
Dict,
List,
NamedTuple,
Optional,
Tuple,
Union,
)
import sqlalchemy
import yaml
from gxformat2 import (
from_galaxy_native,
ImporterGalaxyInterface,
ImportOptions,
python_to_workflow,
)
from gxformat2.abstract import from_dict
from gxformat2.cytoscape import to_cytoscape
from gxformat2.yaml import ordered_dump
from pydantic import (
BaseModel,
SerializerFunctionWrapHandler,
WrapSerializer,
)
from sqlalchemy import (
and_,
Cast,
ColumnElement,
desc,
false,
func,
or_,
select,
true,
)
from sqlalchemy.dialects.postgresql import JSONB
from sqlalchemy.orm import (
aliased,
joinedload,
subqueryload,
)
from typing_extensions import Annotated
from galaxy import (
exceptions,
model,
util,
)
from galaxy.job_execution.actions.post import ActionBox
from galaxy.managers import (
deletable,
sharable,
)
from galaxy.managers.base import (
decode_id,
security_check,
)
from galaxy.managers.context import ProvidesUserContext
from galaxy.managers.executables import artifact_class
from galaxy.model import (
History,
ImplicitCollectionJobs,
ImplicitCollectionJobsJobAssociation,
Job,
StoredWorkflow,
StoredWorkflowTagAssociation,
StoredWorkflowUserShareAssociation,
User,
Workflow,
WorkflowInvocation,
WorkflowInvocationStep,
WorkflowInvocationToSubworkflowInvocationAssociation,
)
from galaxy.model.base import (
ensure_object_added_to_session,
transaction,
)
from galaxy.model.index_filter_util import (
append_user_filter,
raw_text_column_filter,
tag_filter,
text_column_filter,
)
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.schema.invocation import InvocationCancellationUserRequest
from galaxy.schema.schema import WorkflowIndexQueryPayload
from galaxy.structured_app import MinimalManagerApp
from galaxy.tools.parameters import (
params_to_incoming,
visit_input_values,
)
from galaxy.tools.parameters.basic import (
DataCollectionToolParameter,
DataToolParameter,
)
from galaxy.tools.parameters.workflow_utils import (
ConnectedValue,
RuntimeValue,
workflow_building_modes,
)
from galaxy.util.hash_util import md5_hash_str
from galaxy.util.json import (
safe_dumps,
safe_loads,
)
from galaxy.util.sanitize_html import sanitize_html
from galaxy.util.search import (
FilteredTerm,
parse_filters_structured,
RawTextTerm,
)
from galaxy.work.context import WorkRequestContext
from galaxy.workflow.modules import (
module_factory,
ToolModule,
WorkflowModule,
WorkflowModuleInjector,
)
from galaxy.workflow.refactor.execute import WorkflowRefactorExecutor
from galaxy.workflow.refactor.schema import (
RefactorActionExecution,
RefactorActions,
)
from galaxy.workflow.render import (
STANDALONE_SVG_TEMPLATE,
WorkflowCanvas,
)
from galaxy.workflow.reports import generate_report
from galaxy.workflow.resources import get_resource_mapper_function
from galaxy.workflow.steps import (
attach_ordered_steps,
has_cycles,
)
from galaxy.workflow.trs_proxy import TrsProxy
log = logging.getLogger(__name__)
INDEX_SEARCH_FILTERS = {
"name": "name",
"tag": "tag",
"n": "name",
"t": "tag",
"user": "user",
"u": "user",
"is": "is",
}
[docs]class WorkflowsManager(sharable.SharableModelManager, deletable.DeletableManagerMixin):
"""Handle CRUD type operations related to workflows. More interesting
stuff regarding workflow execution, step sorting, etc... can be found in
the galaxy.workflow module.
"""
model_class = model.StoredWorkflow
foreign_key_name = "stored_workflow"
user_share_model = model.StoredWorkflowUserShareAssociation
[docs] def index_query(
self, trans: ProvidesUserContext, payload: WorkflowIndexQueryPayload, include_total_count: bool = False
) -> Tuple[sqlalchemy.engine.Result, Optional[int]]:
show_published = payload.show_published
show_hidden = payload.show_hidden
show_deleted = payload.show_deleted
show_shared = payload.show_shared
if show_shared is None:
show_shared = not show_hidden and not show_deleted
if show_shared and show_deleted:
message = "show_shared and show_deleted cannot both be specified as true"
raise exceptions.RequestParameterInvalidException(message)
if show_shared and show_hidden:
message = "show_shared and show_hidden cannot both be specified as true"
raise exceptions.RequestParameterInvalidException(message)
filters = [
StoredWorkflow.user == trans.user,
]
user = trans.user
if user and show_shared:
filters.append(StoredWorkflowUserShareAssociation.user == user)
if show_published or user is None and show_published is None:
filters.append(StoredWorkflow.published == true())
stmt = select(StoredWorkflow)
if show_shared:
stmt = stmt.outerjoin(StoredWorkflow.users_shared_with)
stmt = stmt.outerjoin(StoredWorkflow.tags)
latest_workflow_load = joinedload(StoredWorkflow.latest_workflow)
if not payload.skip_step_counts:
latest_workflow_load = latest_workflow_load.undefer(Workflow.step_count) # type:ignore[arg-type]
latest_workflow_load = latest_workflow_load.lazyload(Workflow.steps)
stmt = stmt.options(joinedload(StoredWorkflow.annotations))
stmt = stmt.options(latest_workflow_load)
stmt = stmt.where(or_(*filters))
stmt = stmt.where(StoredWorkflow.hidden == (true() if show_hidden else false()))
if payload.search:
search_query = payload.search
parsed_search = parse_filters_structured(search_query, INDEX_SEARCH_FILTERS)
def w_tag_filter(term_text: str, quoted: bool):
nonlocal stmt
alias = aliased(StoredWorkflowTagAssociation)
stmt = stmt.outerjoin(StoredWorkflow.tags.of_type(alias))
return tag_filter(alias, term_text, quoted)
def name_filter(term):
return text_column_filter(StoredWorkflow.name, term)
for term in parsed_search.terms:
if isinstance(term, FilteredTerm):
key = term.filter
q = term.text
if key == "tag":
tf = w_tag_filter(term.text, term.quoted)
stmt = stmt.where(tf)
elif key == "name":
stmt = stmt.where(name_filter(term))
elif key == "user":
stmt = append_user_filter(stmt, StoredWorkflow, term)
elif key == "is":
if q == "published":
stmt = stmt.where(StoredWorkflow.published == true())
elif q == "importable":
stmt = stmt.where(StoredWorkflow.importable == true())
elif q == "deleted":
stmt = stmt.where(StoredWorkflow.deleted == true())
show_deleted = True
elif q == "shared_with_me":
if not show_shared:
message = "Can only use tag is:shared_with_me if show_shared parameter also true."
raise exceptions.RequestParameterInvalidException(message)
stmt = stmt.where(StoredWorkflowUserShareAssociation.user == user)
elif q == "bookmarked":
stmt = (
stmt.join(model.StoredWorkflowMenuEntry)
.where(model.StoredWorkflowMenuEntry.stored_workflow_id == StoredWorkflow.id)
.where(model.StoredWorkflowMenuEntry.user_id == user.id)
)
elif isinstance(term, RawTextTerm):
tf = w_tag_filter(term.text, False)
alias = aliased(User)
stmt = stmt.outerjoin(StoredWorkflow.user.of_type(alias))
stmt = stmt.where(
raw_text_column_filter(
[
StoredWorkflow.name,
tf,
alias.username,
],
term,
)
)
stmt = stmt.where(StoredWorkflow.deleted == (true() if show_deleted else false())).distinct()
if include_total_count:
total_matches = get_count(trans.sa_session, stmt)
else:
total_matches = None
if payload.sort_by is None:
if user:
stmt = stmt.order_by(desc(StoredWorkflow.user == user))
stmt = stmt.order_by(desc(StoredWorkflow.update_time))
else:
sort_column = getattr(StoredWorkflow, payload.sort_by)
if payload.sort_desc:
sort_column = sort_column.desc()
stmt = stmt.order_by(sort_column)
if payload.limit is not None:
stmt = stmt.limit(payload.limit)
if payload.offset is not None:
stmt = stmt.offset(payload.offset)
result = trans.sa_session.scalars(stmt).unique()
return result, total_matches # type:ignore[return-value]
[docs] def get_stored_workflow(self, trans, workflow_id, by_stored_id=True) -> StoredWorkflow:
"""Use a supplied ID (UUID or encoded stored workflow ID) to find
a workflow.
"""
if util.is_uuid(workflow_id):
workflow_uuid = uuid.UUID(workflow_id)
else:
workflow_uuid = None
workflow_id = workflow_id if isinstance(workflow_id, int) else decode_id(self.app, workflow_id)
stored_workflow = _get_stored_workflow(trans.sa_session, workflow_uuid, workflow_id, by_stored_id)
if stored_workflow is None:
if not by_stored_id:
# May have a subworkflow without attached StoredWorkflow object, this was the default prior to 20.09 release.
workflow = trans.sa_session.get(Workflow, workflow_id)
stored_workflow = self.attach_stored_workflow(trans=trans, workflow=workflow)
if stored_workflow:
return stored_workflow
raise exceptions.ObjectNotFound("No such workflow found.")
return stored_workflow
[docs] def get_stored_accessible_workflow(self, trans, workflow_id, by_stored_id=True):
"""Get a stored workflow from a encoded stored workflow id and
make sure it accessible to the user.
"""
stored_workflow = self.get_stored_workflow(trans, workflow_id, by_stored_id=by_stored_id)
# check to see if user has permissions to selected workflow
if stored_workflow.user != trans.user and not trans.user_is_admin and not stored_workflow.importable:
stmt = select(StoredWorkflowUserShareAssociation).filter_by(
user=trans.user, stored_workflow=stored_workflow
)
if get_count(trans.sa_session, stmt) == 0:
message = "Workflow is not owned by or shared with current user"
raise exceptions.ItemAccessibilityException(message)
return stored_workflow
[docs] def attach_stored_workflow(self, trans, workflow):
"""Attach and return stored workflow if possible."""
# Imported Subworkflows are not created with a StoredWorkflow association
# To properly serialize them we do need a StoredWorkflow, so we create and attach one here.
# We hide the new StoredWorkflow to avoid cluttering the default workflow view.
if workflow and workflow.stored_workflow is None and self.check_security(trans, has_workflow=workflow):
stored_workflow = trans.app.model.StoredWorkflow(
user=trans.user, name=workflow.name, workflow=workflow, hidden=True
)
trans.sa_session.add(stored_workflow)
with transaction(trans.sa_session):
trans.sa_session.commit()
return stored_workflow
[docs] def get_owned_workflow(self, trans, encoded_workflow_id):
"""Get a workflow (non-stored) from a encoded workflow id and
make sure it accessible to the user.
"""
workflow_id = decode_id(self.app, encoded_workflow_id)
workflow = trans.sa_session.get(Workflow, workflow_id)
self.check_security(trans, workflow, check_ownership=True)
return workflow
[docs] def check_security(self, trans, has_workflow, check_ownership=True, check_accessible=True):
"""check accessibility or ownership of workflows, storedworkflows, and
workflowinvocations. Throw an exception or returns True if user has
needed level of access.
"""
if not check_ownership and not check_accessible:
return True
# If given an invocation verify ownership of invocation
if isinstance(has_workflow, model.WorkflowInvocation):
# We use the owner of the history that is associated to the invocation as a proxy
# for the owner of the invocation.
security_check(
trans, has_workflow.history, check_ownership=check_ownership, check_accessible=check_accessible
)
return True
# stored workflow contains security stuff - follow that workflow to
# that unless given a stored workflow.
if isinstance(has_workflow, model.Workflow):
stored_workflow = has_workflow.top_level_stored_workflow
else:
stored_workflow = has_workflow
if stored_workflow.user != trans.user and not trans.user_is_admin:
if check_ownership:
raise exceptions.ItemOwnershipException()
# else check_accessible...
stmt = select(StoredWorkflowUserShareAssociation).filter_by(
user=trans.user, stored_workflow=stored_workflow
)
if get_count(trans.sa_session, stmt) == 0:
raise exceptions.ItemAccessibilityException()
return True
[docs] def get_workflow_svg_from_id(self, trans, id, version=None, for_embed=False) -> bytes:
stored = self.get_stored_accessible_workflow(trans, id)
workflow = stored.get_internal_version(version)
return self.get_workflow_svg(trans, workflow, for_embed=for_embed)
[docs] def get_workflow_svg(self, trans, workflow, for_embed=False) -> bytes:
try:
svg = self._workflow_to_svg_canvas(trans, workflow, for_embed=for_embed)
s = STANDALONE_SVG_TEMPLATE % svg.tostring()
return s.encode("utf-8")
except Exception:
message = (
"Galaxy is unable to create the SVG image. Please check your workflow, there might be missing tools."
)
raise exceptions.MessageException(message)
def _workflow_to_svg_canvas(self, trans, workflow, for_embed=False):
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(for_embed=for_embed)
[docs] def get_invocation(
self, trans, decoded_invocation_id: int, eager=False, check_ownership=True, check_accessible=True
) -> WorkflowInvocation:
workflow_invocation = _get_invocation(trans.sa_session, eager, decoded_invocation_id)
if not workflow_invocation:
encoded_wfi_id = trans.security.encode_id(decoded_invocation_id)
message = f"'{encoded_wfi_id}' is not a valid workflow invocation id"
raise exceptions.ObjectNotFound(message)
self.check_security(
trans, workflow_invocation, check_ownership=check_ownership, check_accessible=check_accessible
)
return workflow_invocation
[docs] def get_invocation_report(self, trans, invocation_id, **kwd):
decoded_workflow_invocation_id = (
trans.security.decode_id(invocation_id) if isinstance(invocation_id, str) else invocation_id
)
workflow_invocation = self.get_invocation(
trans, decoded_workflow_invocation_id, check_ownership=False, check_accessible=True
)
generator_plugin_type = kwd.get("generator_plugin_type")
runtime_report_config_json = kwd.get("runtime_report_config_json")
invocation_markdown = kwd.get("invocation_markdown", None)
target_format = kwd.get("format", "json")
if invocation_markdown:
runtime_report_config_json = {"markdown": invocation_markdown}
return generate_report(
trans,
workflow_invocation,
runtime_report_config_json=runtime_report_config_json,
plugin_type=generator_plugin_type,
target_format=target_format,
)
[docs] def request_invocation_cancellation(self, trans, decoded_invocation_id: int):
workflow_invocation = self.get_invocation(trans, decoded_invocation_id, check_ownership=True)
cancelled = workflow_invocation.cancel()
if cancelled:
workflow_invocation.add_message(InvocationCancellationUserRequest(reason="user_request"))
trans.sa_session.add(workflow_invocation)
with transaction(trans.sa_session):
trans.sa_session.commit()
return workflow_invocation
[docs] def get_invocation_step(
self, trans, decoded_workflow_invocation_step_id, check_ownership=True, check_accessible=True
):
try:
workflow_invocation_step = trans.sa_session.get(WorkflowInvocationStep, decoded_workflow_invocation_step_id)
except Exception:
raise exceptions.ObjectNotFound()
self.check_security(
trans,
workflow_invocation_step.workflow_invocation,
check_ownership=check_ownership,
check_accessible=check_accessible,
)
return workflow_invocation_step
[docs] def update_invocation_step(self, trans, decoded_workflow_invocation_step_id, action):
if action is None:
raise exceptions.RequestParameterMissingException(
"Updating workflow invocation step requires an action parameter. "
)
workflow_invocation_step = self.get_invocation_step(trans, decoded_workflow_invocation_step_id)
workflow_invocation = workflow_invocation_step.workflow_invocation
if not workflow_invocation.active:
raise exceptions.RequestParameterInvalidException(
"Attempting to modify the state of a completed workflow invocation."
)
step = workflow_invocation_step.workflow_step
module = module_factory.from_workflow_step(trans, step)
performed_action = module.do_invocation_step_action(step, action)
workflow_invocation_step.action = performed_action
trans.sa_session.add(workflow_invocation_step)
with transaction(trans.sa_session):
trans.sa_session.commit()
return workflow_invocation_step
[docs] def build_invocations_query(
self,
trans: ProvidesUserContext,
stored_workflow_id=None,
history_id=None,
job_id=None,
user_id=None,
include_terminal=True,
limit=None,
offset=None,
sort_by=None,
sort_desc=None,
include_nested_invocations=True,
check_ownership=True,
) -> Tuple[List, int]:
"""Get invocations owned by the current user."""
stmt = select(WorkflowInvocation)
if stored_workflow_id is not None:
stored_workflow = trans.sa_session.get(StoredWorkflow, stored_workflow_id)
if not stored_workflow:
raise exceptions.ObjectNotFound()
stmt = stmt.join(Workflow).where(Workflow.stored_workflow_id == stored_workflow_id)
if user_id is not None:
stmt = stmt.join(History).where(History.user_id == user_id)
if history_id is not None:
stmt = stmt.where(WorkflowInvocation.history_id == history_id)
if job_id is not None:
stmt = stmt.join(WorkflowInvocationStep).where(WorkflowInvocationStep.job_id == job_id)
if not include_terminal:
stmt = stmt.where(WorkflowInvocation.state.in_(WorkflowInvocation.non_terminal_states))
if not include_nested_invocations:
subquery = (
select(WorkflowInvocationToSubworkflowInvocationAssociation.id)
.where(
WorkflowInvocationToSubworkflowInvocationAssociation.subworkflow_invocation_id
== WorkflowInvocation.id
)
.exists()
)
stmt = stmt.where(~subquery)
total_matches = get_count(trans.sa_session, stmt)
if sort_by:
sort_column = getattr(WorkflowInvocation, sort_by)
if sort_desc:
sort_column = sort_column.desc()
else:
sort_column = WorkflowInvocation.id.desc()
stmt = stmt.order_by(sort_column)
if limit is not None:
stmt = stmt.limit(limit)
if offset is not None:
stmt = stmt.offset(offset)
invocations = [
inv
for inv in trans.sa_session.scalars(stmt)
if self.check_security(trans, inv, check_ownership=check_ownership, check_accessible=True)
]
return invocations, total_matches
MissingToolsT = List[Tuple[str, str, Optional[str], str]]
[docs]class CreatedWorkflow(NamedTuple):
stored_workflow: StoredWorkflow
workflow: model.Workflow
missing_tools: MissingToolsT
[docs]class WorkflowSerializer(sharable.SharableModelSerializer):
"""
Interface/service object for serializing stored workflows into dictionaries.
These are used for simple workflow operations - much more detailed serialization operations
that allow recovering the workflow in its entirity or rendering it in a workflow
editor are available inside the WorkflowContentsManager.
"""
model_manager_class = WorkflowsManager
SINGLE_CHAR_ABBR = "w"
[docs]class WorkflowContentsManager(UsesAnnotations):
[docs] def __init__(self, app: MinimalManagerApp, trs_proxy: TrsProxy):
self.app = app
self.trs_proxy = trs_proxy
self._resource_mapper_function = get_resource_mapper_function(app)
[docs] def ensure_raw_description(self, dict_or_raw_description):
if not isinstance(dict_or_raw_description, RawWorkflowDescription):
dict_or_raw_description = RawWorkflowDescription(dict_or_raw_description)
return dict_or_raw_description
[docs] def read_workflow_from_path(self, app, user, path, allow_in_directory=None) -> model.Workflow:
trans = WorkRequestContext(app=self.app, user=user)
as_dict = {"src": "from_path", "path": path}
workflow_class, as_dict, object_id = artifact_class(trans, as_dict, allow_in_directory=allow_in_directory)
assert workflow_class == "GalaxyWorkflow"
# Format 2 Galaxy workflow.
galaxy_interface = Format2ConverterGalaxyInterface()
import_options = ImportOptions()
import_options.deduplicate_subworkflows = True
as_dict = python_to_workflow(as_dict, galaxy_interface, workflow_directory=None, import_options=import_options)
raw_description = RawWorkflowDescription(as_dict, path)
created_workflow = self.build_workflow_from_raw_description(trans, raw_description, WorkflowCreateOptions())
return created_workflow.workflow
[docs] def normalize_workflow_format(self, trans, as_dict):
"""Process incoming workflow descriptions for consumption by other methods.
Currently this mostly means converting format 2 workflows into standard Galaxy
workflow JSON for consumption for the rest of this module. In the future we will
want to be a lot more precise about this - preserve the original description along
side the data model and apply updates in a way that largely preserves YAML structure
so workflows can be extracted.
"""
workflow_directory = None
workflow_path = None
if as_dict.get("src", None) == "from_path":
if not trans.user_is_admin:
raise exceptions.AdminRequiredException()
workflow_path = as_dict.get("path")
workflow_directory = os.path.normpath(os.path.dirname(workflow_path))
workflow_class, as_dict, object_id = artifact_class(trans, as_dict)
if workflow_class == "GalaxyWorkflow" or "yaml_content" in as_dict:
# Format 2 Galaxy workflow.
galaxy_interface = Format2ConverterGalaxyInterface()
import_options = ImportOptions()
import_options.deduplicate_subworkflows = True
try:
as_dict = python_to_workflow(
as_dict, galaxy_interface, workflow_directory=workflow_directory, import_options=import_options
)
except yaml.scanner.ScannerError as e:
raise exceptions.MalformedContents(str(e))
return RawWorkflowDescription(as_dict, workflow_path)
[docs] def build_workflow_from_raw_description(
self,
trans,
raw_workflow_description,
workflow_create_options,
source=None,
add_to_menu=False,
hidden=False,
is_subworkflow=False,
) -> CreatedWorkflow:
data = raw_workflow_description.as_dict
# Put parameters in workflow mode
trans.workflow_building_mode = workflow_building_modes.ENABLED
# If there's a source, put it in the workflow name.
if "name" not in data:
raise exceptions.RequestParameterInvalidException(f"Invalid workflow format detected [{data}]")
workflow_input_name = data["name"]
imported_sufix = f"(imported from {source})"
if source and imported_sufix not in workflow_input_name:
name = f"{workflow_input_name} {imported_sufix}"
else:
name = workflow_input_name
workflow, missing_tool_tups = self._workflow_from_raw_description(
trans,
raw_workflow_description,
workflow_create_options,
name=name,
is_subworkflow=is_subworkflow,
)
if "uuid" in data:
workflow.uuid = data["uuid"]
# Connect up
stored = model.StoredWorkflow()
stored.from_path = raw_workflow_description.workflow_path
stored.name = workflow.name
workflow.stored_workflow = stored
stored.latest_workflow = workflow
stored.user = trans.user
stored.published = workflow_create_options.publish
stored.hidden = hidden
if data["annotation"]:
annotation = sanitize_html(data["annotation"])
self.add_item_annotation(trans.sa_session, stored.user, stored, annotation)
workflow_tags = data.get("tags", [])
trans.tag_handler.set_tags_from_list(user=trans.user, item=stored, new_tags_list=workflow_tags)
# Persist
trans.sa_session.add(stored)
if add_to_menu:
if trans.user.stored_workflow_menu_entries is None:
trans.user.stored_workflow_menu_entries = []
menuEntry = model.StoredWorkflowMenuEntry()
menuEntry.stored_workflow = stored
trans.user.stored_workflow_menu_entries.append(menuEntry)
with transaction(trans.sa_session):
trans.sa_session.commit()
return CreatedWorkflow(stored_workflow=stored, workflow=workflow, missing_tools=missing_tool_tups)
[docs] def update_workflow_from_raw_description(
self, trans, stored_workflow, raw_workflow_description, workflow_update_options
):
raw_workflow_description = self.ensure_raw_description(raw_workflow_description)
# Put parameters in workflow mode
trans.workflow_building_mode = workflow_building_modes.ENABLED
dry_run = workflow_update_options.dry_run
workflow, missing_tool_tups = self._workflow_from_raw_description(
trans,
raw_workflow_description,
workflow_update_options,
name=stored_workflow.name,
dry_run=dry_run,
)
if missing_tool_tups and not workflow_update_options.allow_missing_tools:
errors = []
for missing_tool_tup in missing_tool_tups:
errors.append("Step %i: Requires tool '%s'." % (int(missing_tool_tup[3]) + 1, missing_tool_tup[0]))
raise MissingToolsException(workflow, errors)
# Connect up
if not dry_run:
workflow.stored_workflow = stored_workflow
stored_workflow.latest_workflow = workflow
else:
stored_workflow = model.StoredWorkflow() # detached
stored_workflow.latest_workflow = workflow
workflow.stored_workflow = stored_workflow
data = raw_workflow_description.as_dict
if isinstance(data, str):
data = json.loads(data)
if "tags" in data:
trans.tag_handler.set_tags_from_list(
trans.user,
stored_workflow,
data["tags"],
flush=False,
)
if workflow_update_options.update_stored_workflow_attributes:
update_dict = raw_workflow_description.as_dict
if "name" in update_dict:
sanitized_name = sanitize_html(update_dict["name"])
if not sanitized_name:
raise exceptions.RequestParameterInvalidException("Workflow must have a valid name")
workflow.name = sanitized_name
stored_workflow.name = sanitized_name
if update_dict.get("annotation") is not None:
newAnnotation = sanitize_html(update_dict["annotation"])
sa_session = None if dry_run else trans.sa_session
self.add_item_annotation(sa_session, stored_workflow.user, stored_workflow, newAnnotation)
# Persist
if not dry_run:
with transaction(trans.sa_session):
trans.sa_session.commit()
if stored_workflow.from_path:
self._sync_stored_workflow(trans, stored_workflow)
# Return something informative
errors = []
if workflow.has_errors:
errors.append("Some steps in this workflow have validation errors")
if workflow.has_cycles:
errors.append("This workflow contains cycles")
return workflow, errors
def _workflow_from_raw_description(
self,
trans,
raw_workflow_description,
workflow_state_resolution_options,
name,
is_subworkflow: bool = False,
**kwds,
) -> Tuple[model.Workflow, MissingToolsT]:
# don't commit the workflow or attach its part to the sa session - just build a
# a transient model to operate on or render.
dry_run = kwds.pop("dry_run", False)
data = raw_workflow_description.as_dict
if isinstance(data, str):
data = json.loads(data)
# Create new workflow from source data
workflow = model.Workflow()
workflow.name = name
if "report" in data:
workflow.reports_config = data["report"]
workflow.license = data.get("license")
workflow.creator_metadata = data.get("creator")
if getattr(workflow_state_resolution_options, "archive_source", None):
source_metadata = {}
if workflow_state_resolution_options.archive_source in ("trs_tool", "trs_url"):
source_metadata["trs_tool_id"] = workflow_state_resolution_options.trs_tool_id
source_metadata["trs_version_id"] = workflow_state_resolution_options.trs_version_id
source_metadata["trs_server"] = workflow_state_resolution_options.trs_server
source_metadata["trs_url"] = workflow_state_resolution_options.trs_url
elif not workflow_state_resolution_options.archive_source.startswith("file://"): # URL import
source_metadata["url"] = workflow_state_resolution_options.archive_source
workflow_state_resolution_options.archive_source = None # so trs_id is not set for subworkflows
workflow.source_metadata = source_metadata
# Assume no errors until we find a step that has some
workflow.has_errors = False
# Create each step
steps: List[model.WorkflowStep] = []
# The editor will provide ids for each step that we don't need to save,
# but do need to use to make connections
steps_by_external_id: Dict[str, model.WorkflowStep] = {}
# Preload dependent workflows with locally defined content_ids.
subworkflow_id_map = None
if subworkflows := data.get("subworkflows"):
subworkflow_id_map = {}
for key, subworkflow_dict in subworkflows.items():
subworkflow = self.__build_embedded_subworkflow(
trans, subworkflow_dict, workflow_state_resolution_options
)
subworkflow_id_map[key] = subworkflow
# Keep track of tools required by the workflow that are not available in
# the local Galaxy instance. Each tuple in the list of missing_tool_tups
# will be (tool_id, tool_name, tool_version, step_id).
missing_tool_tups = []
for step_dict in self.__walk_step_dicts(data):
if not dry_run:
self.__load_subworkflows(
trans, step_dict, subworkflow_id_map, workflow_state_resolution_options, dry_run=dry_run
)
module_kwds = workflow_state_resolution_options.model_dump()
module_kwds.update(kwds) # TODO: maybe drop this?
for step_dict in self.__walk_step_dicts(data):
module, step = self.__module_from_dict(trans, steps, steps_by_external_id, step_dict, **module_kwds)
if isinstance(module, ToolModule) and module.tool is None:
missing_tool_tup = (module.tool_id, module.get_name(), module.tool_version, step_dict["id"])
if missing_tool_tup not in missing_tool_tups:
missing_tool_tups.append(missing_tool_tup)
if module.get_errors():
workflow.has_errors = True
# Second pass to deal with connections between steps
self.__connect_workflow_steps(steps, steps_by_external_id, dry_run)
workflow.has_cycles = True
workflow.steps = steps
# Safeguard: workflow was implicitly merged into this Session prior to SQLAlchemy 2.0.
# when AT LEAST ONE step in steps belonged to a session.
for step in steps:
if ensure_object_added_to_session(workflow, object_in_session=step):
break
comments: List[model.WorkflowComment] = []
comments_by_external_id: Dict[str, model.WorkflowComment] = {}
for comment_dict in data.get("comments", []):
comment = model.WorkflowComment.from_dict(comment_dict)
comments.append(comment)
external_id = comment_dict.get("id")
if external_id:
comments_by_external_id[external_id] = comment
workflow.comments = comments
# populate parent_comment
for comment, comment_dict in zip(comments, data.get("comments", [])):
for step_external_id in comment_dict.get("child_steps", []):
child_step = steps_by_external_id.get(step_external_id)
if child_step:
child_step.parent_comment = comment
for comment_external_id in comment_dict.get("child_comments", []):
child_comment = comments_by_external_id.get(comment_external_id)
if child_comment:
child_comment.parent_comment = comment
# we can't reorder subworkflows, as step connections would become invalid
if not is_subworkflow:
# Order the steps if possible
attach_ordered_steps(workflow)
return workflow, missing_tool_tups
[docs] def workflow_to_dict(self, trans, stored, style="export", version=None, history=None):
"""Export the workflow contents to a dictionary ready for JSON-ification and to be
sent out via API for instance. There are three styles of export allowed 'export', 'instance', and
'editor'. The Galaxy team will do its best to preserve the backward compatibility of the
'export' style - this is the export method meant to be portable across Galaxy instances and over
time. The 'editor' style is subject to rapid and unannounced changes. The 'instance' export
option describes the workflow in a context more tied to the current Galaxy instance and includes
fields like 'url' and 'url' and actual unencoded step ids instead of 'order_index'.
"""
def to_format_2(wf_dict, **kwds):
return from_galaxy_native(wf_dict, None, **kwds)
if version == "":
version = None
if version is not None:
version = int(version)
workflow = stored.get_internal_version(version)
if style == "export":
style = self.app.config.default_workflow_export_format
if style == "editor":
wf_dict = self._workflow_to_dict_editor(trans, stored, workflow)
elif style == "legacy":
wf_dict = self._workflow_to_dict_instance(trans, stored, workflow=workflow, legacy=True)
elif style == "instance":
wf_dict = self._workflow_to_dict_instance(trans, stored, workflow=workflow, legacy=False)
elif style == "run":
wf_dict = self._workflow_to_dict_run(trans, stored, workflow=workflow, history=history or trans.history)
elif style == "preview":
wf_dict = self._workflow_to_dict_preview(trans, workflow=workflow)
elif style == "format2":
wf_dict = self._workflow_to_dict_export(trans, stored, workflow=workflow)
wf_dict = to_format_2(wf_dict)
elif style == "format2_wrapped_yaml":
wf_dict = self._workflow_to_dict_export(trans, stored, workflow=workflow)
wf_dict = to_format_2(wf_dict, json_wrapper=True)
elif style == "ga":
wf_dict = self._workflow_to_dict_export(trans, stored, workflow=workflow)
else:
raise exceptions.RequestParameterInvalidException(f"Unknown workflow style {style}")
if version is not None:
wf_dict["version"] = version
# If returning a run-form workflow for a specific version, use that version's name
if style == "run":
wf_dict["name"] = workflow.name
else:
wf_dict["version"] = len(stored.workflows) - 1
return wf_dict
def _sync_stored_workflow(self, trans, stored_workflow):
workflow_path = stored_workflow.from_path
self.store_workflow_to_path(workflow_path, stored_workflow, stored_workflow.latest_workflow, trans=trans)
[docs] def store_workflow_artifacts(self, directory, filename_base, workflow, **kwd):
modern_workflow_path = os.path.join(directory, f"{filename_base}.gxwf.yml")
legacy_workflow_path = os.path.join(directory, f"{filename_base}.ga")
abstract_cwl_workflow_path = os.path.join(directory, f"{filename_base}.abstract.cwl")
for path in [legacy_workflow_path, modern_workflow_path, abstract_cwl_workflow_path]:
self.app.workflow_contents_manager.store_workflow_to_path(path, workflow.stored_workflow, workflow, **kwd)
try:
cytoscape_path = os.path.join(directory, f"{filename_base}.html")
to_cytoscape(modern_workflow_path, cytoscape_path)
except Exception:
# completely optional and currently broken so ignore...
pass
[docs] def store_workflow_to_path(self, workflow_path, stored_workflow, workflow, **kwd):
trans = kwd.get("trans")
if trans is None:
trans = WorkRequestContext(app=self.app, user=kwd.get("user"), history=kwd.get("history"))
workflow = stored_workflow.latest_workflow
with open(workflow_path, "w") as f:
if workflow_path.endswith(".ga"):
wf_dict = self._workflow_to_dict_export(trans, stored_workflow, workflow=workflow)
json.dump(wf_dict, f, indent=4)
elif workflow_path.endswith(".abstract.cwl"):
wf_dict = self._workflow_to_dict_export(trans, stored_workflow, workflow=workflow)
abstract_dict = from_dict(wf_dict)
ordered_dump(abstract_dict, f)
else:
wf_dict = self._workflow_to_dict_export(trans, stored_workflow, workflow=workflow)
wf_dict = from_galaxy_native(wf_dict, None, json_wrapper=True)
f.write(wf_dict["yaml_content"])
def _workflow_to_dict_run(self, trans, stored, workflow, history=None):
"""
Builds workflow dictionary used by run workflow form
"""
if len(workflow.steps) == 0:
raise exceptions.MessageException("Workflow cannot be run because it does not have any steps.")
if has_cycles(workflow):
raise exceptions.MessageException("Workflow cannot be run because it contains cycles.")
trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
module_injector = WorkflowModuleInjector(trans)
has_upgrade_messages = False
step_version_changes = []
missing_tools = []
errors = {}
module_injector.inject_all(workflow, exact_tools=False, ignore_tool_missing_exception=True)
for step in workflow.steps:
try:
module_injector.compute_runtime_state(step)
except exceptions.ToolMissingException as e:
# FIXME: if a subworkflow lacks multiple tools we report only the first missing tool
if e.tool_id not in missing_tools:
missing_tools.append(e.tool_id)
continue
if step.upgrade_messages:
has_upgrade_messages = True
if step.type in ("tool", "subworkflow", None):
if step.module.version_changes:
step_version_changes.extend(step.module.version_changes)
step_errors = step.module.get_errors()
if step_errors:
errors[step.id] = step_errors
if missing_tools:
workflow.annotation = self.get_item_annotation_str(trans.sa_session, trans.user, workflow)
raise exceptions.MessageException(f"Following tools missing: {', '.join(missing_tools)}")
workflow.annotation = self.get_item_annotation_str(trans.sa_session, trans.user, workflow)
step_order_indices = {}
for step in workflow.steps:
step_order_indices[step.id] = step.order_index
step_models = []
for step in workflow.steps:
step_model = None
if step.type == "tool":
incoming: Dict[str, Any] = {}
tool = trans.app.toolbox.get_tool(
step.tool_id, tool_version=step.tool_version, tool_uuid=step.tool_uuid
)
params_to_incoming(incoming, tool.inputs, step.state.inputs, trans.app)
step_model = tool.to_json(
trans, incoming, workflow_building_mode=workflow_building_modes.USE_HISTORY, history=history
)
step_model["post_job_actions"] = [
{
"short_str": ActionBox.get_short_str(pja),
"action_type": pja.action_type,
"output_name": pja.output_name,
"action_arguments": pja.action_arguments,
}
for pja in step.post_job_actions
]
else:
inputs = step.module.get_runtime_inputs(step, connections=step.output_connections)
step_model = {"inputs": [input.to_dict(trans) for input in inputs.values()]}
step_model["when"] = step.when_expression
step_model["replacement_parameters"] = step.module.get_informal_replacement_parameters(step)
step_model["step_type"] = step.type
step_model["step_label"] = step.label
step_model["step_name"] = step.module.get_name()
step_model["step_version"] = step.module.get_version()
step_model["step_index"] = step.order_index
step_model["output_connections"] = [
{
"input_step_index": step_order_indices.get(oc.input_step_id),
"output_step_index": step_order_indices.get(oc.output_step_id),
"input_name": oc.input_name,
"output_name": oc.output_name,
}
for oc in step.output_connections
]
if step.annotations:
step_model["annotation"] = step.annotations[0].annotation
if step.upgrade_messages:
step_model["messages"] = step.upgrade_messages
step_models.append(step_model)
return {
"id": trans.app.security.encode_id(stored.id),
"workflow_id": trans.app.security.encode_id(workflow.id),
"history_id": trans.app.security.encode_id(history.id) if history else None,
"name": stored.name,
"owner": stored.user.username,
"steps": step_models,
"step_version_changes": step_version_changes,
"has_upgrade_messages": has_upgrade_messages,
"workflow_resource_parameters": self._workflow_resource_parameters(trans, stored, workflow),
}
def _workflow_to_dict_preview(self, trans, workflow):
"""
Builds workflow dictionary containing input labels and values.
Used to create embedded workflow previews.
"""
if len(workflow.steps) == 0:
raise exceptions.MessageException("Workflow cannot be run because it does not have any steps.")
if has_cycles(workflow):
raise exceptions.MessageException("Workflow cannot be run because it contains cycles.")
def row_for_param(input_dict, param, raw_value, other_values, prefix, step):
input_dict["label"] = param.get_label()
value = None
if isinstance(param, DataToolParameter) or isinstance(param, DataCollectionToolParameter):
if (prefix + param.name) in step.input_connections_by_name:
conns = step.input_connections_by_name[prefix + param.name]
if not isinstance(conns, list):
conns = [conns]
value_list = [
"Output '%s' from Step %d." % (conn.output_name, int(conn.output_step.order_index) + 1)
for conn in conns
]
value = ",".join(value_list)
else:
value = "Select at Runtime."
else:
value = param.value_to_display_text(raw_value) or "Unavailable."
input_dict["value"] = value
if hasattr(step, "upgrade_messages") and step.upgrade_messages and param.name in step.upgrade_messages:
input_dict["upgrade_messages"] = step.upgrade_messages[param.name]
def do_inputs(inputs, values, prefix, step, other_values=None):
input_dicts = []
for input in inputs.values():
input_dict = {}
input_dict["type"] = input.type
if input.type == "repeat":
repeat_values = values[input.name]
if len(repeat_values) > 0:
input_dict["title"] = input.title_plural
nested_input_dicts = []
for i in range(len(repeat_values)):
nested_input_dict = {}
index = repeat_values[i]["__index__"]
nested_input_dict["title"] = "%i. %s" % (i + 1, input.title)
try:
nested_input_dict["inputs"] = do_inputs(
input.inputs,
repeat_values[i],
f"{prefix + input.name}_{str(index)}|",
step,
other_values,
)
except KeyError:
continue
nested_input_dicts.append(nested_input_dict)
input_dict["inputs"] = nested_input_dicts
elif input.type == "conditional":
group_values = values[input.name]
current_case = group_values["__current_case__"]
new_prefix = f"{prefix + input.name}|"
row_for_param(
input_dict, input.test_param, group_values[input.test_param.name], other_values, prefix, step
)
try:
input_dict["inputs"] = do_inputs(
input.cases[current_case].inputs, group_values, new_prefix, step, other_values
)
except KeyError:
continue
elif input.type == "section":
new_prefix = f"{prefix + input.name}|"
group_values = values[input.name]
input_dict["title"] = input.title
try:
input_dict["inputs"] = do_inputs(input.inputs, group_values, new_prefix, step, other_values)
except KeyError:
continue
else:
row_for_param(
input_dict,
input,
# Use values.get so that unspecified param values don't blow up the display
values.get(input.name),
other_values,
prefix,
step,
)
input_dicts.append(input_dict)
return input_dicts
module_injector = WorkflowModuleInjector(trans)
module_injector.inject_all(workflow, ignore_tool_missing_exception=True, exact_tools=False)
step_dicts = []
for step in workflow.steps:
step_dict = {}
step_dict["order_index"] = step.order_index
step_dict["type"] = step.type
if step.annotations:
step_dict["annotation"] = step.annotations[0].annotation
try:
module_injector.compute_runtime_state(step)
except exceptions.ToolMissingException as e:
step_dict["label"] = f"Unknown Tool with id '{e.tool_id}'"
step_dicts.append(step_dict)
continue
if step.type == "tool":
tool = trans.app.toolbox.get_tool(step.tool_id, step.tool_version)
step_dict["tool_id"] = step.tool_id
step_dict["tool_version"] = step.tool_version
step_dict["label"] = step.label or tool.name
step_dict["inputs"] = do_inputs(tool.inputs, step.state.inputs, "", step)
elif step.type == "subworkflow":
step_dict["label"] = step.label or (step.subworkflow.name if step.subworkflow else "Missing workflow.")
errors = step.module.get_errors()
if errors:
step_dict["errors"] = errors
subworkflow_dict = self._workflow_to_dict_preview(trans, step.subworkflow)
step_dict["inputs"] = subworkflow_dict["steps"]
else:
module = step.module
step_dict["label"] = module.name
step_dict["inputs"] = do_inputs(module.get_runtime_inputs(step), step.state.inputs, "", step)
step_dicts.append(step_dict)
return {
"name": workflow.name,
"steps": step_dicts,
}
def _workflow_resource_parameters(self, trans, stored, workflow):
"""Get workflow scheduling resource parameters for this user and workflow or None if not configured."""
return self._resource_mapper_function(trans=trans, stored_workflow=stored, workflow=workflow)
def _workflow_to_dict_editor(self, trans, stored, workflow, tooltip=True, is_subworkflow=False):
# Pack workflow data into a dictionary and return
data = {}
data["name"] = workflow.name
data["steps"] = {}
data["upgrade_messages"] = {}
data["report"] = workflow.reports_config or {}
data["license"] = workflow.license
data["creator"] = workflow.creator_metadata
data["source_metadata"] = workflow.source_metadata
data["annotation"] = self.get_item_annotation_str(trans.sa_session, trans.user, stored) or ""
data["comments"] = [comment.to_dict() for comment in workflow.comments]
output_label_index = set()
input_step_types = set(workflow.input_step_types)
# For each step, rebuild the form and encode the state
for step in workflow.steps:
# Load from database representation
module = module_factory.from_workflow_step(trans, step, exact_tools=False)
if not module:
raise exceptions.MessageException(f"Unrecognized step type: {step.type}")
# Load label from state of data input modules, necessary for backward compatibility
self.__set_default_label(step, module, step.tool_inputs)
# Fix any missing parameters
upgrade_message_dict = module.check_and_update_state() or {}
version_changes = getattr(module, "version_changes", None)
if version_changes:
upgrade_message_dict[module.get_name()] = "\n".join(version_changes)
# Get user annotation.
config_form = module.get_config_form(step=step)
annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ""
# Pack attributes into plain dictionary
step_dict = {
"id": step.order_index,
"type": module.type,
"label": module.label,
"content_id": module.get_content_id(),
"name": module.get_name(),
"tool_state": module.get_tool_state(),
"errors": module.get_errors(),
"inputs": module.get_all_inputs(connectable_only=True),
"outputs": module.get_all_outputs(),
"config_form": config_form,
"annotation": annotation_str,
"post_job_actions": module.get_post_job_actions({}),
"uuid": str(step.uuid) if step.uuid else None,
"when": step.when_expression,
"workflow_outputs": [],
}
if tooltip:
step_dict["tooltip"] = module.get_tooltip(static_path="/static")
# Connections
input_connections = step.input_connections
input_connections_type = {}
multiple_input = {} # Boolean value indicating if this can be multiple
if isinstance(module, ToolModule) and module.tool:
# Serialize tool version
step_dict["tool_version"] = module.tool.version
# Determine full (prefixed) names of valid input datasets
data_input_names = {}
def callback(input, prefixed_name, **kwargs):
if isinstance(input, DataToolParameter) or isinstance(input, DataCollectionToolParameter):
data_input_names[prefixed_name] = True # noqa: B023
multiple_input[prefixed_name] = input.multiple # noqa: B023
if isinstance(input, DataToolParameter):
input_connections_type[input.name] = "dataset" # noqa: B023
if isinstance(input, DataCollectionToolParameter):
input_connections_type[input.name] = "dataset_collection" # noqa: B023
visit_input_values(module.tool.inputs, module.state.inputs, callback)
# post_job_actions
pja_dict = {}
for pja in step.post_job_actions:
pja_dict[pja.action_type + pja.output_name] = dict(
action_type=pja.action_type, output_name=pja.output_name, action_arguments=pja.action_arguments
)
step_dict["post_job_actions"] = pja_dict
# workflow outputs
outputs = []
output_label_duplicate = set()
for output in step.unique_workflow_outputs:
if output.workflow_step.type not in input_step_types:
output_label = output.label
output_name = output.output_name
output_uuid = str(output.uuid) if output.uuid else None
outputs.append({"output_name": output_name, "uuid": output_uuid, "label": output_label})
if output_label is not None:
if output_label in output_label_index:
if output_label not in output_label_duplicate:
output_label_duplicate.add(output_label)
else:
output_label_index.add(output_label)
step_dict["workflow_outputs"] = outputs
if len(output_label_duplicate) > 0:
output_label_duplicate_string = ", ".join(output_label_duplicate)
upgrade_message_dict["output_label_duplicate"] = (
f"Ignoring duplicate labels: {output_label_duplicate_string}."
)
if upgrade_message_dict:
data["upgrade_messages"][step.order_index] = upgrade_message_dict
# Encode input connections as dictionary
input_conn_dict: model.InputConnDictType = {}
for conn in input_connections:
input_type = "dataset"
if conn.input_name in input_connections_type:
input_type = input_connections_type[conn.input_name]
conn_dict = dict(id=conn.output_step.order_index, output_name=conn.output_name, input_type=input_type)
if conn.input_name in multiple_input:
if conn.input_name in input_conn_dict:
cast(list, input_conn_dict[conn.input_name]).append(conn_dict)
else:
input_conn_dict[conn.input_name] = [conn_dict]
else:
input_conn_dict[conn.input_name] = conn_dict
step_dict["input_connections"] = input_conn_dict
# Position
step_dict["position"] = step.position
# Add to return value
data["steps"][step.order_index] = step_dict
if is_subworkflow:
data["steps"] = self._resolve_collection_type(data["steps"])
return data
[docs] @staticmethod
def get_step_map_over(current_step, steps):
"""
Given a tool step and its input steps guess that maximum level of mapping over.
All data outputs of a step need to be mapped over to this level.
"""
max_map_over = ""
for input_name, input_connections in current_step["input_connections"].items():
if isinstance(input_connections, dict):
# if input does not accept multiple inputs
input_connections = [input_connections]
for input_value in input_connections:
current_data_input = None
for current_input in current_step["inputs"]:
if current_input["name"] == input_name:
current_data_input = current_input
# we've got one of the tools' input data definitions
break
if current_data_input is None:
log.info(f"failed to find input {input_name} for get_step_map_over")
continue
input_step = steps[input_value["id"]]
for input_step_data_output in input_step["outputs"]:
if input_step_data_output["name"] == input_value["output_name"]:
collection_type = input_step_data_output.get("collection_type")
# This is the defined incoming collection type, in reality there may be additional
# mapping over of the workflows' data input, but this should be taken care of by the workflow editor /
# outer workflow.
if collection_type:
if current_data_input.get("input_type") == "dataset" and current_data_input.get("multiple"):
# We reduce the innermost collection
if ":" in collection_type:
# more than one layer of nesting and multiple="true" input,
# we consume the innermost collection
collection_type = ":".join(collection_type.rsplit(":")[:-1])
else:
# We've reduced a list or a pair
collection_type = None
elif current_data_input.get("input_type") == "dataset_collection":
current_collection_types = current_data_input["collection_types"]
if not current_collection_types:
# Accepts any input dataset collection, no mapping
collection_type = None
elif collection_type in current_collection_types:
# incoming collection type is an exact match, no mapping over
collection_type = None
else:
outer_map_over = collection_type
for accepted_collection_type in current_data_input["collection_types"]:
# need to find the lowest level of mapping over,
# for collection_type = 'list:list:list' and accepted_collection_type = ['list:list', 'list']
# it'd be outer_map_over == 'list'
if collection_type.endswith(accepted_collection_type):
_outer_map_over = collection_type[: -(len(accepted_collection_type) + 1)]
if len(_outer_map_over.split(":")) < len(outer_map_over.split(":")):
outer_map_over = _outer_map_over
collection_type = outer_map_over
# If there is mapping over, we're going to assume it is linked, everything else is (probably)
# too hard to display in the workflow editor. With this assumption we should be able to
# set the maximum mapping over level to the most deeply nested map_over
if collection_type and len(collection_type.split(":")) >= len(max_map_over.split(":")):
max_map_over = collection_type
if max_map_over:
return max_map_over
return None
def _resolve_collection_type(self, steps):
"""
Fill in collection type for step outputs.
This can either be via collection_type_source and / or "inherited" from the step's input.
This information is only needed in the workflow editor.
"""
for order_index in sorted(steps):
step = steps[order_index]
if step["type"] == "tool" and not step.get("errors"):
map_over = self.get_step_map_over(step, steps)
for step_data_output in step["outputs"]:
if step_data_output.get("collection_type_source") and step_data_output["collection_type"] is None:
collection_type_source = step_data_output["collection_type_source"]
for input_connection in step["input_connections"].get(collection_type_source, []):
input_step = steps[input_connection["id"]]
for input_step_data_output in input_step["outputs"]:
if input_step_data_output["name"] == input_connection["output_name"]:
step_data_output["collection_type"] = input_step_data_output.get("collection_type")
if map_over:
collection_type = map_over
step_data_output["collection"] = True
if step_data_output.get("collection_type"):
collection_type = f"{map_over}:{step_data_output['collection_type']}"
step_data_output["collection_type"] = collection_type
return steps
def _workflow_to_dict_export(self, trans, stored=None, workflow=None, internal=False, allow_upgrade=False):
"""Export the workflow contents to a dictionary ready for JSON-ification and export.
If internal, use content_ids instead subworkflow definitions.
If `allow_upgrade`, the workflow and sub-workflows might use updated tool versions when refactoring.
"""
annotation_str = ""
tags_list = []
annotation_owner = None
if stored is not None:
if stored.id:
# if the active user doesn't have an annotation on the workflow, default to the owner's annotation.
annotation_owner = stored.user
annotation_str = (
self.get_item_annotation_str(trans.sa_session, trans.user, stored)
or self.get_item_annotation_str(trans.sa_session, annotation_owner, stored)
or ""
)
tags_list = stored.make_tag_string_list()
else:
# dry run with flushed workflow objects, just use the annotation
annotations = stored.annotations
if annotations and len(annotations) > 0:
annotation_str = util.unicodify(annotations[0].annotation)
# Pack workflow data into a dictionary and return
data: Dict[str, Any] = {}
data["a_galaxy_workflow"] = "true" # Placeholder for identifying galaxy workflow
data["format-version"] = "0.1"
data["name"] = workflow.name
data["annotation"] = annotation_str
data["tags"] = tags_list
if workflow.uuid is not None:
data["uuid"] = str(workflow.uuid)
steps: Dict[int, Dict[str, Any]] = {}
data["steps"] = steps
data["comments"] = [comment.to_dict() for comment in workflow.comments]
if workflow.reports_config:
data["report"] = workflow.reports_config
if workflow.creator_metadata:
data["creator"] = workflow.creator_metadata
if workflow.license:
data["license"] = workflow.license
if workflow.source_metadata:
data["source_metadata"] = workflow.source_metadata
# For each step, rebuild the form and encode the state
for step in workflow.steps:
# Load from database representation
module = module_factory.from_workflow_step(trans, step)
if not module:
raise exceptions.MessageException(f"Unrecognized step type: {step.type}")
# Get user annotation if it exists, otherwise get owner annotation.
annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ""
if not annotation_str and annotation_owner:
annotation_str = self.get_item_annotation_str(trans.sa_session, annotation_owner, step) or ""
content_id = module.get_content_id() if allow_upgrade else step.content_id
try:
tool_state = module.get_export_state()
except ValueError:
# Fix state if necessary
module.check_and_update_state()
tool_state = module.get_export_state()
# Step info
step_dict = {
"id": step.order_index,
"type": module.type,
"content_id": content_id,
"tool_id": None,
"tool_version": module.get_version() if allow_upgrade else step.tool_version,
"name": module.get_name(),
"tool_state": json.dumps(tool_state),
"errors": module.get_errors(),
"uuid": str(step.uuid),
"label": step.label or None,
"annotation": annotation_str,
"when": step.when_expression,
}
if step.type == "tool":
step_dict["tool_id"] = content_id if allow_upgrade else step.tool_id
# Add tool shed repository information and post-job actions to step dict.
if isinstance(module, ToolModule):
if module.tool and module.tool.tool_shed:
step_dict["tool_shed_repository"] = {
"name": module.tool.repository_name,
"owner": module.tool.repository_owner,
"changeset_revision": module.tool.changeset_revision,
"tool_shed": module.tool.tool_shed,
}
tool_representation = None
dynamic_tool = step.dynamic_tool
if dynamic_tool:
tool_representation = dynamic_tool.value
step_dict["tool_representation"] = tool_representation
if util.is_uuid(step_dict["content_id"]):
step_dict["content_id"] = None
step_dict["tool_id"] = None
pja_dict = {}
for pja in step.post_job_actions:
pja_dict[pja.action_type + pja.output_name] = dict(
action_type=pja.action_type, output_name=pja.output_name, action_arguments=pja.action_arguments
)
step_dict["post_job_actions"] = pja_dict
if module.type == "subworkflow" and not internal:
del step_dict["content_id"]
del step_dict["errors"]
del step_dict["tool_version"]
del step_dict["tool_state"]
subworkflow = step.subworkflow
subworkflow_as_dict = self._workflow_to_dict_export(trans, stored=None, workflow=subworkflow)
step_dict["subworkflow"] = subworkflow_as_dict
# Data inputs, legacy section not used anywhere within core
input_dicts = []
step_state = module.state.inputs or {}
if module.type != "tool":
name = step_state.get("name") or module.label
if name:
input_dicts.append({"name": name, "description": annotation_str})
for name, val in step_state.items():
if isinstance(val, RuntimeValue) and not isinstance(val, ConnectedValue):
input_dicts.append({"name": name, "description": f"runtime parameter for tool {module.get_name()}"})
elif isinstance(val, dict):
# Input type is described by a dict, e.g. indexed parameters.
for partval in val.values():
if isinstance(partval, RuntimeValue) and not isinstance(val, ConnectedValue):
input_dicts.append(
{"name": name, "description": f"runtime parameter for tool {module.get_name()}"}
)
step_dict["inputs"] = input_dicts
# User outputs
workflow_outputs_dicts = []
for workflow_output in step.unique_workflow_outputs:
workflow_output_dict = dict(
output_name=workflow_output.output_name,
label=workflow_output.label,
uuid=str(workflow_output.uuid) if workflow_output.uuid is not None else None,
)
workflow_outputs_dicts.append(workflow_output_dict)
step_dict["workflow_outputs"] = workflow_outputs_dicts
# All step outputs
step_dict["outputs"] = []
if type(module) is ToolModule:
for output in module.get_data_outputs():
step_dict["outputs"].append({"name": output["name"], "type": output["extensions"][0]})
step_in = {}
for step_input in step.inputs:
if step_input.default_value_set:
step_in[step_input.name] = {"default": step_input.default_value}
if step_in:
step_dict["in"] = step_in
# Connections
input_connections = step.input_connections
if isinstance(module, ToolModule):
# Determine full (prefixed) names of valid input datasets
data_input_names = {}
def callback(input, prefixed_name, **kwargs):
if isinstance(input, DataToolParameter) or isinstance(input, DataCollectionToolParameter):
data_input_names[prefixed_name] = True # noqa: B023
# FIXME: this updates modules silently right now; messages from updates should be provided.
module.check_and_update_state()
if module.tool:
# If the tool is installed we attempt to verify input values
# and connections, otherwise the last known state will be dumped without modifications.
visit_input_values(module.tool.inputs, module.state.inputs, callback)
# Encode input connections as dictionary
input_conn_dict: Dict[str, List[Dict[str, Any]]] = {}
unique_input_names = {conn.input_name for conn in input_connections}
for input_name in unique_input_names:
input_conn_dicts = []
for conn in input_connections:
if conn.input_name != input_name:
continue
input_conn = dict(id=conn.output_step.order_index, output_name=conn.output_name)
if conn.input_subworkflow_step is not None:
subworkflow_step_id = conn.input_subworkflow_step.order_index
input_conn["input_subworkflow_step_id"] = subworkflow_step_id
input_conn_dicts.append(input_conn)
input_conn_dict[input_name] = input_conn_dicts
# Preserve backward compatibility. Previously Galaxy
# assumed input connections would be dictionaries not
# lists of dictionaries, so replace any singleton list
# with just the dictionary so that workflows exported from
# newer Galaxy instances can be used with older Galaxy
# instances if they do no include multiple input
# tools. This should be removed at some point. Mirrored
# hack in _workflow_from_raw_description should never be removed so
# existing workflow exports continue to function.
back_compat_input_conn_dict: model.InputConnDictType = {}
for input_name, input_conn_list in dict(input_conn_dict).items():
if len(input_conn_list) == 1:
back_compat_input_conn_dict[input_name] = input_conn_list[0]
else:
back_compat_input_conn_dict[input_name] = input_conn_list
step_dict["input_connections"] = back_compat_input_conn_dict
# Position
step_dict["position"] = step.position
# Add to return value
steps[step.order_index] = step_dict
return data
def _workflow_to_dict_instance(self, trans, stored, workflow, legacy=True):
encode = self.app.security.encode_id
sa_session = self.app.model.context
item = stored.to_dict(view="element")
item["name"] = workflow.name
item["url"] = trans.url_builder("workflow", id=encode(stored.id))
item["owner"] = stored.user.username
item["email_hash"] = md5_hash_str(stored.user.email)
item["slug"] = stored.slug
inputs = {}
for step in workflow.input_steps:
step_type = step.type
step_label = step.label or step.tool_inputs and step.tool_inputs.get("name")
if step_label:
label = step_label
elif step_type == "data_input":
label = "Input Dataset"
elif step_type == "data_collection_input":
label = "Input Dataset Collection"
elif step_type == "parameter_input":
label = "Input Parameter"
else:
raise ValueError(f"Invalid step_type {step_type}")
if legacy:
index = step.id
else:
index = step.order_index
step_uuid = str(step.uuid) if step.uuid else None
inputs[index] = {"label": label, "value": "", "uuid": step_uuid}
item["inputs"] = inputs
item["annotation"] = self.get_item_annotation_str(sa_session, stored.user, stored)
item["license"] = workflow.license
item["creator"] = workflow.creator_metadata
item["source_metadata"] = workflow.source_metadata
steps = {}
steps_to_order_index = {}
for step in workflow.steps:
steps_to_order_index[step.id] = step.order_index
for step in workflow.steps:
step_id = step.id if legacy else step.order_index
step_type = step.type
step_dict = {
"id": step_id,
"type": step_type,
"tool_id": step.tool_id,
"tool_version": step.tool_version,
"annotation": self.get_item_annotation_str(sa_session, stored.user, step),
"tool_inputs": step.tool_inputs,
"input_steps": {},
"when": step.when_expression,
}
if step_type == "subworkflow":
del step_dict["tool_id"]
del step_dict["tool_version"]
del step_dict["tool_inputs"]
step_dict["workflow_id"] = step.subworkflow.id
for conn in step.input_connections:
step_id = step.id if legacy else step.order_index
source_id = conn.output_step_id
source_step = source_id if legacy else steps_to_order_index[source_id]
step_dict["input_steps"][conn.input_name] = {
"source_step": source_step,
"step_output": conn.output_name,
}
steps[step_id] = step_dict
item["steps"] = steps
return item
def __walk_step_dicts(self, data):
"""Walk over the supplied step dictionaries and return them in a way
designed to preserve step order when possible.
"""
supplied_steps = data["steps"]
# Try to iterate through imported workflow in such a way as to
# preserve step order.
step_indices = list(supplied_steps.keys())
try:
step_indices = sorted(step_indices, key=int)
except ValueError:
# to defensive, were these ever or will they ever not be integers?
pass
discovered_labels = set()
discovered_uuids = set()
discovered_output_labels = set()
discovered_output_uuids = set()
# First pass to build step objects and populate basic values
for step_index in step_indices:
step_dict = supplied_steps[step_index]
uuid = step_dict.get("uuid", None)
if uuid and uuid != "None":
if uuid in discovered_uuids:
raise exceptions.DuplicatedIdentifierException(f"Duplicate step UUID '{uuid}' in request.")
discovered_uuids.add(uuid)
label = step_dict.get("label", None)
if label:
if label in discovered_labels:
raise exceptions.DuplicatedIdentifierException(f"Duplicated step label '{label}' in request.")
discovered_labels.add(label)
if "workflow_outputs" in step_dict:
outputs = step_dict["workflow_outputs"]
# outputs may be list of name (deprecated legacy behavior)
# or dictionary of names to {uuid: <uuid>, label: <label>}
if isinstance(outputs, dict):
for output_name in outputs:
output_dict = outputs[output_name]
output_label = output_dict.get("label", None)
if output_label:
if label in discovered_output_labels:
raise exceptions.DuplicatedIdentifierException(
f"Duplicated workflow output label '{label}' in request."
)
discovered_output_labels.add(label)
output_uuid = step_dict.get("output_uuid", None)
if output_uuid:
if output_uuid in discovered_output_uuids:
raise exceptions.DuplicatedIdentifierException(
f"Duplicate workflow output UUID '{output_uuid}' in request."
)
discovered_output_uuids.add(uuid)
yield step_dict
def __load_subworkflows(
self, trans, step_dict, subworkflow_id_map, workflow_state_resolution_options, dry_run=False
):
step_type = step_dict.get("type", None)
if step_type == "subworkflow":
subworkflow = self.__load_subworkflow_from_step_dict(
trans, step_dict, subworkflow_id_map, workflow_state_resolution_options, dry_run=dry_run
)
step_dict["subworkflow"] = subworkflow
def __module_from_dict(
self,
trans,
steps: List[model.WorkflowStep],
steps_by_external_id: Dict[str, model.WorkflowStep],
step_dict,
**kwds,
) -> Tuple[WorkflowModule, model.WorkflowStep]:
"""Create a WorkflowStep model object and corresponding module
representing type-specific functionality from the incoming dictionary.
"""
dry_run = kwds.get("dry_run", False)
step = model.WorkflowStep()
step.position = step_dict.get("position", model.WorkflowStep.DEFAULT_POSITION)
if step_dict.get("uuid", None) and step_dict["uuid"] != "None":
step.uuid = step_dict["uuid"]
if "label" in step_dict:
step.label = step_dict["label"]
module = module_factory.from_dict(trans, step_dict, detached=dry_run, **kwds)
self.__set_default_label(step, module, step_dict.get("tool_state"))
module.save_to_step(step, detached=dry_run)
if annotation := step_dict.get("annotation"):
annotation = sanitize_html(annotation)
sa_session = None if dry_run else trans.sa_session
self.add_item_annotation(sa_session, trans.get_user(), step, annotation)
# Stick this in the step temporarily
DictConnection = Dict[str, Union[int, str]]
temp_input_connections: Dict[str, Union[List[DictConnection], DictConnection]] = step_dict.get(
"input_connections", {}
)
step.temp_input_connections = temp_input_connections # type: ignore[assignment]
# Create the model class for the step
steps.append(step)
external_id = step_dict["id"]
steps_by_external_id[external_id] = step
step.order_index = external_id
if "workflow_outputs" in step_dict:
workflow_outputs = step_dict["workflow_outputs"]
found_output_names = set()
for workflow_output in workflow_outputs:
# Allow workflow outputs as list of output_names for backward compatibility.
if not isinstance(workflow_output, dict):
workflow_output = {"output_name": workflow_output}
output_name = workflow_output["output_name"]
if output_name in found_output_names:
raise exceptions.ObjectAttributeInvalidException(
f"Duplicate workflow outputs with name [{output_name}] found."
)
if not output_name:
raise exceptions.ObjectAttributeInvalidException("Workflow output with empty name encountered.")
found_output_names.add(output_name)
uuid = workflow_output.get("uuid", None)
label = workflow_output.get("label", None)
m = step.create_or_update_workflow_output(
output_name=output_name,
uuid=uuid,
label=label,
)
if not dry_run:
trans.sa_session.add(m)
if "in" in step_dict:
for input_name, input_dict in step_dict["in"].items():
# This is just a bug in gxformat? I think the input
# defaults should be called input to match the input modules's
# input parameter name.
if input_name == "default":
input_name = "input"
step_input = step.get_or_add_input(input_name)
NO_DEFAULT_DEFINED = object()
default = input_dict.get("default", NO_DEFAULT_DEFINED)
if default is not NO_DEFAULT_DEFINED:
step_input.default_value = default
step_input.default_value_set = True
if "when" in step_dict:
step.when_expression = step_dict["when"]
if dry_run and step in trans.sa_session:
trans.sa_session.expunge(step)
return module, step
def __load_subworkflow_from_step_dict(
self, trans, step_dict, subworkflow_id_map, workflow_state_resolution_options, dry_run=False
):
embedded_subworkflow = step_dict.get("subworkflow", None)
subworkflow_id = step_dict.get("content_id", None)
if embedded_subworkflow and subworkflow_id:
raise exceptions.RequestParameterInvalidException(
"Subworkflow step defines both subworkflow and content_id, only one may be specified."
)
if not embedded_subworkflow and not subworkflow_id:
raise exceptions.RequestParameterInvalidException(
"Subworkflow step must define either subworkflow or content_id."
)
if embedded_subworkflow:
assert not dry_run
subworkflow = self.__build_embedded_subworkflow(
trans, embedded_subworkflow, workflow_state_resolution_options
)
elif subworkflow_id_map is not None:
assert not dry_run
# Interpret content_id as a workflow local thing.
subworkflow = subworkflow_id_map[subworkflow_id[1:]]
else:
subworkflow = self.app.workflow_manager.get_owned_workflow(trans, subworkflow_id)
return subworkflow
def __build_embedded_subworkflow(self, trans, data, workflow_state_resolution_options):
raw_workflow_description = self.ensure_raw_description(data)
subworkflow = self.build_workflow_from_raw_description(
trans,
raw_workflow_description,
workflow_state_resolution_options,
hidden=True,
is_subworkflow=True,
).workflow
return subworkflow
def __connect_workflow_steps(self, steps: List[model.WorkflowStep], steps_by_external_id, dry_run: bool) -> None:
"""Second pass to deal with connections between steps.
Create workflow connection objects using externally specified ids
using during creation or update.
"""
for step in steps:
# Input connections
if step.temp_input_connections: # populated by __module_from_dict
for input_name, conn_list in step.temp_input_connections.items(): # type:ignore[unreachable]
if not conn_list:
continue
if not isinstance(conn_list, list): # Older style singleton connection
conn_list = [conn_list]
for conn_dict in conn_list:
if "output_name" not in conn_dict or "id" not in conn_dict:
template = "Invalid connection [%s] - must be dict with output_name and id fields."
message = template % conn_dict
raise exceptions.MessageException(message)
external_id = conn_dict["id"]
if external_id not in steps_by_external_id:
raise KeyError(f"Failed to find external id {external_id} in {steps_by_external_id.keys()}")
output_step = steps_by_external_id[external_id]
output_name = conn_dict["output_name"]
input_subworkflow_step_index = conn_dict.get("input_subworkflow_step_id", None)
if dry_run:
input_subworkflow_step_index = None
step.add_connection(input_name, output_name, output_step, input_subworkflow_step_index)
step.temp_input_connections = None
def __set_default_label(self, step, module, state):
"""Previously data input modules had a `name` attribute to rename individual steps. Here, this value is transferred
to the actual `label` attribute which is available for all module types, unique, and mapped to its own database column.
"""
if not module.label and module.type in ["data_input", "data_collection_input"]:
new_state = safe_loads(state) or {}
default_label = new_state.get("name")
if default_label and util.unicodify(default_label).lower() not in [
"input dataset",
"input dataset collection",
]:
step.label = module.label = default_label
[docs] def do_refactor(self, trans, stored_workflow, refactor_request):
"""Apply supplied actions to stored_workflow.latest_workflow to build a new version."""
workflow = stored_workflow.latest_workflow
as_dict = self._workflow_to_dict_export(
trans, stored_workflow, workflow=workflow, internal=True, allow_upgrade=True
)
raw_workflow_description = self.normalize_workflow_format(trans, as_dict)
workflow_update_options = WorkflowUpdateOptions(
fill_defaults=False,
allow_missing_tools=True,
dry_run=refactor_request.dry_run,
)
module_injector = WorkflowModuleInjector(trans)
refactor_executor = WorkflowRefactorExecutor(raw_workflow_description, workflow, module_injector)
action_executions = refactor_executor.refactor(refactor_request)
refactored_workflow, errors = self.update_workflow_from_raw_description(
trans,
stored_workflow,
raw_workflow_description,
workflow_update_options,
)
# errors could be three things:
# - we allow missing tools so it won't be that.
# - might have cycles or might have state validation issues, but it still saved...
# so this is really more of a warning - we disregard it the other two places
# it is used also. These same messages will appear in the dictified version we
# we send back anyway
return refactored_workflow, action_executions
[docs] def refactor(self, trans, stored_workflow, refactor_request):
refactored_workflow, action_executions = self.do_refactor(trans, stored_workflow, refactor_request)
return RefactorResponse(
action_executions=action_executions,
workflow=self.workflow_to_dict(trans, refactored_workflow.stored_workflow, style=refactor_request.style),
dry_run=refactor_request.dry_run,
)
[docs] def get_all_tools(self, workflow):
tools = []
for step in workflow.steps:
if step.type == "tool":
if step.tool_id:
if {"tool_id": step.tool_id, "tool_version": step.tool_version} not in tools:
tools.append({"tool_id": step.tool_id, "tool_version": step.tool_version})
elif step.type == "subworkflow":
tools.extend(self.get_all_tools(step.subworkflow))
return tools
[docs] def get_or_create_workflow_from_trs(
self,
trans: ProvidesUserContext,
trs_url: Optional[str],
trs_id: Optional[str] = None,
trs_version: Optional[str] = None,
trs_server: Optional[str] = None,
):
user_id = trans.user and trans.user.id
assert user_id, "Cannot create workflow for anonymous user"
if not trs_url:
assert trs_server and trs_id and trs_version, "trs_url or trs_server, trs_version and trs_id must be passed"
server = self.trs_proxy.get_server(trs_server)
trs_url = server.get_trs_url(trs_id, trs_version)
else:
_, trs_id, trs_version = self.trs_proxy.get_trs_id_and_version_from_trs_url(trs_url=trs_url)
assert trs_id and trs_version and trs_url
workflow = self.get_workflow_by_trs_id_and_version(trs_id=trs_id, trs_version=trs_version, user_id=user_id)
if not workflow:
workflow = self.create_workflow_from_trs_url(trans, trs_url, trs_server)
return workflow
[docs] def create_workflow_from_trs_url(
self, trans: ProvidesUserContext, trs_url: str, trs_server: Optional[str] = None
) -> StoredWorkflow:
_, trs_tool_id, trs_version_id = self.trs_proxy.get_trs_id_and_version_from_trs_url(trs_url=trs_url)
data = self.trs_proxy.get_version_from_trs_url(trs_url)
as_dict = yaml.safe_load(data)
raw_workflow_description = self.normalize_workflow_format(trans, as_dict)
created_workflow = self.build_workflow_from_raw_description(
trans,
raw_workflow_description,
WorkflowCreateOptions(
trs_tool_id=trs_tool_id,
trs_version_id=trs_version_id,
trs_url=trs_url,
trs_server=trs_server,
archive_source="trs_url",
),
)
return created_workflow.stored_workflow
[docs] def get_workflow_by_trs_id_and_version(
self, trs_id: str, trs_version: str, user_id: Optional[int] = None
) -> Optional[model.StoredWorkflow]:
sa_session = self.app.model.session
def to_json(column, keys: List[str]):
assert sa_session.bind
if sa_session.bind.dialect.name == "postgresql":
cast: Union[ColumnElement[Any], Cast[Any]] = func.cast(func.convert_from(column, "UTF8"), JSONB)
for key in keys:
cast = cast.__getitem__(key)
return cast.astext
else:
for key in keys:
column = func.json_extract(column, f"$.{key}")
return column
stmnt = (
select(model.StoredWorkflow)
.join(model.Workflow, model.Workflow.id == model.StoredWorkflow.latest_workflow_id)
.filter(
and_(
to_json(model.Workflow.source_metadata, ["trs_tool_id"]) == trs_id,
to_json(model.Workflow.source_metadata, ["trs_version_id"]) == trs_version,
)
)
)
if user_id:
stmnt = stmnt.filter(
model.StoredWorkflow.user_id == user_id,
)
else:
stmnt = stmnt.filter(model.StoredWorkflow.importable == true())
return sa_session.execute(stmnt).scalar()
[docs]def safe_wraps(v: Any, nxt: SerializerFunctionWrapHandler) -> str:
try:
return nxt(v)
except Exception:
return safe_dumps(v)
[docs]class RefactorResponse(BaseModel):
action_executions: List[RefactorActionExecution]
workflow: Annotated[dict, WrapSerializer(safe_wraps, when_used="json")]
dry_run: bool
[docs]class WorkflowStateResolutionOptions(BaseModel):
# fill in default tool state when updating, may change tool_state
fill_defaults: bool = False
# If True, assume all tool state coming from generated form instead of potentially simpler json stored in DB/exported
from_tool_form: bool = False
# If False, allow running with less exact tool versions
exact_tools: bool = True
[docs]class WorkflowUpdateOptions(WorkflowStateResolutionOptions):
# Only used internally, don't set. If using the API assume updating the workflows
# representation with name or annotation for instance, updates the corresponding
# stored workflow
update_stored_workflow_attributes: bool = True
allow_missing_tools: bool = False
dry_run: bool = False
# Workflow update options but with some different defaults - we allow creating
# workflows with missing tools by default but not updating.
[docs]class WorkflowCreateOptions(WorkflowStateResolutionOptions):
import_tools: bool = False
publish: bool = False
# true or false, effectively defaults to ``publish`` if None/unset
importable: Optional[bool] = None
# following are install options, only used if import_tools is true
install_repository_dependencies: bool = False
install_resolver_dependencies: bool = False
install_tool_dependencies: bool = False
new_tool_panel_section_label: str = ""
tool_panel_section_id: str = ""
tool_panel_section_mapping: Dict = {}
shed_tool_conf: Optional[str] = None
# for workflows imported by archive source
archive_source: Optional[str] = None
trs_tool_id: Optional[str] = None
trs_version_id: Optional[str] = None
trs_server: Optional[str] = None
trs_url: Optional[str] = None
@property
def is_importable(self):
# if self.importable is None, use self.publish that has a default.
if self.importable is None:
return self.publish
else:
return self.importable
@property
def install_options(self):
return {
"install_repository_dependencies": self.install_repository_dependencies,
"install_resolver_dependencies": self.install_resolver_dependencies,
"install_tool_dependencies": self.install_tool_dependencies,
"new_tool_panel_section_label": self.new_tool_panel_section_label,
"tool_panel_section_id": self.tool_panel_section_id,
"tool_panel_section_mapping": self.tool_panel_section_mapping,
"shed_tool_conf": self.shed_tool_conf,
}
[docs]class RawWorkflowDescription:
[docs] def __init__(self, as_dict, workflow_path=None):
self.as_dict = as_dict
self.workflow_path = workflow_path
[docs]class Format2ConverterGalaxyInterface(ImporterGalaxyInterface):
[docs] def import_workflow(self, workflow, **kwds):
raise NotImplementedError(
"Direct format 2 import of nested workflows is not yet implemented, use bioblend client."
)
def _get_stored_workflow(session, workflow_uuid, workflow_id, by_stored_id):
stmt = select(StoredWorkflow)
if workflow_uuid is not None:
stmt = stmt.where(StoredWorkflow.id == Workflow.stored_workflow_id).where(Workflow.uuid == workflow_uuid)
else:
if by_stored_id:
stmt = stmt.where(StoredWorkflow.id == workflow_id)
else:
stmt = stmt.where(StoredWorkflow.id == Workflow.stored_workflow_id).where(Workflow.id == workflow_id)
stmt = stmt.options(
joinedload(StoredWorkflow.annotations),
joinedload(StoredWorkflow.tags),
subqueryload(StoredWorkflow.latest_workflow).joinedload(Workflow.steps).joinedload("*"),
).limit(1)
return session.scalars(stmt).first()
def _get_invocation(session, eager, invocation_id):
stmt = select(WorkflowInvocation)
if eager:
stmt = stmt.options(
subqueryload(WorkflowInvocation.steps)
.joinedload(WorkflowInvocationStep.implicit_collection_jobs)
.joinedload(ImplicitCollectionJobs.jobs)
.joinedload(ImplicitCollectionJobsJobAssociation.job)
.joinedload(Job.input_datasets)
)
stmt = stmt.where(WorkflowInvocation.id == invocation_id).limit(1)
return session.scalars(stmt).first()
[docs]def get_count(session, statement):
stmt = select(func.count()).select_from(statement.subquery())
return session.scalar(stmt)