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Source code for galaxy.managers.workflows
from __future__ import absolute_import
import json
import logging
import uuid
from collections import namedtuple
from six import string_types
from sqlalchemy import and_
from sqlalchemy.orm import joinedload, subqueryload
from galaxy import (
exceptions,
model,
util
)
from galaxy.jobs.actions.post import ActionBox
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.tools.parameters import (
params_to_incoming,
visit_input_values
)
from galaxy.tools.parameters.basic import (
DataCollectionToolParameter,
DataToolParameter,
RuntimeValue,
workflow_building_modes
)
from galaxy.util.json import safe_loads
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import url_for
from galaxy.workflow import modules
from galaxy.workflow.modules import (
is_tool_module_type,
module_factory,
ToolModule,
WorkflowModuleInjector
)
from galaxy.workflow.resources import get_resource_mapper_function
from galaxy.workflow.steps import attach_ordered_steps
from .base import decode_id
log = logging.getLogger(__name__)
[docs]class WorkflowsManager(object):
""" Handle CRUD type operations related to workflows. More interesting
stuff regarding workflow execution, step sorting, etc... can be found in
the galaxy.workflow module.
"""
[docs] def get_stored_workflow(self, trans, workflow_id):
""" Use a supplied ID (UUID or encoded stored workflow ID) to find
a workflow.
"""
if util.is_uuid(workflow_id):
# see if they have passed in the UUID for a workflow that is attached to a stored workflow
workflow_uuid = uuid.UUID(workflow_id)
workflow_query = trans.sa_session.query(trans.app.model.StoredWorkflow).filter(and_(
trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id,
trans.app.model.Workflow.uuid == workflow_uuid
))
else:
workflow_id = decode_id(self.app, workflow_id)
workflow_query = trans.sa_session.query(trans.app.model.StoredWorkflow).\
filter(trans.app.model.StoredWorkflow.id == workflow_id)
stored_workflow = workflow_query.options(joinedload('annotations'),
joinedload('tags'),
subqueryload('latest_workflow').joinedload('steps').joinedload('*')).first()
if stored_workflow is None:
raise exceptions.ObjectNotFound("No such workflow found.")
return stored_workflow
[docs] def get_stored_accessible_workflow(self, trans, workflow_id):
""" 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)
# 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.published:
if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
message = "Workflow is not owned by or shared with current user"
raise exceptions.ItemAccessibilityException(message)
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.query(model.Workflow).get(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 the owner of the history that is associated to the invocation as a proxy
# for the owner of the invocation.
if trans.user != has_workflow.history.user and not trans.user_is_admin():
raise exceptions.ItemOwnershipException()
else:
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...
if trans.sa_session.query(model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
raise exceptions.ItemAccessibilityException()
return True
[docs] def get_invocation(self, trans, decoded_invocation_id):
workflow_invocation = trans.sa_session.query(
self.app.model.WorkflowInvocation
).get(decoded_invocation_id)
if not workflow_invocation:
encoded_wfi_id = trans.security.encode_id(decoded_invocation_id)
message = "'%s' is not a valid workflow invocation id" % encoded_wfi_id
raise exceptions.ObjectNotFound(message)
self.check_security(trans, workflow_invocation, check_ownership=True, check_accessible=False)
return workflow_invocation
[docs] def cancel_invocation(self, trans, decoded_invocation_id):
workflow_invocation = self.get_invocation(trans, decoded_invocation_id)
cancelled = workflow_invocation.cancel()
if cancelled:
trans.sa_session.add(workflow_invocation)
trans.sa_session.flush()
else:
# TODO: More specific exception?
raise exceptions.MessageException("Cannot cancel an inactive workflow invocation.")
return workflow_invocation
[docs] def get_invocation_step(self, trans, decoded_workflow_invocation_step_id):
try:
workflow_invocation_step = trans.sa_session.query(
model.WorkflowInvocationStep
).get(decoded_workflow_invocation_step_id)
except Exception:
raise exceptions.ObjectNotFound()
self.check_security(trans, workflow_invocation_step.workflow_invocation, check_ownership=True, check_accessible=False)
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 an completed workflow invocation.")
step = workflow_invocation_step.workflow_step
module = modules.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)
trans.sa_session.flush()
return workflow_invocation_step
[docs] def build_invocations_query(self, trans, decoded_stored_workflow_id):
"""Get invocations owned by the current user."""
stored_workflow = trans.sa_session.query(
self.app.model.StoredWorkflow
).get(decoded_stored_workflow_id)
if not stored_workflow:
raise exceptions.ObjectNotFound()
invocations = trans.sa_session.query(
model.WorkflowInvocation
).filter_by(
workflow_id=stored_workflow.latest_workflow_id
)
return [inv for inv in invocations if self.check_security(trans,
inv,
check_ownership=True,
check_accessible=False)]
CreatedWorkflow = namedtuple("CreatedWorkflow", ["stored_workflow", "workflow", "missing_tools"])
[docs]class WorkflowContentsManager(UsesAnnotations):
[docs] def __init__(self, app):
self.app = app
self._resource_mapper_function = get_resource_mapper_function(app)
[docs] def build_workflow_from_dict(
self,
trans,
data,
source=None,
add_to_menu=False,
publish=False,
create_stored_workflow=True,
exact_tools=True,
):
# 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 source:
name = "%s (imported from %s)" % (data['name'], source)
else:
name = data['name']
workflow, missing_tool_tups = self._workflow_from_dict(
trans,
data,
name=name,
exact_tools=exact_tools,
)
if 'uuid' in data:
workflow.uuid = data['uuid']
if create_stored_workflow:
# Connect up
stored = model.StoredWorkflow()
stored.name = workflow.name
workflow.stored_workflow = stored
stored.latest_workflow = workflow
stored.user = trans.user
stored.published = publish
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.app.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)
else:
stored = None
# Persist
trans.sa_session.add(workflow)
trans.sa_session.flush()
return CreatedWorkflow(
stored_workflow=stored,
workflow=workflow,
missing_tools=missing_tool_tups
)
[docs] def update_workflow_from_dict(self, trans, stored_workflow, workflow_data):
# Put parameters in workflow mode
trans.workflow_building_mode = workflow_building_modes.ENABLED
workflow, missing_tool_tups = self._workflow_from_dict(
trans,
workflow_data,
name=stored_workflow.name,
)
if missing_tool_tups:
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
workflow.stored_workflow = stored_workflow
stored_workflow.latest_workflow = workflow
# Persist
trans.sa_session.flush()
# 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_dict(self, trans, data, name, **kwds):
if isinstance(data, string_types):
data = json.loads(data)
# Create new workflow from source data
workflow = model.Workflow()
workflow.name = name
# Assume no errors until we find a step that has some
workflow.has_errors = False
# Create each step
steps = []
# 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 = {}
# 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 ).
missing_tool_tups = []
for step_dict in self.__walk_step_dicts(data):
self.__load_subworkflows(trans, step_dict)
for step_dict in self.__walk_step_dicts(data):
module, step = self.__module_from_dict(trans, steps, steps_by_external_id, step_dict, **kwds)
is_tool = is_tool_module_type(module.type)
if is_tool 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)
# Order the steps if possible
attach_ordered_steps(workflow, steps)
return workflow, missing_tool_tups
[docs] def workflow_to_dict(self, trans, stored, style="export"):
""" 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 it best to preserve the backward compatibility of the
'export' stye - 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'.
"""
if style == "editor":
return self._workflow_to_dict_editor(trans, stored)
elif style == "legacy":
return self._workflow_to_dict_instance(stored, legacy=True)
elif style == "instance":
return self._workflow_to_dict_instance(stored, legacy=False)
elif style == "run":
return self._workflow_to_dict_run(trans, stored)
else:
return self._workflow_to_dict_export(trans, stored)
def _workflow_to_dict_run(self, trans, stored):
"""
Builds workflow dictionary used by run workflow form
"""
workflow = stored.latest_workflow
if len(workflow.steps) == 0:
raise exceptions.MessageException('Workflow cannot be run because it does not have any steps.')
if attach_ordered_steps(workflow, workflow.steps):
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 = {}
for step in workflow.steps:
try:
module_injector.inject(step, steps=workflow.steps, exact_tools=False)
except exceptions.ToolMissingException:
if step.tool_id not in missing_tools:
missing_tools.append(step.tool_id)
continue
if step.upgrade_messages:
has_upgrade_messages = True
if step.type == 'tool' or step.type is 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('Following tools missing: %s' % ', '.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 i, step in enumerate(workflow.steps):
step_model = None
if step.type == 'tool':
incoming = {}
tool = trans.app.toolbox.get_tool(step.tool_id, tool_version=step.tool_version)
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)
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(connections=step.output_connections)
step_model = {
'inputs' : [input.to_dict(trans) for input in inputs.values()]
}
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),
'history_id': trans.app.security.encode_id(trans.history.id) if trans.history else None,
'name': stored.name,
'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_resource_parameters(self, trans, stored, workflow):
"""Get workflow scheduling resource parameters for this user and workflow or None if unconfigured.
"""
return self._resource_mapper_function(trans=trans, stored_workflow=stored, workflow=workflow)
def _workflow_to_dict_editor(self, trans, stored):
workflow = stored.latest_workflow
# Pack workflow data into a dictionary and return
data = {}
data['name'] = workflow.name
data['steps'] = {}
data['upgrade_messages'] = {}
# 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('Unrecognized step type: %s' % 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 = module.check_and_update_state()
if upgrade_message:
data['upgrade_messages'][step.order_index] = upgrade_message
if (hasattr(module, "version_changes")) and (module.version_changes):
if step.order_index in data['upgrade_messages']:
data['upgrade_messages'][step.order_index][module.tool.name] = "\n".join(module.version_changes)
else:
data['upgrade_messages'][step.order_index] = {module.tool.name: "\n".join(module.version_changes)}
# Get user annotation.
annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ''
config_form = module.get_config_form()
# 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_state(),
'tooltip': module.get_tooltip(static_path=url_for('/static')),
'errors': module.get_errors(),
'data_inputs': module.get_data_inputs(),
'data_outputs': module.get_data_outputs(),
'config_form': config_form,
'annotation': annotation_str,
'post_job_actions': {},
'uuid': str(step.uuid) if step.uuid else None,
'workflow_outputs': []
}
# Connections
input_connections = step.input_connections
input_connections_type = {}
multiple_input = {} # Boolean value indicating if this can be mutliple
if (step.type is None or step.type == 'tool') and module.tool:
# 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
multiple_input[prefixed_name] = input.multiple
if isinstance(input, DataToolParameter):
input_connections_type[input.name] = "dataset"
if isinstance(input, DataCollectionToolParameter):
input_connections_type[input.name] = "dataset_collection"
visit_input_values(module.tool.inputs, module.state.inputs, callback)
# Filter
# FIXME: this removes connection without displaying a message currently!
input_connections = [conn for conn in input_connections if conn.input_name in data_input_names]
# 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 = []
for output in step.unique_workflow_outputs:
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})
step_dict['workflow_outputs'] = outputs
# Encode input connections as dictionary
input_conn_dict = {}
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:
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
return data
def _workflow_to_dict_export(self, trans, stored=None, workflow=None):
""" Export the workflow contents to a dictionary ready for JSON-ification and export.
"""
if workflow is None:
assert stored is not None
workflow = stored.latest_workflow
annotation_str = ""
tag_str = ""
if stored is not None:
annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, stored) or ''
tag_str = stored.make_tag_string_list()
# Pack workflow data into a dictionary and return
data = {}
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'] = tag_str
if workflow.uuid is not None:
data['uuid'] = str(workflow.uuid)
data['steps'] = {}
# 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('Unrecognized step type: %s' % step.type)
# Get user annotation.
annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ''
content_id = module.get_content_id()
# Export differences for backward compatibility
if module.type == 'tool':
tool_state = module.get_state(nested=False)
else:
tool_state = module.state.inputs
# Step info
step_dict = {
'id': step.order_index,
'type': module.type,
'content_id': content_id,
'tool_id': content_id, # For worklfows exported to older Galaxies,
# eliminate after a few years...
'tool_version': 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
}
# Add tool shed repository information and post-job actions to step dict.
if module.type == 'tool':
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
}
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':
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 "name" in step_state and module.type != 'tool':
name = step_state.get("name")
input_dicts.append({"name": name, "description": annotation_str})
for name, val in step_state.items():
input_type = type(val)
if input_type == RuntimeValue:
input_dicts.append({"name": name, "description": "runtime parameter for tool %s" % module.get_name()})
elif input_type == dict:
# Input type is described by a dict, e.g. indexed parameters.
for partval in val.values():
if type(partval) == RuntimeValue:
input_dicts.append({"name": name, "description": "runtime parameter for tool %s" % 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]})
# Connections
input_connections = step.input_connections
if step.type is None or step.type == 'tool':
# 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
# 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)
# FIXME: this removes connection without displaying a message currently!
input_connections = [conn for conn in input_connections if (conn.input_name in data_input_names or conn.non_data_connection)]
# Encode input connections as dictionary
input_conn_dict = {}
unique_input_names = set([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 compatability. 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_dict should never be removed so
# existing workflow exports continue to function.
for input_name, input_conn in dict(input_conn_dict).items():
if len(input_conn) == 1:
input_conn_dict[input_name] = input_conn[0]
step_dict['input_connections'] = input_conn_dict
# Position
step_dict['position'] = step.position
# Add to return value
data['steps'][step.order_index] = step_dict
return data
def _workflow_to_dict_instance(self, stored, legacy=True):
encode = self.app.security.encode_id
sa_session = self.app.model.context
item = stored.to_dict(view='element', value_mapper={'id': encode})
workflow = stored.latest_workflow
item['url'] = url_for('workflow', id=item['id'])
item['owner'] = stored.user.username
inputs = {}
for step in workflow.input_steps:
step_type = step.type
step_label = step.label or 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"
else:
raise ValueError("Invalid step_type %s" % 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)
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': {}}
if step_type == 'subworkflow':
del step_dict['tool_id']
del step_dict['tool_version']
del step_dict['tool_inputs']
step_dict['workflow_id'] = encode(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 supplid 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("Duplicate step UUID in request.")
discovered_uuids.add(uuid)
label = step_dict.get("label", None)
if label:
if label in discovered_labels:
raise exceptions.DuplicatedIdentifierException("Duplicated step 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("Duplicated workflow output 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("Duplicate workflow output UUID in request.")
discovered_output_uuids.add(uuid)
yield step_dict
def __load_subworkflows(self, trans, step_dict):
step_type = step_dict.get("type", None)
if step_type == "subworkflow":
subworkflow = self.__load_subworkflow_from_step_dict(
trans, step_dict
)
step_dict["subworkflow"] = subworkflow
def __module_from_dict(self, trans, steps, steps_by_external_id, step_dict, **kwds):
""" Create a WorkflowStep model object and corresponding module
representing type-specific functionality from the incoming dictionary.
"""
step = model.WorkflowStep()
# TODO: Consider handling position inside module.
step.position = step_dict['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, **kwds)
self.__set_default_label(step, module, step_dict.get('tool_state'))
module.save_to_step(step)
annotation = step_dict['annotation']
if annotation:
annotation = sanitize_html(annotation)
self.add_item_annotation(trans.sa_session, trans.get_user(), step, annotation)
# Stick this in the step temporarily
step.temp_input_connections = step_dict['input_connections']
# Create the model class for the step
steps.append(step)
steps_by_external_id[step_dict['id']] = step
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 compatiblity.
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("Duplicate workflow outputs with name [%s] found." % output_name)
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,
)
trans.sa_session.add(m)
return module, step
def __load_subworkflow_from_step_dict(self, trans, step_dict):
embedded_subworkflow = step_dict.get("subworkflow", None)
subworkflow_id = step_dict.get("content_id", None)
if embedded_subworkflow and subworkflow_id:
raise Exception("Subworkflow step defines both subworkflow and content_id, only one may be specified.")
if not embedded_subworkflow and not subworkflow_id:
raise Exception("Subworkflow step must define either subworkflow or content_id.")
if embedded_subworkflow:
subworkflow = self.build_workflow_from_dict(
trans,
embedded_subworkflow,
create_stored_workflow=False,
).workflow
else:
workflow_manager = WorkflowsManager(self.app)
subworkflow = workflow_manager.get_owned_workflow(
trans, subworkflow_id
)
return subworkflow
def __connect_workflow_steps(self, steps, steps_by_external_id):
""" 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
for input_name, conn_list in step.temp_input_connections.items():
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)
conn = model.WorkflowStepConnection()
conn.input_step = step
conn.input_name = input_name
conn.output_name = conn_dict['output_name']
conn.output_step = steps_by_external_id[conn_dict['id']]
input_subworkflow_step_index = conn_dict.get('input_subworkflow_step_id', None)
if input_subworkflow_step_index is not None:
conn.input_subworkflow_step = step.subworkflow.step_by_index(input_subworkflow_step_index)
del step.temp_input_connections
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)
default_label = new_state.get('name')
if str(default_label).lower() not in ['input dataset', 'input dataset collection']:
step.label = module.label = default_label