def invoke(self, trans, workflow_id, payload, **kwd):
"""
POST /api/workflows/{encoded_workflow_id}/invocations
Schedule the workflow specified by `workflow_id` to run.
"""
# /usage is awkward in this context but is consistent with the rest of
# this module. Would prefer to redo it all to use /invocation(s).
# Get workflow + accessibility check.
stored_workflow = self.__get_stored_accessible_workflow(
trans, workflow_id)
workflow = stored_workflow.latest_workflow
run_config = build_workflow_run_config(trans, workflow, payload)
workflow_scheduler_id = payload.get("scheduler", None)
# TODO: workflow scheduler hints
work_request_params = dict(scheduler=workflow_scheduler_id)
workflow_invocation = queue_invoke(trans=trans,
workflow=workflow,
workflow_run_config=run_config,
request_params=work_request_params)
return self.encode_all_ids(trans,
workflow_invocation.to_dict(),
recursive=True)
def invoke(self, trans, workflow_id, payload, **kwd):
"""
POST /api/workflows/{encoded_workflow_id}/invocations
Schedule the workflow specified by `workflow_id` to run.
"""
# /usage is awkward in this context but is consistent with the rest of
# this module. Would prefer to redo it all to use /invocation(s).
# Get workflow + accessibility check.
stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id)
workflow = stored_workflow.latest_workflow
run_config = build_workflow_run_config(trans, workflow, payload)
workflow_scheduler_id = payload.get("scheduler", None)
# TODO: workflow scheduler hints
work_request_params = dict(scheduler=workflow_scheduler_id)
workflow_invocation = queue_invoke(
trans=trans, workflow=workflow, workflow_run_config=run_config, request_params=work_request_params
)
return self.encode_all_ids(trans, workflow_invocation.to_dict(), recursive=True)
def create(self, trans, payload, **kwd):
"""
POST /api/workflows
Run or create workflows from the api.
If installed_repository_file or from_history_id is specified a new
workflow will be created for this user. Otherwise, workflow_id must be
specified and this API method will cause a workflow to execute.
:param installed_repository_file The path of a workflow to import. Either workflow_id, installed_repository_file or from_history_id must be specified
:type installed_repository_file str
:param workflow_id: An existing workflow id. Either workflow_id, installed_repository_file or from_history_id must be specified
:type workflow_id: str
:param parameters: If workflow_id is set - see _update_step_parameters()
:type parameters: dict
:param ds_map: If workflow_id is set - a dictionary mapping each input step id to a dictionary with 2 keys: 'src' (which can be 'ldda', 'ld' or 'hda') and 'id' (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively)
:type ds_map: dict
:param no_add_to_history: If workflow_id is set - if present in the payload with any value, the input datasets will not be added to the selected history
:type no_add_to_history: str
:param history: If workflow_id is set - optional history where to run the workflow, either the name of a new history or "hist_id=HIST_ID" where HIST_ID is the id of an existing history. If not specified, the workflow will be run a new unnamed history
:type history: str
:param replacement_params: If workflow_id is set - an optional dictionary used when renaming datasets
:type replacement_params: dict
:param from_history_id: Id of history to extract a workflow from. Either workflow_id, installed_repository_file or from_history_id must be specified
:type from_history_id: str
:param job_ids: If from_history_id is set - optional list of jobs to include when extracting a workflow from history
:type job_ids: str
:param dataset_ids: If from_history_id is set - optional list of HDA `hid`s corresponding to workflow inputs when extracting a workflow from history
:type dataset_ids: str
:param dataset_collection_ids: If from_history_id is set - optional list of HDCA `hid`s corresponding to workflow inputs when extracting a workflow from history
:type dataset_collection_ids: str
:param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history
:type workflow_name: str
:param allow_tool_state_corrections: If set to True, any Tool parameter changes will not prevent running workflow, defaults to False
:type allow_tool_state_corrections: bool
"""
ways_to_create = set([
'workflow_id',
'installed_repository_file',
'from_history_id',
'shared_workflow_id',
'workflow',
]).intersection(payload)
if len(ways_to_create) == 0:
message = "One parameter among - %s - must be specified" % ", ".join(
ways_to_create)
raise exceptions.RequestParameterMissingException(message)
if len(ways_to_create) > 1:
message = "Only one parameter among - %s - must be specified" % ", ".join(
ways_to_create)
raise exceptions.RequestParameterInvalidException(message)
if 'installed_repository_file' in payload:
workflow_controller = trans.webapp.controllers['workflow']
result = workflow_controller.import_workflow(trans=trans,
cntrller='api',
**payload)
return result
if 'from_history_id' in payload:
from_history_id = payload.get('from_history_id')
from_history_id = self.decode_id(from_history_id)
history = self.history_manager.get_accessible(
from_history_id, trans.user, current_history=trans.history)
job_ids = map(self.decode_id, payload.get('job_ids', []))
dataset_ids = payload.get('dataset_ids', [])
dataset_collection_ids = payload.get('dataset_collection_ids', [])
workflow_name = payload['workflow_name']
stored_workflow = extract_workflow(
trans=trans,
user=trans.get_user(),
history=history,
job_ids=job_ids,
dataset_ids=dataset_ids,
dataset_collection_ids=dataset_collection_ids,
workflow_name=workflow_name,
)
item = stored_workflow.to_dict(
value_mapper={'id': trans.security.encode_id})
item['url'] = url_for('workflow', id=item['id'])
return item
if 'shared_workflow_id' in payload:
workflow_id = payload['shared_workflow_id']
return self.__api_import_shared_workflow(trans, workflow_id,
payload)
if 'workflow' in payload:
return self.__api_import_new_workflow(trans, payload, **kwd)
workflow_id = payload.get('workflow_id', None)
if not workflow_id:
message = "Invalid workflow_id specified."
raise exceptions.RequestParameterInvalidException(message)
# Get workflow + accessibility check.
stored_workflow = self.__get_stored_accessible_workflow(
trans, workflow_id)
workflow = stored_workflow.latest_workflow
run_config = build_workflow_run_config(trans, workflow, payload)
history = run_config.target_history
# invoke may throw MessageExceptions on tool erors, failure
# to match up inputs, etc...
outputs, invocation = invoke(
trans=trans,
workflow=workflow,
workflow_run_config=run_config,
populate_state=True,
)
trans.sa_session.flush()
# Build legacy output - should probably include more information from
# outputs.
rval = {}
rval['history'] = trans.security.encode_id(history.id)
rval['outputs'] = []
for step in workflow.steps:
if step.type == 'tool' or step.type is None:
for v in outputs[step.id].itervalues():
rval['outputs'].append(trans.security.encode_id(v.id))
# Newer version of this API just returns the invocation as a dict, to
# facilitate migration - produce the newer style response and blend in
# the older information.
invocation_response = self.__encode_invocation(trans,
invocation,
step_details=kwd.get(
'step_details',
False))
invocation_response.update(rval)
return invocation_response
def create(self, trans, payload, **kwd):
"""
POST /api/workflows
Run or create workflows from the api.
If installed_repository_file or from_history_id is specified a new
workflow will be created for this user. Otherwise, workflow_id must be
specified and this API method will cause a workflow to execute.
:param installed_repository_file The path of a workflow to import. Either workflow_id, installed_repository_file or from_history_id must be specified
:type installed_repository_file str
:param workflow_id: An existing workflow id. Either workflow_id, installed_repository_file or from_history_id must be specified
:type workflow_id: str
:param parameters: If workflow_id is set - see _update_step_parameters()
:type parameters: dict
:param ds_map: If workflow_id is set - a dictionary mapping each input step id to a dictionary with 2 keys: 'src' (which can be 'ldda', 'ld' or 'hda') and 'id' (which should be the id of a LibraryDatasetDatasetAssociation, LibraryDataset or HistoryDatasetAssociation respectively)
:type ds_map: dict
:param no_add_to_history: If workflow_id is set - if present in the payload with any value, the input datasets will not be added to the selected history
:type no_add_to_history: str
:param history: If workflow_id is set - optional history where to run the workflow, either the name of a new history or "hist_id=HIST_ID" where HIST_ID is the id of an existing history. If not specified, the workflow will be run a new unnamed history
:type history: str
:param replacement_params: If workflow_id is set - an optional dictionary used when renaming datasets
:type replacement_params: dict
:param from_history_id: Id of history to extract a workflow from. Either workflow_id, installed_repository_file or from_history_id must be specified
:type from_history_id: str
:param job_ids: If from_history_id is set - optional list of jobs to include when extracting a workflow from history
:type job_ids: str
:param dataset_ids: If from_history_id is set - optional list of HDA `hid`s corresponding to workflow inputs when extracting a workflow from history
:type dataset_ids: str
:param dataset_collection_ids: If from_history_id is set - optional list of HDCA `hid`s corresponding to workflow inputs when extracting a workflow from history
:type dataset_collection_ids: str
:param workflow_name: If from_history_id is set - name of the workflow to create when extracting a workflow from history
:type workflow_name: str
"""
ways_to_create = set(
["workflow_id", "installed_repository_file", "from_history_id", "shared_workflow_id", "workflow"]
).intersection(payload)
if len(ways_to_create) == 0:
message = "One parameter among - %s - must be specified" % ", ".join(ways_to_create)
raise exceptions.RequestParameterMissingException(message)
if len(ways_to_create) > 1:
message = "Only one parameter among - %s - must be specified" % ", ".join(ways_to_create)
raise exceptions.RequestParameterInvalidException(message)
if "installed_repository_file" in payload:
workflow_controller = trans.webapp.controllers["workflow"]
result = workflow_controller.import_workflow(trans=trans, cntrller="api", **payload)
return result
if "from_history_id" in payload:
from_history_id = payload.get("from_history_id")
from_history_id = self.decode_id(from_history_id)
history = self.history_manager.get_accessible(from_history_id, trans.user, current_history=trans.history)
job_ids = map(self.decode_id, payload.get("job_ids", []))
dataset_ids = payload.get("dataset_ids", [])
dataset_collection_ids = payload.get("dataset_collection_ids", [])
workflow_name = payload["workflow_name"]
stored_workflow = extract_workflow(
trans=trans,
user=trans.get_user(),
history=history,
job_ids=job_ids,
dataset_ids=dataset_ids,
dataset_collection_ids=dataset_collection_ids,
workflow_name=workflow_name,
)
item = stored_workflow.to_dict(value_mapper={"id": trans.security.encode_id})
item["url"] = url_for("workflow", id=item["id"])
return item
if "shared_workflow_id" in payload:
workflow_id = payload["shared_workflow_id"]
return self.__api_import_shared_workflow(trans, workflow_id, payload)
if "workflow" in payload:
return self.__api_import_new_workflow(trans, payload, **kwd)
workflow_id = payload.get("workflow_id", None)
if not workflow_id:
message = "Invalid workflow_id specified."
raise exceptions.RequestParameterInvalidException(message)
# Get workflow + accessibility check.
stored_workflow = self.__get_stored_accessible_workflow(trans, workflow_id)
workflow = stored_workflow.latest_workflow
run_config = build_workflow_run_config(trans, workflow, payload)
history = run_config.target_history
# invoke may throw MessageExceptions on tool erors, failure
# to match up inputs, etc...
outputs, invocation = invoke(
trans=trans, workflow=workflow, workflow_run_config=run_config, populate_state=True
)
trans.sa_session.flush()
# Build legacy output - should probably include more information from
# outputs.
rval = {}
rval["history"] = trans.security.encode_id(history.id)
rval["outputs"] = []
for step in workflow.steps:
if step.type == "tool" or step.type is None:
for v in outputs[step.id].itervalues():
rval["outputs"].append(trans.security.encode_id(v.id))
# Newer version of this API just returns the invocation as a dict, to
# facilitate migration - produce the newer style response and blend in
# the older information.
invocation_response = self.__encode_invocation(trans, invocation)
invocation_response.update(rval)
return invocation_response
