def query_by_project_uuid(self, project_uuid, with_labels=True):
"""Query the analysis workflows by the HCA DCP Ingest submission project-UUID, which is essentially one of the
workflow labels.
Note, due to the open issue: https://github.com/broadinstitute/cromwell/issues/3115, if the result of workflows
are more than ~1000, this function will very likely raise an error. The `with_labels` is a flag controlling the
behavior of whether to query the workflows asking for the labels in the response, by default it's set to True,
so please set it to False if you don't want to risk getting error responses.
Args:
project_uuid (str): HCA DCP Ingest submission project-UUID.
with_labels (bool): Optional, whether to query the workflows asking for the labels in the response,
by default it's True
Returns:
List[Workflow]: A list of Workflow objects. E.g. [Workflow_1, ..., Workflow_100]
Raises:
requests.exceptions.HTTPError: When the request to Secondary-analysis service (Cromwell) failed.
"""
query_dict = {"label": {"project_uuid": project_uuid}}
if with_labels:
query_dict['additionalQueryResultFields'] = ['labels']
response = cwm_api.query(query_dict=query_dict, auth=self.auth)
response.raise_for_status()
result = response.json()
all_workflows = [Workflow(wf) for wf in result['results']]
return all_workflows
def query_by_bundle(self, bundle_uuid, bundle_version=None):
"""Query the analysis workflows by their workflow-UUID.
Note, due to the open issue: https://github.com/broadinstitute/cromwell/issues/3115, if the result of workflows
are more than ~1000, this function will very likely raise an error.
Args:
bundle_uuid (str): HCA DCP bundle UUID.
bundle_version (str): Optional, HCA DCP bundle version. By default, it's None.
Returns:
List[Workflow]: A list of Workflow objects. E.g. [Workflow_1, ..., Workflow_100]
Raises:
requests.exceptions.HTTPError: When the request to Secondary-analysis service (Cromwell) failed.
"""
query_dict = {
'label': {
'bundle-uuid': bundle_uuid
},
'additionalQueryResultFields': ['labels']
}
if bundle_version:
query_dict['label']['bundle-version'] = bundle_version
response = cwm_api.query(query_dict=query_dict, auth=self.auth)
response.raise_for_status()
result = response.json()
all_workflows = [Workflow(wf) for wf in result['results']]
return all_workflows
def query_by_workflow_uuid(self, uuid):
"""Query an analysis workflow by its workflow-UUID.
It is a one to one mapping between UUID and workflow in Secondary-analysis service (Cromwell), so the
result should always be a single workflow. The Workflow object returned by this function will look like an
object be loaded from the following dictionary:
{
"end": "2019-01-06T20:35:19.533Z",
"id": "aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeee",
"labels": {
"bundle-uuid": "aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeee",
"bundle-version": "2018-11-02T114842.872218Z",
"caas-collection-name": "xxxx-prod",
"cromwell-workflow-id": "cromwell-aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeee",
"project_shortname": "project name",
"project_uuid": "aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeee",
"workflow-name": "AdapterSmartSeq2SingleCell",
"workflow-version": "smartseq2_v2.1.0"
},
"name": "AdapterSmartSeq2SingleCell",
"start": "2019-01-06T20:18:18.102Z",
"status": "Succeeded",
"submission": "2019-01-06T20:16:30.804Z"
}
Args:
uuid (str): Secondary-analysis service (Cromwell) workflow UUID.
Returns:
Workflow: Workflow object.
Raises:
requests.exceptions.HTTPError: When the request to Secondary-analysis service (Cromwell) failed.
"""
query_dict = {
'id': uuid,
'additionalQueryResultFields': ['labels'],
'label': {
'caas-collection-name': self.cromwell_collection
}
}
response = cwm_api.query(query_dict=query_dict, auth=self.auth)
response.raise_for_status()
result = response.json()
all_workflows = result['results']
total_count = result['totalResultsCount']
assert len(all_workflows) == total_count == 1
return Workflow(all_workflows[0])