def generate_entity_redaction(project_uuid: str,
ingest_url: str) -> 'EntityRedaction':
ingest_client = IngestApi(ingest_url)
project = ingest_client.get_project_by_uuid(project_uuid)
submission_for_project = list(
ingest_client.get_related_entities("submissionEnvelopes", project,
"submissionEnvelopes"))[0]
submissions_for_project = EntityMap.from_list([submission_for_project])
files = list(
ingest_client.get_related_entities("files", submission_for_project,
"files"))
supplementary_files = EntityMap.from_list([
f for f in files
if "supplementary_file" in f["content"]["describedBy"]
])
sequence_files = EntityMap.from_list([
f for f in files if "sequence_file" in f["content"]["describedBy"]
])
assert len(supplementary_files) + len(sequence_files) == len(files)
biomaterials = EntityMap.from_list(
ingest_client.get_related_entities("biomaterials",
submission_for_project,
"biomaterials"))
processes = EntityMap.from_list(
ingest_client.get_related_entities("processes",
submission_for_project,
"processes"))
protocols = EntityMap.from_list(
ingest_client.get_related_entities("protocols",
submission_for_project,
"protocols"))
projects = EntityMap.from_list(
ingest_client.get_related_entities("projects",
submission_for_project,
"projects"))
primary_bundle_manifests = EntityMap.from_list(
ingest_client.get_related_entities("bundleManifests",
submission_for_project,
"bundleManifests"),
["bundleUuid"])
analysis_processes = EntityMap()
analysis_protocols = EntityMap()
analysis_files = EntityMap()
analysis_submissions = EntityMap()
analysis_bundle_manifests = EntityMap()
for file in sequence_files:
input_to_processes = ingest_client.get_related_entities(
"inputToProcesses", file, "processes")
for analysis_process in input_to_processes:
analysis_processes.add([analysis_process])
analysis_protocols.add(
ingest_client.get_related_entities("protocols",
analysis_process,
"protocols"))
analysis_files.add(
ingest_client.get_related_entities("derivedFiles",
analysis_process,
"files"))
analysis_submission = list(
ingest_client.get_related_entities(
"submissionEnvelopes", analysis_process,
"submissionEnvelopes"))[0]
analysis_submissions.add([analysis_submission])
analysis_bundle_manifests.add(
ingest_client.get_related_entities("bundleManifests",
analysis_submission,
"bundleManifests"),
["bundleUuid"])
assert len(projects.uuids()) == 1
return EntityRedaction(sequence_files, supplementary_files,
biomaterials, processes, protocols, projects,
primary_bundle_manifests,
submissions_for_project, analysis_processes,
analysis_protocols, analysis_files,
analysis_bundle_manifests, analysis_submissions)
description='Generates a bundle fqid list given a project uuid')
parser.add_argument('env',
choices=['dev', 'integration', 'staging', 'prod'],
help='environment')
parser.add_argument('project_uuid',
metavar='project-uuid',
type=str,
help='Project uuid')
parser.add_argument('--filename', type=str, help='Output filename')
args = parser.parse_args()
project_uuid = args.project_uuid
filename = args.filename or f'{args.project_uuid}.json'
env = args.env
infix = f'.{env}' if env != 'prod' else ''
url = f'https://api.ingest{infix}.data.humancellatlas.org'
ingest_api = IngestApi(url)
project = ingest_api.get_project_by_uuid(project_uuid)
bundle_manifests = ingest_api.get_related_entities("bundleManifests",
project,
"bundleManifests")
bundle_fqids = [BundleManifest(obj).fqid for obj in bundle_manifests]
with open(filename, 'w') as outfile:
json.dump(bundle_fqids, outfile, indent=4)
print(f'Total bundle count: {len(bundle_fqids)}')
print(f'Saved into file: {filename}')
