def login(parsed_args,
manager=None,
dry_run=False,
api_base=None,
verbose=False):
"""
Login to authorize credentials.
:param manager: API Manager
:param dry_run: If true, will do a dry run with no actual execution of functionality.
:return:
"""
if manager is None:
manager = scp_api.SCPAPIManager(verbose=verbose)
if parsed_args.user_agent:
user_agent = get_user_agent()
manager.login(
token=parsed_args.token,
dry_run=dry_run,
api_base=api_base,
user_agent=user_agent,
)
else:
manager.login(token=parsed_args.token,
dry_run=dry_run,
api_base=api_base)
return manager
def test_get_studies(self, mock_get):
studies = scp_api.SCPAPIManager().get_studies()['studies']
expected_studies = [
" Single nucleus RNA-seq of cell diversity in the adult mouse hippocampus (sNuc-Seq)",
"Study only for unit test"
]
self.assertEqual(studies, expected_studies)
def test_get_studies(self, mock_get):
manager = scp_api.SCPAPIManager()
manager.api_base = 'https://portals.broadinstitute.org/single_cell/api/v1/'
manager.verify_https = True
studies = manager.get_studies()['studies']
expected_studies = [
" Single nucleus RNA-seq of cell diversity in the adult mouse hippocampus (sNuc-Seq)",
"Study only for unit test"
]
self.assertEqual(studies, expected_studies)
def test_get_studies(self, mocked_requests_get):
manager = scp_api.SCPAPIManager()
manager.api_base = "https://singlecell.broadinstitute.org/single_cell/api/v1/"
manager.verify_https = True
manager.head = {"Accept": "application/json"}
studies = manager.get_studies()["studies"]
expected_studies = [
" Single nucleus RNA-seq of cell diversity in the adult mouse hippocampus (sNuc-Seq)",
"Study only for unit test",
]
self.assertEqual(studies, expected_studies)
def login(manager=None, dry_run=False):
'''
Login to authorize credentials.
:param manager: API Manager
:param dry_run: If true, will do a dry run with no actual execution of functionality.
:return:
'''
if manager is None:
manager = scp_api.SCPAPIManager()
manager.login(token=parsed_args.token, dry_run=dry_run)
return (manager)
def test_upload_cluster(self, mocked_requests_get, mocked_requests_post,
mock_upload_via_gsutil):
# manager = scp_api.SCPAPIManager(verbose=True)
manager = scp_api.SCPAPIManager()
manager.api_base = 'https://singlecell.broadinstitute.org/single_cell/api/v1/'
manager.verify_https = True
manager.login(dry_run=True)
return_object = manager.upload_cluster(
file='../tests/data/toy_cluster',
study_name='Study only for unit test',
cluster_name='Test',
description='Test',
x='X',
y='Y',
z='Z')
# HTTP 204 indicates successful parse launch, per
# https://singlecell.broadinstitute.org/single_cell/api/swagger_docs/v1#!/StudyFiles/parse_study_study_file_path
self.assertEqual(return_object['code'], 204)
def test_ingest_version_mismatch(self, mocked_ingest_version_mismatch):
manager = scp_api.SCPAPIManager()
manager.api_base = "https://singlecell.broadinstitute.org/single_cell/api/v1/"
manager.verify_https = True
manager.head = {
"Accept": "application/json",
"User-Agent": "single-cell-portal/0.1.3rc1 (manage-study) scp-ingest-pipeline/0.9.12 (ingest_pipeline.py)",
}
# All SCP servers use single-cell-portal major release v1 or later, sending
# User-Agent string with an outdated package version should fail
with self.assertRaises(SystemExit) as cm:
manager.get_study_attribute(
study_name="Study only for unit test", attribute="accession"
)
# 400 "incompatibile with server" response should trigger custom exit code 79
self.assertEqual(
cm.exception.code, 79
), "expect exit if ingest major version mismatch detected"
def test_upload_unprocessable_entity_study_bucket_false(
self,
mocked_requests_get,
mocked_requests_post,
mock_upload_via_gsutil_study_bucket_false,
mock_delete_via_gsutil,
):
manager = scp_api.SCPAPIManager()
manager.api_base = "https://singlecell.broadinstitute.org/single_cell/api/v1/"
manager.verify_https = True
manager.login(dry_run=True)
with self.assertRaises(SystemExit) as cm:
manager.upload_study_file(
file="gs://fc-36f39ea7-439e-4a49-ad10-6a5a4614300e/metadata.txt",
file_type="Metadata",
study_name=" Single nucleus RNA-seq of cell diversity in the adult mouse hippocampus (sNuc-Seq)",
)
# when file_from_study_bucket = True, uploaded file is deleted from study bucket
self.assertEqual(cm.exception.code, 83), "expect exit-uploaded-file-deleted"
def test_upload_unprocessable_entity_study_bucket_true(
self,
mock_upload_via_gsutil_study_bucket_true,
mocked_requests_post,
mocked_requests_get,
):
manager = scp_api.SCPAPIManager()
manager.api_base = "https://singlecell.broadinstitute.org/single_cell/api/v1/"
manager.verify_https = True
manager.login(dry_run=True)
# 422 response (unprocessable entity) from server
# causes script to exit during file upload request
with self.assertRaises(SystemExit) as cm:
manager.upload_study_file(
file="fc-36f39ea7-1111-4a49-ad10-6a5a4614300e/foo.txt",
file_type="Metadata",
study_name=" Single nucleus RNA-seq of cell diversity in the adult mouse hippocampus (sNuc-Seq)",
)
# when file_from_study_bucket = True, no cleanup in bucket occurs
self.assertEqual(cm.exception.code, 84), "expect exit-no-file-cleanup-needed"
def test_upload_cluster(
self,
mocked_requests_get,
mocked_requests_post,
mock_upload_via_gsutil_study_bucket_true,
):
# manager = scp_api.SCPAPIManager(verbose=True)
manager = scp_api.SCPAPIManager()
manager.api_base = "https://singlecell.broadinstitute.org/single_cell/api/v1/"
manager.verify_https = True
manager.login(dry_run=True)
return_object = manager.upload_cluster(
file="../tests/data/toy_cluster",
study_name="Study only for unit test",
cluster_name="Test",
description="Test",
x="X",
y="Y",
z="Z",
)
# HTTP 204 indicates successful parse launch, per
# https://singlecell.broadinstitute.org/single_cell/api/swagger_docs/v1#!/StudyFiles/parse_study_study_file_path
self.assertEqual(return_object["code"], 204)
