def get_validation_result(archive_submission_uuid: str):
dsp_api = DataSubmissionPortal(config.DSP_API_URL)
submission_url = dsp_api.get_submission_url(archive_submission_uuid)
submission = ArchiveSubmission(dsp_api=dsp_api,
dsp_submission_url=submission_url)
result = submission.get_all_validation_result_details()
return jsonify(result)
def get_blockers(archive_submission_uuid: str):
dsp_api = DataSubmissionPortal(config.DSP_API_URL)
submission_url = dsp_api.get_submission_url(archive_submission_uuid)
submission = ArchiveSubmission(dsp_api=dsp_api,
dsp_submission_url=submission_url)
blockers = submission.get_blockers()
return jsonify(blockers)
def get_validation_errors(archive_submission_uuid: str):
dsp_api = DataSubmissionPortal(config.DSP_API_URL)
submission_url = dsp_api.get_submission_url(archive_submission_uuid)
submission = ArchiveSubmission(dsp_api=dsp_api,
dsp_submission_url=submission_url)
validation_errors = submission.get_validation_error_report()
return jsonify(validation_errors)
def delete_archive_submission(dsp_submission_uuid: str):
ingest_api = IngestAPI(config.INGEST_API_URL)
dsp_api = DataSubmissionPortal(config.DSP_API_URL)
ingest_archive_submission = ingest_api.get_archive_submission_by_dsp_uuid(
dsp_submission_uuid)
dsp_url = ingest_archive_submission['dspUrl']
dsp_api.delete_submission(dsp_url)
logger.info(f'Deleting DSP submission {dsp_url}')
archive_submission_url = ingest_archive_submission['_links']['self'][
'href']
logger.info(f'Deleting Ingest Archive Submission {archive_submission_url}')
response = ingest_api.delete(archive_submission_url)
return response_json(HTTPStatus.OK, data=response)
def archive():
data = request.get_json()
submission_uuid = data.get('submission_uuid')
exclude_types = data.get('exclude_types')
alias_prefix = data.get('alias_prefix')
if not submission_uuid:
error = {
'message':
f'You must supply the parameter submission_uuid referring to an Ingest submission envelope uuid.'
}
return response_json(HTTPStatus.BAD_REQUEST, error)
if config.DIRECT_SUBMISSION:
direct_archiver = direct_archiver_from_config()
submission = direct_archiver.archive_submission(submission_uuid)
response = submission.as_dict(string_lists=True)
else:
ingest_api = IngestAPI(config.INGEST_API_URL)
archiver = IngestArchiver(ingest_api=ingest_api,
dsp_api=DataSubmissionPortal(
config.DSP_API_URL),
exclude_types=exclude_types,
alias_prefix=alias_prefix)
thread = threading.Thread(target=async_archive,
args=(ingest_api, archiver, submission_uuid))
thread.start()
response = {'message': 'successfully triggered!'}
return jsonify(response)
def complete(dsp_submission_uuid: str):
dsp_api = DataSubmissionPortal(config.DSP_API_URL)
ingest_api = IngestAPI(config.INGEST_API_URL)
thread = threading.Thread(target=async_complete,
args=(dsp_api, dsp_submission_uuid, ingest_api))
thread.start()
response = {'message': 'successfully triggered!'}
return response_json(HTTPStatus.ACCEPTED, data=response)
def __init__(self, alias_prefix, output_dir, exclude_types, no_validation):
self.manifests = []
self.ingest_api = IngestAPI(config.INGEST_API_URL)
self.dsp_api = DataSubmissionPortal(config.DSP_API_URL)
now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%S")
self.output_dir = output_dir if output_dir else f"output/ARCHIVER_{now}"
self.archiver = IngestArchiver(ingest_api=self.ingest_api,
dsp_api=self.dsp_api,
exclude_types=self.split_exclude_types(exclude_types),
alias_prefix=alias_prefix,
dsp_validation=not no_validation)
def setUp(self):
self.dsp_api = DataSubmissionPortal()
with open(config.JSON_DIR + 'hca/biomaterials.json',
encoding=config.ENCODING) as data_file:
hca_samples = json.loads(data_file.read())
self.hca_submission = {'samples': hca_samples}
self.ontology_api = MagicMock()
self.ontology_api.expand_curie = MagicMock(
return_value='http://purl.obolibrary.org/obo/UO_0000015')
self.ingest_api = MagicMock()
self.ingest_api.url = 'ingest_url'
self.ingest_api.get_concrete_entity_type = MagicMock(
return_value='donor_organism')
self.converter = SampleConverter(ontology_api=self.ontology_api)
self.converter.ingest_api = self.ingest_api
pass
class TestDataSubmissionPortal(unittest.TestCase):
def setUp(self):
self.dsp_api = DataSubmissionPortal()
with open(config.JSON_DIR + 'hca/biomaterials.json',
encoding=config.ENCODING) as data_file:
hca_samples = json.loads(data_file.read())
self.hca_submission = {'samples': hca_samples}
self.ontology_api = MagicMock()
self.ontology_api.expand_curie = MagicMock(
return_value='http://purl.obolibrary.org/obo/UO_0000015')
self.ingest_api = MagicMock()
self.ingest_api.url = 'ingest_url'
self.ingest_api.get_concrete_entity_type = MagicMock(
return_value='donor_organism')
self.converter = SampleConverter(ontology_api=self.ontology_api)
self.converter.ingest_api = self.ingest_api
pass
def tearDown(self):
self.dsp_api.session.close()
def test_get_token_given_valid_credentials_return_token(self):
aap_user = os.environ.get('AAP_API_USER', '')
aap_password = os.environ.get('AAP_API_PASSWORD', '')
token_client = AAPTokenClient(username=aap_user, password=aap_password)
token = token_client.retrieve_token()
self.assertTrue(token)
def test_get_token_given_invalid_credentials_return_none(self):
username = '******'
password = '******'
token_client = AAPTokenClient(username=username, password=password)
token = token_client.retrieve_token()
self.assertFalse(token)
def test_create_submission(self):
submission = self.dsp_api.create_submission()
delete_url = submission['_links']['self:delete']['href']
self.dsp_api.delete_submission(delete_url)
self.assertTrue(submission['_links']['self']['href'])
def test_get_submission_contents(self):
submission = self.dsp_api.create_submission()
get_contents_url = submission['_links']['contents']['href']
contents = self.dsp_api.get_contents(get_contents_url)
delete_url = submission['_links']['self:delete']['href']
self.dsp_api.delete_submission(delete_url)
self.assertTrue(contents)
def test_create_sample(self):
submission = self.dsp_api.create_submission()
get_contents_url = submission['_links']['contents']['href']
contents = self.dsp_api.get_contents(get_contents_url)
create_sample_url = contents['_links']['samples:create']['href']
samples = self.hca_submission['samples']
sample = samples[0]
sample = {'biomaterial': sample}
converted_sample = self.converter.convert(sample)
created_sample = self.dsp_api.create_entity(create_sample_url,
converted_sample)
# clean up submission in DSP
delete_url = submission['_links']['self:delete']['href']
self.dsp_api.delete_submission(delete_url)
self.assertTrue(created_sample)