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)
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)