def __init__(self,
ingest_api,
dsp_api,
ontology_api=ontology.__api__,
exclude_types=None,
alias_prefix=None,
dsp_validation=True):
self.logger = logging.getLogger(__name__)
self.ingest_api = ingest_api
self.exclude_types = exclude_types if exclude_types else []
self.alias_prefix = f"{alias_prefix}_" if alias_prefix else ""
self.ontology_api = ontology_api
self.dsp_api = dsp_api
self.dsp_validation = dsp_validation
self.converter = {
"project":
ProjectConverter(ontology_api=ontology_api),
"sample":
SampleConverter(ontology_api=ontology_api),
"study":
StudyConverter(ontology_api=ontology_api),
"sequencingRun":
SequencingRunConverter(ontology_api=ontology_api),
"sequencingExperiment":
SequencingExperimentConverter(ontology_api=ontology_api)
}
self.converter['sample'].ingest_api = self.ingest_api
def test_convert_sample(self):
# given:
biomaterial = self.hca_data.get('biomaterial')
with open(config.JSON_DIR + 'dsp/sample.json',
encoding=config.ENCODING) as data_file:
no_release_date = json.loads(data_file.read())
# and:
test_alias = 'hca' + str(randint(0, 1000))
biomaterial['uuid']['uuid'] = test_alias
no_release_date['alias'] = test_alias
no_release_date['attributes']['HCA Biomaterial UUID'] = [{
'value':
test_alias
}]
# and:
with_release_date = deepcopy(no_release_date)
with_release_date['releaseDate'] = '2018-10-11'
# and:
converter = SampleConverter(ontology_api=self.ontology_api)
converter.ingest_api = self.ingest_api
# when:
converted_with_release_date = converter.convert({
'biomaterial': biomaterial,
'project': {
'releaseDate': '2018-10-11T14:33:22.111Z'
}
})
# and:
converted_no_release_date = converter.convert({
'biomaterial': biomaterial,
'project': {
'releaseDate': None
}
})
# then:
self.assertEqual(with_release_date, converted_with_release_date)
self.assertEqual(no_release_date, converted_no_release_date)
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 test_convert_sample(self):
biomaterial = self.hca_data.get('biomaterial')
with open(config.JSON_DIR + 'dsp/sample.json', encoding=config.ENCODING) as data_file:
expected_json = json.loads(data_file.read())
test_alias = 'hca' + str(randint(0, 1000))
biomaterial['uuid']['uuid'] = test_alias
expected_json['alias'] = test_alias
expected_json['attributes']['HCA Biomaterial UUID'] = [{'value': test_alias}]
input = {
'biomaterial': biomaterial
}
converter = SampleConverter(ontology_api=self.ontology_api)
converter.ingest_api = self.ingest_api
actual_json = converter.convert(input)
self.assertEqual(expected_json, actual_json)
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)