def get_latest_submittable_schemas(self, ingest_api_url):
ingest_api = IngestApi(url=ingest_api_url)
urls = []
for schema in ingest_api.get_schemas(high_level_entity="type",
latest_only=True):
url = schema["_links"]["json-schema"]["href"]
urls.append(url)
return urls
def test_get_latest_schema_url__empty_result(self, mock_session):
# given
ingest_api = IngestApi(token_manager=self.token_manager)
ingest_api.get_schemas = MagicMock(return_value=[])
# when
result = ingest_api.get_latest_schema_url('type', 'project', 'project')
# then
self.assertEqual(result, None)
def get_hca_entity_types(
ingest_api_url="http://api.ingest.data.humancellatlas.org"):
'''
takes a while to run so only run once per ingest.
'''
ingest_api = IngestApi(url=ingest_api_url)
res = ingest_api.get_schemas(high_level_entity="type", latest_only=True)
hca_schemas = {}
for schema in res:
concreteEntity = schema.get('concreteEntity')
domainEntity = schema.get('domainEntity')
if domainEntity not in hca_schemas:
hca_schemas[domainEntity] = [concreteEntity + '_json']
else:
hca_schemas[domainEntity].append(concreteEntity + '_json')
return hca_schemas
def test_get_latest_schema_url(self, mock_session):
# given
ingest_api = IngestApi(token_manager=self.token_manager)
latest_schema_url = 'latest-project-schema-url'
ingest_api.get_schemas = MagicMock(return_value=[{
'_links': {
'json-schema': {
'href': latest_schema_url
}
}
}])
# when
result = ingest_api.get_latest_schema_url('type', 'project', 'project')
# then
self.assertEqual(result, latest_schema_url)
def main(environment, auth_token, doi):
pub_info = get_pub_info(doi)
if environment == "prod":
env = ""
elif environment == "staging":
env = "staging."
else:
env = "dev."
ingest_api_url = "http://api.ingest.{}archive.data.humancellatlas.org".format(
env)
ingest_api = IngestApi(ingest_api_url)
latest_project_schema = ingest_api.get_schemas(
high_level_entity="type",
domain_entity="project",
concrete_entity="project")[0]['_links']['json-schema']['href']
project_json = construct_project_json(pub_info, latest_project_schema)
submission_headers = {
'Authorization': 'Bearer {}'.format(auth_token),
'Content-Type': 'application/json'
}
response = rq.post("{}/projects".format(ingest_api_url),
data=json.dumps(project_json),
headers=submission_headers)
if response:
print("Project with uuid '{}' successfully created in {}.".format(
response.json()['uuid']['uuid'], environment))
print(
"View the created project here: https://{}contribute.data.humancellatlas.org/projects/detail?uuid={}"
.format(env,
response.json()['uuid']['uuid']))
with open("log.txt", "a") as log_file:
log_file.write(doi + "\t" + response.json()['uuid']['uuid'] + "\n")
else:
print("No project created, check if your token is still valid.")
