def download_studies(self):
ret_data, retcode = self.study_api_instance.download_studies(
user=self._user, auths=self._auths)
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=ret_data, status=retcode))
return ret_data
def update_study(self, study_code, study_detail):
ret_data, retcode = self.study_api_instance.update_study(
study_code, study_detail, user=self._user, auths=self._auths)
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=ret_data, status=retcode))
return ret_data
def delete_sampling_event(self, sampling_event_id):
ret, retcode = self.se_api_instance.delete_sampling_event(
sampling_event_id, user=self._user, auths=self._auths)
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=ret, status=retcode))
def get_country_metadata(self, country_value):
metadata, retcode = self.metadata_api_instance.get_country_metadata(
country_value, user=self._user, auths=self._auths)
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=metadata, status=retcode))
return metadata
def create_sampling_event(self, sampling_event):
created, retcode = self.se_api_instance.create_sampling_event(
sampling_event, user=self._user, auths=self._auths)
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=f'"{created}"\n', status=retcode))
return created
def download_sampling_event(self, sampling_event_id):
existing, retcode = self.se_api_instance.download_sampling_event(
sampling_event_id, user=self._user, auths=self._auths)
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=existing, status=retcode))
return existing
def download_partner_location(self, partner_name):
ret, retcode = self.location_api_instance.download_partner_location(
partner_name, user=self._user, auths=self._auths)
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=ret, status=retcode))
return ret
def update_location(self, location_id, location):
updated, retcode = self.location_api_instance.update_location(
location_id, location, user=self._user, auths=self._auths)
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=updated, status=retcode))
return updated
def merge_individuals(self, individual_id1, individual_id2):
found_events, retcode = self.i_api_instance.merge_individuals(
individual_id1, individual_id2, user=self._user, auths=self._auths)
self._logger.debug("PUT /v1/individual/{}/{} {}".format(
individual_id1, individual_id2, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def download_sampling_events_by_location(self, location_id):
found_events, retcode = self.se_api_instance.download_sampling_events_by_location(
location_id, start=0, count=0, user=self._user, auths=self._auths)
self._logger.debug("GET /v1/samplingEvents/location/{} {}".format(
location_id, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def download_individual(self, individual_id):
found_events, retcode = self.i_api_instance.download_individual(
individual_id, user=self._user, auths=self._auths)
self._logger.debug("GET /v1/individual/{} {}".format(
individual_id, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def download_location(self, location_id):
ret, retcode = self.location_api_instance.download_location(
location_id, user=self._user, auths=self._auths)
self._logger.debug("GET /v1/location/{} {}".format(
location_id, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=ret, status=retcode))
return ret
def delete_assay_datum(self, assay_datum_id):
found_events, retcode = self.ad_api_instance.delete_assay_datum(
assay_datum_id, user=self._user, auths=self._auths)
self._logger.debug("DELETE /v1/derivativeSample/{} {}".format(
assay_datum_id, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def create_individual(self, individual):
found_events, retcode = self.i_api_instance.create_individual(
individual, user=self._user, auths=self._auths)
self._logger.debug("POST /v1/individual {} {}".format(
individual, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def download_derivative_sample(self, derivative_sample_id):
found_events, retcode = self.ds_api_instance.download_derivative_sample(
derivative_sample_id, user=self._user, auths=self._auths)
self._logger.debug("GET /v1/derivativeSample/{} {}".format(
derivative_sample_id, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def delete_original_sample(self, original_sample_id):
found_events, retcode = self.os_api_instance.delete_original_sample(
original_sample_id, user=self._user, auths=self._auths)
self._logger.debug("DELETE /v1/originalSample/{} {}".format(
original_sample_id, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def delete_event_set(self, event_set_id):
api_response, retcode = self.es_api_instance.delete_event_set(
event_set_id, user=self._user, auths=self._auths)
if retcode >= 400:
if retcode != 422: # Already exists
self._logger.debug(
"Exception when calling EventSetApi->delete_event_set: \n")
raise ApiException(
http_resp=HTTPResponse(body=api_response, status=retcode))
return api_response
def update_sampling_event(self, sampling_event_id, sampling_event):
ret, retcode = self.se_api_instance.update_sampling_event(
sampling_event_id,
sampling_event,
user=self._user,
auths=self._auths)
self._logger.debug("POST /v1/samplingEvent/{} {}".format(
sampling_event_id, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=f'"{ret}"\n', status=retcode))
return ret
def merge_sampling_events(self, sampling_event_id1, sampling_event_id2):
ret, retcode = self.se_api_instance.merge_sampling_events(
sampling_event_id1,
sampling_event_id2,
user=self._user,
auths=self._auths)
self._logger.debug("PUT /v1/samplingEvent/merge/{}/{} {}".format(
sampling_event_id1, sampling_event_id2, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=ret, status=retcode))
return ret
def merge_original_samples(self, original_sample_id1, original_sample_id2):
found_events, retcode = self.os_api_instance.merge_original_samples(
original_sample_id1,
original_sample_id2,
user=self._user,
auths=self._auths)
self._logger.debug("PUT /v1/originalSample/{}/{} {}".format(
original_sample_id1, original_sample_id2, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def download_sampling_events_by_study(self,
study_name,
start=None,
count=None):
found_events, retcode = self.se_api_instance.download_sampling_events_by_study(
study_name, start, count, user=self._user, auths=self._auths)
self._logger.debug("GET /v1/samplingEvents/study/{} {}".format(
study_name, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def download_assay_data_by_attr(self, attr_type, attr_value):
found_events, retcode = self.ad_api_instance.download_assay_data_by_attr(
attr_type,
urllib.parse.quote_plus(attr_value),
user=self._user,
auths=self._auths)
self._logger.debug("GET /v1/derivativeSamples/attr/{}/{} {}".format(
attr_type, attr_value, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def merge_derivative_samples(self, derivative_sample_id1,
derivative_sample_id2):
found_events, retcode = self.ds_api_instance.merge_derivative_samples(
derivative_sample_id1,
derivative_sample_id2,
user=self._user,
auths=self._auths)
self._logger.debug("PUT /v1/derivativeSample/merge/{}/{} {}".format(
derivative_sample_id1, derivative_sample_id2, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def download_individuals_by_attr(self, prop_name, prop_value, study_name):
found_events, retcode = self.i_api_instance.download_individuals_by_attr(
prop_name,
urllib.parse.quote_plus(prop_value),
study_name,
user=self._user,
auths=self._auths)
self._logger.debug("GET /v1/individuals/attr/{}/{} {}".format(
prop_name, prop_value, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events
def create_response(self, ret, retcode, response_type=None):
if retcode >= 400:
raise ApiException(status=retcode, reason='')
if ret and response_type:
if isinstance(ret, Model):
response_dict = ret.to_dict()
else:
response_dict = ret
resp_data = json.dumps(response_dict,
ensure_ascii=False,
cls=JSONEncoder)
mr = MockResponse(resp_data, retcode)
response = RESTResponse(mr)
ret = self.api_client.deserialize(response, response_type)
return ret
def download_sampling_events_by_event_set(self,
event_set_name,
start=None,
count=None):
found_events, retcode = self.se_api_instance.download_sampling_events_by_event_set(
urllib.parse.quote_plus(event_set_name),
start,
count,
user=self._user,
auths=self._auths)
self._logger.debug("GET /v1/samplingEvents/event_set/{} {}".format(
event_set_name, retcode))
if retcode >= 400:
raise ApiException(
http_resp=HTTPResponse(body=found_events, status=retcode))
return found_events