def test_download_samples_by_study(self, api_factory):
api_instance = api_factory.SamplingEventApi()
os_api_instance = api_factory.OriginalSampleApi()
study_api = api_factory.StudyApi()
try:
samp = openapi_client.SamplingEvent(None, doc_accuracy='month')
created = api_instance.create_sampling_event(samp)
osamp = openapi_client.OriginalSample(None,
study_name='2006-MD-UP')
osamp.sampling_event_id = created.sampling_event_id
os_created = os_api_instance.create_original_sample(osamp)
events = api_instance.download_sampling_events_by_study(
'2006-MD-UP')
assert events.count == 1, "Event expected"
os_api_instance.delete_original_sample(
os_created.original_sample_id)
api_instance.delete_sampling_event(created.sampling_event_id)
except ApiException as error:
self.check_api_exception(
api_factory, "SamplingEventApi->create_sampling_event", error)
def test_ds_event_set_lookup(self, api_factory):
api_instance = api_factory.OriginalSampleApi()
se_api_instance = api_factory.SamplingEventApi()
es_api_instance = api_factory.EventSetApi()
ds_api_instance = api_factory.DerivativeSampleApi()
try:
event_set_name = 'test_ds_event_set_lookup'
study_code = '7004-MD-UP'
created_es = es_api_instance.create_event_set(event_set_name)
sampling_event = openapi_client.SamplingEvent(None,
date(2017, 10, 10),
doc_accuracy='month')
created_se = se_api_instance.create_sampling_event(sampling_event)
created_set = es_api_instance.create_event_set_item(
event_set_name, created_se.sampling_event_id)
created, created1, created2 = self.create_test_samples(
api_factory, study_code)
created.sampling_event_id = created_se.sampling_event_id
api_instance.update_original_sample(created.original_sample_id,
created)
results = ds_api_instance.download_derivative_samples_by_event_set(
event_set_name)
looked_up = results.derivative_samples[0]
fetched = ds_api_instance.download_derivative_sample(
looked_up.derivative_sample_id)
assert created1 == fetched or created2 == fetched, "create response != download response"
assert results.attr_types == ['test1', 'test2']
se_api_instance.delete_sampling_event(created_se.sampling_event_id)
es_api_instance.delete_event_set(event_set_name)
ds_api_instance.delete_derivative_sample(
created1.derivative_sample_id)
ds_api_instance.delete_derivative_sample(
created2.derivative_sample_id)
api_instance.delete_original_sample(created.original_sample_id)
with pytest.raises(ApiException, status=404):
results = api_instance.download_original_samples_by_event_set(
event_set_name)
except ApiException as error:
self.check_api_exception(
api_factory, "OriginalSampleApi->create_original_sample",
error)
def test_delete_missing_member(self, api_factory):
api_instance = api_factory.EventSetApi()
event_api_instance = api_factory.SamplingEventApi()
try:
event_set = 'EventSet12'
created = api_instance.create_event_set(event_set)
samp = openapi_client.SamplingEvent(None, date(2017, 10, 10))
created = event_api_instance.create_sampling_event(samp)
created_set = api_instance.create_event_set_item(
event_set, created.sampling_event_id)
api_instance.delete_event_set_item(event_set,
created.sampling_event_id)
with pytest.raises(ApiException, status=404):
api_instance.delete_event_set_item(event_set,
created.sampling_event_id)
api_instance.delete_event_set(event_set)
event_api_instance.delete_sampling_event(created.sampling_event_id)
except ApiException as error:
self.check_api_exception(api_factory,
"EventSetsApi->create_event_set", error)
def create_sampling_event_from_values(self, values):
doc = None
doc_accuracy = None
study_id = None
ret = None
idents = []
if 'sample_individual_id' in values:
idents.append(
openapi_client.Attr('individual_id',
values['sample_individual_id'],
self._event_set))
if 'roma_pk_id' in values:
idents.append(
openapi_client.Attr('roma_pk_id', values['roma_pk_id'],
self._event_set))
if 'doc' in values:
if isinstance(values['doc'], datetime.date):
doc = values['doc']
else:
if 'year' in values:
if isinstance(values['year'], datetime.date):
doc = values['year']
values['doc_accuracy'] = 'year'
if 'doc_accuracy' in values:
doc_accuracy = values['doc_accuracy']
if 'study_id' in values:
study_id = values['study_id']
samp = openapi_client.SamplingEvent(None, doc=doc)
if doc_accuracy:
samp.doc_accuracy = doc_accuracy
samp.attrs = idents
#print(values)
#print(samp)
return samp
def test_ds_event_set_lookup_no_ds(self, api_factory):
api_instance = api_factory.OriginalSampleApi()
se_api_instance = api_factory.SamplingEventApi()
es_api_instance = api_factory.EventSetApi()
ds_api_instance = api_factory.DerivativeSampleApi()
try:
event_set_name = 'test_ds_event_set_lookup'
study_code = '7005-MD-UP'
created_es = es_api_instance.create_event_set(event_set_name)
sampling_event = openapi_client.SamplingEvent(None,
date(2017, 10, 10),
doc_accuracy='month')
created_se = se_api_instance.create_sampling_event(sampling_event)
created_set = es_api_instance.create_event_set_item(
event_set_name, created_se.sampling_event_id)
if api_factory.is_authorized(None):
res = ds_api_instance.download_derivative_samples_by_event_set(
event_set_name)
assert not res.derivative_samples
else:
with pytest.raises(ApiException, status=403):
ds_api_instance.download_derivative_samples_by_event_set(
event_set_name)
se_api_instance.delete_sampling_event(created_se.sampling_event_id)
es_api_instance.delete_event_set(event_set_name)
except ApiException as error:
self.check_api_exception(
api_factory, "OriginalSampleApi->create_original_sample",
error)
def test_create_member(self, api_factory):
api_instance = api_factory.EventSetApi()
event_api_instance = api_factory.SamplingEventApi()
try:
event_set = 'EventSet2'
created = api_instance.create_event_set(event_set)
samp = openapi_client.SamplingEvent(None, date(2017, 10, 10))
created = event_api_instance.create_sampling_event(samp)
created_set = api_instance.create_event_set_item(
event_set, created.sampling_event_id)
if not api_factory.is_authorized(None):
pytest.fail(
'Unauthorized call to create_event_set_item succeeded')
fetched_set = api_instance.download_event_set(event_set)
if not api_factory.is_authorized(None):
pytest.fail(
'Unauthorized call to download_event_set succeeded')
assert fetched_set.members.sampling_events[
0].sampling_event_id == created.sampling_event_id
assert fetched_set.members.count == 1
api_instance.delete_event_set_item(event_set,
created.sampling_event_id)
fetched_set = api_instance.download_event_set(event_set)
assert fetched_set.members.count == 0
api_instance.delete_event_set(event_set)
event_api_instance.delete_sampling_event(created.sampling_event_id)
except ApiException as error:
self.check_api_exception(api_factory,
"EventSetsApi->create_event_set", error)
def create_test_samples(self, api_factory):
created_es = None
created_se = None
created = None
created1 = None
created2 = None
try:
api_instance = api_factory.OriginalSampleApi()
loc_api_instance = api_factory.LocationApi()
se_api_instance = api_factory.SamplingEventApi()
es_api_instance = api_factory.EventSetApi()
ds_api_instance = api_factory.DerivativeSampleApi()
study_api = api_factory.StudyApi()
event_set_name = 'test_hist_event_set_lookup'
study_name = '8004-MD-UP'
created_es = es_api_instance.create_event_set(event_set_name)
loc = openapi_client.Location(None, 28.463, 91.495, 'country',
'Trongsa, Trongsa, Bhutan',
'history_locations.txt', 'BTN')
location = loc_api_instance.create_location(loc)
sampling_event = openapi_client.SamplingEvent(None,
date(2017, 10, 10),
doc_accuracy='month')
sampling_event.location_id = location.location_id
created_se = se_api_instance.create_sampling_event(sampling_event)
es_api_instance.create_event_set_item(event_set_name,
created_se.sampling_event_id)
samp = openapi_client.OriginalSample(None,
study_name=study_name,
partner_species='PF')
samp.attrs = [
openapi_client.Attr(attr_type='ds_os_attr',
attr_value='123456')
]
created = api_instance.create_original_sample(samp)
study_detail = study_api.download_study(study_name)
study_detail.partner_species[0].taxa = [
openapi_client.Taxonomy(taxonomy_id=5833)
]
study_api.update_study(study_name, study_detail)
samp1 = openapi_client.DerivativeSample(None)
samp2 = openapi_client.DerivativeSample(None)
samp1.attrs = [
openapi_client.Attr(attr_type='test1',
attr_value='test1',
attr_source='ds_os_attr')
]
samp2.attrs = [
openapi_client.Attr(attr_type='test2',
attr_value='test2',
attr_source='ds_os_attr')
]
samp1.original_sample_id = created.original_sample_id
samp2.original_sample_id = created.original_sample_id
created1 = ds_api_instance.create_derivative_sample(samp1)
created2 = ds_api_instance.create_derivative_sample(samp2)
created.sampling_event_id = created_se.sampling_event_id
api_instance.update_original_sample(created.original_sample_id,
created)
except ApiException as error:
self.check_api_exception(
api_factory, "OriginalSampleApi->create_original_sample",
error)
return created_es, created_se, created, created1, created2
def test_update_event_set(self, api_factory):
api_instance = api_factory.EventSetApi()
event_api_instance = api_factory.SamplingEventApi()
try:
event_set = 'EventSet8'
created = api_instance.create_event_set(event_set)
samp = openapi_client.SamplingEvent(None, date(2017, 10, 10))
created = event_api_instance.create_sampling_event(samp)
samp2 = openapi_client.SamplingEvent(None, date(2017, 10, 11))
created2 = event_api_instance.create_sampling_event(samp2)
created_set = api_instance.create_event_set_item(
event_set, created.sampling_event_id)
fetched_set1 = api_instance.download_event_set(event_set)
assert fetched_set1.members.sampling_events[
0].sampling_event_id == created.sampling_event_id
assert fetched_set1.members.count == 1
assert fetched_set1.notes is None
evsn = openapi_client.EventSetNote('note8', 'note8text')
fetched_set1.notes = [evsn]
fetched_set1.members.sampling_events.append(created2)
fetched_set1.members.count = 2
api_instance.update_event_set(event_set, fetched_set1)
fetched_set2 = api_instance.download_event_set(event_set)
assert fetched_set2.members.count == 2
assert len(fetched_set2.notes) == 1
fetched_set2.members = None
api_instance.update_event_set(event_set, fetched_set2)
fetched_set3 = api_instance.download_event_set(event_set)
assert fetched_set3.members.count == 2
assert len(fetched_set3.notes) == 1
api_instance.delete_event_set_item(event_set,
created.sampling_event_id)
api_instance.delete_event_set_item(event_set,
created2.sampling_event_id)
fetched_set = api_instance.download_event_set(event_set)
assert fetched_set.members.count == 0
api_instance.delete_event_set(event_set)
event_api_instance.delete_sampling_event(created.sampling_event_id)
event_api_instance.delete_sampling_event(
created2.sampling_event_id)
except ApiException as error:
self.check_api_exception(api_factory,
"EventSetsApi->create_event_set", error)