def test_ds_parent_create(self, api_factory):
api_instance = api_factory.DerivativeSampleApi()
try:
parent_samp = openapi_client.DerivativeSample(None)
parent_created = api_instance.create_derivative_sample(parent_samp)
samp = openapi_client.DerivativeSample(None)
samp.parent_derivative_sample_id = parent_created.derivative_sample_id
created = api_instance.create_derivative_sample(samp)
if not api_factory.is_authorized(None):
pytest.fail(
'Unauthorized call to create_derivative_sample succeeded')
fetched = api_instance.download_derivative_sample(
created.derivative_sample_id)
assert created == fetched, "create response != download response"
fetched.derivative_sample_id = None
assert samp == fetched, "upload != download response"
api_instance.delete_derivative_sample(
parent_created.derivative_sample_id)
api_instance.delete_derivative_sample(created.derivative_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "DerivativeSampleApi->create_derivative_sample",
error)
def test_ds_update(self, api_factory):
api_instance = api_factory.DerivativeSampleApi()
try:
samp = openapi_client.DerivativeSample(None)
samp.attrs = [
openapi_client.Attr(attr_type='oxford', attr_value='1234567')
]
created = api_instance.create_derivative_sample(samp)
looked_up = api_instance.download_derivative_samples_by_attr(
'oxford', '1234567')
looked_up = looked_up.derivative_samples[0]
new_samp = openapi_client.DerivativeSample(None)
updated = api_instance.update_derivative_sample(
looked_up.derivative_sample_id, new_samp)
fetched = api_instance.download_derivative_sample(
looked_up.derivative_sample_id)
assert updated == fetched, "update response != download response"
fetched.derivative_sample_id = None
assert new_samp == fetched, "update != download response"
api_instance.delete_derivative_sample(
looked_up.derivative_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "DerivativeSampleApi->create_derivative_sample",
error)
def test_ds_attr_merge(self, api_factory):
api_instance = api_factory.DerivativeSampleApi()
try:
ident1 = openapi_client.Attr(attr_type='oxford_id',
attr_value='1234')
ident2 = openapi_client.Attr(attr_type='roma_id',
attr_value='12345')
ident3 = openapi_client.Attr(attr_type='lims_id',
attr_value='123456')
samp1 = openapi_client.DerivativeSample(None)
samp1.attrs = [ident1]
created1 = api_instance.create_derivative_sample(samp1)
samp2 = openapi_client.DerivativeSample(None)
samp2.attrs = [ident2]
created2 = api_instance.create_derivative_sample(samp2)
samp3 = openapi_client.DerivativeSample(None)
samp3.attrs = [ident1, ident2, ident3]
with pytest.raises(ApiException, status=422):
created3 = api_instance.create_derivative_sample(samp3)
api_instance.delete_derivative_sample(
created1.derivative_sample_id)
api_instance.delete_derivative_sample(
created2.derivative_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "DerivativeSampleApi->create_derivative_sample",
error)
def test_ds_os_attr_lookup(self, api_factory):
api_instance = api_factory.OriginalSampleApi()
ds_api_instance = api_factory.DerivativeSampleApi()
try:
samp = openapi_client.OriginalSample(None, study_name='7000-MD-UP')
samp.attrs = [
openapi_client.Attr(attr_type='ds_os_attr',
attr_value='123456')
]
created = api_instance.create_original_sample(samp)
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)
results = ds_api_instance.download_derivative_samples_by_os_attr(
'ds_os_attr', '123456')
assert results.count == 2
assert results.derivative_samples[
0].derivative_sample_id != results.derivative_samples[
1].derivative_sample_id
assert results.derivative_samples[
0].original_sample_id == results.derivative_samples[
1].original_sample_id
assert results.derivative_samples[
0].original_sample_id == created.original_sample_id
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)
except ApiException as error:
self.check_api_exception(
api_factory, "OriginalSampleApi->create_original_sample",
error)
def create_derivative_sample_from_values(self, values):
d_sample = openapi_client.DerivativeSample(None)
idents = []
if 'derivative_sample_id' in values:
idents.append(
openapi_client.Attr('derivative_sample_id',
values['derivative_sample_id'],
self._event_set))
if 'derivative_sample_source' in values:
idents.append(
openapi_client.Attr('derivative_sample_source',
values['derivative_sample_source'],
self._event_set))
if 'sanger_sample_id' in values:
idents.append(
openapi_client.Attr('sanger_sample_id',
values['sanger_sample_id'],
self._event_set))
if 'sample_lims_id' in values and values['sample_lims_id']:
idents.append(
openapi_client.Attr('sanger_lims_id', values['sample_lims_id'],
self._event_set))
if 'dna_prep' in values:
d_sample.dna_prep = values['dna_prep']
d_sample.attrs = idents
return d_sample
def test_ds_study_lookup_paged(self, api_factory):
api_instance = api_factory.OriginalSampleApi()
ds_api_instance = api_factory.DerivativeSampleApi()
try:
study_code = '7003-MD-UP'
os_samp = openapi_client.OriginalSample(None,
study_name=study_code)
os_created = api_instance.create_original_sample(os_samp)
for i in range(5):
samp = openapi_client.DerivativeSample(None)
samp.original_sample_id = os_created.original_sample_id
created = ds_api_instance.create_derivative_sample(samp)
fetched1 = ds_api_instance.download_derivative_samples_by_study(
study_code, start=0, count=2)
assert len(fetched1.derivative_samples
) == 2, "Wrong number of original_samples returned"
assert fetched1.count == 5, "Wrong total of original_samples returned"
ffetched = ds_api_instance.download_derivative_samples(
search_filter='studyId:' + study_code, start=0, count=2)
assert ffetched == fetched1
fetched2 = ds_api_instance.download_derivative_samples_by_study(
study_code, start=2, count=5)
#Gets second tranche and also attempts to retrieve more than exist
assert len(fetched2.derivative_samples
) == 3, "Wrong number of original_samples returned"
assert fetched2.count == 5, "Wrong total of original_samples returned"
ids = []
for derivative_sample in fetched1.derivative_samples + fetched2.derivative_samples:
assert not derivative_sample.derivative_sample_id in ids, "derivativeSample returned twice"
ids.append(derivative_sample.derivative_sample_id)
#Check that it's the correct number of *unique* events
#Clean up
fetch_all = ds_api_instance.download_derivative_samples_by_study(
study_code)
for derivative_sample in fetch_all.derivative_samples:
ds_api_instance.delete_derivative_sample(
derivative_sample.derivative_sample_id)
api_instance.delete_original_sample(os_created.original_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "OriginalSampleApi->create_original_sample",
error)
def test_ds_nested_delete_os(self, api_factory):
api_instance = api_factory.DerivativeSampleApi()
os_api_instance = api_factory.OriginalSampleApi()
try:
parent_samp = openapi_client.OriginalSample(None)
parent_created = os_api_instance.create_original_sample(
parent_samp)
samp = openapi_client.DerivativeSample(None)
samp.original_sample_id = parent_created.original_sample_id
created = api_instance.create_derivative_sample(samp)
child_samp = openapi_client.DerivativeSample(None)
child_samp.parent_derivative_sample_id = created.derivative_sample_id
child_created = api_instance.create_derivative_sample(child_samp)
api_instance.delete_derivative_sample(created.derivative_sample_id)
fetched = api_instance.download_derivative_sample(
child_created.derivative_sample_id)
assert fetched.original_sample_id == parent_created.original_sample_id
api_instance.delete_derivative_sample(
child_created.derivative_sample_id)
os_api_instance.delete_original_sample(
parent_created.original_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "DerivativeSampleApi->create_derivative_sample",
error)
def create_test_samples(self, api_factory, study_name):
api_instance = api_factory.OriginalSampleApi()
ds_api_instance = api_factory.DerivativeSampleApi()
study_api = api_factory.StudyApi()
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)
return created, created1, created2
def test_ds_update_duplicate(self, api_factory):
api_instance = api_factory.DerivativeSampleApi()
try:
samp = openapi_client.DerivativeSample(None)
samp.attrs = [
openapi_client.Attr(attr_type='oxford',
attr_value='12345678',
attr_source='upd')
]
created = api_instance.create_derivative_sample(samp)
looked_up = api_instance.download_derivative_samples_by_attr(
'oxford', '12345678')
looked_up = looked_up.derivative_samples[0]
new_samp = openapi_client.DerivativeSample(None)
new_samp.attrs = [
openapi_client.Attr(attr_type='oxford',
attr_value='123456789',
attr_source='upd')
]
new_created = api_instance.create_derivative_sample(new_samp)
with pytest.raises(ApiException, status=422):
updated = api_instance.update_derivative_sample(
looked_up.derivative_sample_id, new_samp)
api_instance.delete_derivative_sample(
looked_up.derivative_sample_id)
api_instance.delete_derivative_sample(
new_created.derivative_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "DerivativeSampleApi->create_derivative_sample",
error)
def test_ds_delete(self, api_factory):
api_instance = api_factory.DerivativeSampleApi()
try:
samp = openapi_client.DerivativeSample(None)
created = api_instance.create_derivative_sample(samp)
api_instance.delete_derivative_sample(created.derivative_sample_id)
with pytest.raises(ApiException, status=404):
fetched = api_instance.download_derivative_sample(
created.derivative_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "DerivativeSampleApi->create_derivative_sample",
error)
def test_ds_attr_lookup_encode(self, api_factory):
api_instance = api_factory.DerivativeSampleApi()
try:
test_id = 'MDG/DK_0005'
samp = openapi_client.DerivativeSample(None)
samp.attrs = [
openapi_client.Attr(attr_type='partner_id',
attr_value=test_id,
attr_source='encode')
]
created = api_instance.create_derivative_sample(samp)
fetched = api_instance.download_derivative_sample(
created.derivative_sample_id)
assert created == fetched, "create response != download response"
fetched.derivative_sample_id = None
assert samp == fetched, "upload != download response"
results = api_instance.download_derivative_samples_by_attr(
'partner_id', urllib.parse.quote_plus(test_id))
looked_up = results.derivative_samples[0]
fetched = api_instance.download_derivative_sample(
looked_up.derivative_sample_id)
assert created == fetched, "create response != download response"
fetched.derivative_sample_id = None
assert samp == fetched, "upload != download response"
api_instance.delete_derivative_sample(created.derivative_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "DerivativeSampleApi->create_derivative_sample",
error)
def test_ds_duplicate_key(self, api_factory):
api_instance = api_factory.DerivativeSampleApi()
try:
samp = openapi_client.DerivativeSample(None)
samp.attrs = [
openapi_client.Attr(attr_type='oxford',
attr_value='1234',
attr_source='same')
]
created = api_instance.create_derivative_sample(samp)
with pytest.raises(ApiException, status=422):
created = api_instance.create_derivative_sample(samp)
api_instance.delete_derivative_sample(created.derivative_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "DerivativeSampleApi->create_derivative_sample",
error)
def test_ds_update_missing(self, api_factory):
api_instance = api_factory.DerivativeSampleApi()
try:
new_samp = openapi_client.DerivativeSample(None)
fake_id = uuid.uuid4()
new_samp.derivative_sample_id = str(fake_id)
if api_factory.is_authorized(None):
with pytest.raises(ApiException, status=404):
updated = api_instance.update_derivative_sample(
new_samp.derivative_sample_id, new_samp)
else:
with pytest.raises(ApiException, status=403):
updated = api_instance.update_derivative_sample(
new_samp.derivative_sample_id, new_samp)
except ApiException as error:
self.check_api_exception(
api_factory, "DerivativeSampleApi->update_derivative_sample",
error)
def test_ad_attr_lookup(self, api_factory):
api_instance = api_factory.AssayDataApi()
ds_api_instance = api_factory.DerivativeSampleApi()
try:
samp1 = openapi_client.DerivativeSample(None)
created1 = ds_api_instance.create_derivative_sample(samp1)
samp = openapi_client.AssayDatum(None)
samp.attrs = [
openapi_client.Attr(attr_type='oxford', attr_value='123456')
]
samp.derivative_sample_id = created1.derivative_sample_id
created = api_instance.create_assay_datum(samp)
results = api_instance.download_assay_data_by_attr(
'oxford', '123456')
looked_up = results.assay_data[0]
fetched = api_instance.download_assay_datum(
looked_up.assay_datum_id)
assert created == fetched, "create response != download response"
fetched.assay_datum_id = None
assert samp == fetched, "upload != download response"
api_instance.delete_assay_datum(created.assay_datum_id)
ds_api_instance.delete_derivative_sample(
created1.derivative_sample_id)
except ApiException as error:
self.check_api_exception(api_factory,
"AssayDataApi->create_assay_datum", error)
def test_ad_os_attr_lookup(self, api_factory):
api_instance = api_factory.AssayDataApi()
os_api_instance = api_factory.OriginalSampleApi()
ds_api_instance = api_factory.DerivativeSampleApi()
try:
samp = openapi_client.OriginalSample(None, study_name='5000-MD-UP')
samp.attrs = [
openapi_client.Attr(attr_type='ds_os_attr',
attr_value='ad123456')
]
created = os_api_instance.create_original_sample(samp)
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)
ad_samp = openapi_client.AssayDatum(None)
ad_samp.attrs = [
openapi_client.Attr(attr_type='oxford', attr_value='123456')
]
ad_samp.derivative_sample_id = created1.derivative_sample_id
ad_created = api_instance.create_assay_datum(ad_samp)
results = ds_api_instance.download_derivative_samples_by_os_attr(
'ds_os_attr', 'ad123456')
results = api_instance.download_assay_data_by_os_attr(
'ds_os_attr', 'ad123456')
looked_up = results.assay_data[0]
fetched = api_instance.download_assay_datum(
looked_up.assay_datum_id)
assert ad_created == fetched, "create response != download response"
fetched.assay_datum_id = None
assert ad_samp == fetched, "upload != download response"
assert looked_up == ad_created
api_instance.delete_assay_datum(ad_created.assay_datum_id)
ds_api_instance.delete_derivative_sample(
created1.derivative_sample_id)
ds_api_instance.delete_derivative_sample(
created2.derivative_sample_id)
os_api_instance.delete_original_sample(created.original_sample_id)
except ApiException as error:
self.check_api_exception(api_factory,
"AssayDataApi->create_assay_datum", 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