def test_update_study_bad_taxa(self, api_factory):
api_instance = api_factory.OriginalSampleApi()
study_api = api_factory.StudyApi()
try:
samp = openapi_client.OriginalSample(
None, study_name='2005-MD-UP', partner_species='P. falciparum')
created = api_instance.create_original_sample(samp)
study1 = study_api.download_study('2005-MD-UP')
assert study1.partner_species[
0].partner_species == 'P. falciparum', 'Species not set'
# Taxa or study name are the only things you can update
# partner_species belong to the sampling event
taxa = openapi_client.Taxonomy(999999)
study1.partner_species[0].taxa = [taxa]
with pytest.raises(ApiException, status=422):
study2 = study_api.update_study('2004-MD-UP', study1)
#assert study2.partner_species[0].taxa[0].taxonomy_id == 999999, 'taxa not updated'
api_instance.delete_original_sample(created.original_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "SamplingEventApi->create_sampling_event", error)
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_download_studies(self, api_factory):
api_instance = api_factory.OriginalSampleApi()
study_api = api_factory.StudyApi()
samp = openapi_client.OriginalSample(None, study_name='2000-MD-UP')
try:
created = api_instance.create_original_sample(samp)
studies = study_api.download_studies()
if not api_factory.is_authorized(None):
pytest.fail('Unauthorized call to download_studies succeeded')
found = False
for study in studies.studies:
if study.name == '2000-MD-UP' and study.code == '2000':
found = True
assert found, 'Study does not exist'
api_instance.delete_original_sample(created.original_sample_id)
except ApiException as error:
self.check_api_exception(
api_factory, "SamplingEventApi->create_sampling_event", error)
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_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 test_update_partner_species(self, api_factory):
api_instance = api_factory.OriginalSampleApi()
try:
samp = openapi_client.OriginalSample(None, study_name='3001-MD-UP',
partner_species='P. falciparum')
created = api_instance.create_original_sample(samp)
new_samp = openapi_client.OriginalSample(None, study_name='3001-MD-UP',
partner_species='P. vivax')
updated = api_instance.update_original_sample(
created.original_sample_id, new_samp)
fetched = api_instance.download_original_sample(
created.original_sample_id)
assert updated == fetched, "update response != download response"
fetched.original_sample_id = None
assert new_samp == fetched, "update != download response"
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_original_sample_from_values(self, values):
study_id = None
if 'study_id' in values:
study_id = values['study_id']
o_sample = openapi_client.OriginalSample(None, study_name=study_id)
idents = []
if 'sample_roma_id' in values:
idents.append(openapi_client.Attr ('roma_id', values['sample_roma_id'],
self._event_set))
if 'sample_partner_id' in values and values['sample_partner_id']:
idents.append(openapi_client.Attr ('partner_id', values['sample_partner_id'],
self._event_set))
if 'sample_partner_id_1' in values and values['sample_partner_id_1']:
idents.append(openapi_client.Attr ('partner_id', values['sample_partner_id_1'],
self._event_set))
if 'sample_oxford_id' in values and values['sample_oxford_id']:
idents.append(openapi_client.Attr ('oxford_id', values['sample_oxford_id'],
self._event_set))
if 'sample_alternate_oxford_id' in values and len(values['sample_alternate_oxford_id']) > 0:
idents.append(openapi_client.Attr ('alt_oxford_id',
values['sample_alternate_oxford_id'],
self._event_set))
if 'sample_source_id' in values and values['sample_source_id'] and values['sample_source_type']:
idents.append(openapi_client.Attr (values['sample_source_type'],
values['sample_source_id'],
self._event_set))
if 'sample_source_id1' in values and values['sample_source_id1'] and values['sample_source_type1']:
idents.append(openapi_client.Attr (values['sample_source_type1'],
values['sample_source_id1'],
self._event_set))
if 'sample_source_id2' in values and values['sample_source_id2'] and values['sample_source_type2']:
idents.append(openapi_client.Attr (values['sample_source_type2'],
values['sample_source_id2'],
self._event_set))
if 'days_in_culture' in values:
o_sample.days_in_culture = int(float(values['days_in_culture']))
if 'species' in values and values['species'] and len(values['species']) > 0:
o_sample.partner_species = values['species']
o_sample.attrs = idents
return o_sample
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_download_study(self, api_factory):
api_instance = api_factory.OriginalSampleApi()
study_api = api_factory.StudyApi()
samp = openapi_client.OriginalSample(None,
study_name='2002-MD-UP',
partner_species='P. falciparum')
try:
created = api_instance.create_original_sample(samp)
study1 = study_api.download_study('2002-MD-UP')
study2 = study_api.download_study('2002')
assert study1 == study2, 'Study does not match'
assert study1.partner_species[
0].partner_species == 'P. falciparum', 'Species not set'
api_instance.delete_original_sample(created.original_sample_id)
except ApiException as error:
self.check_api_exception(api_factory,
"LocationApi->create_location", 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
def test_multiple_partner_species(self, api_factory):
api_instance = api_factory.OriginalSampleApi()
study_api_instance = api_factory.StudyApi()
study_ident = '3000-MD-UP'
try:
samp1 = openapi_client.OriginalSample(None, study_name=study_ident,
partner_species='P. falciparum')
created1 = api_instance.create_original_sample(samp1)
fetched1 = api_instance.download_original_sample(created1.original_sample_id)
assert created1 == fetched1, "create response != download response"
fetched1.original_sample_id = None
assert samp1 == fetched1, "upload != download response"
samp2 = openapi_client.OriginalSample(None, study_name=study_ident,
partner_species='P. falciparum')
created2 = api_instance.create_original_sample(samp2)
fetched2 = api_instance.download_original_sample(created2.original_sample_id)
assert created2 == fetched2, "create response != download response"
fetched2.original_sample_id = None
assert samp2 == fetched2, "upload != download response"
samp3 = openapi_client.OriginalSample(None, study_name=study_ident,
partner_species='P. falciparum + P. vivax')
created3 = api_instance.create_original_sample(samp3)
fetched3 = api_instance.download_original_sample(created3.original_sample_id)
assert created3 == fetched3, "create response != download response"
fetched3.original_sample_id = None
assert samp3 == fetched3, "upload != download response"
samp4 = openapi_client.OriginalSample(None, study_name=study_ident,
partner_species='P. falciparum + P. vivax')
created4 = api_instance.create_original_sample(samp4)
fetched4 = api_instance.download_original_sample(created4.original_sample_id)
assert created4 == fetched4, "create response != download response"
fetched4.original_sample_id = None
assert samp4 == fetched4, "upload != download response"
study_detail = study_api_instance.download_study(study_ident)
for species in study_detail.partner_species:
if species.partner_species == 'P. falciparum':
species.taxa = [openapi_client.Taxonomy(taxonomy_id=5833)]
else:
species.taxa = [openapi_client.Taxonomy(taxonomy_id=5833),
openapi_client.Taxonomy(taxonomy_id=5855)]
study_api_instance.update_study(study_ident, study_detail)
fetched1 = api_instance.download_original_sample(created1.original_sample_id)
assert len(fetched1.partner_taxonomies) == 1
assert (int)(fetched1.partner_taxonomies[0].taxonomy_id) == 5833
fetched3 = api_instance.download_original_sample(created3.original_sample_id)
assert len(fetched3.partner_taxonomies) == 2
assert (int)(fetched3.partner_taxonomies[0].taxonomy_id) == 5833 and (int)(fetched3.partner_taxonomies[1].taxonomy_id) == 5855
fetched = api_instance.download_original_samples_by_taxa(5833)
assert len(fetched.original_samples) == 4
for original_sample in fetched.original_samples:
if original_sample.original_sample_id == fetched1.original_sample_id:
assert original_sample == fetched1
if original_sample.original_sample_id == fetched2.original_sample_id:
assert original_sample == fetched2
if original_sample.original_sample_id == fetched3.original_sample_id:
assert original_sample == fetched3
if original_sample.original_sample_id == fetched4.original_sample_id:
assert original_sample == fetched4
api_instance.delete_original_sample(created1.original_sample_id)
api_instance.delete_original_sample(created2.original_sample_id)
api_instance.delete_original_sample(created3.original_sample_id)
api_instance.delete_original_sample(created4.original_sample_id)
except ApiException as error:
self.check_api_exception(api_factory,
"OriginalSampleApi->test_multiple_partner_species", error)
