def test_patch_biospecimen_genomic_file(self, mock):
"""
Test updating an existing biospecimen_genomic_file
"""
indexd = MockIndexd()
mock.Session().post = indexd.post
mock.Session().get = indexd.get
mock.Session().put = indexd.put
response = self._make_biospecimen_genomic_file(mock)
orig = BiospecimenGenomicFile.query.count()
resp = json.loads(response.data.decode('utf-8'))
biospecimen_genomic_file = resp['results']
kf_id = biospecimen_genomic_file['kf_id']
body = {}
self.assertEqual(orig, BiospecimenGenomicFile.query.count())
response = self.client.patch(url_for(BS_GF_URL, kf_id=kf_id),
headers=self._api_headers(),
data=json.dumps(body))
resp = json.loads(response.data.decode('utf-8'))
# Status code
self.assertEqual(response.status_code, 200)
# Message
self.assertIn('biospecimen_genomic_file', resp['_status']['message'])
self.assertIn('updated', resp['_status']['message'])
# Content - check only patched fields are updated
bgf = BiospecimenGenomicFile.query.get(kf_id)
self.assertEqual(orig, BiospecimenGenomicFile.query.count())
def test_post_biospecimen_genomic_file(self, mock):
"""
Test creating a new biospecimen_genomic_file
"""
indexd = MockIndexd()
mock.Session().post = indexd.post
mock.Session().get = indexd.get
mock.Session().put = indexd.put
response = self._make_biospecimen_genomic_file(mock)
resp = json.loads(response.data.decode('utf-8'))
self.assertEqual(response.status_code, 201)
self.assertIn('biospecimen_genomic_file', resp['_status']['message'])
self.assertIn('created', resp['_status']['message'])
# Content check
biospecimen_genomic_file = resp['results']
bsgf = BiospecimenGenomicFile.query.get(
biospecimen_genomic_file['kf_id'])
# Relations check
bs_kfid = resp['_links']['biospecimen'].split('/')[-1]
gf_kfid = resp['_links']['genomic_file'].split('/')[-1]
assert bsgf.biospecimen_id == bs_kfid
assert bsgf.genomic_file_id == gf_kfid
assert Biospecimen.query.get(bs_kfid) is not None
assert GenomicFile.query.get(gf_kfid) is not None
def test_get_biospecimen_genomic_file(self, mock):
"""
Test retrieving a biospecimen_genomic_file by id
"""
indexd = MockIndexd()
mock.Session().post = indexd.post
mock.Session().get = indexd.get
mock.Session().put = indexd.put
resp = self._make_biospecimen_genomic_file(mock)
resp = json.loads(resp.data.decode('utf-8'))
kf_id = resp['results']['kf_id']
response = self.client.get(url_for(BS_GF_URL, kf_id=kf_id),
headers=self._api_headers())
resp = json.loads(response.data.decode('utf-8'))
self.assertEqual(response.status_code, 200)
biospecimen_genomic_file = resp['results']
bsgf = BiospecimenGenomicFile.query.get(kf_id)
self.assertEqual(kf_id, biospecimen_genomic_file['kf_id'])
self.assertEqual(kf_id, bsgf.kf_id)
def test_delete(self, mock):
"""
Test delete cavatica_task
"""
indexd = MockIndexd()
mock.Session().post = indexd.post
mock.Session().get = indexd.get
mock.Session().put = indexd.put
# Create and save cavatica_tasks and dependents
participants, cavatica_tasks = self._create_and_save_cavatica_tasks()
kf_id = cavatica_tasks[0].kf_id
# Delete cavatica_task
ct = CavaticaTask.query.get(kf_id)
db.session.delete(ct)
db.session.commit()
# Check database
self.assertEqual(0, CavaticaTaskGenomicFile.query.
filter_by(cavatica_task_id=kf_id).count())
self.assertEqual(1, CavaticaTask.query.count())
self.assertNotIn(cavatica_tasks[0], CavaticaTask.query.all())
self.assertEqual(8, GenomicFile.query.count())
def test_create_and_find(self, mock):
"""
Test create cavatica_task
"""
indexd = MockIndexd()
mock.Session().post = indexd.post
mock.Session().get = indexd.get
mock.Session().put = indexd.put
# Create and save cavatica_tasks and dependents
participants, cavatica_tasks = self._create_and_save_cavatica_tasks()
GenomicFile.query.limit(5).all()
# Check database
# Count checks
# 4 participants, 2 genomic files per participant
# 2 cavatica_tasks, all genomic files are in both cavatica_tasks
self.assertEqual(8, GenomicFile.query.count())
self.assertEqual(2, CavaticaTask.query.count())
self.assertEqual(16, CavaticaTaskGenomicFile.query.count())
self.assertEqual(8, CavaticaTaskGenomicFile.query.filter_by(
is_input=False).count())
self.assertEqual(8, CavaticaTaskGenomicFile.query.filter_by(
is_input=True).count())
# CavaticaTask content checks
for p in participants:
gfs = (p.biospecimens[0].genomic_files)
for gf in gfs:
gf_cavatica_tasks = [
ctgf.cavatica_task
for ctgf in gf.cavatica_task_genomic_files]
for gf_cavatica_task in gf_cavatica_tasks:
self.assertIn(gf_cavatica_task, cavatica_tasks)
self.assertEqual(
True,
(gf_cavatica_task.name == 'kf-alignment1'
or gf_cavatica_task.name == 'kf-alignment2'))
