def bet(record):
import nipype
from nipype.interfaces.fsl import BET
from nipype.utils.filemanip import hash_infile
nipype.config.enable_provenance()
in_file_uri = record['t1_uri']
os.chdir('/tmp')
fname = 'anatomy.nii.gz'
with open(fname, 'wb') as fd:
response = requests.get(in_file_uri, stream=True)
if not response.ok:
response.raise_for_status()
for chunk in response.iter_content(1024):
fd.write(chunk)
# Check if interface has run with this input before
sha = hash_infile(os.path.abspath(fname), crypto=hashlib.sha512)
select = SelectQuery(config=app.config)
res = select.execute_select('E0921842-1EDB-49F8-A4B3-BA51B85AD407')
sha_recs = res[res.sha512.str.contains(sha)]
bet_recs = res[res.interface.str.contains('BET')]
results = dict()
if sha_recs.empty or \
(not sha_recs.empty and bet_recs.empty):
better = BET()
better.inputs.in_file = os.path.abspath(fname)
result = better.run()
prov = result.provenance.rdf().serialize(format='json-ld')
results.update({'prov': prov})
else:
results.update({'prov': res.to_json(orient='records')})
return results
def post(self):
args = parser.parse_args()
result = []
select = SelectQuery()
df = select.execute_select(args['query_uuid'],
turtle_str=args['turtle_file'])
for record in df.to_dict(outtype='records'):
task_id = record['task']
task = celery.tasks[task_id]
res = task.apply_async([record])
record.update({"task_id": res.task_id})
result.append(record)
return result
class SelectQueryTestCase(unittest.TestCase):
def setUp(self):
self.query = SelectQuery()
def test_init(self):
self.assertIsInstance(self.query, SelectQuery)
self.assertGreater(len(self.query.sparql_meta), 0)
def test_execute_select(self):
res = self.query.execute_select(0)
self.assertIsInstance(res, pd.DataFrame)
def setUp(self):
self.query = SelectQuery()