class CromwellUnitTests(unittest.TestCase):
@classmethod
def setUpClass(self):
resources = c.resource_dir
self.cromwell = Cromwell(host='btl-cromwell')
self.json = os.path.join(resources, 'hello.json')
self.wdl = os.path.join(resources, 'hello_world.wdl')
self.labels = {'username': '******', 'foo': 'bar'}
def _initiate_workflow(self):
wf = self.cromwell.jstart_workflow(self.wdl, self.json)
time.sleep(5)
return wf
def test_start_workflow(self):
wf = self._initiate_workflow()
wfid = wf['id']
self.assertTrue('id' in wf and 'status' in wf)
self.assertEqual(wf['status'], 'Submitted')
self.assertEqual(len(wfid), 36)
self.cromwell.stop_workflow(wfid)
def test_build_long_url(self):
wf = self._initiate_workflow()
wfid = wf['id']
url_dict = {
'name': 'test_build_long_url',
'id': wfid,
'start': datetime.datetime.now() - datetime.timedelta(days=1),
'end': datetime.datetime.now()
}
query_url = self.cromwell.build_query_url('http://btl-cromwell:9000/api/workflows/v1/query?', url_dict)
r = requests.get(query_url)
self.assertEquals(r.status_code, 200)
self.cromwell.stop_workflow(wfid)
def test_label_workflow(self):
wf = self._initiate_workflow()
wfid = wf['id']
r = self.cromwell.label_workflow(wfid, self.labels)
self.assertEquals(r.status_code, 200)
self.cromwell.stop_workflow(wfid)
def test_explain(self):
wf = self._initiate_workflow()
wfid = wf['id']
time.sleep(10)
result = self.cromwell.explain_workflow(wfid)
self.assertIsInstance(result, tuple)
self.cromwell.stop_workflow(wfid)
def test_stop_workflow(self):
wf = self._initiate_workflow()
wfid = wf['id']
result = self.cromwell.stop_workflow(wfid)
print(result)
self.cromwell.stop_workflow(wfid)
@classmethod
def tearDownClass(self):
print("Done!")
class QueryUnitTests(unittest.TestCase):
@classmethod
def setUpClass(self):
resources = c.resource_dir
self.cromwell = Cromwell(host='btl-cromwell')
self.json = os.path.join(resources, 'hw.json')
self.wdl = os.path.join(resources, 'hw.wdl')
self.labels = {'username': '******', 'foo': 'bar'}
def _initiate_workflow(self):
wf = self.cromwell.jstart_workflow(self.wdl, self.json)
time.sleep(5)
return wf
def test_query_status(self):
wf = self._initiate_workflow()
wfid = wf['id']
result = self.cromwell.query_status(wfid)
self.assertTrue('id' in result and 'status' in result)
self.cromwell.stop_workflow(wfid)
def test_query_metadata(self):
wf = self._initiate_workflow()
wfid = wf['id']
result = self.cromwell.query_metadata(wfid)
self.assertTrue('id' in result and 'submission' in result)
self.cromwell.stop_workflow(wfid)
def test_query_logs(self):
wf = self._initiate_workflow()
wfid = wf['id']
result = self.cromwell.query_logs(wfid)
self.assertTrue('id' in result)
self.cromwell.stop_workflow(wfid)
def test_build_long_url(self):
wf = self._initiate_workflow()
wfid = wf['id']
url_dict = {
'name': 'test_build_long_url',
'id': wfid,
'start': datetime.datetime.now() - datetime.timedelta(days=1),
'end': datetime.datetime.now()
}
query_url = self.cromwell.build_query_url(
'http://btl-cromwell:9000/api/workflows/v1/query?', url_dict)
r = requests.get(query_url)
self.assertEquals(r.status_code, 200)
self.cromwell.stop_workflow(wfid)
def test_query(self):
wf = self._initiate_workflow()
wfid = wf['id']
url_dict = {
'name': 'gatk',
'id': [wfid],
'start': datetime.datetime.now() - datetime.timedelta(days=1),
'end': datetime.datetime.now()
}
result = self.cromwell.query(url_dict)
self.assertTrue(isinstance(result['results'], list), True)
self.cromwell.stop_workflow(wfid)
def test_label_workflow(self):
wf = self._initiate_workflow()
wfid = wf['id']
r = self.cromwell.label_workflow(wfid, self.labels)
self.assertEquals(r.status_code, 200)
self.cromwell.stop_workflow(wfid)
def test_query_labels(self):
wf = self._initiate_workflow()
wfid = wf['id']
labels = {'username': '******', 'foo': 'bar'}
self.cromwell.label_workflow(wfid, self.labels)
# This sleep is needed to make sure the label workflow completes before we query for it.
time.sleep(5)
r = self.cromwell.query_labels(labels)
# Here, the most recent workflow that matches the query will be the last item so we can use that to check
# this assertion.
self.assertTrue(wfid in r['results'][-1]['id'])
self.cromwell.stop_workflow(wfid)
def test_query_filter_by_statuses(self):
from argparse import Namespace
from widdler import call_list
wf = self._initiate_workflow()
wfid = wf['id']
result = call_list(
Namespace(server="btl-cromwell",
all=False,
no_notify=True,
verbose=True,
interval=None,
username="******",
days=1,
filter=['Succeeded', 'Failed']))
statuses = set(d['status'] for d in result)
self.assertEqual(len(statuses), 2)
self.assertIn('Succeeded', statuses)
self.assertIn('Failed', statuses)
self.cromwell.stop_workflow(wfid)
def test_query_filter_by_name(self):
from argparse import Namespace
from widdler import call_list
user_result = call_list(
Namespace(server="btl-cromwell",
all=False,
no_notify=True,
verbose=True,
interval=None,
username="******",
days=1,
filter=None))
user_wfids = set(d['id'] for d in user_result)
all_result = call_list(
Namespace(server="btl-cromwell",
all=False,
no_notify=True,
verbose=True,
interval=None,
username="******",
days=1,
filter=None))
all_wfids = set(d['id'] for d in all_result)
self.assertGreater(len(all_wfids), len(user_wfids))
def test_query_filter_by_days(self):
from argparse import Namespace
from widdler import call_list
result = call_list(
Namespace(server="btl-cromwell",
all=False,
no_notify=True,
verbose=True,
interval=None,
username="******",
days=1,
filter=None))
all_dates = set(d['start'].split('T')[0] for d in result)
self.assertEqual(len(all_dates), 1)
def test_query_backend(self):
self.assertTrue('defaultBackend' in self.cromwell.query_backend())
@classmethod
def tearDownClass(self):
print("Done!")