def test_creates_runs1(self, submit_job):
"""
Test that sending data through the API view 'post' method starts a Run
Checks to make sure that a Run is successfully created
"""
# Load fixtures
test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR,
"10075_D_single_TN_pair.file.json")
call_command("loaddata", test_files_fixture, verbosity=0)
test_files_fixture = os.path.join(
settings.TEST_FIXTURE_DIR,
"10075_D_single_TN_pair.filemetadata.json")
call_command("loaddata", test_files_fixture, verbosity=0)
test_files_fixture = os.path.join(settings.TEST_FIXTURE_DIR,
"argos_reference_files.json")
call_command("loaddata", test_files_fixture, verbosity=0)
number_of_runs = len(Run.objects.all())
self.assertEqual(number_of_runs, 0)
pipeline_name = "argos"
request_ids = ["10075_D"]
request = MockRequest()
request.data = dict()
request.data["request_ids"] = request_ids
request.data["pipeline_name"] = pipeline_name
view = OperatorViewSet()
response = view.post(request)
number_of_runs = len(Run.objects.all())
self.assertEqual(number_of_runs, 1)
def test_create_demo_operator_run(self, submit_job):
"""
Test case for creating a Demo Operator run
"""
# there should be no Runs
self.assertEqual(len(Run.objects.all()), 0)
self.assertEqual(len(Port.objects.all()), 0)
self.assertEqual(len(File.objects.all()), 2)
self.assertEqual(len(FileMetadata.objects.all()), 2)
# make a fake http request with some data
# and send it to the API endpoint for starting a run
request = MockRequest()
request.data = {
"request_ids": ["1"],
"pipeline_name": DemoOperator._pipeline_name
}
view = OperatorViewSet()
response = view.post(request)
# there should be 1 run now
self.assertEqual(len(Run.objects.all()), 1)
self.assertEqual(len(Port.objects.all()), 3)
self.assertEqual(len(File.objects.all()), 2)
self.assertEqual(len(FileMetadata.objects.all()), 2)
def test_post_to_view1(self):
"""
Test that data sent through the API view 'post' method returns a successful status and expected response
"""
pipeline_name = 'argos'
request_ids = ['foo', 'bar']
request = MockRequest()
request.data = {}
request.data['request_ids'] = request_ids
request.data['pipeline_name'] = pipeline_name
view = OperatorViewSet()
response = view.post(request)
self.assertEqual(response.data, {'details': "Operator Job submitted {}".format(request_ids)})
self.assertEqual(response.status_code, 200)
def test_live_demo_operator_run(self):
"""
A test case for submitting a job to Ridgeback for the Demo Operator
Need to enable a specific env var to run this test since it should submit a job to Ridgeback
Make sure that a Ridgeback instance is running! Set with env var BEAGLE_RIDGEBACK_URL
This one takes about 3-6min to run on LSF with Ridgeback
NOTE: see this one also; https://github.com/mskcc/beagle/blob/master/runner/tests/run/test_run.py#L291 RunObjectTest.test_run_complete_job
Usage
------
$ BEAGLE_RIDGEBACK_URL=http://silo:5003 LIVE_DEMO=1 PRESERVE=1 python manage.py test runner.tests.operator.demo_operator.test_demo_operator.TestDemoOperator.test_live_demo_operator_run
"""
self.preserve = os.environ.get("PRESERVE")
enable_testcase = os.environ.get("LIVE_DEMO")
request_id = "test_live_demo_operator_run"
if enable_testcase:
print(">>> running TestDemoOperator.test_live_demo_operator_run")
print(">>> using RIDGEBACK_URL: ", settings.RIDGEBACK_URL)
# sanity check: there are no runs to start with
self.assertEqual(len(OperatorRun.objects.all()), 0)
self.assertEqual(len(Run.objects.all()), 0)
# make a file
path = os.path.join(self.tmpdir, "file.txt")
with open(path, "w") as f:
f.write("some data\n")
# make db entries
file_instance = File.objects.create(
file_name=os.path.basename(path),
path=path,
file_group=self.filegroup)
filemetadata_instance = FileMetadata.objects.create(
file=file_instance, metadata={"requestId": request_id})
# check the number of files present, there should be two from setUp and a third from this test
self.assertEqual(len(File.objects.all()), 3)
# make a request to start the run
request = MockRequest()
request.data = {
"request_ids": [request_id],
"pipeline_name": DemoOperator._pipeline_name
}
view = OperatorViewSet()
response = view.post(request)
print(">>> response: ", response, response.data)
# check the Beagle response code for the submitted run
self.assertEqual(response.status_code, 200)
# there should be 1 run now in the Beagle db
self.assertEqual(len(Run.objects.all()), 1)
self.assertEqual(len(OperatorRun.objects.all()), 1)
# get the Run and OperatorRun instances for this run
run_instance = Run.objects.all().first()
operator_run_instance = OperatorRun.objects.all().first()
# wait for the run to finish in Ridgeback
wait_on_runs(run_instance, operator_run_instance)
# check for the output from the Run
print(">>> operator run located at; ", self.tmpdir)
for port in Port.objects.all():
pprint(port.__dict__)
# get the output file
output_port = Port.objects.get(name="output_file")
print(output_port.files.all())
# there should be an extra File object for the output
self.assertEqual(len(File.objects.all()), 4)
self.assertEqual(len(output_port.files.all()), 1)
for file_instance in File.objects.all():
pprint(file_instance.__dict__, indent=4)