def test_run_creation_from_cwl(self, mock_get_pipeline):
with open('runner/tests/run/pair-workflow.cwl', 'r') as f:
app = json.load(f)
with open('runner/tests/run/inputs.json', 'r') as f:
inputs = json.load(f)
mock_get_pipeline.return_value = app
run = RunObject.from_cwl_definition(str(self.run.id), inputs)
run.ready()
for inp in run.inputs:
if inp.name == 'pair':
self.assertEqual(inp.db_value[0]['R1'][0]['location'],
'bid://%s' % str(self.file1.id))
self.assertEqual(inp.value[0]['R1'][0]['path'],
self.file1.path)
self.assertEqual(inp.db_value[0]['R2'][0]['location'],
'bid://%s' % str(self.file2.id))
self.assertEqual(inp.value[0]['R2'][0]['path'],
self.file2.path)
self.assertEqual(inp.db_value[1]['R1'][0]['location'],
'bid://%s' % str(self.file3.id))
self.assertEqual(inp.value[1]['R1'][0]['path'],
self.file3.path)
self.assertEqual(inp.db_value[1]['R2'][0]['location'],
'bid://%s' % str(self.file4.id))
self.assertEqual(inp.value[1]['R2'][0]['path'],
self.file4.path)
def create_run_task(run_id, inputs, output_directory=None):
logger.info("Creating and validating Run for %s" % run_id)
run = RunObject.from_cwl_definition(run_id, inputs)
run.ready()
RunObject.to_db(run)
submit_job.delay(run_id, output_directory)
logger.info("Run %s Ready" % run_id)
def test_run_to_db(self, mock_get_pipeline):
with open('runner/tests/run/pair-workflow.cwl', 'r') as f:
app = json.load(f)
with open('runner/tests/run/inputs.json', 'r') as f:
inputs = json.load(f)
mock_get_pipeline.return_value = app
run = RunObject.from_cwl_definition(str(self.run.id), inputs)
run.to_db()
try:
run_obj = Run.objects.get(id=run.run_id)
except Run.DoesNotExist as e:
pass
self.assertEqual(str(run_obj.id), run.run_id)
def create_run_task(run_id, inputs, output_directory=None):
logger.info("Creating and validating Run")
try:
run = RunObject.from_cwl_definition(run_id, inputs)
run.ready()
except RunCreateException as e:
run = RunObject.from_db(run_id)
run.fail({'details': str(e)})
RunObject.to_db(run)
logger.info("Run %s Failed" % run_id)
else:
RunObject.to_db(run)
submit_job.delay(run_id, output_directory)
logger.info("Run %s Ready" % run_id)
def test_multiple_failed_on_same_job(self, mock_get_pipeline):
with open('runner/tests/run/pair-workflow.cwl', 'r') as f:
app = json.load(f)
with open('runner/tests/run/inputs.json', 'r') as f:
inputs = json.load(f)
mock_get_pipeline.return_value = app
run = RunObject.from_cwl_definition(str(self.run.id), inputs)
run.to_db()
operator_run = OperatorRun.objects.first()
operator_run.runs.add(run.run_obj)
num_failed_runs = operator_run.num_failed_runs
fail_job(run.run_id, {'details': 'Error has happened'})
fail_job(run.run_id, {'details': 'Error has happened'})
fail_job(run.run_id, {'details': 'Error has happened'})
operator_run.refresh_from_db()
self.assertEqual(operator_run.num_failed_runs, num_failed_runs + 1)
def test_run_complete_job(self, mock_get_pipeline):
with open('runner/tests/run/pair-workflow.cwl', 'r') as f:
app = json.load(f)
with open('runner/tests/run/inputs.json', 'r') as f:
inputs = json.load(f)
mock_get_pipeline.return_value = app
run = RunObject.from_cwl_definition(str(self.run.id), inputs)
run.to_db()
operator_run = OperatorRun.objects.first()
operator_run.runs.add(run.run_obj)
num_completed_runs = operator_run.num_completed_runs
complete_job(run.run_id, self.outputs)
operator_run.refresh_from_db()
self.assertEqual(operator_run.num_completed_runs,
num_completed_runs + 1)
run_obj = RunObject.from_db(run.run_id)
file_obj = File.objects.filter(path=self.outputs['maf']['location'].
replace('file://', '')).first()
run_obj.to_db()
for out in run_obj.outputs:
if out.name == 'maf':
self.assertEqual(out.value['location'],
self.outputs['maf']['location'])
self.assertEqual(FileProcessor.get_bid_from_file(file_obj),
out.db_value['location'])
port = Port.objects.filter(run_id=run_obj.run_id, name='bams').first()
self.assertEqual(len(port.files.all()), 4)
expected_result = (
'/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_1.rg.md.abra.printreads.bam',
'/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_1.rg.md.abra.printreads.bai',
'/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_2.rg.md.abra.printreads.bam',
'/output/argos_pair_workflow/425194f6-a974-4c2f-995f-f27d7ba54ddc/outputs/test_2.rg.md.abra.printreads.bai'
)
self.assertTrue(port.files.all()[0].path in expected_result)
self.assertTrue(port.files.all()[1].path in expected_result)
self.assertTrue(port.files.all()[2].path in expected_result)
self.assertTrue(port.files.all()[3].path in expected_result)
