def _register_file(val, size, group_id, metadata, file_list):
file_obj = copy.deepcopy(val)
file_obj.pop("basename", None)
file_obj.pop("nameroot", None)
file_obj.pop("nameext", None)
uri = file_obj.pop('location', None)
checksum = file_obj.pop("checksum", None)
try:
file_obj_db = FileProcessor.create_file_obj(
uri, size, checksum, group_id, metadata)
except FileConflictException as e:
logger.warning(str(e))
# TODO: Check what to do in case file already exist in DB.
file_obj_db = FileProcessor.get_file_obj(uri)
FileProcessor.update_file(file_obj_db, file_obj_db.path, metadata)
secondary_files = file_obj.pop('secondaryFiles', [])
secondary_file_list = []
secondary_files_obj = PortProcessor.process_files(
secondary_files,
PortAction.REGISTER_OUTPUT_FILES,
group_id=group_id,
metadata=metadata,
file_list=secondary_file_list)
if secondary_files_obj:
file_obj['secondaryFiles'] = secondary_files_obj
file_obj['location'] = FileProcessor.get_bid_from_file(file_obj_db)
if file_list is not None:
file_list.append('bid://%s' %
FileProcessor.get_bid_from_file(file_obj_db))
file_list.extend([f['location'] for f in secondary_files_obj])
return file_obj
def from_db(cls, port_id):
try:
port = Port.objects.get(id=port_id)
except Port.DoesNotExist:
raise PortObjectConstructException('Port with id:')
return cls(str(port.run.id),
port.name,
port.port_type,
port.schema,
port.secondary_files,
port.db_value,
port.value,
[FileProcessor.get_bid_from_file(f) for f in port.files.all()],
port_id=port_id,
notify=port.notify)
def test_run_complete_job(
self, mock_populate_job_group_notifier, mock_get_pipeline, memcache_task_lock, send_notification
):
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_populate_job_group_notifier.return_value = None
mock_get_pipeline.return_value = app
memcache_task_lock.return_value = True
send_notification.return_value = False
run = RunObjectFactory.from_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 = RunObjectFactory.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)
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)