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 test_create_file_obj_bad_file_group(self):
file_group_id = str(uuid.uuid4())
with self.assertRaises(Exception) as context:
file_obj = FileProcessor.create_file_obj(
"file:///path/to/file.unknown_data_type", 123345, "sha1$calculated checksum", file_group_id, {}
)
self.assertTrue("Invalid FileGroup id: %s" % file_group_id in context.exception)
def test_create_file_type_unknown(self):
file_obj = FileProcessor.create_file_obj(
'file:///path/to/file.unknown_data_type', 123345,
'sha1$calculated checksum', str(self.file_group.id), {})
self.assertEqual(file_obj.file_type, self.file_type_unknown)
def test_create_file_setting_proper_file_type_based_on_extension(self):
file_obj = FileProcessor.create_file_obj(
'file:///path/to/file.fastq.gz', 123345,
'sha1$calculated checksum', str(self.file_group.id), {})
self.assertEqual(file_obj.file_type, self.file_type_fastq)
