def _covert_to_cwl_format(val):
file_obj = copy.deepcopy(val)
location = file_obj.pop('location', None)
if location:
try:
file_db_object = FileProcessor.get_file_obj(location)
except FileHelperException as e:
raise PortProcessorException('File %s not found' % location)
path = file_db_object.path
path_obj = Path(path)
checksum = FileProcessor.get_file_checksum(file_db_object)
if checksum:
file_obj['checksum'] = checksum
size = FileProcessor.get_file_size(file_db_object)
if size:
file_obj['size'] = size
file_obj['basename'] = path_obj.name
file_obj['nameext'] = path_obj.suffix
file_obj['nameroot'] = path_obj.stem
file_obj['path'] = path
secondary_files = file_obj.pop('secondaryFiles', [])
secondary_files_value = PortProcessor.process_files(
secondary_files, PortAction.CONVERT_TO_CWL_FORMAT)
if secondary_files_value:
file_obj['secondaryFiles'] = secondary_files_value
return file_obj
def _convert_to_path(val):
file_obj = copy.deepcopy(val)
location = file_obj.pop("location", None)
if not location and val.get("contents"):
logger.debug("Processing file literal %s", str(val))
return val
try:
path = FileProcessor.get_file_path(location)
except FileHelperException as e:
raise PortProcessorException("File %s not found" % location)
secondary_files = file_obj.pop("secondaryFiles", [])
secondary_files_value = PortProcessor.process_files(secondary_files, PortAction.CONVERT_TO_PATH)
if secondary_files_value:
file_obj["secondaryFiles"] = secondary_files_value
file_obj["path"] = path
return file_obj
def _process_file(file_obj, action, **kwargs):
if action == PortAction.CONVERT_TO_BID:
return PortProcessor._update_location_to_bid(file_obj, kwargs.get('file_list'))
if action == PortAction.FIX_DB_VALUES:
return PortProcessor._fix_locations_in_db(file_obj, kwargs.get('file_list'))
if action == PortAction.CONVERT_TO_PATH:
return PortProcessor._convert_to_path(file_obj)
if action == PortAction.CONVERT_TO_CWL_FORMAT:
return PortProcessor._covert_to_cwl_format(file_obj)
if action == PortAction.REGISTER_OUTPUT_FILES:
return PortProcessor._register_file(file_obj,
kwargs.get('size'),
kwargs.get('group_id'),
kwargs.get('metadata'),
kwargs.get('file_list'))
if action == PortAction.SEND_AS_NOTIFICATION:
return PortProcessor._send_as_notification(file_obj, kwargs.get('job_group'))
else:
raise PortProcessorException('Unknown PortProcessor action: %s' % action)
def _process_file(file_obj, action, **kwargs):
if action == PortAction.CONVERT_TO_BID:
return PortProcessor._update_location_to_bid(file_obj, kwargs.get("file_list"))
if action == PortAction.FIX_DB_VALUES:
return PortProcessor._fix_locations_in_db(file_obj, kwargs.get("file_list"))
if action == PortAction.CONVERT_TO_PATH:
return PortProcessor._convert_to_path(file_obj)
if action == PortAction.CONVERT_TO_CWL_FORMAT:
return PortProcessor._covert_to_cwl_format(file_obj)
if action == PortAction.REGISTER_OUTPUT_FILES:
return PortProcessor._register_file(
file_obj, kwargs.get("size"), kwargs.get("group_id"), kwargs.get("metadata"), kwargs.get("file_list")
)
if action == PortAction.SEND_AS_NOTIFICATION:
return PortProcessor._send_as_notification(file_obj, kwargs.get("job_group"))
if action == PortAction.NEXTFLOW_TEMPLATE:
return file_obj["path"]
else:
raise PortProcessorException("Unknown PortProcessor action: %s" % action)