def __init__(self,
workflow_uri_path: str,
root_directory: str,
stove_provenance_directory: str,
executor: Optional[JobExecutor] = None,
loading_context: Optional[LoadingContext] = None,
runtime_context: Optional[RuntimeContext] = None) -> None:
"""Easy way to load a CWL document for execution."""
super().__init__(root_directory=root_directory,
executor=executor,
loading_context=loading_context,
runtime_context=runtime_context)
self.store_provenance_directory = stove_provenance_directory
self.loading_context, self.workflow_object, self.uri = fetch_document(
workflow_uri_path, self.loading_context)
make_fs_access = self.runtime_context.make_fs_access \
if self.runtime_context.make_fs_access is not None else StdFsAccess
ro = ResearchObject(make_fs_access(""), )
self.runtime_context.research_obj = ro
log_file_io = ro.open_log_file_for_activity(ro.engine_uuid)
prov_log_handler = logging.StreamHandler(cast(IO[str], log_file_io))
prov_log_handler.setFormatter(ProvLogFormatter())
_logger.addHandler(prov_log_handler)
_logger.debug("[provenance] Logging to %s", log_file_io)
def research_object() -> Generator[ResearchObject, None, None]:
re_ob = ResearchObject(StdFsAccess(""))
yield re_ob
re_ob.close()
