from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, normalizeFilesDirs
from cwltool.load_tool import load_tool
from cwltool.errors import WorkflowException
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, normalizeFilesDirs
from cwltool.load_tool import load_tool
from cwltool.errors import WorkflowException
- runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
+ runner = arvados_cwl.ArvCwlRunner(api_client=arvados.safeapi.ThreadSafeApiCache(
+ api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
output_name=output_name, output_tags=output_tags)
make_fs_access = functools.partial(CollectionFsAccess,
output_name=output_name, output_tags=output_tags)
make_fs_access = functools.partial(CollectionFsAccess,
logging.getLogger('arvados').setLevel(logging.DEBUG)
logging.getLogger("cwltool").setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
logging.getLogger("cwltool").setLevel(logging.DEBUG)
args.make_fs_access = make_fs_access
args.trash_intermediate = False
args.intermediate_output_ttl = 0
args.make_fs_access = make_fs_access
args.trash_intermediate = False
args.intermediate_output_ttl = 0
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)