import functools
from arvados.api import OrderedJsonModel
-from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, getListing, normalizeFilesDirs
+from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, normalizeFilesDirs
from cwltool.load_tool import load_tool
from cwltool.errors import WorkflowException
-from .fsaccess import CollectionFetcher
+from .fsaccess import CollectionFetcher, CollectionFsAccess
logger = logging.getLogger('arvados.cwl-runner')
return v
def keeppathObj(v):
- v["location"] = keeppath(v["location"])
+ if "location" in v:
+ v["location"] = keeppath(v["location"])
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
- adjustDirObjs(job_order_object, functools.partial(getListing, arvados_cwl.fsaccess.CollectionFsAccess("", api_client=api)))
output_name = None
output_tags = None
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
output_name=output_name, output_tags=output_tags)
+ make_fs_access = functools.partial(CollectionFsAccess,
+ collection_cache=runner.collection_cache)
+
t = load_tool(toolpath, runner.arv_make_tool,
fetcher_constructor=functools.partial(CollectionFetcher,
- api_client=api,
- keep_client=arvados.keep.KeepClient(api_client=api, num_retries=4)))
+ api_client=runner.api,
+ fs_access=make_fs_access(""),
+ num_retries=runner.num_retries))
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]
args.basedir = os.getcwd()
args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
+ args.make_fs_access = make_fs_access
+
runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
if isinstance(e, WorkflowException):