from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, normalizeFilesDirs
from cwltool.load_tool import load_tool
from cwltool.errors import WorkflowException
+from arvados_cwl.context import ArvRuntimeContext
from .fsaccess import CollectionFetcher, CollectionFsAccess
debug = job_order_object["arv:debug"]
del job_order_object["arv:debug"]
- runner = arvados_cwl.ArvCwlRunner(api_client=arvados.safeapi.ThreadSafeApiCache(
+ arvargs = argparse.Namespace()
+ arvargs.work_api = "jobs"
+ arvargs.output_name = output_name
+ arvargs.output_tags = output_tags
+ arvargs.thread_count = 1
+
+ runner = arvados_cwl.ArvCwlExecutor(api_client=arvados.safeapi.ThreadSafeApiCache(
api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
- output_name=output_name, output_tags=output_tags)
+ arvargs=arvargs)
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=runner.api,
- fs_access=make_fs_access(""),
- num_retries=runner.num_retries))
+ t = load_tool(toolpath, runner.loadingContext)
if debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
logging.getLogger("cwltool").setLevel(logging.DEBUG)
- args = argparse.Namespace()
+ args = ArvRuntimeContext(vars(arvargs))
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.on_error = on_error
args.priority = arvados_cwl.DEFAULT_PRIORITY
args.do_validate = True
args.disable_js_validation = False
+ args.tmp_outdir_prefix = "tmp"
- runner.arv_executor(t, job_order_object, **vars(args))
+ runner.arv_executor(t, job_order_object, args, logger=logger)
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)