Merge branch '11017-docker-migration'

[arvados.git] / sdk / cwl / arvados_cwl / crunch_script.py

diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index 4b1b42843b67ae8ee2efb372186f54043355aa1d..f33619391d89ef2583d406a6ed25a22cb87f5159 100644 (file)
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -23,6 +23,8 @@ from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, getListing
 from cwltool.load_tool import load_tool
 from cwltool.errors import WorkflowException
 
+from .fsaccess import CollectionFetcher
+
 logger = logging.getLogger('arvados.cwl-runner')
 
 def run():
@@ -67,6 +69,7 @@ def run():
         output_name = None
         output_tags = None
         enable_reuse = True
+        on_error = "continue"
         if "arv:output_name" in job_order_object:
             output_name = job_order_object["arv:output_name"]
             del job_order_object["arv:output_name"]
@@ -79,14 +82,22 @@ def run():
             enable_reuse = job_order_object["arv:enable_reuse"]
             del job_order_object["arv:enable_reuse"]
 
+        if "arv:on_error" in job_order_object:
+            on_error = job_order_object["arv:on_error"]
+            del job_order_object["arv:on_error"]
+
         runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
                                           output_name=output_name, output_tags=output_tags)
 
-        t = load_tool(toolpath, runner.arv_make_tool)
+        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)))
 
         args = argparse.Namespace()
         args.project_uuid = arvados.current_job()["owner_uuid"]
         args.enable_reuse = enable_reuse
+        args.on_error = on_error
         args.submit = False
         args.debug = False
         args.quiet = False
@@ -94,7 +105,7 @@ def run():
         args.basedir = os.getcwd()
         args.name = None
         args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
-        outputObj = runner.arv_executor(t, job_order_object, **vars(args))
+        runner.arv_executor(t, job_order_object, **vars(args))
     except Exception as e:
         if isinstance(e, WorkflowException):
             logging.info("Workflow error %s", e)