13627: a-c-r migration to cwltool loading/runtimeContext API

[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 7fbbd29d50d72f385b5e1ea95f2b093405518baf..94e9c8fc84abcd2511935d63b7c413e77da38948 100644 (file)
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -27,6 +27,7 @@ from cwltool.process import shortname
 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, normalizeFilesDirs
 from cwltool.load_tool import load_tool
 from cwltool.errors import WorkflowException
+from cwltool.context import RuntimeContext
 
 from .fsaccess import CollectionFetcher, CollectionFsAccess
 
@@ -75,6 +76,8 @@ def run():
         output_tags = None
         enable_reuse = True
         on_error = "continue"
+        debug = False
+
         if "arv:output_name" in job_order_object:
             output_name = job_order_object["arv:output_name"]
             del job_order_object["arv:output_name"]
@@ -91,7 +94,12 @@ def run():
             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()),
+        if "arv:debug" in job_order_object:
+            debug = job_order_object["arv:debug"]
+            del job_order_object["arv:debug"]
+
+        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,
@@ -103,12 +111,17 @@ def run():
                                                   fs_access=make_fs_access(""),
                                                   num_retries=runner.num_retries))
 
-        args = argparse.Namespace()
+        if debug:
+            logger.setLevel(logging.DEBUG)
+            logging.getLogger('arvados').setLevel(logging.DEBUG)
+            logging.getLogger("cwltool").setLevel(logging.DEBUG)
+
+        args = RuntimeContext()
         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.debug = debug
         args.quiet = False
         args.ignore_docker_for_reuse = False
         args.basedir = os.getcwd()
@@ -117,8 +130,12 @@ def run():
         args.make_fs_access = make_fs_access
         args.trash_intermediate = False
         args.intermediate_output_ttl = 0
+        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)
     except Exception as e:
         if isinstance(e, WorkflowException):
             logging.info("Workflow error %s", e)