14198: Bringing unit tests up to date WIP

[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 5024e95f77df785abf668c68364dadc4d49fb2a4..7512d5bef27f28014f650d897d24e3d59cb7b3c4 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 arvados_cwl.context import ArvRuntimeContext
 
 from .fsaccess import CollectionFetcher, CollectionFsAccess
 
@@ -97,25 +98,27 @@ def run():
             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
@@ -134,7 +137,7 @@ def run():
         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)