Merge branch '2411-check-copyright'

[arvados.git] / crunch_scripts / cwl-runner

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 3f2d53d038576b0694a3eea257c8b396ca9e16e0..0c79844d5fc91c68aac1d532aa1af8833a39da8e 100755 (executable)
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -1,15 +1,33 @@
 #!/usr/bin/env python
-
-# Crunch script integration for running arvados-cwl-runner (importing
-# arvados_cwl module) inside a crunch job.
+# Copyright (C) The Arvados Authors. All rights reserved.
 #
+# SPDX-License-Identifier: Apache-2.0
+
+# Crunch script integration for running arvados-cwl-runner inside a crunch job.
+
+import arvados_cwl
+import sys
+
+try:
+    # Use the crunch script defined in the arvados_cwl package.  This helps
+    # prevent the crunch script from going out of sync with the rest of the
+    # arvados_cwl package.
+    import arvados_cwl.crunch_script
+    arvados_cwl.crunch_script.run()
+    sys.exit()
+except ImportError:
+    pass
+
+# When running against an older arvados-cwl-runner package without
+# arvados_cwl.crunch_script, fall back to the old code.
+
+
 # This gets the job record, transforms the script parameters into a valid CWL
 # input object, then executes the CWL runner to run the underlying workflow or
 # tool.  When the workflow completes, record the output object in an output
 # collection for this runner job.
 
 import arvados
-import arvados_cwl
 import arvados.collection
 import arvados.util
 import cwltool.main
@@ -57,7 +75,13 @@ try:
     normalizeFilesDirs(job_order_object)
     adjustDirObjs(job_order_object, functools.partial(getListing, arvados_cwl.fsaccess.CollectionFsAccess("", api_client=api)))
 
-    runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
+    output_name = None
+    if "arv:output_name" in job_order_object:
+        output_name = job_order_object["arv:output_name"]
+        del job_order_object["arv:output_name"]
+
+    runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
+                                      output_name=output_name)
 
     t = load_tool(job_order_object, runner.arv_make_tool)