8654: Fix keeppath and add ensure_unique_name to upload.

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 81755b8ca5b4cb52c3d75cad56c115cbfc9f0117..003e4185772431c57dd8f0ee4010c303ddb27dd4 100755 (executable)
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -22,7 +22,7 @@ try:
 
     def keeppath(v):
         if arvados.util.keep_locator_pattern.match(v):
-            job_order_object[k] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
+            return "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
 
     adjustFiles(job_order_object, keeppath)
 

diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index 046f7066373559452b2c8b24ab58041365b6cb73..643d3f542d96dff1815a7496dd716382cc9c7099 100644 (file)
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -151,7 +151,7 @@ def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPatter
         body = {"owner_uuid": project, "manifest_text": collection.manifest_text()}
         if name is not None:
             body["name"] = name
-        item = api.collections().create(body=body).execute()
+        item = api.collections().create(body=body, ensure_unique_name=True).execute()
         pdh = item["portable_data_hash"]
         logger.info("Uploaded to %s", item["uuid"])