Crunch-job needs to call the python executable from our sdk package for

[arvados.git] / crunch_scripts / crunchutil / vwd.py

diff --git a/crunch_scripts/crunchutil/vwd.py b/crunch_scripts/crunchutil/vwd.py
index ca4116d7cee9015cbeb03bfaaf3ea4ca7dadfe03..3245da14b3e3658f1a6ddc4da68e9960e1b7849d 100644 (file)
--- a/crunch_scripts/crunchutil/vwd.py
+++ b/crunch_scripts/crunchutil/vwd.py
@@ -1,3 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 import arvados
 import os
 import stat
@@ -73,6 +77,12 @@ def checkin(target_dir):
                     if pdh is not None:
                         # 2. load collection
                         if pdh not in collections:
+                            # 2.1 make sure it is flushed (see #5787 note 11)
+                            fd = os.open(real[0], os.O_RDONLY)
+                            os.fsync(fd)
+                            os.close(fd)
+
+                            # 2.2 get collection from API server
                             collections[pdh] = arvados.collection.CollectionReader(pdh,
                                                                                    api_client=outputcollection._my_api(),
                                                                                    keep_client=outputcollection._my_keep(),