9701: Merge branch 'master' into 9701-collection-pack-small-files-alt

[arvados.git] / sdk / python / arvados / commands / put.py

diff --git a/sdk/python/arvados/commands/put.py b/sdk/python/arvados/commands/put.py
index b2c40f12f8c361ae988dde139c2b26b830adb372..1a274104fc76c5ec6449dee5b8387fe3d478170b 100644 (file)
--- a/sdk/python/arvados/commands/put.py
+++ b/sdk/python/arvados/commands/put.py
@@ -320,6 +320,7 @@ class ArvPutUploadJob(object):
         """
         Start supporting thread & file uploading
         """
+        self._checkpointer.daemon = True
         self._checkpointer.start()
         try:
             for path in self.paths:
@@ -334,12 +335,13 @@ class ArvPutUploadJob(object):
             # Stop the thread before doing anything else
             self._stop_checkpointer.set()
             self._checkpointer.join()
-        # Successful upload, one last _update()
-        self._update()
-        if self.resume:
-            self._cache_file.close()
-            # Correct the final written bytes count
-            self.bytes_written -= self.bytes_skipped
+            # Commit all & one last _update()
+            self.manifest_text()
+            self._update()
+            if self.resume:
+                self._cache_file.close()
+                # Correct the final written bytes count
+                self.bytes_written -= self.bytes_skipped
 
     def save_collection(self):
         with self._collection_lock:
@@ -387,7 +389,8 @@ class ArvPutUploadJob(object):
             # Update cache, if resume enabled
             if self.resume:
                 with self._state_lock:
-                    self._state['manifest'] = self._my_collection().manifest_text()
+                    # Get the manifest text without comitting pending blocks
+                    self._state['manifest'] = self._my_collection()._get_manifest_text(".", strip=False, normalize=False, only_committed=True)
         if self.resume:
             self._save_state()
         # Call the reporter, if any