Merge branch '21535-multi-wf-delete'

[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 f6f85ba69619ba930cca9efd20d3b4f134f28527..d1961c8c8ac9face6513ec47d8897ee5a326466b 100644 (file)
--- a/sdk/python/arvados/commands/put.py
+++ b/sdk/python/arvados/commands/put.py
@@ -2,10 +2,6 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
-from __future__ import division
-from future.utils import listitems, listvalues
-from builtins import str
-from builtins import object
 import argparse
 import arvados
 import arvados.collection
@@ -576,6 +572,9 @@ class ArvPutUploadJob(object):
                     files.sort()
                     for f in files:
                         filepath = os.path.join(root, f)
+                        if not os.path.isfile(filepath):
+                            self.logger.warning("Skipping non-regular file '{}'".format(filepath))
+                            continue
                         # Add its size to the total bytes count (if applicable)
                         if self.follow_links or (not os.path.islink(filepath)):
                             if self.bytes_expected is not None:
@@ -693,7 +692,7 @@ class ArvPutUploadJob(object):
         Recursively get the total size of the collection
         """
         size = 0
-        for item in listvalues(collection):
+        for item in collection.values():
             if isinstance(item, arvados.collection.Collection) or isinstance(item, arvados.collection.Subcollection):
                 size += self._collection_size(item)
             else:
@@ -975,7 +974,7 @@ class ArvPutUploadJob(object):
     def collection_file_paths(self, col, path_prefix='.'):
         """Return a list of file paths by recursively go through the entire collection `col`"""
         file_paths = []
-        for name, item in listitems(col):
+        for name, item in col.items():
             if isinstance(item, arvados.arvfile.ArvadosFile):
                 file_paths.append(os.path.join(path_prefix, name))
             elif isinstance(item, arvados.collection.Subcollection):
@@ -1055,7 +1054,7 @@ class ArvPutUploadJob(object):
                     locators.append(loc)
                 return locators
         elif isinstance(item, arvados.collection.Collection):
-            l = [self._datablocks_on_item(x) for x in listvalues(item)]
+            l = [self._datablocks_on_item(x) for x in item.values()]
             # Fast list flattener method taken from:
             # http://stackoverflow.com/questions/952914/making-a-flat-list-out-of-list-of-lists-in-python
             return [loc for sublist in l for loc in sublist]
@@ -1133,7 +1132,7 @@ def main(arguments=None, stdout=sys.stdout, stderr=sys.stderr,
     logging.getLogger('arvados').handlers[0].setFormatter(formatter)
 
     if api_client is None:
-        api_client = arvados.api('v1', request_id=request_id)
+        api_client = arvados.api('v1', request_id=request_id, num_retries=args.retries)
 
     if install_sig_handlers:
         arv_cmd.install_signal_handlers()