From ce7841bc87310c3cb9fe7b925781ed550f9ca5a3 Mon Sep 17 00:00:00 2001
From: Blake Fitch <blake.fitch@tuebingen.mpg.de>
Date: Wed, 3 Jul 2024 13:21:45 +0200
Subject: [PATCH] separate case of skipping zero len file from removing
(unlinking) preexisting iRODS object for replace_existing flag
---
pymods/irods_utils/irods_utils.py | 20 ++++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/pymods/irods_utils/irods_utils.py b/pymods/irods_utils/irods_utils.py
index 70d5a69..a19d3c6 100644
--- a/pymods/irods_utils/irods_utils.py
+++ b/pymods/irods_utils/irods_utils.py
@@ -391,14 +391,18 @@ def confirmed_put( irods_sesh, file_pathname, new_obj_ipath, metadata_dict=None,
logging.error( f"FATAL: Failed to get size of file to upload. file_pathname: {file_pathname} ex: {ex}" )
raise
- if upload_file_size == 0 and existing_obj != None and replace_existing and skip_on_zero_len :
- logging.warning( f"got zero len file with replace_existing -- removing current data object. ipath: {new_obj_ipath}" )
- try:
- existing_obj.unlink(force=True)
- return 0
- except Exception as ex:
- logging.warning( "Failed remove zero line file on replace_existing and skip_on_zero_len. ipath: {new_obj_ipath} ex: {ex} " )
- raise
+ # Return if zero sized objects are to be discarded. Check if an existing object needs to be removed.
+ if upload_file_size == 0 and skip_on_zero_len:
+ if existing_obj != None and replace_existing:
+ logging.warning( f"Got zero len file. Removing existing iRODS obj. file_pathname: {file_pathname} ipath: {new_obj_ipath}" )
+ try:
+ existing_obj.unlink(force=True)
+ except Exception as ex:
+ logging.error( "Failed remove existing zero line file on replace_existing and skip_on_zero_len. ipath: {new_obj_ipath} ex: {ex} " )
+ raise
+ else:
+ logging.debug( f"Got zero len file with skip_on_zero_len set. Returning. file_pathname: {file_pathname} ipath: {new_obj_ipath}" )
+ return 0
# Make a timestamped partial tmp file name which, if the upload somehow fails here, will be left behind
# Hopefully this does not happen much, but we have seen at least on case so far.
--
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