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Do not retry query for OS errors #84

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Mar 13, 2025
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9 changes: 9 additions & 0 deletions genomicsdb/scripts/genomicsdb_query.py
Original file line number Diff line number Diff line change
Expand Up @@ -675,6 +675,15 @@ def process(config):
logging.info(f"Processed {msg}")
# exit out of the loop as the query has completed
return 0
except OSError as e:
# See https://docs.python.org/3/library/exceptions.html#OSError, possible errors are :
# File not found: Attempting to open a file that does not exist
# Permission denied: Trying to access a file or directory without the necessary permissions.
# Disk full: Running out of storage space while writing to a file.
# Invalid file path: Providing an incorrect or malformed file path.
# Device errors: Problems with hardware devices, such as a disconnected drive.
logging.critical(f"Cannot continue - OS Error encountered while processing {msg} : {e}")
raise e
except Exception as e:
# Try to handle read errors with expired access tokens for azure urls
# e.g. GenomicsDBIteratorException exception : Error while reading from TileDB array
Expand Down