Checks genomicsdb_query output directory and retry once with a new genomicsdb instance when azure access tokens expire #81
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added 3 commits
February 13, 2025 11:23
nalinigans
changed the title
mlathara
reviewed
Feb 15, 2025
| writer = None | ||
| logging.info(f"Processed {msg}") | ||
| return 0 | ||
| except Exception as e: |
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Can we check for a specific exception here, or even check the exception message to only target the signature for what we think is expired tokens?
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Most of the time we see a GenomicsDBIteratorException. But, we cannot be really sure.
| allow_retry = False | ||
| try: | ||
| if not gdb.workspace_exists(export_config.workspace): | ||
| logging.info(f"Retrying query with a new instance of gdb for {msg}...") |
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Could you explain what we're trying to do with this check?
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I m trying to check if the gdb is functional. If it is, it is probably not an expired token, I will document that better in the code. And maybe improve the logging message. Comments?
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Add additional checks for genomicsdb_query when output's parent directory does not exist and exit out gracefully.