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Second pass at retry for expired azure access tokens #82

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Merged
nalinigans merged 1 commit into from
Feb 20, 2025
Merged

Second pass at retry for expired azure access tokens #82

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13 changes: 9 additions & 4 deletions genomicsdb/scripts/genomicsdb_query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -676,20 +676,25 @@ def process(config):
# exit out of the loop as the query has completed
return 0
except Exception as e:
# Try handle read errors from TileDB storage for azure urls
# Try to handle read errors with expired access tokens for azure urls
# e.g. GenomicsDBIteratorException exception : Error while reading from TileDB array
if allow_retry and "GenomicsDB" in str(type(e)) and "TileDB" in str(e):
# VariantQueryProcessorException : Could not open array <array> at workspace <workspace>
if allow_retry:
if os.environ.get("GENOMICSDB_PRINT_EXCEPTION", None):
logging.info(f"Exception({e}) encountered with genomicdb query")
# Check for the possibility of an expired access token
allow_retry = False
try:
# If the check for workspace under consideration succeeds and the workspace exists as it should,
# genomicsdb instance is functional! Probably not an expired token, so re-raise outer exception
if not gdb.workspace_exists(export_config.workspace):
logging.info(f"Retrying query with a new instance of gdb for {msg}...")
logging.info(f"Retrying after workspace check with a new instance of genomicsdb for {msg}...")
gdb = None
continue
except Exception as ex:
logging.info(f"Exception({ex}) encountered. Retrying query with a new instance of gdb for {msg}...")
if os.environ.get("GENOMICSDB_PRINT_EXCEPTION", None):
logging.info(f"Exception({ex}) encountered with genomicdb workspace check")
logging.info(f"Retrying query with a new instance of genomicsdb for {msg}...")
gdb = None
continue
logging.critical(f"Unexpected exception while processing {msg} : {e}")
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