Some changes to the ngs cohort extract files #7113
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ericsong
commented
Feb 27, 2021
ericsong
commented
- Add ngs_cohort_extract.py to the Dockerfile
- Don't swallow exceptions thrown in the python script; results in succeeding workflows even if the script fails.
| create_position_table(fq_temp_table_dataset, min_variant_samples) | ||
| make_new_pet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, cohort) | ||
| populate_final_extract_table(fq_temp_table_dataset, fq_destination_dataset, destination_table, fq_sample_mapping_table) | ||
| except Exception as err: |
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I think this will just eat the exception, but then continue on to print the "Final cohort extract written to..." error message (which isn't true?)
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the try/catch is being removed so it will no longer eat the exception. it seems counter intuitive to remove the try/catch but i'm not sure the best way to handle this. maybe add a comment that states exceptions are not being caught so the calling script will error out when an exception occurs. i feel like we could into a cycle otherwise where we try to add exception handling back in.
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ah -- duh, of course. My mistake.
I think the reason the exception handing was in there though was so that we would get the dump_job_stats() output even in the case of failures (so you could see how much $$/bytes were consumed before the failure).
In that case, I'd suggst we have a
try:
finally:
dump_job_stats
without explicitly catching the exception
…tract python script (#7113) * add ngs to cohort extract docker * throw error if there's an exception * add back try block to print job stats * whitespace changes * remove unused var
…tract python script (#7113) * add ngs to cohort extract docker * throw error if there's an exception * add back try block to print job stats * whitespace changes * remove unused var
