Add skipping mechanism for list of studies #360
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SandyRogers
requested changes
Jun 3, 2024
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Thanks @KateSakharova ! Couple of tiny suggestions inline.
Please can you also change the PR base branch to develop? Thanks!
emgapi/metagenomics_exchange.py
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| pass | ||
| raise http_error | ||
| return response | ||
| except ValueError: # Catch JSON decoding errors |
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Wouldn't this raise an requests.exceptions.JSONDecodeError rather than a ValueError 🤔 ?
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you are right, one is a subclass of another. Fixed!
| @@ -131,6 +131,9 @@ def process_to_index_and_update_records(self, analyses_to_index_and_update): | |||
| mgya=annotation_job.accession, | |||
| sequence_accession=sequence_accession, | |||
| ) | |||
| if not response: | |||
| logging.info(f"Error occured {annotation_job}") | |||
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Suggested change
| logging.info(f"Error occured {annotation_job}") | |
| logging.warning(f"Error occurred {annotation_job}") |
I suppose it is bad enough for a warning :)
mberacochea
reviewed
Jun 3, 2024
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If ME post request doesn't work - it raised error and fail for whole run. This fix will skip that study raising HTTP error and continue with next study in list