Ids 641 end to end ingestion test on staging server #445
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…to IDS-641-end-to-end-ingestion-test-on-staging-server
…ytardis_ingestion into IDS-641-end-to-end-ingestion-test-on-staging-server
…ytardis_ingestion into IDS-641-end-to-end-ingestion-test-on-staging-server
uoa-noel
requested changes
Oct 23, 2024
| @@ -72,7 +73,7 @@ def _is_completed_df( | |||
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| def _filter_completed_dfs( | |||
| config: ConfigFromEnv, datafiles: list[RawDatafile], min_file_age: Optional[int] | |||
| ) -> list[RawDatafile]: | |||
| ) -> Tuple[list[RawDatafile], list[RawDatafile]]: | |||
| """Inspects through a list of datafiles, return datafiles which have completed ingestion.""" | |||
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Update comment to clarify what's being returned.
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| network_base_path = Path( | ||
| "//files.auckland.ac.nz/research/resmed202000005-biru-shared-drive" | ||
| ) | ||
| modified_source_path_base = network_base_path / source_path.parent.relative_to( | ||
| "/mnt/biru_shared_drive" | ||
| ) |
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Because this command is meant to be generic to different workflows, I'm wondering if it's necessary to prepend BIRU drive paths here?
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| # save file verification status to a csv file for idw project | ||
| if profile_name == "idw": | ||
| logger.info("Saving files verification status into a csv file.") | ||
| _save_data_status(source_data_path, verified_dfs, unverified_dfs) |
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I think it would be useful to have a separate command for the reporting functionality. The ids clean command mainly deletes files, whereas this functionality creates a report. To prevent accidental deleting of files it's better for the CLI user to run it as a separate command...
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In this PR:
Added
_save_data_statusfunction to save file verification status into a CSV file for BIRU users to determine if they want to delete some ingested files when the auto clean-up script is disabled. It can be disabled, too, depending on the cleanup strategy's decision.Tested
cmd_clean.pyin the ingestion_biru.py.