Support for OMOP ES batches #274
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…ch setup as needed. For now, all tests are doing it the "old" way. Delete duplicated test resources.
back to multi-batch when it's implemented.
person has procedures in both batches, there is some overlap in the PERSON_LINKS.parquet file
jeremyestein
changed the title
split over two batches.
jeremyestein
changed the title
stefpiatek
approved these changes
Feb 5, 2024
cli/src/pixl_cli/_io.py
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| # should it really be 'extract_*'? | ||
| batch_dirs = list(extract_path.glob("batch_*")) |
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Yeah we're given extract_*, though we could ask if OMOP ES could change it? Worth dropping a message in pixl-omop channel in UCLH Foundry slack.
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Also, should we sort these?
| @@ -47,20 +47,75 @@ def messages_from_state_file(filepath: Path) -> list[Message]: | |||
| return [deserialise(line) for line in filepath.open().readlines() if string_is_non_empty(line)] | |||
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| def config_from_log_file(parquet_path: Path) -> tuple[str, datetime]: | |||
| log_file = parquet_path / "extract_summary.json" | |||
| def determine_batch_structure(extract_path: Path) -> tuple[str, datetime, list[Path]]: | |||
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maybe parse_batch_structure?
milanmlft
approved these changes
Feb 5, 2024
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Thanks for the detailed docstrings! ❤️
Just one small suggestion; maybe add the example file structure from the issue to the cli/README.md as well? And clarify that we support this multi-batch structure.
└── omop_extract
├── extract_1
│ ├── extract_summary.json
│ ├── private
│ └── public
├── extract_2
│ ├── extract_summary.json
│ ├── private
│ └── public
└── extract_3
├── extract_summary.json
├── private
└── public
1 task
of the pipeline - probably needs some changing to make more consistent!
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Will fix #231
TODO:
extract_Nvsbatch_N), change code and docs when decided