added a validation_reporting directory for AMICA #7
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Contributor
Caroline-99
commented
Dec 17, 2025
Caroline-99
commented
- Added a proper validation-reporting package (src/amica/validation_reporting/) with config, loaders, pure stats, and Markdown renderers so the CXG outputs can be summarized without copy-pasted scripts.
- Added scripts/generate_validation_reports.py (main script) as the main entry point under scripts/, exposing flags for directory overrides, report selection, ontology controls, and reuse via amica.validation_reporting.generate_reports.
- Documented the workflow (docs/validation_reporting.md), covering required inputs, CLI usage, and ontology requirements, and verified the script against the real output/ data (raw and filtered report regenerated).
ubyndr
reviewed
Dec 19, 2025
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| Key flags: | ||
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| - `--output-root`: base directory that contains `raw_output/`, `pandasaurus_cxg_outputs_30/`, and `reports/`. Defaults to `resources/cxg/output`. | ||
| - `--raw-output-dir`, `--match-type-dir`, `--reports-dir`: override individual directories if they live elsewhere. | ||
| - `--skip-filtered`, `--skip-examples`, `--skip-raw-stats`: toggle which reports are generated. | ||
| - `--skip-ontology`: skip the online OLS lookup entirely. | ||
| - `--ontology-adapter`: use a custom oaklib adapter string (e.g., `pronto:/path/to/cl.owl`) for offline runs. Defaults to `ols:cl`. |
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Could you expand the docstring/README to explain when someone should use --raw-output-dir, --match-type-dir, or --reports-dir, and what happens if those directories are missing? Similarly, can you describe the intended use cases for the --skip-* toggles and clarify whether --skip-ontology impacts the accuracy of the filtered stats?
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@ubyndr I have updated the doc. Could you please review it and let me know if I need to add anything else? Thank you
ubyndr
requested changes
Dec 19, 2025
ubyndr
approved these changes
Jan 13, 2026
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