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Enforce required sex parameter in Gradio CLI app
Browse files- Remove 'Unknown' as default sex value
- Add validation to ensure sex is provided for single slide processing
- Update help text to indicate sex is required parameter
- Remove fallback to 'Unknown' when sex is missing
- src/mosaic/gradio_app.py +5 -3
src/mosaic/gradio_app.py
CHANGED
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@@ -140,8 +140,8 @@ def main():
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"--sex",
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type=str,
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choices=SEX_OPTIONS,
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-
default=
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help="Sex of the patient (for single slide processing)",
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)
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parser.add_argument(
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"--tissue-site",
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@@ -231,6 +231,8 @@ def main():
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# Single slide processing mode
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if not args.output_dir:
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raise ValueError("Please provide --output-dir to save results")
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settings_df = pd.DataFrame(
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[
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[
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@@ -320,7 +322,7 @@ def main():
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slide_path=slide_path,
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seg_config=row["Segmentation Config"],
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site_type=row["Site Type"],
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-
sex=row
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tissue_site=row.get("Tissue Site", "Unknown"),
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cancer_subtype=row["Cancer Subtype"],
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cancer_subtype_name_map=cancer_subtype_name_map,
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"--sex",
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type=str,
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choices=SEX_OPTIONS,
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+
default=None,
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+
help="Sex of the patient (required for single slide processing)",
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)
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parser.add_argument(
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"--tissue-site",
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# Single slide processing mode
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if not args.output_dir:
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raise ValueError("Please provide --output-dir to save results")
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+
if not args.sex:
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raise ValueError("Please provide --sex (Male or Female) for single slide processing")
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settings_df = pd.DataFrame(
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[
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[
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slide_path=slide_path,
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seg_config=row["Segmentation Config"],
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site_type=row["Site Type"],
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+
sex=row["Sex"],
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tissue_site=row.get("Tissue Site", "Unknown"),
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cancer_subtype=row["Cancer Subtype"],
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cancer_subtype_name_map=cancer_subtype_name_map,
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