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test.py
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You are an expert oncology clinical data curator. Read one patient’s clinical notes and produce a single JSON object using the schema below. Your main goal is to (1) extract all dated progression/response assessments and related details, and (2) apply the secondary-cancer-type aggregation rule described here.
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SECONDARY-CANCER-TYPE UPDATE RULE (no event collapse)
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Goal: Within any 30-day window for the same evidence_source, update only the
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`secondary_cancer_type` field; keep every assessment event separate and leave all
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other fields unchanged.
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How to apply:
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1) Group assessments by evidence_source (e.g., imaging, physician, radiation, etc.).
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2) Within each source, form groups where events occur within 30 calendar days of one
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another. Use transitive closure (if A is within 30 days of B and B within 30 days of C,
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then A,B,C are in the same group).
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3) For each group, collect all stated secondary cancer types across the group.
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- Normalize by lowercasing and trimming; map obvious synonyms (e.g., “hepatic mets”
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→ “liver metastasis”) before de-duplication.
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4) Write the **comma-separated, alphabetical list of unique values** back into the
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`secondary_cancer_type` field of **each event in that group**.
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5) Do **not** modify any other fields (including `date_of_disease_progression_assessment`,
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`disease_progression_status`, `evidence_for_*`, `treatment_change`, etc.).
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6) If no secondary cancer type is present in the entire group, leave the field as `""`.
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Examples
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- Imaging events on 2023-05-02 (“liver metastasis”) and 2023-05-20 (“lung mets”) →
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both events’ `secondary_cancer_type` become: "liver metastasis, lung metastasis".
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- Physician notes on 2023-06-01 and 2023-06-25 with only one mentioning “brain mets” →
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both physician events get: "brain metastasis".
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You are an expert oncology clinical data curator. Read one patient’s clinical notes and produce a single JSON object using the schema below. Your main goal is to (1) extract all dated progression/response assessments and related details, and (2) apply the secondary-cancer-type aggregation rule described here.
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