Initial commit
This commit is contained in:
Zhongwei Li
334
skills/clinical-reports/scripts/validate_case_report.py
Executable file
334
skills/clinical-reports/scripts/validate_case_report.py
Executable file
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#!/usr/bin/env python3
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"""
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Validate case reports against CARE (CAse REport) guidelines.
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This script checks a clinical case report for compliance with CARE guidelines
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and provides a checklist of required elements.
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Usage:
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python validate_case_report.py <input_file.md|.txt>
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python validate_case_report.py <input_file> --output report.json
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"""
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import argparse
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import json
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import re
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from pathlib import Path
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from typing import Dict, List, Tuple
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class CareValidator:
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"""Validator for CARE guideline compliance."""
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# CARE checklist items with regex patterns
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CARE_REQUIREMENTS = {
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"title": {
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"name": "Title contains 'case report'",
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"pattern": r"(?i)(case\s+report|case\s+study)",
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"section": "Title",
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"required": True
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},
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"keywords": {
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"name": "Keywords provided (2-5)",
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"pattern": r"(?i)keywords?[:]\s*(.+)",
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"section": "Keywords",
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"required": True
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},
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"abstract": {
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"name": "Abstract present",
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"pattern": r"(?i)##?\s*abstract",
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"section": "Abstract",
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"required": True
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},
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"introduction": {
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"name": "Introduction explaining novelty",
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"pattern": r"(?i)##?\s*introduction",
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"section": "Introduction",
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"required": True
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},
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"patient_info": {
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"name": "Patient demographics present",
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"pattern": r"(?i)(patient\s+information|demographics?)",
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"section": "Patient Information",
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"required": True
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},
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"clinical_findings": {
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"name": "Clinical findings documented",
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"pattern": r"(?i)(clinical\s+findings?|physical\s+exam)",
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"section": "Clinical Findings",
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"required": True
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},
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"timeline": {
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"name": "Timeline of events",
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"pattern": r"(?i)(timeline|chronology)",
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"section": "Timeline",
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"required": True
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},
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"diagnostic": {
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"name": "Diagnostic assessment",
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"pattern": r"(?i)diagnostic\s+(assessment|evaluation|workup)",
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"section": "Diagnostic Assessment",
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"required": True
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},
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"therapeutic": {
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"name": "Therapeutic interventions",
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"pattern": r"(?i)(therapeutic\s+intervention|treatment)",
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"section": "Therapeutic Interventions",
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"required": True
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},
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"followup": {
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"name": "Follow-up and outcomes",
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"pattern": r"(?i)(follow[\-\s]?up|outcomes?)",
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"section": "Follow-up and Outcomes",
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"required": True
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},
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"discussion": {
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"name": "Discussion with literature review",
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"pattern": r"(?i)##?\s*discussion",
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"section": "Discussion",
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"required": True
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},
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"consent": {
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"name": "Informed consent statement",
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"pattern": r"(?i)(informed\s+consent|written\s+consent|consent.*obtained)",
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"section": "Informed Consent",
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"required": True
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},
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}
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# HIPAA identifiers to check for
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HIPAA_PATTERNS = {
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"dates": r"\b(0?[1-9]|1[0-2])/(0?[1-9]|[12][0-9]|3[01])/\d{4}\b",
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"phone": r"\b\d{3}[-.]?\d{3}[-.]?\d{4}\b",
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"email": r"\b[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\.[A-Z|a-z]{2,}\b",
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"ssn": r"\b\d{3}-\d{2}-\d{4}\b",
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"mrn": r"(?i)(mrn|medical\s+record)[:]\s*\d+",
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"zip_full": r"\b\d{5}-\d{4}\b",
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}
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def __init__(self, filename: str):
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"""Initialize validator with input file."""
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self.filename = Path(filename)
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self.content = self._read_file()
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self.results = {}
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def _read_file(self) -> str:
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"""Read input file content."""
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try:
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with open(self.filename, 'r', encoding='utf-8') as f:
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return f.read()
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except FileNotFoundError:
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raise FileNotFoundError(f"File not found: {self.filename}")
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except Exception as e:
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raise Exception(f"Error reading file: {e}")
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def validate_care_compliance(self) -> Dict[str, Dict]:
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"""Validate compliance with CARE guidelines."""
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results = {}
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for key, item in self.CARE_REQUIREMENTS.items():
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pattern = item["pattern"]
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found = bool(re.search(pattern, self.content))
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results[key] = {
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"name": item["name"],
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"section": item["section"],
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"required": item["required"],
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"found": found,
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"status": "PASS" if found else "FAIL" if item["required"] else "WARNING"
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}
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self.results["care_compliance"] = results
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return results
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def check_deidentification(self) -> Dict[str, List[str]]:
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"""Check for potential HIPAA identifier violations."""
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violations = {}
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for identifier, pattern in self.HIPAA_PATTERNS.items():
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matches = re.findall(pattern, self.content)
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if matches:
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violations[identifier] = matches[:5] # Limit to first 5 examples
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self.results["hipaa_violations"] = violations
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return violations
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def check_word_count(self) -> Dict[str, int]:
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"""Check word count and provide limits guidance."""
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words = len(re.findall(r'\b\w+\b', self.content))
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word_count = {
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"total_words": words,
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"typical_min": 1500,
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"typical_max": 3000,
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"status": "ACCEPTABLE" if 1500 <= words <= 3500 else "CHECK"
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}
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self.results["word_count"] = word_count
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return word_count
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def check_references(self) -> Dict[str, any]:
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"""Check for presence of references."""
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ref_patterns = [
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r"##?\s*references",
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r"\[\d+\]",
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r"\d+\.\s+[A-Z][a-z]+.*\d{4}", # Numbered references
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]
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has_refs = any(re.search(p, self.content, re.IGNORECASE) for p in ref_patterns)
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ref_count = len(re.findall(r"\[\d+\]", self.content))
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references = {
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"has_references": has_refs,
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"estimated_count": ref_count,
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"recommended_min": 10,
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"status": "ACCEPTABLE" if ref_count >= 10 else "LOW"
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}
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self.results["references"] = references
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return references
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def generate_report(self) -> Dict:
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"""Generate comprehensive validation report."""
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if not self.results:
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self.validate_care_compliance()
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self.check_deidentification()
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self.check_word_count()
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self.check_references()
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# Calculate overall compliance
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care = self.results["care_compliance"]
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total_required = sum(1 for v in care.values() if v["required"])
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passed = sum(1 for v in care.values() if v["required"] and v["found"])
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compliance_rate = (passed / total_required * 100) if total_required > 0 else 0
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report = {
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"filename": str(self.filename),
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"compliance_rate": round(compliance_rate, 1),
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"care_compliance": care,
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"hipaa_violations": self.results["hipaa_violations"],
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"word_count": self.results["word_count"],
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"references": self.results["references"],
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"overall_status": "PASS" if compliance_rate >= 90 and not self.results["hipaa_violations"] else "NEEDS_REVISION"
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}
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return report
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def print_report(self):
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"""Print human-readable validation report."""
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report = self.generate_report()
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print("=" * 70)
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print(f"CARE Guideline Validation Report")
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print(f"File: {report['filename']}")
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print("=" * 70)
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print()
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print(f"Overall Compliance: {report['compliance_rate']}%")
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print(f"Status: {report['overall_status']}")
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print()
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print("CARE Checklist:")
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print("-" * 70)
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for key, item in report["care_compliance"].items():
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status_symbol = "✓" if item["found"] else "✗"
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print(f"{status_symbol} [{item['status']:8}] {item['name']}")
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print()
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if report["hipaa_violations"]:
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print("HIPAA DE-IDENTIFICATION WARNINGS:")
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print("-" * 70)
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for identifier, examples in report["hipaa_violations"].items():
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print(f"⚠ {identifier.upper()}: {len(examples)} instance(s) found")
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for ex in examples[:3]:
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print(f" Example: {ex}")
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print()
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else:
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print("✓ No obvious HIPAA identifiers detected")
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print()
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wc = report["word_count"]
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print(f"Word Count: {wc['total_words']} words")
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print(f" Typical range: {wc['typical_min']}-{wc['typical_max']} words")
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print(f" Status: {wc['status']}")
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print()
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refs = report["references"]
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print(f"References: {refs['estimated_count']} citation(s) detected")
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print(f" Recommended minimum: {refs['recommended_min']}")
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print(f" Status: {refs['status']}")
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print()
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print("=" * 70)
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# Recommendations
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issues = []
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if report['compliance_rate'] < 100:
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missing = [v["name"] for v in report["care_compliance"].values() if v["required"] and not v["found"]]
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issues.append(f"Missing required sections: {', '.join(missing)}")
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if report["hipaa_violations"]:
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issues.append("HIPAA identifiers detected - review de-identification")
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if refs["status"] == "LOW":
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issues.append("Low reference count - consider adding more citations")
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if issues:
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print("RECOMMENDATIONS:")
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for i, issue in enumerate(issues, 1):
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print(f"{i}. {issue}")
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else:
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print("✓ Case report meets CARE guidelines!")
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print("=" * 70)
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def main():
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"""Main entry point."""
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parser = argparse.ArgumentParser(
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description="Validate clinical case reports against CARE guidelines"
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)
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parser.add_argument(
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"input_file",
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help="Path to case report file (Markdown or text)"
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)
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parser.add_argument(
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"--output",
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"-o",
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help="Output JSON report to file"
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)
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parser.add_argument(
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"--json",
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action="store_true",
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help="Output JSON to stdout instead of human-readable report"
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)
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args = parser.parse_args()
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try:
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validator = CareValidator(args.input_file)
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report = validator.generate_report()
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if args.json:
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print(json.dumps(report, indent=2))
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else:
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validator.print_report()
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if args.output:
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with open(args.output, 'w') as f:
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json.dumps(report, f, indent=2)
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print(f"\nJSON report saved to: {args.output}")
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# Exit with non-zero if validation failed
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exit_code = 0 if report["overall_status"] == "PASS" else 1
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return exit_code
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except Exception as e:
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print(f"Error: {e}", file=sys.stderr)
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return 1
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if __name__ == "__main__":
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import sys
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sys.exit(main())
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