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skills/clinical-reports/scripts/validate_trial_report.py

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+#!/usr/bin/env python3
+"""
+Validate clinical trial reports against ICH-E3 structure.
+
+Checks Clinical Study Reports (CSR) for ICH-E3 compliance.
+
+Usage:
+    python validate_trial_report.py <csr_file.md>
+"""
+
+import argparse
+import json
+import re
+from pathlib import Path
+
+
+ICH_E3_SECTIONS = {
+    "title_page": "Title Page",
+    "synopsis": "Synopsis (2)",
+    "toc": "Table of Contents (3)",
+    "abbreviations": "List of Abbreviations (4)",
+    "ethics": "Ethics (Section 2)",
+    "investigators": "Investigators and Study Administrative Structure (Section 3)",
+    "introduction": "Introduction (Section 4)",
+    "objectives": "Study Objectives and Plan (Section 5)",
+    "study_patients": "Study Patients (Section 6)",
+    "efficacy": "Efficacy Evaluation (Section 7)",
+    "safety": "Safety Evaluation (Section 8)",
+    "discussion": "Discussion and Overall Conclusions (Section 9)",
+    "tables_figures": "Tables, Figures, and Graphs (Section 10)",
+    "references": "References (Section 11)",
+    "appendices": "Appendices (Section 12-14)",
+}
+
+
+def validate_ich_e3(filename: str) -> dict:
+    """Validate CSR structure against ICH-E3."""
+    with open(filename, 'r', encoding='utf-8') as f:
+        content = f.read()
+    
+    results = {}
+    for section_id, section_name in ICH_E3_SECTIONS.items():
+        # Simple pattern matching for section headers
+        pattern = rf"(?i)##?\s*{re.escape(section_name.split('(')[0].strip())}"
+        found = bool(re.search(pattern, content))
+        results[section_id] = {"name": section_name, "found": found}
+    
+    compliance_rate = sum(1 for r in results.values() if r["found"]) / len(results) * 100
+    
+    return {
+        "filename": filename,
+        "compliance_rate": round(compliance_rate, 1),
+        "sections": results,
+        "status": "PASS" if compliance_rate >= 90 else "NEEDS_REVISION"
+    }
+
+
+def main():
+    """Main entry point."""
+    parser = argparse.ArgumentParser(description="Validate CSR against ICH-E3")
+    parser.add_argument("input_file", help="Path to CSR file")
+    parser.add_argument("--json", action="store_true", help="Output JSON")
+    
+    args = parser.parse_args()
+    
+    try:
+        report = validate_ich_e3(args.input_file)
+        
+        if args.json:
+            print(json.dumps(report, indent=2))
+        else:
+            print(f"\nICH-E3 Compliance: {report['compliance_rate']}%")
+            print(f"Status: {report['status']}\n")
+            print("Section Checklist:")
+            for section, details in report["sections"].items():
+                symbol = "✓" if details["found"] else "✗"
+                print(f"{symbol} {details['name']}")
+        
+        return 0 if report["status"] == "PASS" else 1
+        
+    except Exception as e:
+        print(f"Error: {e}")
+        return 1
+
+
+if __name__ == "__main__":
+    import sys
+    sys.exit(main())
+