Initial commit
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Zhongwei Li
335
skills/clinical-decision-support/scripts/validate_cds_document.py
Executable file
335
skills/clinical-decision-support/scripts/validate_cds_document.py
Executable file
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#!/usr/bin/env python3
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"""
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Validate Clinical Decision Support Documents for Quality and Completeness
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Checks for:
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- Evidence citations for all recommendations
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- Statistical reporting completeness
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- Biomarker nomenclature consistency
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- Required sections present
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- HIPAA de-identification
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- GRADE recommendation format
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Dependencies: None (pure Python)
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"""
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import re
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import argparse
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from pathlib import Path
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from collections import defaultdict
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class CDSValidator:
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"""Validator for clinical decision support documents."""
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def __init__(self, filepath):
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self.filepath = filepath
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with open(filepath, 'r', encoding='utf-8', errors='ignore') as f:
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self.content = f.read()
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self.errors = []
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self.warnings = []
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self.info = []
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def validate_all(self):
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"""Run all validation checks."""
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print(f"Validating: {self.filepath}")
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print("="*70)
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self.check_required_sections()
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self.check_evidence_citations()
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self.check_recommendation_grading()
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self.check_statistical_reporting()
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self.check_hipaa_identifiers()
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self.check_biomarker_nomenclature()
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return self.generate_report()
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def check_required_sections(self):
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"""Check if required sections are present."""
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# Cohort analysis required sections
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cohort_sections = [
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'cohort characteristics',
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'biomarker',
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'outcomes',
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'statistical analysis',
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'clinical implications',
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'references'
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]
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# Treatment recommendation required sections
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rec_sections = [
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'evidence',
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'recommendation',
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'monitoring',
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'references'
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]
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content_lower = self.content.lower()
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# Check which document type
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is_cohort = 'cohort' in content_lower
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is_recommendation = 'recommendation' in content_lower
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if is_cohort:
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missing = [sec for sec in cohort_sections if sec not in content_lower]
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if missing:
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self.warnings.append(f"Cohort analysis may be missing sections: {', '.join(missing)}")
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else:
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self.info.append("All cohort analysis sections present")
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if is_recommendation:
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missing = [sec for sec in rec_sections if sec not in content_lower]
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if missing:
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self.errors.append(f"Recommendation document missing required sections: {', '.join(missing)}")
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else:
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self.info.append("All recommendation sections present")
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def check_evidence_citations(self):
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"""Check that recommendations have citations."""
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# Find recommendation statements
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rec_pattern = r'(recommend|should|prefer|suggest|consider)(.*?)(?:\n\n|\Z)'
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recommendations = re.findall(rec_pattern, self.content, re.IGNORECASE | re.DOTALL)
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# Find citations
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citation_patterns = [
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r'\[\d+\]', # Numbered citations [1]
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r'\(.*?\d{4}\)', # Author year (Smith 2020)
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r'et al\.', # Et al citations
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r'NCCN|ASCO|ESMO', # Guideline references
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]
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uncited_recommendations = []
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for i, (_, rec_text) in enumerate(recommendations):
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has_citation = any(re.search(pattern, rec_text) for pattern in citation_patterns)
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if not has_citation:
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snippet = rec_text[:60].strip() + '...'
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uncited_recommendations.append(snippet)
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if uncited_recommendations:
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self.warnings.append(f"Found {len(uncited_recommendations)} recommendations without citations")
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for rec in uncited_recommendations[:3]: # Show first 3
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self.warnings.append(f" - {rec}")
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else:
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self.info.append(f"All {len(recommendations)} recommendations have citations")
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def check_recommendation_grading(self):
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"""Check for GRADE-style recommendation strength."""
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# Look for GRADE notation (1A, 1B, 2A, 2B, 2C)
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grade_pattern = r'GRADE\s*[12][A-C]|Grade\s*[12][A-C]|\(?\s*[12][A-C]\s*\)?'
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grades = re.findall(grade_pattern, self.content, re.IGNORECASE)
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# Look for strong/conditional language
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strong_pattern = r'(strong|we recommend|should)'
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conditional_pattern = r'(conditional|weak|we suggest|may consider|could consider)'
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strong_count = len(re.findall(strong_pattern, self.content, re.IGNORECASE))
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conditional_count = len(re.findall(conditional_pattern, self.content, re.IGNORECASE))
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if grades:
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self.info.append(f"Found {len(grades)} GRADE-style recommendations")
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else:
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self.warnings.append("No GRADE-style recommendation grading found (1A, 1B, 2A, etc.)")
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if strong_count > 0 or conditional_count > 0:
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self.info.append(f"Recommendation language: {strong_count} strong, {conditional_count} conditional")
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else:
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self.warnings.append("No clear recommendation strength language (strong/conditional) found")
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def check_statistical_reporting(self):
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"""Check for proper statistical reporting."""
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# Check for p-values
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p_values = re.findall(r'p\s*[=<>]\s*[\d.]+', self.content, re.IGNORECASE)
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# Check for confidence intervals
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ci_pattern = r'95%\s*CI|confidence interval'
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cis = re.findall(ci_pattern, self.content, re.IGNORECASE)
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# Check for hazard ratios
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hr_pattern = r'HR\s*[=:]\s*[\d.]+'
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hrs = re.findall(hr_pattern, self.content)
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# Check for sample sizes
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n_pattern = r'n\s*=\s*\d+'
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sample_sizes = re.findall(n_pattern, self.content, re.IGNORECASE)
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if not p_values:
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self.warnings.append("No p-values found - statistical significance not reported")
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else:
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self.info.append(f"Found {len(p_values)} p-values")
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if hrs and not cis:
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self.warnings.append("Hazard ratios reported without confidence intervals")
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if not sample_sizes:
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self.warnings.append("Sample sizes (n=X) not clearly reported")
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# Check for common statistical errors
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if 'p=0.00' in self.content or 'p = 0.00' in self.content:
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self.warnings.append("Found p=0.00 (should report as p<0.001 instead)")
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def check_hipaa_identifiers(self):
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"""Check for potential HIPAA identifiers."""
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# 18 HIPAA identifiers (simplified check for common ones)
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identifiers = {
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'Names': r'Dr\.\s+[A-Z][a-z]+|Patient:\s*[A-Z][a-z]+',
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'Specific dates': r'\d{1,2}/\d{1,2}/\d{4}', # MM/DD/YYYY
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'Phone numbers': r'\d{3}[-.]?\d{3}[-.]?\d{4}',
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'Email addresses': r'[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}',
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'SSN': r'\d{3}-\d{2}-\d{4}',
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'MRN': r'MRN\s*:?\s*\d+',
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}
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found_identifiers = []
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for identifier_type, pattern in identifiers.items():
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matches = re.findall(pattern, self.content)
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if matches:
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found_identifiers.append(f"{identifier_type}: {len(matches)} instance(s)")
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if found_identifiers:
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self.errors.append("Potential HIPAA identifiers detected:")
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for identifier in found_identifiers:
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self.errors.append(f" - {identifier}")
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self.errors.append(" ** Ensure proper de-identification before distribution **")
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else:
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self.info.append("No obvious HIPAA identifiers detected (basic check only)")
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def check_biomarker_nomenclature(self):
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"""Check for consistent biomarker nomenclature."""
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# Common biomarker naming issues
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issues = []
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# Check for gene names (should be italicized in LaTeX)
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gene_names = ['EGFR', 'ALK', 'ROS1', 'BRAF', 'KRAS', 'HER2', 'TP53', 'BRCA1', 'BRCA2']
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for gene in gene_names:
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# Check if gene appears but not in italics (\textit{} or \emph{})
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if gene in self.content:
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if f'\\textit{{{gene}}}' not in self.content and f'\\emph{{{gene}}}' not in self.content:
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if '.tex' in self.filepath.suffix:
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issues.append(f"{gene} should be italicized in LaTeX (\\textit{{{gene}}})")
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# Check for protein vs gene naming
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# HER2 (protein) vs ERBB2 (gene) - both valid
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# Check for mutation nomenclature (HGVS format)
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hgvs_pattern = r'p\.[A-Z]\d+[A-Z]' # e.g., p.L858R
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hgvs_mutations = re.findall(hgvs_pattern, self.content)
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if hgvs_mutations:
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self.info.append(f"Found {len(hgvs_mutations)} HGVS protein nomenclature (e.g., p.L858R)")
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# Warn about non-standard mutation format
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if 'EGFR mutation' in self.content and 'exon' not in self.content.lower():
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self.warnings.append("EGFR mutation mentioned - specify exon/variant (e.g., exon 19 deletion)")
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if issues:
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self.warnings.extend(issues)
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def generate_report(self):
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"""Generate validation report."""
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print("\n" + "="*70)
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print("VALIDATION REPORT")
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print("="*70)
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if self.errors:
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print(f"\n❌ ERRORS ({len(self.errors)}):")
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for error in self.errors:
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print(f" {error}")
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if self.warnings:
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print(f"\n⚠️ WARNINGS ({len(self.warnings)}):")
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for warning in self.warnings:
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print(f" {warning}")
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if self.info:
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print(f"\n✓ PASSED CHECKS ({len(self.info)}):")
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for info in self.info:
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print(f" {info}")
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# Overall status
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print("\n" + "="*70)
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if self.errors:
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print("STATUS: ❌ VALIDATION FAILED - Address errors before distribution")
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return False
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elif self.warnings:
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print("STATUS: ⚠️ VALIDATION PASSED WITH WARNINGS - Review recommended")
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return True
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else:
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print("STATUS: ✓ VALIDATION PASSED - Document meets quality standards")
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return True
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def save_report(self, output_file):
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"""Save validation report to file."""
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with open(output_file, 'w') as f:
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f.write("CLINICAL DECISION SUPPORT DOCUMENT VALIDATION REPORT\n")
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f.write("="*70 + "\n")
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f.write(f"Document: {self.filepath}\n")
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f.write(f"Validated: {Path.cwd()}\n\n")
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if self.errors:
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f.write(f"ERRORS ({len(self.errors)}):\n")
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for error in self.errors:
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f.write(f" - {error}\n")
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f.write("\n")
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if self.warnings:
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f.write(f"WARNINGS ({len(self.warnings)}):\n")
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for warning in self.warnings:
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f.write(f" - {warning}\n")
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f.write("\n")
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if self.info:
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f.write(f"PASSED CHECKS ({len(self.info)}):\n")
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for info in self.info:
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f.write(f" - {info}\n")
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print(f"\nValidation report saved to: {output_file}")
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def main():
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parser = argparse.ArgumentParser(description='Validate clinical decision support documents')
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parser.add_argument('input_file', type=str, help='Document to validate (.tex, .md, .txt)')
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parser.add_argument('-o', '--output', type=str, default=None,
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help='Save validation report to file')
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parser.add_argument('--strict', action='store_true',
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help='Treat warnings as errors')
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args = parser.parse_args()
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# Validate
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validator = CDSValidator(args.input_file)
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passed = validator.validate_all()
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# Save report if requested
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if args.output:
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validator.save_report(args.output)
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# Exit code
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if args.strict and (validator.errors or validator.warnings):
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exit(1)
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elif validator.errors:
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exit(1)
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else:
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exit(0)
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if __name__ == '__main__':
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main()
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# Example usage:
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# python validate_cds_document.py cohort_analysis.tex
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# python validate_cds_document.py treatment_recommendations.tex -o validation_report.txt
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# python validate_cds_document.py document.tex --strict # Warnings cause failure
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