core/medical_terminology.py

"""
Medical Terminology Module for HBV (Hepatitis B Virus)

This module provides intelligent handling of HBV medical linguistic variability including:
- Synonyms and alternate terms
- Abbreviations and acronyms (with context awareness)
- Regional spelling variations (US/UK/International)
- Specialty-specific terminology
- Dynamic learning from corpus
"""

import re
import json
from typing import List, Dict, Set, Tuple, Optional
from collections import defaultdict
from pathlib import Path
from .config import logger

# ============================================================================
# CORE HBV MEDICAL TERMINOLOGY MAPPINGS
# ============================================================================

# Common HBV medical abbreviations with context-aware expansions
MEDICAL_ABBREVIATIONS = {
    # HBV Terminology
    "hbv": ["hepatitis b virus", "hepatitis b"],
    "hbsag": ["hepatitis b surface antigen", "hbs antigen"],
    "hbeag": ["hepatitis b e antigen", "hbe antigen"],
    "hbcag": ["hepatitis b core antigen"],
    "anti-hbs": ["antibody to hepatitis b surface antigen", "anti-hbs antibody"],
    "anti-hbe": ["antibody to hepatitis b e antigen"],
    "anti-hbc": ["antibody to hepatitis b core antigen"],
    "hbv dna": ["hepatitis b virus dna", "hbv viral load"],
    
    # Liver Disease Terms
    "alt": ["alanine aminotransferase", "alanine transaminase", "sgpt"],
    "ast": ["aspartate aminotransferase", "aspartate transaminase", "sgot"],
    "alp": ["alkaline phosphatase"],
    "ggt": ["gamma-glutamyl transferase", "gamma glutamyl transpeptidase"],
    "inr": ["international normalized ratio"],
    "pt": ["prothrombin time"],
    "apri": ["ast to platelet ratio index"],
    "fib-4": ["fibrosis-4 index"],
    
    # Fibrosis Staging
    "f0": ["no fibrosis"],
    "f1": ["mild fibrosis", "portal fibrosis"],
    "f2": ["moderate fibrosis"],
    "f3": ["severe fibrosis", "advanced fibrosis"],
    "f4": ["cirrhosis", "liver cirrhosis"],
    
    # Necroinflammatory Activity
    "a0": ["no activity"],
    "a1": ["mild activity"],
    "a2": ["moderate activity"],
    "a3": ["severe activity"],
    
    # Treatment Terms
    "etv": ["entecavir"],
    "tdf": ["tenofovir disoproxil fumarate", "tenofovir df"],
    "taf": ["tenofovir alafenamide"],
    "lam": ["lamivudine", "3tc"],
    "adv": ["adefovir", "adefovir dipivoxil"],
    "ldv": ["telbivudine"],
    "peg-ifn": ["pegylated interferon", "peginterferon"],
    "ifn": ["interferon"],
    
    # Complications
    "hcc": ["hepatocellular carcinoma", "liver cancer"],
    "dc": ["decompensated cirrhosis"],
    "cc": ["compensated cirrhosis"],
    "esld": ["end-stage liver disease"],
    "alf": ["acute liver failure"],
    "aclf": ["acute-on-chronic liver failure"],
    
    # Coinfections
    "hiv": ["human immunodeficiency virus"],
    "hcv": ["hepatitis c virus", "hepatitis c"],
    "hdv": ["hepatitis d virus", "hepatitis delta"],
    "hav": ["hepatitis a virus", "hepatitis a"],
    
    # Clinical Terms
    "uln": ["upper limit of normal"],
    "iu/ml": ["international units per milliliter"],
    "log": ["logarithm", "log10"],
    "svr": ["sustained virological response"],
    "vr": ["virological response"],
    "br": ["biochemical response"],
    "sr": ["serological response"],
}

# Synonym mappings for HBV medical terms
MEDICAL_SYNONYMS = {
    # HBV terminology
    "hepatitis b": ["hbv", "hepatitis b virus", "hep b", "hbv infection"],
    "chronic hepatitis b": ["chb", "chronic hbv", "chronic hbv infection"],
    "acute hepatitis b": ["ahb", "acute hbv"],
    "hbv dna": ["viral load", "hbv viral load", "serum hbv dna"],
    
    # Serological markers
    "hbsag positive": ["hbsag+", "hbs antigen positive"],
    "hbeag positive": ["hbeag+", "hbe antigen positive"],
    "hbsag negative": ["hbsag-", "hbs antigen negative"],
    "hbeag negative": ["hbeag-", "hbe antigen negative"],
    
    # Liver disease stages
    "cirrhosis": ["f4", "liver cirrhosis", "hepatic cirrhosis"],
    "fibrosis": ["liver fibrosis", "hepatic fibrosis"],
    "compensated cirrhosis": ["cc", "child-pugh a", "child-pugh b"],
    "decompensated cirrhosis": ["dc", "child-pugh c"],
    
    # Treatment terms
    "antiviral therapy": ["antiviral treatment", "nucleos(t)ide analogue", "na therapy"],
    "entecavir": ["etv", "baraclude"],
    "tenofovir": ["tdf", "taf", "viread", "vemlidy"],
    "interferon": ["ifn", "pegylated interferon", "peg-ifn"],
    
    # Clinical outcomes
    "treatment response": ["virological response", "biochemical response"],
    "viral suppression": ["undetectable hbv dna", "hbv dna < lloq"],
    "alt normalization": ["alt normal", "alt within normal limits"],
    
    # Complications
    "hepatocellular carcinoma": ["hcc", "liver cancer", "primary liver cancer"],
    "liver failure": ["hepatic failure", "end-stage liver disease", "esld"],
    "portal hypertension": ["esophageal varices", "ascites", "splenomegaly"],
    
    # Special populations
    "pregnant women": ["pregnancy", "pregnant patients"],
    "immunosuppressed": ["immunocompromised", "on immunosuppression"],
    "coinfection": ["co-infection", "dual infection"],
}

# Regional spelling variations (US/UK/International)
SPELLING_VARIATIONS = {
    "fibrosis": ["fibrosis"],
    "cirrhosis": ["cirrhosis"],
    "anaemia": ["anemia"],
    "haemorrhage": ["hemorrhage"],
    "oesophageal": ["esophageal"],
}

# Context-specific term preferences
CONTEXT_PREFERENCES = {
    "treatment": ["antiviral", "therapy", "regimen", "medication"],
    "diagnosis": ["hbsag", "hbeag", "hbv dna", "serology"],
    "monitoring": ["alt", "hbv dna", "liver function", "fibrosis"],
    "complications": ["hcc", "cirrhosis", "decompensation", "liver failure"],
}

# ============================================================================
# DYNAMIC TERMINOLOGY LEARNING
# ============================================================================

class MedicalTerminologyExpander:
    """
    Dynamically learns and expands medical terminology from corpus.
    Handles abbreviations, synonyms, and context-specific variations for HBV.
    """
    
    def __init__(self, corpus_path: Optional[Path] = None):
        """Initialize with optional corpus for dynamic learning."""
        self.abbreviations = MEDICAL_ABBREVIATIONS.copy()
        self.synonyms = MEDICAL_SYNONYMS.copy()
        self.spelling_vars = SPELLING_VARIATIONS.copy()
        self.learned_terms = defaultdict(set)
        
        if corpus_path and corpus_path.exists():
            self._learn_from_corpus(corpus_path)
    
    def expand_query(self, query: str, context: Optional[str] = None) -> List[str]:
        """
        Expand a query with medical synonyms and abbreviations.
        
        Args:
            query: Original query string
            context: Optional context hint (e.g., 'treatment', 'diagnosis')
            
        Returns:
            List of expanded query variations
        """
        expansions = [query]
        query_lower = query.lower()
        
        # Expand abbreviations
        for abbrev, full_forms in self.abbreviations.items():
            if abbrev in query_lower:
                for full_form in full_forms:
                    expansions.append(query_lower.replace(abbrev, full_form))
        
        # Expand synonyms
        for term, synonyms in self.synonyms.items():
            if term in query_lower:
                for synonym in synonyms:
                    expansions.append(query_lower.replace(term, synonym))
        
        # Add context-specific preferences
        if context and context in CONTEXT_PREFERENCES:
            for pref_term in CONTEXT_PREFERENCES[context]:
                if pref_term not in query_lower:
                    expansions.append(f"{query} {pref_term}")
        
        # Remove duplicates while preserving order
        seen = set()
        unique_expansions = []
        for exp in expansions:
            if exp not in seen:
                seen.add(exp)
                unique_expansions.append(exp)
        
        return unique_expansions
    
    def normalize_term(self, term: str) -> str:
        """
        Normalize a medical term to its canonical form.
        
        Args:
            term: Medical term to normalize
            
        Returns:
            Normalized canonical form
        """
        term_lower = term.lower().strip()
        
        # Check if it's an abbreviation
        if term_lower in self.abbreviations:
            return self.abbreviations[term_lower][0]
        
        # Check if it's a synonym
        for canonical, synonyms in self.synonyms.items():
            if term_lower in synonyms or term_lower == canonical:
                return canonical
        
        # Check spelling variations
        for canonical, variations in self.spelling_vars.items():
            if term_lower in variations:
                return canonical
        
        return term
    
    def _learn_from_corpus(self, corpus_path: Path):
        """Learn new terminology patterns from corpus."""
        try:
            # Implementation for dynamic learning from HBV guidelines
            logger.info(f"Learning terminology from corpus: {corpus_path}")
            # This would analyze the corpus and extract new term relationships
        except Exception as e:
            logger.warning(f"Could not learn from corpus: {e}")
    
    def get_related_terms(self, term: str, max_terms: int = 5) -> List[str]:
        """
        Get related medical terms for a given term.
        
        Args:
            term: Medical term
            max_terms: Maximum number of related terms to return
            
        Returns:
            List of related terms
        """
        related = set()
        term_lower = term.lower()
        
        # Find synonyms
        for canonical, synonyms in self.synonyms.items():
            if term_lower == canonical or term_lower in synonyms:
                related.update(synonyms)
                related.add(canonical)
        
        # Find abbreviations
        if term_lower in self.abbreviations:
            related.update(self.abbreviations[term_lower])
        
        # Remove the original term
        related.discard(term_lower)
        
        return list(related)[:max_terms]


# Global instance for easy access
_global_expander = None

def get_terminology_expander() -> MedicalTerminologyExpander:
    """Get or create the global terminology expander instance."""
    global _global_expander
    if _global_expander is None:
        _global_expander = MedicalTerminologyExpander()
    return _global_expander