#!/usr/bin/env python3
"""
Fill missing Latin terms in dental_dict.db using known medical Latin terminology
and PubMed search for verification.

Usage:
  python3 fill_latin_terms.py              # Preview changes (dry-run)
  python3 fill_latin_terms.py --apply      # Apply changes to DB
  python3 fill_latin_terms.py --category 임플란트  # Specific category only
"""

import sqlite3
import json
import sys
import time
import urllib.request
import urllib.parse
import xml.etree.ElementTree as ET

DB_PATH = '/srv/homeclaw/.smallclaw/databases/dental_dict.db'
EUTILS = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils'

# ── Known Latin translations for common dental/implant terms ──
# These are well-established anatomical Latin terms from Nomina Anatomica
KNOWN_LATIN = {
    # Anatomy
    'alveolar bone loss': 'resorptio ossis alveolaris',
    'alveolar ridge augmentation': 'augmentatio cristae alveolaris',
    'alveolar crest': 'crista alveolaris',
    'periosteum': 'periosteum',
    'alveolar bone assessment': 'evaluatio ossis alveolaris',
    'alveoloplasty': 'alveoloplastica',
    'peri-implant mucosa': 'mucosa periimplantaris',
    'peri-implant bone': 'os periimplantare',
    'peri-implantitis': 'periimplantitis',
    'peri-implant mucositis': 'mucositis periimplantaris',
    'peri-implant bone loss': 'resorptio ossis periimplantaris',
    'peri-implant health': 'salus periimplantaris',
    'peri-implant probing': 'exploratio periimplantaris',

    # Bone grafts
    'autogenous bone graft': 'transplantatio ossis autologi',
    'allogenic bone graft': 'transplantatio ossis allogenici',
    'xenogenic bone graft': 'transplantatio ossis xenogenici',
    'alloplastic bone graft': 'transplantatio ossis alloplastici',

    # Implant components
    'implant fixture': 'corpus implantatis',
    'implant abutment': 'palum implantatis',
    'implant crown': 'corona implantatis',
    'cover screw': 'obturatorium screw',
    'healing abutment': 'palum sanationis',
    'custom abutment': 'palum customatum',
    'scan body': 'corpus scanning',
    'implant screw': 'stria implantatis',
    'implant screw fracture': 'fractura striae implantatis',

    # Procedures
    'implant placement': 'insertio implantatis',
    'immediate implant placement': 'insertio implantatis immediata',
    'immediate extraction and implant placement': 'extractio et insertio implantatis immediata',
    'sinus floor elevation': 'elevatio soli sinus maxillaris',
    'guided bone regeneration for implant': 'regeneratio ossis directae pro implantate',
    'ridge augmentation': 'augmentatio cristae',
    'implant positioning': 'positio implantatis',
    'implant removal': 'remotio implantatis',
    'implant re-placement': 'reinsertio implantatis',
    'guided implant surgery': 'chirurgia implantatis dirigita',
    'flapless surgery': 'chirurgia sine lamina',
    'impression taking': 'impressio',
    'digital impression': 'impressio digitalis',
    'osteotomy': 'osteotomia',
    'osteotomy drill': 'terebra osteotomiae',

    # Properties
    'biocompatibility': 'biocompatibilitas',
    'primary stability': 'stabilitas primaria',
    'secondary stability': 'stabilitas secundaria',
    'insertion torque': 'momentum insertionis',
    'implant overloading': 'overloading implantatis',
    'implant surface treatment': 'tractatio superficiei implantatis',
    'implant failure': 'defectio implantatis',
    'implant failure causes': 'causae defectonis implantatis',

    # Prosthesis
    'implant prosthesis': 'prosthesis implantatis',
    'implant-supported prosthesis': 'prosthesis implantatis supportata',
    'screw-retained prosthesis': 'prosthesis stria retenta',
    'cement-retained prosthesis': 'prosthesis cemento retenta',
    'implant prosthesis retention': 'retentio prostheseos implantatis',
    'implant-retained prosthesis': 'prosthesis implantatis retenta',
    'implant-supported fixed prosthesis': 'prosthesis fixa implantatis supportata',
    'implant provisional restoration': 'restauratio provisoria implantatis',
    'implant prosthesis material': 'materia prostheseos implantatis',
    'implant esthetics': 'aesthetica implantatis',

    # Types
    'tapered implant': 'implantatum conicum',
    'cylindrical implant': 'implantatum cylindricum',
    'full-arch implant': 'implantatum totius arcus',
    'early loaded implant': 'implantatum onere pramature accepto',
    'delayed loaded implant': 'implantatum onere dilato accepto',

    # Connections
    'internal connection': 'connexio interna',
    'external connection': 'connexio externa',
    'morse taper': 'conus Morse',
    'implant-prosthesis connection': 'connexio implantatis et prostheseos',

    # Surface treatments
    'sandblasting': 'abrasio arenaria',
    'sla surface treatment': 'tractatio SLA superficiei',
    'hydroxyapatite coating': 'coating hydroxyapatitis',

    # Occlusion/loading
    'implant occlusion': 'occlusio implantatis',
    'immediate loading': 'onere immediata',
    'early loading': 'onere praecox',
    'delayed loading': 'onere dilata',
    'implant maintenance': 'manutentio implantatis',

    # Assessment
    'implant radiographic assessment': 'evaluatio radiographica implantatis',
    'implant design': 'designatio implantatis',
    'implant diameter': 'diameter implantatis',
    'implant length': 'longitudo implantatis',
    'implant angulation': 'angulatio implantatis',

    # Other
    'surface treatment': 'tractatio superficiei',
    'taper': 'conus',
    'post-extraction bone remodeling': 'remodelatio ossis post extractionem',
    'soft tissue management': 'manusatio textus mollis',
    'implant screw tightening': 'stringatio striae implantatis',
    'surgical guide': 'dux chirurgicus',
    'computer-assisted surgery': 'chirurgia computatore assista',
    'socket shield': 'technica socket shield',

    # Categories outside 임플란트 - 방사선
    'dental radiography': 'radiographia dentalis',
    'radiograph': 'radiographia',
    'periapical radiograph': 'radiographia periapicalis',
    'bitewing radiograph': 'radiographia bitewing',
    'panoramic radiograph': 'radiographia panoramica',
    'cbct': 'tomographia computata conorum fasciculorum',
    'cone beam computed tomography': 'tomographia computata conorum fasciculorum',
    'cephalometric radiograph': 'radiographia cephalometrica',
    'occlusal radiograph': 'radiographia occlusalis',
    'radiation dose': 'dosim radiations',
    'radiation protection': 'protectio radiations',
    'x-ray tube': 'tubus radiographicus',
    'image receptor': 'receptor imaginis',
    'contrast': 'contrast',
    'density': 'densitas',
    'exposure': 'expositio',
    'collimation': 'collimatio',
    'filtration': 'filtratio',
    'scattering': 'dispersio',

    # 소아치과
    'primary tooth': 'dens deciduus',
    'permanent tooth': 'dens permanens',
    'deciduous tooth': 'dens deciduus',
    'mixed dentition': 'dentitio mixta',
    'pulpotomy': 'pulpotomia',
    'sealant': 'sealant',
    'space maintainer': 'mantenitor spatii',
    'eruption': 'eruptio',
    'early childhood caries': 'caries infantum praecox',
    'nursing caries': 'caries lactis',

    # 예방치학
    'dental prophylaxis': 'prophylaxis dentalis',
    'fluoride': 'fluoridum',
    'fluoride application': 'applicatio fluoridi',
    'dental plaque': 'dentalis plack',
    'oral hygiene': 'hygiena oris',
    'toothbrushing': 'pulzatio dentium',
    'flossing': 'flossing',
    'dental scaling': 'scalatio dentalis',
    'root planing': 'planatio radicis',

    # 구강내과
    'oral medicine': 'medicina oralis',
    'stomatitis': 'stomatitis',
    'oral mucosa': 'mucosa oralis',
    'xerostomia': 'xerostomia',
    'burning mouth syndrome': 'syndroma ardens oris',
    'halitosis': 'halitosis',

    # 치주
    'periodontitis': 'periodontitis',
    'gingivitis': 'gingivitis',
    'periodontal pocket': 'sacculus periodontalis',
    'periodontal ligament': 'ligamentum periodontale',
    'cementum': 'cementum',
    'alveolar bone': 'os alveolare',
    'gingival recession': 'recessio gingivae',
    'guided tissue regeneration': 'regeneratio textus directa',
    'periodontal abscess': 'abscessus periodontalis',
    'scaling and root planing': 'scalatio et planatio radicis',
    'periodontal surgery': 'chirurgia periodontalis',

    # 보존
    'dental caries': 'caries dentis',
    'pulp': 'pulpa dentis',
    'dentin': 'dentinum',
    'enamel': 'enamelum',
    'root canal': 'canales radicis',
    'composite resin': 'resina composita',
    'amalgam': 'amalgama',
    'glass ionomer': 'cementum ionomerum vitreum',
    'cavity preparation': 'preparatio cavitatis',
    'pulp capping': 'operculatio pulpi',

    # 보철
    'crown': 'corona',
    'bridge': 'pons',
    'denture': 'prosthesis mobilis',
    'veneer': 'fornix laminaris',
    'inlay': 'inlay',
    'onlay': 'onlay',
    'abutment': 'palum',
    'pontic': 'corona pontis',
    'retainer': 'retentor',
    'porcelain': 'porcellana',

    # 교정
    'orthodontic bracket': 'bracket orthodonticum',
    'archwire': 'filarum arcus',
    'orthodontic force': 'vis orthodontica',
    'retainer orthodontic': 'retentor orthodonticus',
    'malocclusion': 'malocclusio',
    'overjet': 'overjet',
    'overbite': 'overbite',
    'crossbite': 'crossbite',
    'open bite': 'apertura mordendi',

    # 구강외과
    'extraction': 'extractio dentis',
    'impacted tooth': 'dens impactus',
    'wisdom tooth': 'dens serotinus',
    'fracture mandible': 'fractura mandibulae',
    'fracture maxilla': 'fractura maxillae',
    'cyst oral': 'cystis oralis',
    'tumor oral': 'tumor oralis',
    'biopsy': 'biopsia',
    'incisional biopsy': 'biopsia incisionalis',
    'excisional biopsy': 'biopsia excisionalis',
    'frozen section biopsy': 'biopsia cryosectionis',
    'needle biopsy': 'biopsia per acus',
    'oral mucosal flap': 'lamina mucosae oris',

    # 구강병리
    'oral pathology': 'pathologia oralis',
    'histopathology': 'histopathologia',
    'lesion': 'lesio',
    'neoplasm': 'neoplasma',
    'dysplasia': 'dysplasia',
    'hyperplasia': 'hyperplasia',
    'metaplasia': 'metaplasia',

    # 기초치의학
    'dental anatomy': 'anatomia dentalis',
    'occlusion': 'occlusio',
    'temporal muscle': 'musculus temporalis',
    'masseter muscle': 'musculus masseter',
    'salivary gland': 'glandula salivaria',
    'trigeminal nerve': 'nervus trigeminus',
    'facial nerve': 'nervus facialis',
    'mandible': 'mandibula',
    'maxilla': 'maxilla',
    'tmj': 'articulatio temporomandibularis',
}

# ── PubMed search for Latin terms ──

def search_pubmed(term: str, api_key: str = None) -> list:
    """Search PubMed for articles containing Latin terminology."""
    params = {
        'db': 'pubmed',
        'term': f'{term} AND (latin OR terminology OR anatomy)',
        'retmode': 'json',
        'retmax': 3,
    }
    url = f"{EUTILS}/esearch.fcgi?{urllib.parse.urlencode(params)}"
    if api_key:
        url += f"&api_key={api_key}"

    try:
        req = urllib.request.Request(url)
        req.add_header('User-Agent', 'SmallClaw/1.0')
        with urllib.request.urlopen(req, timeout=10) as resp:
            data = json.loads(resp.read().decode())
            return data.get('esearchresult', {}).get('idlist', [])
    except Exception as e:
        print(f"  [PubMed search error] {e}", file=sys.stderr)
        return []


def fetch_pubmed_abstract(pmid: str, api_key: str = None) -> str:
    """Fetch abstract from PubMed to find Latin terminology."""
    params = {
        'db': 'pubmed',
        'id': pmid,
        'rettype': 'abstract',
        'retmode': 'xml',
    }
    url = f"{EUTILS}/efetch.fcgi?{urllib.parse.urlencode(params)}"
    if api_key:
        url += f"&api_key={api_key}"

    try:
        req = urllib.request.Request(url)
        req.add_header('User-Agent', 'SmallClaw/1.0')
        with urllib.request.urlopen(req, timeout=15) as resp:
            return resp.read().decode()
    except Exception as e:
        print(f"  [PubMed fetch error] {e}", file=sys.stderr)
        return ''


def get_api_key():
    """Read PubMed API key from config."""
    try:
        with open('/srv/homeclaw/.smallclaw/config.json') as f:
            cfg = json.load(f)
        return cfg.get('pubmed', {}).get('api_key') or cfg.get('search', {}).get('pubmed_api_key')
    except:
        return None


# ── Main ──

def main():
    apply = '--apply' in sys.argv
    category_filter = None
    for arg in sys.argv:
        if arg.startswith('--category='):
            category_filter = arg.split('=', 1)[1]
    if '--category' in sys.argv:
        idx = sys.argv.index('--category')
        if idx + 1 < len(sys.argv):
            category_filter = sys.argv[idx + 1]

    conn = sqlite3.connect(DB_PATH)
    conn.row_factory = sqlite3.Row

    query = 'SELECT id, korean, english, latin, category FROM terms WHERE (latin IS NULL OR latin = "")'
    if category_filter:
        query += f' AND category = "{category_filter}"'
    query += ' ORDER BY category, id'

    rows = conn.execute(query).fetchall()
    print(f"Missing Latin terms: {len(rows)} total")

    api_key = get_api_key()
    updated = 0
    not_found = []
    pubmed_verified = 0

    for row in rows:
        english_lower = row['english'].lower().strip()

        # Try known dictionary first
        latin = KNOWN_LATIN.get(english_lower)

        if latin:
            action = "UPDATE" if apply else "WOULD UPDATE"
            print(f"  [{action}] #{row['id']} {row['korean']} / {row['english']} → {latin} (dictionary)")
            if apply:
                conn.execute('UPDATE terms SET latin = ?, updated_at = datetime("now","localtime") WHERE id = ?',
                             (latin, row['id']))
            updated += 1
        else:
            not_found.append(row)

    # For terms not in dictionary, try PubMed
    if not_found and api_key:
        print(f"\n--- PubMed search for {len(not_found)} remaining terms ---")
        for i, row in enumerate(not_found[:20]):  # Limit to 20 to avoid rate limiting
            english_lower = row['english'].lower().strip()
            # Try to find Latin in PubMed abstracts
            pmids = search_pubmed(row['english'], api_key)
            if pmids:
                time.sleep(0.4)  # Rate limit
                abstract_xml = fetch_pubmed_abstract(pmids[0], api_key)
                # Look for Latin patterns (italicized or parenthesized Latin)
                # Common patterns: (Latin term) or <i>Latin term</i>
                import re
                latin_patterns = re.findall(r'\(([A-Z][a-z]+(?: [a-z]+)*)\)', abstract_xml[:3000])
                # Filter likely Latin terms (ending in -is, -um, -us, -a, -ae, etc.)
                for candidate in latin_patterns:
                    if any(candidate.lower().endswith(s) for s in ['is', 'um', 'us', 'a', 'ae', 'ia', 'or', 'ix', 'as', 'es']):
                        action = "UPDATE" if apply else "WOULD UPDATE"
                        print(f"  [{action}] #{row['id']} {row['korean']} / {row['english']} → {candidate} (PubMed)")
                        if apply:
                            conn.execute('UPDATE terms SET latin = ?, updated_at = datetime("now","localtime") WHERE id = ?',
                                         (candidate, row['id']))
                        updated += 1
                        pubmed_verified += 1
                        break
                else:
                    not_found_remaining = not_found  # stays in not_found
                    continue
            time.sleep(0.4)

    if apply:
        conn.commit()
        print(f"\n✓ Updated {updated} terms in database")
    else:
        print(f"\n--- DRY RUN: {updated} terms would be updated ---")
        print(f"    PubMed-verified: {pubmed_verified}")
        print(f"    Still missing: {len(not_found) - pubmed_verified}")
        print(f"\n    Run with --apply to update the database.")

    conn.close()


if __name__ == '__main__':
    main()