Learn_System/backend/src/controllers/biochemController.js

'use strict';
const db = require('../db/db');
const { awardXP, checkAchievements } = require('./gamificationController');
const chem = require('../services/chem');

/* ── Helpers ─────────────────────────────────────────────────────────── */
const MAX_V = { H:1, C:4, N:3, O:2, P:5, S:6, Cl:1, Na:1, Ca:2, K:1, Mg:2, Fe:3, Br:1, I:1, F:1 };

function hillFormula(atoms) {
  const cnt = {};
  for (const a of atoms) cnt[a.s] = (cnt[a.s] || 0) + 1;
  const parts = [];
  if (cnt.C) { parts.push('C' + (cnt.C > 1 ? cnt.C : '')); delete cnt.C; }
  if (cnt.H) { parts.push('H' + (cnt.H > 1 ? cnt.H : '')); delete cnt.H; }
  for (const el of Object.keys(cnt).sort()) parts.push(el + (cnt[el] > 1 ? cnt[el] : ''));
  return parts.join('');
}

function valencyIssues(atoms, bonds) {
  const sums = {};
  for (const b of bonds) {
    sums[b.f] = (sums[b.f] || 0) + b.o;
    sums[b.t] = (sums[b.t] || 0) + b.o;
  }
  return atoms
    .filter(a => (sums[a.id] || 0) > (MAX_V[a.s] ?? 4))
    .map(a => ({ id: a.id, symbol: a.s, used: sums[a.id] || 0, max: MAX_V[a.s] ?? 4 }));
}

/* ── Structural (connectivity) match: Morgan-style canonical hash ──────────
 * Сравнивает связность двух молекул независимо от id/координат/нумерации.
 * Инвариант атома итеративно уточняется по соседям и порядкам связей;
 * каноническая подпись = отсортированные инварианты атомов + рёбер.
 */
function _bf(b) { return b.from != null ? b.from : b.f; }
function _bt(b) { return b.to != null ? b.to : b.t; }
function _bo(b) { return (b.order != null ? b.order : b.o) || 1; }
function _hashStr(s) { let h = 5381; for (let i = 0; i < s.length; i++) h = ((h << 5) + h + s.charCodeAt(i)) | 0; return (h >>> 0).toString(36); }

function canonicalHash(atoms, bonds) {
  const adj = {};
  atoms.forEach(a => adj[a.id] = []);
  for (const b of bonds) {
    const f = _bf(b), t = _bt(b), o = _bo(b);
    if (adj[f] && adj[t]) { adj[f].push({ id: t, o }); adj[t].push({ id: f, o }); }
  }
  let inv = {};
  atoms.forEach(a => inv[a.id] = a.s);
  for (let iter = 0; iter < atoms.length; iter++) {
    const next = {};
    for (const a of atoms) {
      const neigh = adj[a.id].map(n => inv[n.id] + ':' + n.o).sort().join(',');
      next[a.id] = _hashStr(inv[a.id] + '|' + neigh);
    }
    inv = next;
  }
  const atomSig = atoms.map(a => inv[a.id]).sort().join(';');
  const edgeSig = bonds.map(b => [inv[_bf(b)], inv[_bt(b)]].sort().join('-') + '#' + _bo(b)).sort().join(',');
  return atomSig + '||' + edgeSig;
}

function structuralMatch(a1, b1, a2, b2) {
  if (!Array.isArray(a1) || !Array.isArray(a2)) return false;
  if (a1.length !== a2.length || (b1 || []).length !== (b2 || []).length) return false;
  return canonicalHash(a1, b1 || []) === canonicalHash(a2, b2 || []);
}

/* ── Prepared statements ─────────────────────────────────────────────── */
const stmts = {
  getElements:    db.prepare('SELECT * FROM bio_elements ORDER BY radius ASC'),
  getMolecules:   db.prepare("SELECT id,formula,name_ru,name_lat,category,difficulty,description,topic_tags,atoms_json,bonds_json FROM bio_molecules WHERE is_library=1 ORDER BY difficulty,name_ru"),
  getMolCat:      db.prepare("SELECT id,formula,name_ru,name_lat,category,difficulty,description,topic_tags,atoms_json,bonds_json FROM bio_molecules WHERE is_library=1 AND category=? ORDER BY difficulty,name_ru"),
  getMolSearch:   db.prepare("SELECT id,formula,name_ru,name_lat,category,difficulty,description,topic_tags,atoms_json,bonds_json FROM bio_molecules WHERE is_library=1 AND (name_ru LIKE ? OR formula LIKE ?) ORDER BY difficulty,name_ru"),
  getMolById:     db.prepare('SELECT * FROM bio_molecules WHERE id=?'),
  getMolByFormula:db.prepare('SELECT id,name_ru,name_lat,category,description,topic_tags FROM bio_molecules WHERE formula=? LIMIT 1'),
  getReactions:   db.prepare('SELECT * FROM bio_reactions ORDER BY name_ru'),
  getChallenges:  db.prepare('SELECT * FROM bio_challenges ORDER BY difficulty,order_n'),
  getChallenge:   db.prepare('SELECT * FROM bio_challenges WHERE id=?'),
  checkDone:      db.prepare('SELECT 1 FROM bio_user_challenges WHERE user_id=? AND challenge_id=?'),
  markDone:       db.prepare('INSERT OR IGNORE INTO bio_user_challenges (user_id,challenge_id) VALUES (?,?)'),
  getDoneIds:     db.prepare('SELECT challenge_id FROM bio_user_challenges WHERE user_id=?'),
  getSaved:       db.prepare('SELECT bm.*, bmo.name_ru AS mol_name FROM bio_user_molecules bm LEFT JOIN bio_molecules bmo ON bmo.id=bm.molecule_id WHERE bm.user_id=? ORDER BY bm.created_at DESC'),
  saveMol:        db.prepare('INSERT INTO bio_user_molecules (user_id,molecule_id,name,formula,atoms_json,bonds_json) VALUES (?,?,?,?,?,?)'),
  deleteSaved:    db.prepare('DELETE FROM bio_user_molecules WHERE id=? AND user_id=?'),
};

/* ── GET /api/biochem/elements ───────────────────────────────────────── */
function getElements(_req, res) {
  res.json(stmts.getElements.all());
}

/* ── GET /api/biochem/molecules ──────────────────────────────────────── */
function getMolecules(req, res) {
  const { cat, q } = req.query;
  let rows;
  if (q) {
    const like = `%${q}%`;
    rows = stmts.getMolSearch.all(like, like);
  } else if (cat) {
    rows = stmts.getMolCat.all(cat);
  } else {
    rows = stmts.getMolecules.all();
  }
  rows = rows.map(r => ({
    ...r,
    topic_tags: tryParse(r.topic_tags, []),
    atoms_json: tryParse(r.atoms_json, []),
    bonds_json: tryParse(r.bonds_json, []),
  }));
  res.json(rows);
}

/* ── GET /api/biochem/molecules/:id ─────────────────────────────────── */
function getMolecule(req, res) {
  const mol = stmts.getMolById.get(req.params.id);
  if (!mol) return res.status(404).json({ error: 'Not found' });
  res.json({
    ...mol,
    atoms_json:  tryParse(mol.atoms_json, []),
    bonds_json:  tryParse(mol.bonds_json, []),
    topic_tags:  tryParse(mol.topic_tags, []),
  });
}

/* ── POST /api/biochem/validate ─────────────────────────────────────── */
function validate(req, res) {
  const { atoms, bonds } = req.body;
  if (!Array.isArray(atoms) || !Array.isArray(bonds))
    return res.status(400).json({ error: 'atoms[] and bonds[] required' });
  if (atoms.length === 0) return res.json({ valid: false, formula: '', issues: [] });

  // Единое химическое ядро (Фаза 2.1): формула + валентность с подсказками (2.4)
  const { valid, formula, issues } = chem.validate(atoms, bonds);
  const known = valid ? stmts.getMolByFormula.get(formula) : null;
  res.json({ valid, formula, issues, known: known || null });
}

/* ── POST /api/biochem/analyze — полный химический анализ структуры (2.2) ─ */
function analyze(req, res) {
  const { atoms, bonds } = req.body || {};
  if (!Array.isArray(atoms))
    return res.status(400).json({ error: 'atoms[] обязателен' });
  if (atoms.length === 0)
    return res.json({ formula: '', mass: 0, dbe: null, valency: [] });
  try {
    res.json(chem.analyze(atoms, Array.isArray(bonds) ? bonds : []));
  } catch (e) {
    res.status(500).json({ error: e.message });
  }
}

/* ── GET /api/biochem/reactions ─────────────────────────────────────── */
function getReactions(_req, res) {
  const rows = stmts.getReactions.all().map(r => ({
    ...r,
    reactant_ids: tryParse(r.reactant_ids, []),
    product_ids:  tryParse(r.product_ids, []),
    topic_tags:   tryParse(r.topic_tags, []),
  }));
  res.json(rows);
}

/* ── GET /api/biochem/challenges ────────────────────────────────────── */
function getChallenges(req, res) {
  const challenges = stmts.getChallenges.all();
  const doneSet = new Set(stmts.getDoneIds.all(req.user.id).map(r => r.challenge_id));
  res.json(challenges.map(c => ({
    ...c,
    data_json: tryParse(c.data_json, null),
    done: doneSet.has(c.id),
  })));
}

/* ── POST /api/biochem/challenges/:id/solve ─────────────────────────── */
function solveChallenge(req, res) {
  const challenge = stmts.getChallenge.get(req.params.id);
  if (!challenge) return res.status(404).json({ error: 'Challenge not found' });

  if (stmts.checkDone.get(req.user.id, challenge.id))
    return res.status(400).json({ error: 'already_completed' });

  const type = challenge.type || 'build';

  /* ── identify: shown structure → pick name ── */
  if (type === 'identify') {
    const { answer } = req.body;
    if (typeof answer !== 'string' || !answer)
      return res.status(400).json({ error: 'answer required' });
    const mol = stmts.getMolByFormula.get(challenge.target_formula);
    if (!mol || answer !== mol.name_ru)
      return res.status(400).json({ error: 'wrong_answer' });
    stmts.markDone.run(req.user.id, challenge.id);
    awardXP(req.user.id, challenge.xp_reward, `biochem_challenge:${challenge.id}`);
    checkAchievements(req.user.id);
    return res.json({ ok: true, xp: challenge.xp_reward });
  }

  /* ── formula: shown name → pick formula ── */
  if (type === 'formula') {
    const { answer } = req.body;
    if (typeof answer !== 'string' || !answer)
      return res.status(400).json({ error: 'answer required' });
    if (answer !== challenge.target_formula)
      return res.status(400).json({ error: 'wrong_answer' });
    stmts.markDone.run(req.user.id, challenge.id);
    awardXP(req.user.id, challenge.xp_reward, `biochem_challenge:${challenge.id}`);
    checkAchievements(req.user.id);
    return res.json({ ok: true, xp: challenge.xp_reward });
  }

  /* ── classify: shown molecule → pick class ── */
  if (type === 'classify') {
    const { answer } = req.body;
    if (typeof answer !== 'string' || !answer)
      return res.status(400).json({ error: 'answer required' });
    const data = tryParse(challenge.data_json, {});
    if (answer !== data.answer)
      return res.status(400).json({ error: 'wrong_answer' });
    stmts.markDone.run(req.user.id, challenge.id);
    awardXP(req.user.id, challenge.xp_reward, `biochem_challenge:${challenge.id}`);
    checkAchievements(req.user.id);
    return res.json({ ok: true, xp: challenge.xp_reward });
  }

  /* ── complete: shown partial reaction → pick missing component ── */
  if (type === 'complete') {
    const { answer } = req.body;
    if (typeof answer !== 'string' || !answer)
      return res.status(400).json({ error: 'answer required' });
    const data = tryParse(challenge.data_json, {});
    if (answer !== data.answer)
      return res.status(400).json({ error: 'wrong_answer' });
    stmts.markDone.run(req.user.id, challenge.id);
    awardXP(req.user.id, challenge.xp_reward, `biochem_challenge:${challenge.id}`);
    checkAchievements(req.user.id);
    return res.json({ ok: true, xp: challenge.xp_reward });
  }

  /* ── balance: fill coefficients to balance equation ── */
  if (type === 'balance') {
    const { coefficients } = req.body;
    const data = tryParse(challenge.data_json, {});
    const expected = data.coefficients || [];
    if (!Array.isArray(coefficients) ||
        coefficients.length !== expected.length ||
        !coefficients.every((c, i) => parseInt(c) === expected[i]))
      return res.status(400).json({ error: 'wrong_answer' });
    stmts.markDone.run(req.user.id, challenge.id);
    awardXP(req.user.id, challenge.xp_reward, `biochem_challenge:${challenge.id}`);
    checkAchievements(req.user.id);
    return res.json({ ok: true, xp: challenge.xp_reward });
  }

  /* ── match: pair left items with right items ── */
  if (type === 'match') {
    const { pairs } = req.body;
    const data = tryParse(challenge.data_json, {});
    const answerMap = new Map((data.pairs || []).map(p => [p.left, p.right]));
    if (!Array.isArray(pairs) ||
        pairs.length !== answerMap.size ||
        !pairs.every(p => answerMap.get(p.left) === p.right))
      return res.status(400).json({ error: 'wrong_answer' });
    stmts.markDone.run(req.user.id, challenge.id);
    awardXP(req.user.id, challenge.xp_reward, `biochem_challenge:${challenge.id}`);
    checkAchievements(req.user.id);
    return res.json({ ok: true, xp: challenge.xp_reward });
  }

  /* ── build (default): draw the molecule ── */
  const { atoms, bonds } = req.body;
  if (!Array.isArray(atoms) || !Array.isArray(bonds))
    return res.status(400).json({ error: 'atoms[] and bonds[] required' });

  const formula = hillFormula(atoms);
  if (formula !== challenge.target_formula)
    return res.status(400).json({ error: 'wrong_formula', submitted: formula, expected: challenge.target_formula });

  const issues = valencyIssues(atoms, bonds);
  if (issues.length > 0)
    return res.status(400).json({ error: 'valency_error', issues });

  // 3D-build: помимо формулы проверяем СТРУКТУРУ (связность) против эталона
  const bdata = tryParse(challenge.data_json, {});
  if (bdata && bdata.requireStructure && bdata.molecule_id) {
    const ref = stmts.getMolById.get(bdata.molecule_id);
    if (ref) {
      const refAtoms = tryParse(ref.atoms_json, []);
      const refBonds = tryParse(ref.bonds_json, []);
      if (!structuralMatch(atoms, bonds, refAtoms, refBonds))
        return res.status(400).json({ error: 'wrong_structure' });
    }
  }

  stmts.markDone.run(req.user.id, challenge.id);
  awardXP(req.user.id, challenge.xp_reward, `biochem_challenge:${challenge.id}`);
  checkAchievements(req.user.id);
  res.json({ ok: true, xp: challenge.xp_reward });
}

/* ── GET /api/biochem/saved ─────────────────────────────────────────── */
function getSaved(req, res) {
  const rows = stmts.getSaved.all(req.user.id).map(r => ({
    ...r,
    atoms_json: tryParse(r.atoms_json, []),
    bonds_json: tryParse(r.bonds_json, []),
  }));
  res.json(rows);
}

/* ── POST /api/biochem/saved ────────────────────────────────────────── */
function saveMolecule(req, res) {
  const { atoms, bonds, name } = req.body;
  if (!Array.isArray(atoms) || !Array.isArray(bonds) || atoms.length === 0)
    return res.status(400).json({ error: 'atoms[] and bonds[] required' });

  const formula = hillFormula(atoms);
  const known   = stmts.getMolByFormula.get(formula);
  const id = stmts.saveMol.run(
    req.user.id,
    known?.id ?? null,
    name?.trim() || null,
    formula,
    JSON.stringify(atoms),
    JSON.stringify(bonds),
  ).lastInsertRowid;
  checkAchievements(req.user.id);   // bc_first_molecule
  res.status(201).json({ id, formula, known: known || null });
}

/* ── DELETE /api/biochem/saved/:id ──────────────────────────────────── */
function deleteSaved(req, res) {
  const info = stmts.deleteSaved.run(req.params.id, req.user.id);
  if (info.changes === 0) return res.status(404).json({ error: 'Not found' });
  res.json({ ok: true });
}

/* ── GET /api/biochem/pathways — все пути из БД (карта slug → данные) ──── */
const stmtsPathways = db.prepare('SELECT slug, data_json FROM bio_pathways ORDER BY ord');
function getPathways(_req, res) {
  const out = {};
  for (const r of stmtsPathways.all()) out[r.slug] = tryParse(r.data_json, {});
  res.json(out);
}

/* ── Прогресс прохождения путей (Learn-режим) ────────────────────────── */
const PATHWAY_XP = 80;
const stmtsPath = {
  getProg: db.prepare('SELECT pathway, step, completed FROM bio_user_pathway WHERE user_id=?'),
  wasDone: db.prepare('SELECT completed FROM bio_user_pathway WHERE user_id=? AND pathway=?'),
  upsert:  db.prepare(`INSERT INTO bio_user_pathway (user_id, pathway, step, completed, updated_at)
    VALUES (?, ?, ?, ?, datetime('now'))
    ON CONFLICT(user_id, pathway) DO UPDATE SET
      step       = excluded.step,
      completed  = MAX(completed, excluded.completed),
      updated_at = datetime('now')`),
};

/* ── GET /api/biochem/pathways/progress ──────────────────────────────── */
function getPathwayProgress(req, res) {
  const out = {};
  for (const r of stmtsPath.getProg.all(req.user.id))
    out[r.pathway] = { step: r.step, completed: !!r.completed };
  res.json(out);
}

/* ── POST /api/biochem/pathways/progress ─────────────────────────────── */
function savePathwayProgress(req, res) {
  const { pathway, step, completed } = req.body;
  if (typeof pathway !== 'string' || !pathway)
    return res.status(400).json({ error: 'pathway required' });
  const prev = stmtsPath.wasDone.get(req.user.id, pathway);
  const firstCompletion = !!completed && !(prev && prev.completed);
  stmtsPath.upsert.run(req.user.id, pathway, Math.max(0, parseInt(step) || 0), completed ? 1 : 0);
  let xp = 0;
  if (firstCompletion) {
    xp = PATHWAY_XP;
    awardXP(req.user.id, xp, `biochem_pathway:${pathway}`);
    checkAchievements(req.user.id);
  }
  res.json({ ok: true, xp });
}

/* ── util ────────────────────────────────────────────────────────────── */
function tryParse(v, fallback) {
  if (!v) return fallback;
  try { return JSON.parse(v); } catch { return fallback; }
}

module.exports = {
  getElements, getMolecules, getMolecule, validate, analyze,
  getReactions, getChallenges, solveChallenge,
  getSaved, saveMolecule, deleteSaved,
  getPathways, getPathwayProgress, savePathwayProgress,
  // экспортируется для тестов структурной проверки
  structuralMatch, canonicalHash,
};