Roadmap 2,3,4
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@@ -2,6 +2,25 @@ const express = require('express');
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const router = express.Router();
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const { getDatabase } = require('../db/init');
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const MAX_CACHE_SIZE = 1000;
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const ancestorCache = new Map();
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const coiCache = new Map();
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function getFromCache(cache, key, computeFn) {
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if (cache.has(key)) {
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const val = cache.get(key);
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cache.delete(key);
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cache.set(key, val);
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return val;
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}
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const val = computeFn();
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if (cache.size >= MAX_CACHE_SIZE) {
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cache.delete(cache.keys().next().value);
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}
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cache.set(key, val);
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return val;
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}
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/**
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* getAncestorMap(db, dogId, maxGen)
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* Returns Map<id, [{ id, name, generation }, ...]>
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@@ -9,24 +28,27 @@ const { getDatabase } = require('../db/init');
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* pairings are correctly detected by calculateCOI.
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*/
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function getAncestorMap(db, dogId, maxGen = 6) {
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const map = new Map();
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const cacheKey = `${dogId}-${maxGen}`;
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return getFromCache(ancestorCache, cacheKey, () => {
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const map = new Map();
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function recurse(id, gen) {
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if (gen > maxGen) return;
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const dog = db.prepare('SELECT id, name FROM dogs WHERE id = ?').get(id);
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if (!dog) return;
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if (!map.has(id)) map.set(id, []);
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map.get(id).push({ id: dog.id, name: dog.name, generation: gen });
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if (map.get(id).length === 1) {
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const parents = db.prepare(`
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SELECT p.parent_id FROM parents p WHERE p.dog_id = ?
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`).all(id);
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parents.forEach(p => recurse(p.parent_id, gen + 1));
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function recurse(id, gen) {
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if (gen > maxGen) return;
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const dog = db.prepare('SELECT id, name FROM dogs WHERE id = ?').get(id);
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if (!dog) return;
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if (!map.has(id)) map.set(id, []);
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map.get(id).push({ id: dog.id, name: dog.name, generation: gen });
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if (map.get(id).length === 1) {
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const parents = db.prepare(`
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SELECT p.parent_id FROM parents p WHERE p.dog_id = ?
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`).all(id);
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parents.forEach(p => recurse(p.parent_id, gen + 1));
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}
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}
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}
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recurse(parseInt(dogId), 0);
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return map;
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recurse(parseInt(dogId), 0);
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return map;
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});
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}
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/**
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@@ -68,54 +90,57 @@ function isDirectRelation(db, sireId, damId) {
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* self-loops.
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*/
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function calculateCOI(db, sireId, damId) {
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const sid = parseInt(sireId);
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const did = parseInt(damId);
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const sireMap = getAncestorMap(db, sid);
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const damMap = getAncestorMap(db, did);
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const cacheKey = `${sireId}-${damId}`;
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return getFromCache(coiCache, cacheKey, () => {
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const sid = parseInt(sireId);
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const did = parseInt(damId);
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const sireMap = getAncestorMap(db, sid);
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const damMap = getAncestorMap(db, did);
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// Common ancestors: in BOTH maps, but:
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// - not the dam itself appearing in sireMap (would be a loop)
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// - not the sire itself appearing in damMap already handled below
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// We collect all IDs present in both, excluding only the direct
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// subjects (did from sireMap side, sid excluded already since we
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// iterate sireMap keys — but sid IS in sireMap at gen 0, and if
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// damMap also has sid, that is the parent×offspring case we WANT).
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const commonIds = [...sireMap.keys()].filter(
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id => damMap.has(id) && id !== did
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);
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// Common ancestors: in BOTH maps, but:
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// - not the dam itself appearing in sireMap (would be a loop)
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// - not the sire itself appearing in damMap already handled below
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// We collect all IDs present in both, excluding only the direct
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// subjects (did from sireMap side, sid excluded already since we
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// iterate sireMap keys — but sid IS in sireMap at gen 0, and if
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// damMap also has sid, that is the parent×offspring case we WANT).
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const commonIds = [...sireMap.keys()].filter(
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id => damMap.has(id) && id !== did
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);
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let coi = 0;
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const processedPaths = new Set();
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const commonAncestorList = [];
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let coi = 0;
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const processedPaths = new Set();
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const commonAncestorList = [];
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commonIds.forEach(ancId => {
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const sireOccs = sireMap.get(ancId);
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const damOccs = damMap.get(ancId);
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commonIds.forEach(ancId => {
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const sireOccs = sireMap.get(ancId);
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const damOccs = damMap.get(ancId);
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sireOccs.forEach(so => {
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damOccs.forEach(do_ => {
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const key = `${ancId}-${so.generation}-${do_.generation}`;
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if (!processedPaths.has(key)) {
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processedPaths.add(key);
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coi += Math.pow(0.5, so.generation + do_.generation + 1);
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}
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sireOccs.forEach(so => {
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damOccs.forEach(do_ => {
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const key = `${ancId}-${so.generation}-${do_.generation}`;
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if (!processedPaths.has(key)) {
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processedPaths.add(key);
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coi += Math.pow(0.5, so.generation + do_.generation + 1);
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}
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});
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});
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const closestSire = sireOccs.reduce((a, b) => a.generation < b.generation ? a : b);
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const closestDam = damOccs.reduce((a, b) => a.generation < b.generation ? a : b);
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commonAncestorList.push({
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id: ancId,
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name: sireOccs[0].name,
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sireGen: closestSire.generation,
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damGen: closestDam.generation
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});
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});
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const closestSire = sireOccs.reduce((a, b) => a.generation < b.generation ? a : b);
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const closestDam = damOccs.reduce((a, b) => a.generation < b.generation ? a : b);
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commonAncestorList.push({
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id: ancId,
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name: sireOccs[0].name,
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sireGen: closestSire.generation,
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damGen: closestDam.generation
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});
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return {
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coefficient: coi,
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commonAncestors: commonAncestorList
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};
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});
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return {
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coefficient: coi,
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commonAncestors: commonAncestorList
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};
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}
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// =====================================================================
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@@ -195,6 +220,63 @@ router.get('/relations/:sireId/:damId', (req, res) => {
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}
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});
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// GET /api/pedigree/:id/cancer-lineage
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router.get('/:id/cancer-lineage', (req, res) => {
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try {
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const db = getDatabase();
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// Get ancestor map up to 5 generations
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const ancestorMap = getAncestorMap(db, req.params.id, 5);
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// Collect all unique ancestor IDs
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const ancestorIds = Array.from(ancestorMap.keys());
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if (ancestorIds.length === 0) {
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return res.json({ lineage_cases: [], stats: { total_ancestors: 0, ancestors_with_cancer: 0 } });
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}
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// Query cancer history for all ancestors
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const placeholders = ancestorIds.map(() => '?').join(',');
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const cancerRecords = db.prepare(`
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SELECT c.*, d.name, d.sex
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FROM cancer_history c
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JOIN dogs d ON c.dog_id = d.id
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WHERE c.dog_id IN (${placeholders})
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`).all(...ancestorIds);
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// Structure the response
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const cases = cancerRecords.map(record => {
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// Find the closest generation this ancestor appears in
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const occurrences = ancestorMap.get(record.dog_id);
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const closestGen = occurrences.reduce((min, occ) => occ.generation < min ? occ.generation : min, 999);
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return {
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...record,
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generation_distance: closestGen
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};
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});
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// Sort by generation distance (closer relatives first)
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cases.sort((a, b) => a.generation_distance - b.generation_distance);
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// Count unique dogs with cancer (excluding generation 0 if we only want stats on ancestors)
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const ancestorCases = cases.filter(c => c.generation_distance > 0);
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const uniqueAncestorsWithCancer = new Set(ancestorCases.map(c => c.dog_id)).size;
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// Number of ancestors is total unique IDs minus 1 for the dog itself
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const numAncestors = ancestorIds.length > 0 && ancestorMap.get(parseInt(req.params.id)) ? ancestorIds.length - 1 : ancestorIds.length;
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res.json({
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lineage_cases: cases,
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stats: {
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total_ancestors: numAncestors,
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ancestors_with_cancer: uniqueAncestorsWithCancer
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}
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});
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} catch (error) {
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res.status(500).json({ error: error.message });
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}
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});
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// =====================================================================
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// Wildcard routes last
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// =====================================================================
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