Merge pull request #286 from RobokopU24/feature/explore-page

Explore page

api_routes/routes.js

@@ -9,6 +9,8 @@ const { handleAxiosError } = require('./utils');
 const services = require('./services');
 const external_apis = require('./external');
 
+const { getDrugDiseasePairs } = require('../explore/query/drug-disease');
+
 const samples = JSON.parse(fs.readFileSync(path.join(__dirname, './sample-query-cache.json')));
 
 router.use('/', external_apis);
@@ -58,6 +60,25 @@ router.route('/quick_answer')
     }
   });
 
+router.route('/explore/drug-disease')
+  .post(async (req, res) => {
+    const { sort, filters, pagination } = req.body;
+
+    if (!pagination || !Number.isInteger(pagination.offset) || !Number.isInteger(pagination.limit)) return res.status(400).json({ error: 'Missing pagination' });
+    if (pagination.limit < 1 || pagination.offset < 0) return res.status(400).json({ error: 'Invalid limit or offset value' });
+
+    const limit = Math.min(pagination.limit, 500);
+    const { offset } = pagination;
+
+    try {
+      const results = await getDrugDiseasePairs({ sort, filters, pagination: { limit, offset } });
+      return res.status(200).json(results);
+    } catch (error) {
+      console.error('Error in explore page query:', error, req.body);
+      return res.status(500).json({ error: 'Internal server error' });
+    }
+  });
+
 router.route('/answer')
   .post(async (req, res) => {
     const { questionId, ara } = req.query;

explore/db_utils.js

@@ -0,0 +1,37 @@
+const run = async (db, sql, params) => new Promise((res, rej) => {
+  db.run(sql, params, (err) => {
+    if (err) rej(err);
+    else res();
+  });
+});
+
+const get = async (db, sql, params) => new Promise((res, rej) => {
+  db.get(sql, params, (err, row) => {
+    if (err) rej(err);
+    else res(row);
+  });
+});
+
+const all = async (db, sql, params) => new Promise((res, rej) => {
+  db.all(sql, params, (err, rows) => {
+    if (err) rej(err);
+    else res(rows);
+  });
+});
+
+/**
+ * Same as normal template literal but 'sql' tag allows syntax highlighting in editor
+ */
+const sql = (strings, ...args) => strings.reduce((str, curr, i) => str + curr + (args[i] || ''), '');
+
+module.exports = {
+  /**
+   * Promise-based wrappers for node-sqlite3. Attempts to mirror API, first param is db instance
+   */
+  db_p: {
+    run,
+    get,
+    all,
+  },
+  sql,
+};

explore/query/drug-disease.js

@@ -0,0 +1,133 @@
+/* eslint-disable no-restricted-syntax */
+/* eslint-disable no-use-before-define */
+const path = require('path');
+const sqlite3 = require('sqlite3');
+const { db_p, sql } = require('../db_utils');
+
+require('dotenv').config({ path: path.resolve(__dirname, '../../.env') });
+
+const db = new sqlite3.Database(process.env.EXPLORE_DB);
+
+/**
+ * @param {{
+ *  sort?: {
+ *    drug_name?: "asc" | "desc",
+ *    disease_name?: "asc" | "desc",
+ *    score?: "asc" | "desc",
+ *    known?: "asc" | "desc",
+ *  }
+ *  filters?: {
+ *    drug_name?: string,
+ *    drug_id?: string,
+ *    disease_name?: string,
+ *    disease_id?: string,
+ *  },
+ *  pagination: {
+ *    limit: number,
+ *    offset: number,
+ *  }
+ * }} params
+ * @returns {Promise<{
+ *  rows: {
+ *    drug_name: string,
+ *    drug_id: string,
+ *    disease_name: string,
+ *    disease_id: string,
+ *    score: number,
+ *    known: number
+ *  }[],
+ *  num_of_results: number,
+ *  limit: number,
+ *  offset: number,
+ * }>}
+ */
+async function getDrugDiseasePairs({ sort, filters, pagination }) {
+  const { whereClause, whereParams } = buildWhereClause(filters);
+  const orderByClause = buildOrderByClause(sort);
+
+  const { paginationClause, paginationParams } = buildPaginationClause(pagination.limit, pagination.offset);
+
+  const params = [...whereParams, ...paginationParams];
+
+  const query = sql`\
+    SELECT * FROM drug_disease_pairs${whereClause}${orderByClause}${paginationClause}\
+  `;
+  const countQuery = sql`\
+    SELECT COUNT(*) AS total FROM drug_disease_pairs${whereClause}\
+  `;
+
+  return new Promise((resolve, reject) => {
+    db.parallelize(() => {
+      Promise.all([
+        db_p.all(db, query, params),
+        db_p.get(db, countQuery, whereParams),
+      ])
+        .then(([rows, { total }]) => {
+          resolve({
+            rows,
+            num_of_results: total,
+            ...pagination,
+          });
+        })
+        .catch(reject);
+    });
+  });
+}
+
+function buildWhereClause(filters) {
+  const whereClauses = [];
+  const params = [];
+
+  if (filters) {
+    if (filters.drug_name) {
+      whereClauses.push('drug_name LIKE ?');
+      params.push(`%${filters.drug_name}%`);
+    }
+    if (filters.drug_id) {
+      whereClauses.push('drug_id LIKE ?');
+      params.push(`%${filters.drug_id}%`);
+    }
+    if (filters.disease_name) {
+      whereClauses.push('disease_name LIKE ?');
+      params.push(`%${filters.disease_name}%`);
+    }
+    if (filters.disease_id) {
+      whereClauses.push('disease_id LIKE ?');
+      params.push(`%${filters.disease_id}%`);
+    }
+  }
+
+  const whereClause =
+    (whereClauses.length > 0 ? ` WHERE ${whereClauses.join(' AND ')}` : '');
+  return { whereClause, whereParams: params };
+}
+
+function buildOrderByClause(sort) {
+  let orderByClause = '';
+  if (sort) {
+    const orderClauses = [];
+    for (const [column, direction] of Object.entries(sort)) {
+      if (
+        ['drug_name', 'disease_name', 'score', 'known'].includes(column) &&
+        ['asc', 'desc'].includes(direction)
+      ) {
+        orderClauses.push(`${column} ${direction.toUpperCase()}`);
+      }
+    }
+    if (orderClauses.length > 0) {
+      orderByClause += ` ORDER BY ${orderClauses.join(', ')}`;
+    }
+  }
+  return orderByClause;
+}
+
+function buildPaginationClause(limit, offset) {
+  return {
+    paginationClause: ' LIMIT ? OFFSET ?',
+    paginationParams: [limit, offset],
+  };
+}
+
+module.exports = {
+  getDrugDiseasePairs,
+};

explore/scripts/init-drug-disease.js

@@ -0,0 +1,66 @@
+/* eslint-disable no-continue */
+/* eslint-disable no-console */
+/* eslint-disable no-restricted-syntax */
+
+const fs = require('fs');
+const path = require('path');
+const sqlite3 = require('sqlite3');
+const { db_p, sql } = require('../db_utils');
+
+require('dotenv').config({ path: path.resolve(__dirname, '../../.env') });
+
+const input = '../data/raw/DrugtoDiseasePrediction-full-9-30-24.json';
+const lowerScoreLimit = 0.5;
+
+const db = new sqlite3.Database(process.env.EXPLORE_DB);
+
+(async () => {
+  await db_p.run(db, sql`
+    CREATE TABLE IF NOT EXISTS drug_disease_pairs (
+      drug_name    TEXT    NOT NULL,
+      drug_id      TEXT    NOT NULL,
+      disease_name TEXT    NOT NULL,
+      disease_id   TEXT    NOT NULL,
+      score        REAL    NOT NULL,
+      known        BOOLEAN NOT NULL  CHECK (known IN (0, 1))
+    )
+  `);
+  await db_p.run(db, sql`DELETE FROM drug_disease_pairs`);
+
+  const rawMaps = JSON.parse(
+    fs.readFileSync(path.resolve(__dirname, input), 'utf-8'),
+  );
+
+  await db_p.run(db, sql`BEGIN TRANSACTION`);
+  for (const [id, score] of Object.entries(rawMaps.Score).sort((a, b) => b[1] - a[1])) {
+    if (score < lowerScoreLimit) continue;
+
+    const drug = {
+      id: rawMaps.DrugID[id],
+      name: rawMaps.DrugName[id],
+    };
+    const disease = {
+      id: rawMaps.DiseaseID[id],
+      name: rawMaps.DiseaseName[id],
+    };
+    const known = rawMaps.Known[id] === '1';
+
+    const command = sql`INSERT INTO drug_disease_pairs VALUES (?, ?, ?, ?, ?, ?)`;
+    const params = [
+      drug.name,
+      drug.id,
+      disease.name,
+      disease.id,
+      score,
+      known ? '1' : '0',
+    ];
+
+    try {
+      db_p.run(db, command, params);
+    } catch (err) {
+      console.error('Error:', err, 'Params:', params);
+    }
+  }
+
+  await db_p.run(db, sql`COMMIT`);
+})();