feat(app): add cors and correct parse of literature id (#8)

Author: carcruz

app.js

@@ -1,16 +1,32 @@
 import express from "express";
+import cors from "cors";
+
 import logger from "./utils/logger.js";
 import httpLogger from "./middlewares/httpLogger.js";
 import literatureRouter from "./routes/literature.js";
 import healthRouter from "./routes/health.js";
-import { normalizePort } from "./utils/index.js";
+import { normalizePort, isProduction, isDevelopment } from "./utils/index.js";
 
-var port = normalizePort(process.env.PORT || "8080");
+const port = normalizePort(process.env.PORT || "8080");
+const originRegExp = /^(.*\.)?opentargets\.(org|xwz)$/;
 
 const app = express();
+
 app.use(httpLogger);
 app.use(express.json());
 
+if (isDevelopment) {
+  app.use(cors());
+}
+
+if (isProduction) {
+  app.use(
+    cors({
+      origin: [originRegExp],
+    })
+  );
+}
+
 app.use("/literature", literatureRouter);
 app.use("/health", healthRouter);
 

controllers/publication.js

@@ -2,7 +2,7 @@ import axios from "axios";
 import { XMLParser } from "fast-xml-parser";
 
 function URLPublicationFullText({ id }) {
-  const baseUrl = `https://www.ebi.ac.uk/europepmc/webservices/rest/PMC${id}/fullTextXML`;
+  const baseUrl = `https://www.ebi.ac.uk/europepmc/webservices/rest/${id}/fullTextXML`;
   const requestOptions = {
     method: "GET",
     headers: {

controllers/publicationSummary.js

@@ -46,7 +46,7 @@ export const getPublicationSummary = async ({
   targetSymbol,
   diseaseName,
   pmcId,
-  wbTracer,
+  wbTracer = null,
 }) => {
   const prompt = createPrompt({ targetSymbol, diseaseName });
 
@@ -58,11 +58,9 @@ export const getPublicationSummary = async ({
   });
 
   const docs = await textSplitter.createDocuments([text]);
-
   logger.info(JSON.stringify({ wordCount, docsLength: docs.length }));
-
   const chain = loadQAMapReduceChain(model);
-  logger.info("reauest to gpt");
+  logger.info("request to openai");
   if (wbTracer !== null) {
     wandb.log({
       targetSymbol: targetSymbol,

package-lock.json

@@ -4,21 +4,23 @@
   "private": true,
   "type": "module",
   "scripts": {
-    "start": "node app.js",
+    "start": "NODE_ENV=development node app.js",
     "start:prod": "NODE_ENV=production node app.js",
-    "dev": "nodemon app.js"
+    "dev": "NODE_ENV=development nodemon app.js"
   },
   "dependencies": {
     "@wandb/sdk": "^0.5.1",
     "axios": "^1.4.0",
     "cookie-parser": "~1.4.4",
+    "cors": "^2.8.5",
     "debug": "~2.6.9",
     "dotenv": "^16.0.3",
     "express": "~4.16.1",
     "fast-xml-parser": "^4.2.2",
     "http-errors": "~1.6.3",
     "langchain": "^0.0.78",
     "morgan": "~1.9.1",
+    "node-cache": "^5.1.2",
     "node-fetch": "^3.3.1",
     "pug": "2.0.0-beta11",
     "winston": "^3.8.2",

package.json

@@ -1,11 +1,13 @@
 import express from "express";
 import { WandbTracer } from "@wandb/sdk/integrations/langchain";
+import * as dotenv from "dotenv";
+
 import { getPublicationPlainText } from "../controllers/publication.js";
 import {
   getPublicationSummary,
   streamTest,
 } from "../controllers/publicationSummary.js";
-import * as dotenv from "dotenv";
+import { isDevelopment } from "../utils/index.js";
 import logger from "../utils/logger.js";
 
 dotenv.config();
@@ -46,13 +48,15 @@ router.post("/publication/summary/", async (req, res) => {
   const { pmcId, targetSymbol, diseaseName } = req.body.payload;
 
   const prettyDiseaseName = diseaseName.replace(/\s/g, "_");
-  const wbIdWithRandom = `${pmcId}_${targetSymbol}_${prettyDiseaseName}_${Math.floor(
-    Math.random() * 1000
-  )}`;
-  const wbTracer = await WandbTracer.init(
-    { project: "ot-explain", id: wbIdWithRandom },
-    false
-  );
+  const queryId = `${pmcId}_${targetSymbol}_${prettyDiseaseName}`;
+  const wbIdWithRandom = `${queryId}_${Math.floor(Math.random() * 1000)}`;
+  let wbTracer = null;
+  if (isDevelopment) {
+    wbTracer = await WandbTracer.init(
+      { project: "ot-explain", id: wbIdWithRandom },
+      false
+    );
+  }
 
   logger.info(`Request on pub summary`);
 

routes/literature.js

@@ -0,0 +1,46 @@
+import NodeCache from "node-cache";
+
+class Cache {
+  constructor(ttlSeconds) {
+    this.cache = new NodeCache({
+      stdTTL: ttlSeconds,
+      checkperiod: ttlSeconds * 0.2,
+      useClones: false,
+    });
+  }
+
+  get(key, storeFunction) {
+    const value = this.cache.get(key);
+    if (value) {
+      return Promise.resolve(value);
+    }
+
+    return storeFunction().then((result) => {
+      this.cache.set(key, result);
+      return result;
+    });
+  }
+
+  del(keys) {
+    this.cache.del(keys);
+  }
+
+  delStartWith(startStr = "") {
+    if (!startStr) {
+      return;
+    }
+
+    const keys = this.cache.keys();
+    for (const key of keys) {
+      if (key.indexOf(startStr) === 0) {
+        this.del(key);
+      }
+    }
+  }
+
+  flush() {
+    this.cache.flushAll();
+  }
+}
+
+export default Cache;

services/cacheService.js

@@ -10,3 +10,6 @@ export function normalizePort(val) {
   }
   return false;
 }
+
+export const isDevelopment = process.env.NODE_ENV === "development";
+export const isProduction = process.env.NODE_ENV === "production";