Merge pull request #13 from shamseen/external-api

Calls ENA search endpoint via fixed search

controllers/searchController.js

@@ -0,0 +1,38 @@
+const express = require('express');
+const router = express.Router();
+const ENADataService = require('../dataServices/enaDataService');
+const ena = new ENADataService();
+
+// TEST GET!
+router.get('/', async (req, res) => {
+
+    try {
+        const found = ena.enaData;
+        res.status(200).json(found);
+
+    } catch (err) {
+        console.log(err);
+        res.status(400).json({
+            msg: err.message
+        });
+    }
+});
+
+// 
+router.get('/:query', async (req, res) => {
+    // const filter = { [req.params.prop]: req.params.val };
+    // TODO: parse query, search mongo too
+
+    try {
+        const found = [];
+        // const found = await enaService.search();
+        res.status(200).json(found);
+
+    } catch (err) {
+        res.status(400).json({
+            msg: err.message
+        });
+    }
+});
+
+module.exports = router;

dataServices/enaDataService.js

@@ -0,0 +1,79 @@
+// structure from https://www.codementor.io/@evanbechtol/node-service-oriented-architecture-12vjt9zs9i
+
+/* -------------------------------------------------------------- */
+// European Nucleotide Archive (ENA): database of sequences
+// The European Bioinformatics Institute exposes an API to access ENA
+// In ENA, record IDs are called accessions 
+/* -------------------------------------------------------------- */
+const axios = require('axios')
+
+
+class ENADataService {
+    /* -  populating with fixed search on instantiation - */
+    constructor() {
+        this.searchENA();
+    }
+
+    /* -- variables for JOINs -- */
+    // static baseURL = 'https://www.ebi.ac.uk/ena/portal/api/search?dataPortal=ena&query=';
+    // static resultLimit = 10;
+
+    /* -- API Calls -- */
+    // BLOCKED: ena POST endpoint docs are missing, waiting to hear back
+
+    // using a custom rule i made on their side instead
+    async searchENA() {
+        try {
+            const response = await axios.get('https://www.ebi.ac.uk/ena/portal/api/search?rule=8624c855-9921-4b98-b763-ac0d79b6a567');
+
+            this.enaData = response.data; // axios returns JSON already
+            return this.enaData;
+
+        } catch (error) {
+            // console.log(error);
+
+            return error.message;
+        }
+    }
+
+    /* -- Search Functionality -- */
+
+    filterByAccession(accType, value, arr) {
+
+    }
+
+    filterByKeyword(keyword, arr) {
+
+    }
+
+    search(seq_accession, study_accession, keyword) {
+        let results = [...this.enaData];
+
+        if (seq_accession !== '')
+            results = this.filterByAccession('accession', seq_accession, results);
+
+        if (study_accession !== '')
+            results = this.filterByAccession('study_accession', study_accession, results);
+
+        if (keyword !== '')
+            results = this.filterByKeyword(keyword, results);
+
+        return results;
+    }
+
+    /* Returns array of:
+     {
+        "accession": "CP034527",
+        "study_accession": "PRJNA504496",
+        "scientific_name": "eukaryotic synthetic construct",
+        "cell_type": "",
+        "dataclass": "STD",
+        "description": "Eukaryotic synthetic construct chromosome 3.",
+        "mol_type": "other DNA",
+        "plasmid": "",
+        "keywords": ""
+    }
+    */
+}
+
+module.exports = ENADataService;

package.json

@@ -10,6 +10,7 @@
     "dev": "nodemon server.js"
   },
   "dependencies": {
+    "axios": "^0.21.1",
     "cors": "^2.8.5",
     "dotenv": "^9.0.2",
     "express": "^4.17.1",

server.js

@@ -1,5 +1,5 @@
 /* --- Required modules --- */
-require('dotenv').config()          // inject .env into process.env
+require('dotenv').config();          // inject .env into process.env
 const express = require('express'); // http server
 const cors = require('cors');       // expose resources for external websites
 const mongoose = require('mongoose'); // talks to mongo db
@@ -14,7 +14,7 @@ mongoose.connect(process.env.MONGO_URI, {
   useNewUrlParser: true,
   useCreateIndex: true,
   useFindAndModify: false
-})
+});
 // confirm connection
 mongoose.connection.once('connected', () => console.log('>> mongoose is connected to mongoDB'));
 
@@ -29,11 +29,12 @@ app.use((req, res, next) => {
 app.use(cors());              // exposes endpoints for apps to request
 
 /* --- Routes --- */
-app.use('/pngcats', require('./controllers/pngcatsController'))
+app.use('/pngcats', require('./controllers/pngcatsController'));
+app.use('/search', require('./controllers/searchController'));
 
 app.get('/', (req, res) => {
-  res.send(`<h1>.pnGCAT API</h1>`)
+  res.send(`<h1>.pnGCAT API</h1>`);
 })
 
 /* --- Leggggoooooooo --- */
-app.listen(PORT, () => console.log(`>> API Server: Listening on port ${PORT}. waiting for database...`))
+app.listen(PORT, () => console.log(`>> API Server: Listening on port ${PORT}. waiting for database...`));

yarn.lock

@@ -35,6 +35,13 @@ [email protected]:
   resolved "https://registry.yarnpkg.com/array-flatten/-/array-flatten-1.1.1.tgz#9a5f699051b1e7073328f2a008968b64ea2955d2"
   integrity sha1-ml9pkFGx5wczKPKgCJaLZOopVdI=
 
+axios@^0.21.1:
+  version "0.21.1"
+  resolved "https://registry.yarnpkg.com/axios/-/axios-0.21.1.tgz#22563481962f4d6bde9a76d516ef0e5d3c09b2b8"
+  integrity sha512-dKQiRHxGD9PPRIUNIWvZhPTPpl1rf/OxTYKsqKUDjBwYylTvV7SjSHJb9ratfyzM6wCdLCOYLzs73qpg5c4iGA==
+  dependencies:
+    follow-redirects "^1.10.0"
+
 bl@^2.2.1:
   version "2.2.1"
   resolved "https://registry.yarnpkg.com/bl/-/bl-2.2.1.tgz#8c11a7b730655c5d56898cdc871224f40fd901d5"
@@ -212,6 +219,11 @@ finalhandler@~1.1.2:
     statuses "~1.5.0"
     unpipe "~1.0.0"
 
+follow-redirects@^1.10.0:
+  version "1.14.1"
+  resolved "https://registry.yarnpkg.com/follow-redirects/-/follow-redirects-1.14.1.tgz#d9114ded0a1cfdd334e164e6662ad02bfd91ff43"
+  integrity sha512-HWqDgT7ZEkqRzBvc2s64vSZ/hfOceEol3ac/7tKwzuvEyWx3/4UegXh5oBOIotkGsObyk3xznnSRVADBgWSQVg==
+
 forwarded@~0.1.2:
   version "0.1.2"
   resolved "https://registry.yarnpkg.com/forwarded/-/forwarded-0.1.2.tgz#98c23dab1175657b8c0573e8ceccd91b0ff18c84"