Wrote tests and Travis CI configuration file and separated mongoose related code into db/mongoose.js

.travis.yml

@@ -0,0 +1,19 @@
+language: node_js
+
+node_js:
+  - 'lts/*'
+
+services: mongodb
+
+before_install:
+  # Set up environment variables
+  # Tests are ran on a separate database named 'regsitry-test'
+  - export MONGODB_URL=mongodb://127.0.0.1:27017/registry-test
+
+install:
+  # Install all the project dependencies
+  - npm install
+
+script:
+  # Run test script
+  - npm run test

app.js

@@ -12,6 +12,7 @@ var index = require('./routes/index');
 var instances = require('./routes/instances');
 var synchronize = require('./routes/synchronize');
 const swaggerUi = require('swagger-ui-express');
+require('./db/mongoose');
 // Swagger.json file is used to generate the API-DOCS
 const swaggerDocument = require('./swagger.json');
 const scheduledAutomaticUpdate = require('./scheduled/automaticUpdate');

createUser.js

@@ -1,11 +1,5 @@
 const User = require('./models/user');
-const mongoose = require('mongoose');
-
-mongoose.connect(process.env.MONGODB_URL);
-
-const db = mongoose.connection;
-db.on('error', console.error.bind(console, 'MongoDB connection error:'));
-
+require('./db/mongoose');
 const readline = require('readline');
 
 const rl = readline.createInterface({

db/mongoose.js

@@ -0,0 +1,11 @@
+// Registry Connection
+var mongoose = require('mongoose');
+
+mongoose.connect(process.env.MONGODB_URL, {
+    useNewUrlParser: true,
+    useUnifiedTopology: true,
+    useCreateIndex: true
+});
+
+var db = mongoose.connection;
+db.on('error', console.error.bind(console, 'MongoDB connection error:'));

models/instance.js

@@ -3,11 +3,7 @@
  */
 // Registry Connection
 var mongoose = require('mongoose');
-
-mongoose.connect(process.env.MONGODB_URL);
-
-var db = mongoose.connection;
-db.on('error', console.error.bind(console, 'MongoDB connection error:'));
+require('../db/mongoose');
 
 // Schema Modeling
 var Schema = mongoose.Schema;

models/user.js

@@ -41,4 +41,4 @@ module.exports.comparePassword = function(candidatePassowrd, hash, callback){
 
 module.exports.getUserByUsername = function(username, callback){
 	User.findOne({user:username}, callback);
-}
+}

package.json

@@ -3,7 +3,11 @@
   "version": "0.0.0",
   "private": true,
   "scripts": {
-    "start": "node ./bin/www"
+    "start": "node ./bin/www",
+    "test": "jest --forceExit --maxWorkers=10"
+  },
+  "jest": {
+    "testEnvironment": "node"
   },
   "dependencies": {
     "async": "^2.6.2",
@@ -32,5 +36,10 @@
     "serve-favicon": "^2.5.0",
     "swagger-express": "~1.0.5",
     "swagger-ui-express": "^2.0.15"
+  },
+  "devDependencies": {
+    "env-cmd": "^10.0.1",
+    "jest": "^25.1.0",
+    "supertest": "^4.0.2"
   }
 }

tests/fixtures/db.js

@@ -0,0 +1,81 @@
+const User = require('../../models/user');
+const Instance = require('../../models/instance');
+
+// User credentials required for testing
+const userOne = {
+  user: 'testuser',
+  password: 'asdfghj'
+};
+
+// Mine data to be stored in the database
+const flyMine = {
+  "name": "FlyMine",
+  "namespace": "flymine",
+  "neighbours": [
+    "MODs"
+  ],
+  "organisms": [
+    "Drosophila"
+  ],
+  "url": "http://www.flymine.org/query",
+  "description": "FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans",
+  "location": {
+    "latitude": "52.2003399",
+    "longitude": "0.120109"
+  },
+  "twitter": "@intermineorg"
+};
+
+// Mine data to be stored in the database
+const chickpeaMine = {
+  "name": "ChickpeaMine",
+  "namespace": "chickpeamine",
+  "neighbours": [
+    "Plants"
+  ],
+  "url": "http://mines.legumeinfo.org/chickpeamine",
+  "organisms": [
+    "A. ipaensis", "A. duranensis", "A. thaliana", "C. arietinum desi", "C. arietinum kabuli", "G. max", "M. truncatula", "P. vulgaris"
+  ],
+  "description": "A mine with chickpea data (both desi and kabuli varieties) from the Legume Information Systems (LIS) tripal.chado database",
+  "location": {
+    "latitude": "72.2003399",
+    "longitude": "10.120109"
+  },
+  "twitter": "@LegumeFed"
+};
+
+// Updates to be apllied on FlyMine during testing
+const flymineUpdate = {
+  "neighbours": [
+    "Plants"
+  ],
+  "namespace": "flymine"
+};
+
+// Update involving change of namespace
+const changeNamespace = {
+  "neighbours": [
+    "Plants"
+  ],
+  "namespace": "flymine alpha"
+};
+
+// Run before tests
+const setupDatabase = async () => {
+  // Clear the test-database
+  await Instance.deleteMany();
+  await User.deleteMany();
+
+  // Create a new user for testing
+  await new User(userOne).save();
+};
+
+module.exports = {
+  setupDatabase,
+  userOne,
+  flyMine,
+  chickpeaMine,
+  flymineUpdate,
+  changeNamespace
+};

tests/instances.test.js

@@ -0,0 +1,105 @@
+const request = require('supertest');
+const app = require('../app');
+const { 
+    setupDatabase, 
+    userOne, 
+    flyMine, 
+    chickpeaMine, 
+    flymineUpdate, 
+    changeNamespace
+} = require('./fixtures/db');
+
+jest.setTimeout(15000);
+
+beforeAll(async () => {
+    await setupDatabase();
+
+    // Save an instance to the database before testing
+    await request(app).post('/service/instances/')
+        .auth(userOne.user, userOne.password)
+        .send(chickpeaMine);
+});
+
+test('POST /instances : Should add an instance to the InterMine Registry', async () => {
+    await request(app).post('/service/instances/')
+        .auth(userOne.user, userOne.password)
+        .send(flyMine)
+        .expect(201);
+});
+
+test('POST /instances : Shoud not add an existing namespace to the InterMine Registry', async () => {
+    await request(app).post('/service/instances/')
+        .auth(userOne.user, userOne.password)
+        .send(flyMine)
+        .expect(409);
+});
+
+test('GET /instances : Should get all InterMine Registry instances information when there are no params', async () => {
+    const response = await request(app).get('/service/instances/')
+        .send()
+        .expect(200);
+
+    // No of returned instances should be correct
+    expect(response.body.instances).toHaveLength(2);
+});
+
+test('GET /instances : Should get the correct InterMine Registry instance information when parameter q is passed', async () => {
+    const response = await request(app).get('/service/instances?q=flymine')
+        .send()
+        .expect(200);
+
+    // Response namespace should be correct
+    expect(response.body.instances[0].namespace).toMatch('flymine');
+});
+
+test('GET /instances : Should not return any InterMine Registry instances with "isProduction": true when parameter "mines=dev" is passed', async () => {
+    const response = await request(app).get('/service/instances?mines=dev')
+        .send()
+        .expect(200);
+
+    // Check value of 'isProduction' for each instance
+    // Value of 'isProduction' should not be true
+    const instances = response.body.instances;
+    instances.forEach(instance => expect(instance.isProduction).not.toBe(true));
+});
+
+test('GET /instances : Should not return any InterMine Registry instances with "isProduction": false when parameter "mines=prod" is passed', async () => {
+    const response = await request(app).get('/service/instances?mines=prod')
+        .send()
+        .expect(200);
+
+    // Check value of "isProduction" for each instance
+    // Value of 'isProduction' should not be false
+    const instances = response.body.instances;
+    instances.forEach(instance => expect(instance.isProduction).not.toBe(false));
+});
+
+test('GET /instances : Should return a count of InterMine Registry instances when parameter "mines=all" is passed', async () => {
+    const response = await request(app).get('/service/instances?mines=all')
+        .send()
+        .expect(200);
+
+    // No of returned instances should be correct
+    expect(response.body.instances).toHaveLength(2);
+});
+
+test('PUT /instances : Should update the given InterMine Registry instance only', async () => {
+    await request(app).put('/service/instances/2')
+        .auth(userOne.user, userOne.password)
+        .send(flymineUpdate)
+        .expect(201);
+});
+
+test('PUT /instances : Should not allow a namespace to be changed', async () => {
+    await request(app).put('/service/instances/2')
+        .auth(userOne.user, userOne.password)
+        .send(changeNamespace)
+        .expect(409);
+});
+
+test('DELETE /instances : Should delete the given InterMine Registry instance only', async () => {
+    await request(app).delete('/service/instances/2')
+        .auth(userOne.user, userOne.password)
+        .send()
+        .expect(200);
+});