Update basic packages and testing packages

.gitignore

@@ -53,3 +53,6 @@ node_modules
 # Ignore everything in the data/hl7-uploads folder for now
 data/hl7-uploads/*
 !data/hl7-uploads/.gitkeep
+
+# No need to commit code coverage reports
+.nyc_output

.nycrc

@@ -0,0 +1,11 @@
+{
+  "nyc": {
+    "all": true,
+    "include": [
+      "server/**/*.js"
+    ],
+    "exclude": [
+      "**/*.test.js"
+    ]
+  }
+}

config/mongo.js

@@ -8,7 +8,7 @@ const debug = require('debug')('hl7-telescoper-api-server:index');
 
 // connect to mongo db
 const mongoUri = config.mongo.host;
-mongoose.connect(mongoUri, { keepAlive: 1, useNewUrlParser: true });
+mongoose.connect(mongoUri, { keepAlive: 1, useNewUrlParser: true, useUnifiedTopology: true });
 mongoose.connection.on('error', () => {
   throw new Error(`unable to connect to database: ${mongoUri}`);
 });

package.json

@@ -3,6 +3,11 @@
   "version": "5.0.0",
   "description": "A server side application for the Amida HL7-Telescoper Project",
   "author": "Perry Ogwuche <[email protected]>",
+  "contributors": [
+    "Alan Thompson <[email protected]>",
+    "Grant Orndorff <[email protected]>",
+    "James Zhu <[email protected]>"
+  ],
   "main": "index.js",
   "private": false,
   "engines": {
@@ -20,8 +25,8 @@
     "pretest": "cross-env NODE_ENV=test yarn drop-database",
     "test": "cross-env NODE_ENV=test ./node_modules/.bin/mocha --ui bdd --reporter spec --colors server --recursive",
     "test:watch": "yarn test -- --watch",
-    "test:coverage": "cross-env NODE_ENV=test ./node_modules/.bin/istanbul cover _mocha -- --ui bdd --reporter spec --colors server --recursive",
-    "test:check-coverage": "yarn test:coverage && istanbul check-coverage",
+    "test:coverage": "yarn pretest && cross-env NODE_ENV=test nyc ./node_modules/.bin/mocha --ui bdd --reporter spec --colors server --recursive",
+    "test:check-coverage": "yarn test:coverage && nyc check-coverage",
     "report-coverage": "coveralls < ./coverage/lcov.info"
   },
   "repository": {
@@ -48,39 +53,40 @@
     "compression": "1.7.2",
     "cookie-parser": "1.4.3",
     "cors": "2.8.4",
-    "debug": "^2.4.5",
     "dotenv": "^4.0.0",
     "express": "4.16.3",
     "express-jwt": "5.3.1",
-    "express-validation": "1.0.2",
+    "express-validation": "1.0.3",
     "express-winston": "2.5.0",
     "health-level-seven-parser": "1.2.2",
     "helmet": "3.12.0",
     "http-status": "1.0.1",
     "joi": "10.6.0",
     "jsonwebtoken": "8.5.1",
     "method-override": "^2.3.10",
-    "mongoose": "5.6.4",
+    "mongoose": "5.7.9",
     "morgan": "1.9.1",
     "multer": "1.4.1",
     "passport": "0.4.0",
     "passport-jwt": "4.0.0",
     "winston": "2.4.1"
   },
   "devDependencies": {
+    "@istanbuljs/nyc-config-babel": "2.1.1",
+    "babel-plugin-istanbul": "5.2.0",
     "chai": "4.1.2",
-    "commitizen": "^2.9.6",
-    "coveralls": "^3.0.0",
+    "commitizen": "^4.0.3",
+    "coveralls": "^3.0.7",
     "cross-env": "5.1.4",
     "cz-conventional-changelog": "1.2.0",
-    "eslint": "3.16.1",
+    "eslint": "6.6.0",
     "eslint-config-airbnb-base": "7.1.0",
     "eslint-plugin-import": "1.16.0",
-    "eslint-watch": "2.1.14",
+    "eslint-watch": "6.0.1",
     "husky": "0.14.3",
-    "istanbul": "1.1.0-alpha.1",
-    "mocha": "3.5.0",
-    "supertest": "3.0.0",
+    "mocha": "6.2.2",
+    "nyc": "14.1.1",
+    "supertest": "4.0.2",
     "supertest-as-promised": "4.0.2",
     "validate-commit-msg": "^2.14.0"
   },

server/hl7/hl7.controller.js

@@ -86,10 +86,10 @@ function parseFile(req, res, next) {
         rawMessage,
         parsedMessage: parseRawHl7(rawMessage),
       })
-    ));
+      ));
   })
-  .then(() => res.status(201).send(`Successfully uploaded ${getFileName(req.user.files[0].filename)}`))
-  .catch(err => next(new APIError(err, httpStatus.INTERNAL_SERVER_ERROR)));
+    .then(() => res.status(201).send(`Successfully uploaded ${getFileName(req.user.files[0].filename)}`))
+    .catch(err => next(new APIError(err, httpStatus.INTERNAL_SERVER_ERROR)));
 }
 
 /**
@@ -196,12 +196,12 @@ function _getMessageByIdOrIndex(value, fileId) {
         { fileId }
       ]
     })
-    .exec((err, message) => {
-      if (err) {
-        reject(err);
-      }
-      resolve(message);
-    });
+      .exec((err, message) => {
+        if (err) {
+          reject(err);
+        }
+        resolve(message);
+      });
   });
 }
 

server/hl7/hl7.test.js

@@ -1,3 +1,5 @@
+const fs = require('fs');
+const path = require('path');
 const mongoose = require('mongoose');
 const request = require('supertest-as-promised');
 const httpStatus = require('http-status');
@@ -25,6 +27,20 @@ const user = {
 };
 let userToken = '';
 before((done) => {
+  // Delete the test file if it exists (else subsequent tests will fail)
+  const jsonPath = path.join(__dirname, '..', '..', 'data', 'hl7-uploads', '500HL7Messages.txt');
+  try {
+    if (fs.existsSync(jsonPath)) {
+      try {
+        fs.unlinkSync(jsonPath);
+      } catch (err) {
+        console.error(err); // eslint-disable-line no-console
+      }
+    }
+  } catch (err) {
+    console.error(err); // eslint-disable-line no-console
+  }
+
   // create a user
   request(app)
     .post('/api/users')