Merge pull request #45 from CBIIT/release-v2.2.1

Release v2.2.1

.gitignore

@@ -3,4 +3,6 @@ node_modules
 npm-debug.log
 client/static/dist
 gdc-docs
-geckodriver.exe
+geckodriver.exe
+.env
+.vscode

app.js

@@ -5,10 +5,9 @@ var config = require('./server/config');
 var logger = require('./server/components/logger');
 var app = express();
 
-
 require('./server/config/express')(app);
 require('./routes')(app);
 
-app.listen(config.port, function(){
-	logger.info('GDCMVS listening on port :' + config.port);
-});
+app.listen(config.port, () => {
+  logger.info('GDCMVS listening on port :' + config.port);
+});

client/index.html

@@ -1,6 +1,6 @@
 
-<% include views/header.html %>
+<%- include('views/header.html'); -%>
 
-<% include views/body.html %>
+<%- include('views/body.html'); -%>
 
-<% include views/footer.html %>
+<%- include('views/footer.html'); -%>

package.json

@@ -1,6 +1,6 @@
 {
   "name": "gdcmvs",
-  "version": "v2.2.0",
+  "version": "v2.2.1",
   "description": "GDC Metadata Validation Services",
   "main": "app.js",
   "scripts": {
@@ -21,42 +21,43 @@
   },
   "dependencies": {
     "body-parser": "^1.18.3",
-    "commander": "^2.20.1",
+    "commander": "^5.1.0",
     "compression": "^1.7.3",
-    "cookie-parser": "^1.4.3",
-    "ejs": "^2.7.1",
+    "cookie-parser": "^1.4.5",
+    "dotenv": "^8.2.0",
+    "ejs": "^3.1.3",
     "elasticsearch": "^15.2.0",
     "express": "^4.17.1",
-    "googleapis": "^27.0.0",
-    "helmet": "^3.21.1",
-    "lodash": "^4.17.15",
-    "method-override": "^2.3.10",
-    "morgan": "^1.9.1",
+    "googleapis": "^54.1.0",
+    "helmet": "^3.23.3",
+    "lodash": "^4.17.19",
+    "method-override": "^3.0.0",
+    "morgan": "^1.10.0",
     "node-fetch": "^2.6.0",
-    "rotating-file-stream": "^1.4.4",
-    "swagger-ui-express": "^4.1.2",
+    "rotating-file-stream": "^2.1.3",
+    "swagger-ui-express": "^4.1.4",
     "winston": "^2.4.4",
     "winston-daily-rotate-file": "^1.7.2",
-    "yamljs": "^0.2.10"
+    "yamljs": "^0.3.0"
   },
   "devDependencies": {
-    "@babel/core": "^7.6.3",
-    "@babel/preset-env": "^7.6.3",
-    "babel-eslint": "^10.0.3",
-    "babel-loader": "^8.0.6",
-    "clean-webpack-plugin": "^2.0.2",
-    "css-loader": "^2.1.1",
-    "eslint": "^5.16.0",
-    "eslint-loader": "^2.2.1",
+    "@babel/core": "^7.10.5",
+    "@babel/preset-env": "^7.10.4",
+    "babel-eslint": "^10.1.0",
+    "babel-loader": "^8.1.0",
+    "clean-webpack-plugin": "^3.0.0",
+    "css-loader": "^3.6.0",
+    "eslint": "^7.4.0",
+    "eslint-loader": "^4.0.2",
     "filemanager-webpack-plugin": "^2.0.5",
-    "mini-css-extract-plugin": "^0.6.0",
-    "mocha": "^5.2.0",
+    "mini-css-extract-plugin": "^0.9.0",
+    "mocha": "^8.0.1",
     "node-excel-export": "^1.4.4",
-    "node-xlsx": "^0.12.1",
+    "node-xlsx": "^0.15.0",
     "optimize-css-assets-webpack-plugin": "^5.0.3",
     "selenium-webdriver": "^3.5.0",
-    "style-loader": "^0.23.1",
-    "webpack": "^4.41.0",
-    "webpack-cli": "^3.3.9"
+    "style-loader": "^1.2.1",
+    "webpack": "^4.43.0",
+    "webpack-cli": "^3.3.12"
   }
 }

routes.js

@@ -34,4 +34,4 @@ module.exports = function (app) {
 	app.get('*', function (req, res) {
 		res.status(404).sendFile(app.get('views') + '/404.html');
 	});
-};
+};

server/components/logger.js

@@ -2,31 +2,29 @@
  * back-end logger for application
  */
 
-'use strict';
-
 const winston = require('winston');
 const config = require('../config');
 winston.emitErrs = true;
 
 const tsFormat = () => (new Date()).toLocaleTimeString();
 
 var logger = new winston.Logger({
-    transports: [
-	    new (require('winston-daily-rotate-file'))({
-	      filename: config.logDir + '/-warning.log',
-	      timestamp: tsFormat,
-	      datePattern: 'yyyy-MM-dd',
-	      prepend: true,
-	      level: 'warn'
-	    }),
-        new winston.transports.Console({
-            level: 'debug',
-            handleExceptions: true,
-            json: false,
-            colorize: true
-        })
-    ],
-    exitOnError: false
+  transports: [
+    new (require('winston-daily-rotate-file'))({
+      filename: config.logDir + '/-warning.log',
+      timestamp: tsFormat,
+      datePattern: 'yyyy-MM-dd',
+      prepend: true,
+      level: 'warn'
+    }),
+    new winston.transports.Console({
+      level: 'debug',
+      handleExceptions: true,
+      json: false,
+      colorize: true
+    })
+  ],
+  exitOnError: false
 });
 
-module.exports = logger;
+module.exports = logger;

server/config/express.js

@@ -12,42 +12,40 @@ const fs = require('fs');
 const rfs = require('rotating-file-stream');
 
 module.exports = app => {
-
-    let env = config.env;
-
-    app.set('views', config.root + '/client');
-    app.engine('html', require('ejs').renderFile);
-    app.set('view engine', 'html');
-    app.use(compression());
-    app.use(bodyParser.urlencoded({
-        limit: '4mb', // 100kb default is too small
-        extended: false
-    }));
-    app.use(bodyParser.json({
-        limit: '4mb' // 100kb default is too small
-    }));
-    app.use(methodOverride());
-    app.use(cookieParser());
-    app.use(express.static(path.join(config.root, 'client/static')));
-    app.set('viewPath', 'client');
-
-    if ('dev' === env) {
-        app.use(morgan('dev'));
-    }
-    else if('prod' === env || 'test' === env){
-        let logDirectory = config.logDir;
-
-        // ensure log directory exists
-        fs.existsSync(logDirectory) || fs.mkdirSync(logDirectory);
-
-        // create a rotating write stream
-        var accessLogStream = rfs('access.log', {
-            interval: '1d', // rotate daily
-            path: logDirectory
-        })
-
-        morgan.format('log-format', ':remote-addr - - [:date[clf]] ":method :url HTTP/:http-version" :status ":referrer" ":user-agent"');
-        // setup the logger
-        app.use(morgan('log-format', {stream: accessLogStream}));
-    }
-};
+  let env = config.env;
+
+  app.set('views', config.root + '/client');
+  app.engine('html', require('ejs').renderFile);
+  app.set('view engine', 'html');
+  app.use(compression());
+  app.use(bodyParser.urlencoded({
+    limit: '4mb', // 100kb default is too small
+    extended: false
+  }));
+  app.use(bodyParser.json({
+    limit: '4mb' // 100kb default is too small
+  }));
+  app.use(methodOverride());
+  app.use(cookieParser());
+  app.use(express.static(path.join(config.root, 'client/static')));
+  app.set('viewPath', 'client');
+
+  if (env === 'dev') {
+    app.use(morgan('dev'));
+  } else if (env === 'prod' || env === 'test') {
+    let logDirectory = config.logDir;
+
+    // ensure log directory exists
+    fs.existsSync(logDirectory) || fs.mkdirSync(logDirectory);
+
+    // create a rotating write stream
+    var accessLogStream = rfs.createStream('access.log', {
+      interval: '1d', // rotate daily
+      path: logDirectory
+    });
+
+    morgan.format('log-format', ':remote-addr - - [:date[clf]] ":method :url HTTP/:http-version" :status ":referrer" ":user-agent"');
+    // setup the logger
+    app.use(morgan('log-format', { stream: accessLogStream }));
+  }
+};

server/config/index.js

@@ -3,60 +3,64 @@
 const path = require('path');
 const _ = require('lodash');
 
+if (process.env.NODE_ENV !== 'prod') {
+  require('dotenv').config();
+};
+
 const all = {
-	// Root path of server
-    root: path.normalize(__dirname + '/../..'),
-
-	// Server port
-	port: process.env.PORT || 3000,
-
-	// Server port
-    logDir: process.env.LOGDIR || '/local/content/mvs/logs',
-
-	// Node environment (dev, test, stage, prod), must select one.
-	env: process.env.NODE_ENV || 'prod',
-
-	//general gdc index name
-	indexName: 'gdc',
-
-	//suggestion index name for typeahead
-	suggestionName: 'gdc-suggestion',
-
-	//NCIT details index name;
-	ncitDetails: 'ncit-details',
-
-	//index name for properties
-	index_p: 'gdc-p',
-
-	//index name for values
-	index_v: 'gdc-v',
-
-	// GDC searchable nodes
-	searchable_nodes : ["case", "demographic", "diagnosis", "exposure", "family_history", "follow_up", "molecular_test",
-		"treatment", "slide", "sample", "read_group", "portion", "analyte", "aliquot", "slide_image", "analysis_metadata",
-		"clinical_supplement", "experiment_metadata", "pathology_detail", "pathology_report", "run_metadata", "biospecimen_supplement",
-		"submitted_aligned_reads", "submitted_genomic_profile", "submitted_methylation_beta_value", "submitted_tangent_copy_number",
-		"submitted_unaligned_reads", "data_release", "root"
-	],
-
-	// GDC drugs properties
-	drugs_properties : ["therapeutic_agents"],
-
-	//get data from caDSR
-	caDSR_url:[
-			"https://cdebrowser.nci.nih.gov/cdebrowserServer/rest/search?publicId=",
-			"https://cdebrowser.nci.nih.gov/cdebrowserServer/rest/CDEData?deIdseq="
-			],
-
-	//get synonyms from NCIt
-	NCIt_url: [
-		'https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&code=',
-		'https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&type=synonym&code=',
-		'http://nciws-d790.nci.nih.gov:15080/evsrestapi2/api/v1/ctrp/concept/',
-		'https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=CTCAE&type=synonym&code=',
-		'https://evsrestapi.nci.nih.gov/evsrestapi/api/v1/ctrp/concept/',
-		'https://evsrestapi-stage.nci.nih.gov/evsrestapi/api/v1/conceptList?db=weekly&properties=Code,Preferred_Name,FULL_SYN,DEFINITION&concepts='
-	]
+  // Root path of server
+  root: path.resolve(__dirname, '../../'),
+
+  // Server port
+  port: process.env.PORT || 3000,
+
+  // Server port
+  logDir: process.env.LOGDIR || '/local/content/mvs/logs',
+
+  // Node environment (dev, test, stage, prod), must select one.
+  env: process.env.NODE_ENV || 'prod',
+
+  // general gdc index name
+  indexName: 'gdc',
+
+  // suggestion index name for typeahead
+  suggestionName: 'gdc-suggestion',
+
+  // NCIT details index name;
+  ncitDetails: 'ncit-details',
+
+  // index name for properties
+  index_p: 'gdc-p',
+
+  // index name for values
+  index_v: 'gdc-v',
+
+  // GDC searchable nodes
+  searchable_nodes: ['case', 'demographic', 'diagnosis', 'exposure', 'family_history', 'follow_up', 'molecular_test',
+    'treatment', 'slide', 'sample', 'read_group', 'portion', 'analyte', 'aliquot', 'slide_image', 'analysis_metadata',
+    'clinical_supplement', 'experiment_metadata', 'pathology_detail', 'pathology_report', 'run_metadata', 'biospecimen_supplement',
+    'submitted_aligned_reads', 'submitted_genomic_profile', 'submitted_methylation_beta_value', 'submitted_tangent_copy_number',
+    'submitted_unaligned_reads', 'data_release', 'root'
+  ],
+
+  // GDC drugs properties
+  drugs_properties: ['therapeutic_agents'],
+
+  // get data from caDSR
+  caDSR_url: [
+    'https://cdebrowser.nci.nih.gov/cdebrowserServer/rest/search?publicId=',
+    'https://cdebrowser.nci.nih.gov/cdebrowserServer/rest/CDEData?deIdseq='
+  ],
+
+  // get synonyms from NCIt
+  NCIt_url: [
+    'https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&code=',
+    'https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&type=synonym&code=',
+    'http://nciws-d790.nci.nih.gov:15080/evsrestapi2/api/v1/ctrp/concept/',
+    'https://ncit.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=CTCAE&type=synonym&code=',
+    'https://evsrestapi.nci.nih.gov/evsrestapi/api/v1/ctrp/concept/',
+    'https://evsrestapi-stage.nci.nih.gov/evsrestapi/api/v1/conceptList?db=weekly&properties=Code,Preferred_Name,FULL_SYN,DEFINITION&concepts='
+  ]
 };
 
-module.exports = _.merge(all, require('./' + all.env + '.js'));
+module.exports = _.merge(all, require('./' + all.env + '.js'));