Merge branch 'BV-BRC:master' into main

Author: chris-c-thomas

app.js

@@ -36,6 +36,20 @@ app.use(favicon(path.join(__dirname, '/public/favicon.ico')));
 app.use(logger('dev'));
 app.use(cookieParser(config.get('cookieSecret')));
 
+const proxyConfig = config.get('proxyConfig');
+if (proxyConfig) {
+  const proxy = require("express-http-proxy");
+  var prox;
+
+  for (const prox of proxyConfig) {
+    console.log(prox);
+    app.use(prox.local, proxy(prox.site, {
+      proxyReqPathResolver: req => req.originalUrl.replace(prox.local, ""),
+      https: true
+    }));
+  }
+}
+
 app.use(function (req, res, next) {
   // console.log("Config.production: ", config.production);
   // console.log("Session Data: ", req.session);
@@ -52,6 +66,7 @@ app.use(function (req, res, next) {
     probModelSeedServiceURL: config.get('probModelSeedServiceURL'), // for dashboard
     shockServiceURL: config.get('shockServiceURL'), // for dashboard
     workspaceServiceURL: config.get('workspaceServiceURL'),
+    workspaceDownloadServiceURL: config.get('workspaceDownloadServiceURL'),
     appBaseURL: config.get('appBaseURL'),
     appServiceURL: config.get('appServiceURL'),
     dataServiceURL: config.get('dataServiceURL'),

bin/p3-web

@@ -1,4 +1,8 @@
 #!/usr/bin/env node
+
+const https = require('https');
+const fs = require('fs');
+
 var debug = require('debug')('p3-web');
 var app = require('../app');
 var conf = require('../config');
@@ -7,6 +11,21 @@ debug('Launching p3-www...');
 
 app.set('port', conf.get('http_port') || 3000);
 
-var server = app.listen(app.get('port'), function () {
-  debug('Express server listening on port ' + server.address().port);
-});
+const sslConfig = conf.get('sslConfig');
+var server;
+
+if (sslConfig) {
+  // Read SSL cert and key
+  const sslOptions = {
+    key: fs.readFileSync(sslConfig.ssl_key),
+    cert: fs.readFileSync(sslConfig.ssl_cert)
+  };
+  server = https.createServer(sslOptions, app).listen(app.get('port'), function () {
+    debug('Express server listening on SSL port ' + server.address().port);
+  });
+}
+else {
+  server = app.listen(app.get('port'), function () {
+    debug('Express server listening on port ' + server.address().port);
+  });
+}

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "p3-web",
-  "version": "3.49.1",
+  "version": "3.50.5",
   "private": true,
   "scripts": {
     "start": "node ./bin/p3-web",
@@ -29,6 +29,7 @@
     "ejs": "^3.1.10",
     "express": "^4.19.2",
     "express-formidable": "^1.2.0",
+    "express-http-proxy": "^2.1.1",
     "feedparser": "^2.2.10",
     "flag-icons": "^7.2.1",
     "formidable": "^2.1.2",

package.json

@@ -43,6 +43,9 @@
 
 .DataItemValue {
     vertical-align: top;
+    word-wrap: break-word;
+    overflow-wrap: break-word;
+    white-space: normal;
 }
 
 .DataItemSectionNotFound {

public/js/archaeopteryx/archaeopteryx-js

@@ -1076,7 +1076,7 @@ define([], function () {
         field: 'host_capture_status', type: 'str', facet: true, facet_hidden: true, search: true
       },
       {
-        field: 'host_health', type: 'str', facet: false, facet_hidden: true, search: true
+        field: 'host_health', type: 'str', facet: true, facet_hidden: true, search: true
       },
       {
         field: 'exposure', type: 'str', facet: false, facet_hidden: true, search: true

public/js/p3/resources/DataItemFormatter.css

@@ -506,6 +506,12 @@ define(['./formatter'], function (formatter) {
       hidden: false,
       group: 'Host Info'
     },
+    host_scientific_name: {
+      label: 'Host Scientific Name',
+      field: 'host_scientific_name',
+      hidden: true,
+      group: 'Host Info'
+    },
     host_gender: {
       label: 'Host Sex',
       field: 'host_gender',

public/js/p3/widget/AdvancedSearchFields.js

@@ -149,7 +149,7 @@ define([
 
     var mini = options && options.mini || false;
 
-    var table = domConstruct.create('table', {}, parent);
+    var table = domConstruct.create('table', { 'style': 'table-layout: fixed;' }, parent);
     var tbody = domConstruct.create('tbody', {}, table);
 
     sections.forEach(function (section) {

public/js/p3/widget/ColumnsGenome.js

@@ -763,6 +763,7 @@ define([
 
       on(_row, 'remove', (evt) => {
         this._Searches[evt.idx].destroyRecursive()
+        delete this._Searches[evt.idx];
       })
       on(_row, 'create', lang.hitch(this, 'createAdvancedSearchRow'))
       this._Searches[this._SearchesIdx] = _row
@@ -804,12 +805,13 @@ define([
       // TODO: implement this and trigger when context has changed
     },
     buildFilterQueryFromAdvancedSearch: function () {
+      this._filter = {};
       Object.keys(this._Searches).map((idx) => {
         const col = this._Searches[idx]
         const condition = col.getValues()
         let q;
         if (condition.type === 'str') {
-          q = `${condition.op === 'NOT' ? 'ne' : 'eq'}(${condition.column},${condition.value})`
+          q = `${condition.op === 'NOT' ? 'ne' : 'eq'}(${condition.column},${encodeURIComponent(condition.value)})`;
         } else if (condition.type === 'date') {
           const encode = (date) => {
             if (!date) {
@@ -862,7 +864,9 @@ define([
           }
         }
         if (this._filter.hasOwnProperty(condition.column)) {
-          this._filter[condition.column].push(q)
+          if (!this._filter[condition.column].includes(q)) {
+            this._filter[condition.column].push(q);
+          }
         } else {
           this._filter[condition.column] = [q]
         }