Release53

.gitignore

@@ -1,6 +1,7 @@
 # See http://help.github.com/ignore-files/ for more about ignoring files.
 # ignore static files generated during build process
 /static/app.html.fragment
+/static/static.html.fragment
 /static/blogFeed.json
 
 # deploy key

.travis.yml

@@ -1,6 +1,6 @@
 language: node_js
 node_js:
-- 6.3.1
+- 7.9.0
 before_script:
 - npm install -g grunt-cli
 script: grunt package

Gruntfile.js

@@ -5,6 +5,8 @@ var moment = require('moment');
 var fs = require('fs');
 
 var grameneRelease = require('./package.json').gramene.dbRelease;
+var reactomeURL = require('./package.json').gramene.reactomeURL;
+
 var webserviceVersion = 'v' + grameneRelease;
 
 module.exports = function (grunt) {
@@ -29,11 +31,11 @@ module.exports = function (grunt) {
     },
 
     exec: {
-      generateStaticApp: {
-        cmd: 'node scripts/babel.js'
+      generateStaticWelcome: {
+        cmd: 'node scripts/babel.js -c app'
       },
-      blogFeed: {
-        cmd: 'node scripts/getBlogFeed.js'
+      generateStaticApp: {
+        cmd: 'node scripts/babel.js -c static'
       }
     },
 
@@ -96,7 +98,7 @@ module.exports = function (grunt) {
       },
       html: {
         files: ['*.template.html'],
-        tasks: ['packageIndexHtml']
+        tasks: ['packageIndexHtml','packageStaticHtml']
       },
       styles: {
         files: ['styles/*.less'],
@@ -121,7 +123,7 @@ module.exports = function (grunt) {
           {expand: true, cwd: 'assets/', src: ['**'], dest: 'build/assets/'},
           {
             expand: true,
-            cwd: 'node_modules/gramene-dalliance', 
+            cwd: 'node_modules/dalliance',
             src: [
               'css/*-scoped.css',
               'css/font-awesome.min.css',
@@ -131,8 +133,12 @@ module.exports = function (grunt) {
             dest: 'build/assets/gramene-dalliance/'
           },
           {
-            src: 'node_modules/gramene-dalliance/prebuilt/worker-all.js',
+            src: 'node_modules/dalliance/prebuilt/worker-all.js',
             dest: 'build/assets/gramene-dalliance/worker-all.js'
+          },
+          {
+            src: 'node_modules/dalliance/prebuilt/dalliance-all.js',
+            dest: 'build/assets/gramene-dalliance/dalliance-all.js'
           }
         ]
       },
@@ -195,7 +201,8 @@ module.exports = function (grunt) {
         footer: footer,
         content: content,
         loadingMessage: loadingMessage,
-        hideIntro: hideIntro
+        hideIntro: hideIntro,
+        reactomeURL: reactomeURL
       };
 
       return template(props);
@@ -205,9 +212,77 @@ module.exports = function (grunt) {
 
     var atlas = grunt.file.read('./static/atlasWidget.template.html')
     grunt.file.write('build/atlasWidget.html', atlas);
+
+    // var htaccess = "RewriteBase /\n"
+    //  + "RewriteRule ^index\.html$ - [L]\n"
+    //  + "RewriteCond %{REQUEST_FILENAME} !-f\n"
+    //  + "RewriteCond %{REQUEST_FILENAME} !-d\n"
+    //  + "RewriteRule . /index.html [L]\n";
+    // grunt.file.write('build/.htaccess', htaccess);
   });
-
-  grunt.registerTask('generateStaticFiles', ['exec:blogFeed', 'copy:assets', 'copy:icons', 'exec:generateStaticApp', 'packageIndexHtml']);
+
+  grunt.registerTask('packageStaticHtml', 'Build static.html for distribution.', function () {
+    var footer = (function compileFooterTemplate() {
+      function defaultServer() {
+        const PROD_SERVER = 'http://data.gramene.org/';
+        const DEV_SERVER = 'http://devdata.gramene.org/';
+        var defaultServer;
+
+        if (process.env.GRAMENE_SERVER) {
+          defaultServer = process.env.GRAMENE_SERVER;
+        }
+        else if (props.tag || props.branch === 'master') {
+          defaultServer = PROD_SERVER;
+        }
+        else {
+          defaultServer = DEV_SERVER;
+        }
+
+        defaultServer += webserviceVersion + '/swagger';
+
+        return defaultServer;
+      }
+
+      var template = _.template(grunt.file.read('./static/footer.template.html'));
+
+      var props = {
+        jobId: process.env.TRAVIS_JOB_ID,
+        jobNumber: process.env.TRAVIS_JOB_NUMBER,
+        branch: process.env.TRAVIS_BRANCH,
+        tag: process.env.TRAVIS_TAG,
+        user: process.env.USER,
+        date: moment().format('MMMM Do YYYY [at] h:mm:ss a'),
+        isDev: process.env.isDev,
+        grameneRelease: grameneRelease
+      };
+
+      props.defaultServer = defaultServer();
+      console.log("This build will use " + props.defaultServer + " as default web service server");
+
+      return template(props);
+    })();
+
+    var index = (function compileIndexTemplate() {
+      var template = _.template(grunt.file.read('./static/index.template.html'));
+      var content = grunt.file.read('./static/static.html.fragment');
+      var loadingMessage = grunt.file.read('./static/loading-message.html.fragment');
+      var hideIntro = grunt.file.read('./static/hide-intro.html.fragment');
+
+      var props = {
+        footer: footer,
+        content: content,
+        loadingMessage: loadingMessage,
+        hideIntro: hideIntro,
+        reactomeURL: reactomeURL
+      };
+
+      return template(props);
+    })();
+
+    grunt.file.write('build/static.html', index);
+  });
+
+  grunt.registerTask('generateStaticFiles', ['copy:assets', 'copy:icons', 'exec:generateStaticApp', 'exec:generateStaticWelcome', 'packageStaticHtml', 'packageIndexHtml']);
   grunt.registerTask('test', ['jasmine_node']);
   grunt.registerTask('default', ['env:dev', 'generateStaticFiles', 'less:dev', 'browserify:dev', 'watch']);
   grunt.registerTask('package', ['env:prod', 'generateStaticFiles', 'less:production', 'browserify:production', 'test']);

package.json

@@ -1,10 +1,12 @@
 {
   "name": "gramoogle",
-  "version": "2.5.1",
+  "version": "3.0.0",
   "description": "Gramene search interface",
   "main": "index.js",
   "gramene": {
-    "dbRelease": 52
+    "dbRelease": 53,
+    "reactomeURL": "//plantreactome.gramene.org",
+    "ensemblURL": "//ensembl.gramene.org"
   },
   "scripts": {
     "build": "grunt package",
@@ -23,25 +25,44 @@
   "homepage": "https://github.com/warelab/gramoogle",
   "dependencies": {
     "axios": "^0.9.1",
+    "body-parser": "^1.16.0",
+    "component-closest": "^1.0.1",
+    "compression": "^1.6.2",
+    "cors": "^2.8.1",
+    "dalliance": "git://github.com/ajo2995/dalliance.git#cran",
+    "email": "^0.2.6",
+    "express": "^4.14.0",
+    "flat-to-nested": "^1.0.2",
     "gramene-bins-client": "^2.2.9",
     "gramene-client-cache": "1.0.0",
-    "gramene-dalliance": "^0.13.2",
     "gramene-dbxrefs": "^3.0.2",
-    "gramene-genetree-vis": "3.1.4",
+    "gramene-genetree-vis": "git://github.com/warelab/gramene-genetree-vis.git",
     "gramene-search-client": "^3.0.4",
     "gramene-search-vis": "^4.1.2",
     "gramene-taxonomy-with-genomes": "^3.0.8",
-    "gramene-trees-client": "2.4.7",
+    "gramene-trees-client": "git://github.com/warelab/gramene-trees-client.git#consensus",
+    "history": "^4.5.1",
+    "is-email": "^1.0.0",
     "lodash": "^4.3.0",
+    "mysql": "^2.13.0",
+    "node-schedule": "^1.2.0",
     "normalize.less": "^1.0.0",
     "numeral": "^1.5.3",
+    "path": "^0.12.7",
     "q": "^1.2.0",
     "query-string": "^4.2.2",
-    "react": "^15.0.1",
-    "react-bootstrap": "^0.30.0",
-    "react-dom": "^15.0.1",
+    "react": "^15.4.2",
+    "react-bootstrap": "^0.30.7",
+    "react-dom": "^15.4.2",
+    "react-ga": "^2.2.0",
+    "react-recaptcha": "^2.2.6",
+    "react-router": "^3.0.2",
+    "react-tree-menu": "^1.5.0",
+    "reactify": "^1.1.1",
     "reflux": "^0.4.1",
     "rss-parser": "latest",
+    "soap": "^0.18.0",
+    "tree-model": "^1.0.6",
     "xml2js": "^0.4.16"
   },
   "devDependencies": {

scripts/actions/docActions.js

@@ -30,7 +30,7 @@ function getClientPromise(collection) {
   return client[collection];
 }
 
-DocActions.needDocs.listen(function (collection, id, postprocessFn) {
+DocActions.needDocs.listen(function (collection, id, postprocessFn, callbackFn) {
   var cacheKey, clientCall;
   cacheKey = [collection,id];
   console.log('DocActions.needDocs', collection, id);
@@ -43,7 +43,13 @@ DocActions.needDocs.listen(function (collection, id, postprocessFn) {
 
   var promise, cached;
   if ((cached = docCache.get(cacheKey))) {
-    promise = Q(cached);
+    promise = Q(cached)
+      .then(function callbackMaybe(result) {
+        if (callbackFn) {
+          callbackFn(result.docs);
+        }
+        return result;
+      });
   }
   else {
     docCache.set(id, 'loading…');
@@ -71,6 +77,12 @@ DocActions.needDocs.listen(function (collection, id, postprocessFn) {
         }
         return result;
       })
+      .then(function callbackMaybe(result) {
+        if (callbackFn) {
+          callbackFn(result.docs);
+        }
+        return result;
+      })
       .then(function addToCache(result) {
         docCache.set(cacheKey, result);
         return result;

scripts/actions/drupalActions.js

@@ -0,0 +1,26 @@
+import Reflux from "reflux";
+import {getBlogFeed} from "../welcome/getDrupalContent.js";
+// import Q from 'q';
+
+const DrupalActions = Reflux.createActions([
+  {'refreshBlogFeed': {asyncResult: true}},
+  // {'fetchDrupalPage': {asyncResult: true}}
+]);
+
+// console.log(DrupalActions);
+
+DrupalActions.refreshBlogFeed.listen(function () {
+  console.log("Will refreshBlog Feed");
+  getBlogFeed()
+    .then(this.completed)
+    .catch(this.failed);
+});
+
+// DrupalActions.fetchDrupalPage.listen(function (url) {
+//   console.log("Will fetchDrupalPage from", url);
+//   getDrupalPage(url)
+//     .then(this.completed)
+//     .catch(this.failed);
+// });
+
+export default DrupalActions;

scripts/actions/welcomeActions.js

@@ -1,21 +1,12 @@
 import Reflux from "reflux";
-import getBlogFeed from "../welcome/getBlogFeed.js";
 import Q from 'q';
 
 const WelcomeActions = Reflux.createActions([
-    {'refreshBlogFeed': {asyncResult: true}},
     {'flashSearchBox': {asyncResult: true}}
 ]);
 
 console.log(WelcomeActions);
 
-WelcomeActions.refreshBlogFeed.listen(function () {
-  console.log("Will refreshBlog Feed");
-  getBlogFeed()
-      .then(this.completed)
-      .catch(this.failed);
-});
-
 WelcomeActions.flashSearchBox.listen(function (delayMs = 500) {
   const deferred = Q.defer();
   setTimeout(()=>deferred.resolve("finish"), delayMs);

scripts/babel.js

@@ -3,6 +3,9 @@
 'use strict';
 
 var fs = require('fs');
+var argv = require('minimist')(process.argv.slice(2));
+
+var serverRenderMode = argv.c;
 
 require('babel-register')({
   presets: ['es2015', 'react']
@@ -16,4 +19,4 @@ var ReactDOMServer = require('react-dom/server');
 
 var App = React.createFactory(require('./components/appStatic.jsx').default);
 
-fs.writeFileSync('static/app.html.fragment', ReactDOMServer.renderToString(new App({context: 'compile'})));
+fs.writeFileSync(`static/${serverRenderMode}.html.fragment`, ReactDOMServer.renderToString(new App({serverRenderMode})));