Merge 226b1f7 into 04d9a6d

.gitignore

@@ -37,3 +37,4 @@ restapi.doc
 package-lock.json
 jb_run.js
 jb_setup.js
+.DS_Store

.jshintrc

@@ -10,18 +10,17 @@
     "browser": true,
     "dojo": true,
     "evil": true,     // allow eval
+    "esversion": 6,
     "laxbreak": true,
     "laxcomma": true,
     "loopfunc": true,
     "funcscope": true,
     "maxlen": 10000,
-    "indent": 4,
     "shadow": true,
     "maxerr": 250,
     "sub": true,
     "predef": [ "require", "define", "SockJS", "Stomp", "bbop", "amigo" ],
     "maxcomplexity": 40,
-    "indent": 2,
     "undef": true,
     "trailing": true,
     "devel": true

.travis.yml

@@ -52,7 +52,7 @@ cache:
     - $HOME/.gradle/wrapper/
 script:
   - travis_wait ./gradlew handleJBrowse copy-resources gwtc && ./grailsw refresh-dependencies --stacktrace && ./grailsw test-app -coverage -xml --stacktrace
-  - node web-app/jbrowse/src/dojo/dojo.js load=build --require "web-app/jbrowse/src/JBrowse/init.js" --profile "web-app/jbrowse/plugins/WebApollo/js/WebApollo"
+  #- node web-app/jbrowse/src/dojo/dojo.js load=build --require "web-app/jbrowse/src/JBrowse/init.js" --profile "web-app/jbrowse/plugins/WebApollo/js/WebApollo"
   - jshint client/apollo/js
 after_success:
   - ./grailsw coveralls

build.gradle

@@ -313,6 +313,10 @@ def cloneRepoNpm(String url, String directory, String branch){
         logger.quiet "Using npm to install: ${finalUrl}"
         commandLine "npm","install",finalUrl,"--ignore-scripts"
     }
+    println "CURRENT DIRECTORY"
+    println new File(".").absolutePath
+//    commandLine "npm","install",finalUrl,"--ignore-scripts"
+
 
     File npmDirectory = new File('node_modules')
     if(finalUrl.contains("#") && (finalUrl.endsWith("jbrowse") || finalUrl.split("#")[0].endsWith("jbrowse"))) {

client/apollo/.gitignore

@@ -0,0 +1 @@
+node_modules

client/apollo/LICENSE.md

@@ -0,0 +1,13 @@
+-------
+Copyright (c) 2015, Regents of the University of California. 
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+Neither the name of the Lawrence Berkeley National Lab nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

client/apollo/README.md

@@ -0,0 +1 @@
+Install this plugin into your JBrowse from npm.  `cd jbrowse; npm install @gmod/apollo-jbrowse-plugin`

client/apollo/js/FeatureEdgeMatchManager.js

@@ -1,9 +1,10 @@
- define( ['dojo/_base/declare',
-          'jquery',
+const $ = require('jquery')
+
+define( ['dojo/_base/declare',
           'WebApollo/View/Track/DraggableHTMLFeatures',
           'WebApollo/View/Track/AnnotTrack'
          ],
-        function( declare, $, DraggableFeatureTrack, AnnotTrack ) {
+        function( declare, DraggableFeatureTrack, AnnotTrack ) {
 
 var FeatureEdgeMatchManager = declare( null,
 

client/apollo/js/SequenceSearch.js

@@ -1,17 +1,18 @@
+const $ = require('jquery')
+
 define( [
             'dojo/_base/declare',
             'dojo/_base/array',
             'dojo/dom-construct',
             'dojo/dom-attr',
             'dojo/dom',
-            'jquery'
 ], 
     function( declare,
         array,
         domConstruct,
         domAttr,
-        dom,
-        $ ) {
+        dom
+        ) {
 
 return declare(null, {
 constructor: function(contextPath) {

client/apollo/js/View/Track/AnnotTrack.js

@@ -1,14 +1,13 @@
+const $ = require('jquery');
+const jui = require('jqueryui');
+const {draggable,droppable,resizable,autocomplete,dialog} = $.ui;
+
+
 define([
         'dojo/_base/declare',
         'dojo/_base/array',
         'dojo/on',
         'dojo/request',
-        'jquery',
-        'jqueryui/draggable',
-        'jqueryui/droppable',
-        'jqueryui/resizable',
-        'jqueryui/autocomplete',
-        'jqueryui/dialog',
         'dijit/registry',
         'dijit/Menu',
         'dijit/MenuItem',
@@ -49,12 +48,8 @@ define([
               array,
               on,
               request,
-              $,
-              draggable,
-              droppable,
-              resizable,
-              autocomplete,
-              dialog,
+
+
               registry,
               dijitMenu,
               dijitMenuItem,

client/apollo/js/View/Track/DraggableBLASTFeatures.js

@@ -1,9 +1,10 @@
+const $ = require('jquery')
+
 define( [
          'dojo/_base/declare',
          'WebApollo/View/Track/DraggableHTMLFeatures',
-		 'jquery'
          ],
-	function(declare, DraggableFeatureTrack,$) {
+	function(declare, DraggableFeatureTrack) {
 
 	    var DraggableBLASTFeatures = declare(DraggableFeatureTrack, {   
 		    constructor: function(args)  {  },

client/apollo/js/View/Track/DraggableHTMLFeatures.js

@@ -1,3 +1,7 @@
+const $ = require('jquery')
+require('jqueryui')
+const { draggable } = $.ui;
+
 define( [
             'dojo/_base/declare',
             'dojo/_base/array',
@@ -9,8 +13,6 @@ define( [
             'dijit/MenuSeparator',
             'dijit/PopupMenuItem',
             'dijit/Dialog',
-            'jquery',
-            'jqueryui/draggable',
             'JBrowse/Util', 
             'JBrowse/Model/SimpleFeature', 
             'WebApollo/SequenceOntologyUtils'
@@ -25,8 +27,6 @@ define( [
         dijitMenuSeparator,
         dijitPopupMenuItem,
         dijitDialog,
-        $,
-        draggable,
         Util, 
         SimpleFeature,
         SeqOnto ) {
@@ -1039,8 +1039,8 @@ var draggableTrack = declare( HTMLFeatureTrack,
                 //     for more explanation of event handling changes in JQuery 1.7
 
                 // _mouseDown(event) triggering boostrapping of feature drag 
-                // $featdiv.data("draggable")._mouseDown(event);  
-                $featdiv.draggable().data("draggable")._mouseDown(event);
+                // $featdiv.data("draggable")._mouseDown(event);
+                // $featdiv.draggable().data("draggable")._mouseDown(event);
                 // $featdiv.trigger(event);
             }
         }

client/apollo/js/View/Track/SequenceTrack.js

@@ -1,3 +1,5 @@
+const $ = require('jquery')
+
 define( [
     'dojo/_base/declare',
     'dojo/request/xhr',
@@ -6,8 +8,7 @@ define( [
     'WebApollo/View/Track/DraggableHTMLFeatures',
     'WebApollo/JSONUtils',
     'WebApollo/Permission',
-    'dojox/widget/Standby',
-    'jquery/jquery'
+    'dojox/widget/Standby'
      ],
 function( declare,
     xhr,
@@ -16,8 +17,7 @@ function( declare,
     DraggableFeatureTrack,
     JSONUtils,
     Permission,
-    Standby,
-    $
+    Standby
 ) {
 
 var SequenceTrack = declare( "SequenceTrack", DraggableFeatureTrack,

client/apollo/js/main.js

@@ -1,13 +1,4 @@
-require({
-           packages: [
-               { name: 'jqueryui', location: '../plugins/WebApollo/jslib/jqueryui' },
-               { name: 'jquery', location: '../plugins/WebApollo/jslib/jquery', main: 'jquery' }
-           ]
-       },
-       [],
-       function() {
-
-define.amd.jQuery = true;
+const $ = require('jquery')
 
 define([
            'dojo/_base/declare',
@@ -38,8 +29,6 @@ define([
            'JBrowse/View/FileDialog/TrackList/GFF3Driver',
            'JBrowse/CodonTable',
            'dojo/io-query',
-           'jquery/jquery',
-           'lazyload/lazyload'
        ],
     function( declare,
             lang,
@@ -68,9 +57,8 @@ define([
             HelpMixin,
             GFF3Driver,
             CodonTable,
-            ioQuery,
-            $,
-            LazyLoad ) {
+            ioQuery
+            ) {
 
 return declare( [JBPlugin, HelpMixin],
 {
@@ -389,9 +377,15 @@ return declare( [JBPlugin, HelpMixin],
         }
 
         // move Tool menu in front of Help menu
-        var toolsMenu = dijit.byId('dropdownbutton_tools');
-        var helpMenu = dijit.byId('dropdownbutton_help');
-        domConstruct.place(toolsMenu.domNode,helpMenu.domNode,'before');
+        var intervalFunction  = function(){
+            var toolsMenu = dijit.byId('dropdownbutton_tools');
+            var helpMenu = dijit.byId('dropdownbutton_help');
+            if(toolsMenu && helpMenu){
+                domConstruct.place(toolsMenu.domNode,helpMenu.domNode,'before');
+                clearInterval(intervalID); // Will clear the timer.
+            }
+        };
+        var intervalID = setInterval(intervalFunction, 100); // Will alert every second.
         this.searchMenuInitialized = true;
     },
 
@@ -750,5 +744,3 @@ return declare( [JBPlugin, HelpMixin],
 });
 
 });
-
-});

client/apollo/json/annot.json

@@ -1,7 +1,8 @@
 {
     "plugins" : [
       {
-         "location" : "./plugins/WebApollo",
+        "pluginsDir" : "./plugins/WebApollo",
+         "location" : "./plugins/WebApollo/js",
          "name" : "WebApollo"
       }
    ],

client/apollo/package.json

@@ -0,0 +1,31 @@
+{
+  "name": "@gmod/apollo-jbrowse-plugin",
+  "version": "1.0.0",
+  "description": "JBrowse client plugin for Apollo",
+  "main": "index.js",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1"
+  },
+  "author": "Nathan Dunn",
+  "license": "SEE LICENSE IN LICENSE.md",
+  "dependencies": {
+    "jquery": "^3.3.1",
+    "jqueryui": "^1.11.1"
+  },
+  "devDependencies": {},
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/GMOD/Apollo.git"
+  },
+  "keywords": [
+    "genome",
+    "curation"
+  ],
+  "bugs": {
+    "url": "https://github.com/GMOD/Apollo/issues"
+  },
+  "homepage": "https://github.com/GMOD/Apollo#readme",
+  "jbrowsePlugin": {
+    "name": "WebApollo"
+  }
+}

grails-app/conf/Config.groovy

@@ -397,10 +397,10 @@ auditLog {
 jbrowse {
     git {
         url = "https://github.com/gmod/jbrowse"
-//        branch = "master"
-        tag = "15dfd2309f2d508d8bed782d0f68b38dd9927bb4"
-        alwaysPull = false
-        alwaysRecheck = false
+        branch = "dev"
+//        tag = "15dfd2309f2d508d8bed782d0f68b38dd9927bb4"
+        alwaysPull = true
+        alwaysRecheck = true
     }
 //    url {
 //        // always use dev for apollo

grails-app/controllers/org/bbop/apollo/JbrowseController.groovy

@@ -458,7 +458,8 @@ class JbrowseController {
                 }
             }
             // add core plugin: https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Browser.js#L244
-            pluginKeys.add("RegexSequenceSearch")
+//            pluginKeys.add("RegexSequenceSearch")
+            pluginKeys.add("WebApollo")
             for (plugin in plugins) {
                 if (!pluginKeys.contains(plugin.key)) {
                     pluginKeys.add(plugin.key)

package.json

@@ -28,6 +28,7 @@
   },
   "homepage": "https://github.com/GMOD/Apollo#readme",
   "dependencies": {
-    "@gmod/jbrowse": "github:gmod/jbrowse#15dfd2309f2d508d8bed782d0f68b38dd9927bb4"
+    "@gmod/client/apollo": "client/apollo",
+    "@gmod/jbrowse": "github:gmod/jbrowse#dev"
   }
 }

sample-h2-apollo-config.groovy

@@ -78,7 +78,7 @@ environments {
 //    git {
 //        url= "https://github.com/GMOD/jbrowse"
 //         tag = "15dfd2309f2d508d8bed782d0f68b38dd9927bb4"
-////        branch = "master"
+////        branch = "dev"
 //        alwaysPull = true
 //        alwaysRecheck = true
 //    }

sample-mysql-apollo-config.groovy

@@ -77,7 +77,7 @@ environments {
 //    git {
 //        url= "https://github.com/GMOD/jbrowse"
 //         tag = "15dfd2309f2d508d8bed782d0f68b38dd9927bb4"
-////        branch = "master"
+////        branch = "dev"
 //        alwaysPull = true
 //        alwaysRecheck = true
 //    }

sample-postgres-apollo-config.groovy

@@ -122,7 +122,7 @@ environments {
 //    git {
 //        url= "https://github.com/GMOD/jbrowse"
 //         tag = "15dfd2309f2d508d8bed782d0f68b38dd9927bb4"
-////        branch = "master"
+////        branch = "dev"
 //        alwaysPull = true
 //        alwaysRecheck = true
 //