Add chart plugins back to plugins directory of visualization framework

config/plugins/visualizations/charts/package.json

@@ -1,18 +1,41 @@
 {
-  "name": "galaxy-charts",
-  "version": "0.0.0",
-  "description": "Charts visualization plugin for the Galaxy informatics framework",
-  "main": " ",
+  "name": "galaxy-charts-plugins",
+  "version": "0.1.0",
+  "description": "Charts visualization plugin.",
   "keywords": [
     "galaxy",
     "visualization",
     "d3"
   ],
-  "author": "Aysam Guerler",
-  "license": "BSD",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/guerler/galaxy-charts"
+  },
+  "license": "AFL-3.0",
+  "dependencies": {
+    "amdi18n-loader": "^0.2.0",
+    "grunt": "^0.4.5",
+    "grunt-bower-install-simple": "^1.1.0",
+    "grunt-check-modules": "^1.0.0",
+    "grunt-cli": "^0.1.13",
+    "grunt-contrib-clean": "^0.6.0",
+    "grunt-contrib-copy": "^0.5.0",
+    "grunt-contrib-less": "^1.1.0",
+    "grunt-contrib-uglify": "^0.8.0",
+    "grunt-contrib-watch": "^0.6.1",
+    "grunt-exec": "^0.4.6",
+    "grunt-spritesmith": "^4.7.1",
+    "i18n-webpack-plugin": "^0.2.7",
+    "webpack": "^1.10.1",
+    "webpack-dev-server": "^1.7.0",
+    "backbone": "^1.3.3",
+    "bootstrap": "^3.3.7",
+    "cytoscape": "^2.7.10",
+    "jquery": "^3.1.1",
+    "cytoscape-edgehandles": "^2.6.0"
+  },
   "devDependencies": {
-    "grunt": "~0.4.1",
-    "grunt-cli": "~0.1.9",
-    "grunt-contrib-requirejs": "~0.4.3"
+    "css-loader": "^0.24.0",
+    "style-loader": "^0.13.1"
   }
 }

config/plugins/visualizations/charts/static/app.js → config/plugins/visualizations/charts/static/client/app.js

@@ -31,7 +31,7 @@ define( [ 'mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils
             }, function( err ) {
                 self.$el.append( $( '<div/>' ).addClass( 'errormessagelarge' )
                         .append( $( '<p/>' ).text( 'Unable to access the plugin repository:' ) )
-                        .append( $( '<pre/>' ).text( 'charts_repository_url = ' + repository_root + 'package.json' ) )
+                        .append( $( '<pre/>' ).text( 'charts_repository_url = ' + repository_root ) )
                         .append( $( '<p/>' ).html( 'Please verify that your internet connection works properly and that the above url is correct. Contact your admin if this error persists.' ) ) );
             });
         },

config/plugins/visualizations/charts/static/views/description.js → config/plugins/visualizations/charts/static/client/views/description.js

@@ -14,7 +14,7 @@ define( [ 'utils/utils' ], function( Utils ) {
         },
         render: function() {
             if ( this.chart.get( 'type' ) ) {
-                this.$image.attr( 'src', repository_root + 'src/visualizations/' + this.app.split( this.chart.get( 'type' ) ) + '/logo.png' );
+                this.$image.attr( 'src', repository_root + '/visualizations/' + this.app.split( this.chart.get( 'type' ) ) + '/logo.png' );
                 this.$title.html( this.chart.definition.title + ' (' + this.chart.definition.library + ')' );
                 this.$text.html( Utils.linkify( this.chart.definition.description || '' ) );
                 this.$el.show();

config/plugins/visualizations/charts/static/views/types.js → config/plugins/visualizations/charts/static/client/views/types.js

@@ -33,7 +33,7 @@ define( [ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs' ], function( Utils,
                     $el.append( $( self._templateThumbnailItem( {
                         id      : type_id,
                         title   : ( type.zoomable ? '<span class="fa fa-search-plus"/>' : '' ) + title + ' (' + type.library + ')',
-                        url     : repository_root + 'src/visualizations/' + self.app.split( type_id ) + '/logo.png'
+                        url     : repository_root + '/visualizations/' + self.app.split( type_id ) + '/logo.png'
                     })).tooltip( { title: type.description, placement: 'bottom' } ) );
                 }
             });
@@ -50,7 +50,7 @@ define( [ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs' ], function( Utils,
                     id          : type_id,
                     title       : ( type.zoomable ? '<span class="fa fa-search-plus"/>' : '' ) + type.title + ' (' + type.library + ')',
                     description : type.description || 'No description available.',
-                    url         : repository_root + 'src/visualizations/' + self.app.split( type_id ) + '/logo.png'
+                    url         : repository_root + '/visualizations/' + self.app.split( type_id ) + '/logo.png'
                 });
             });
             if ( index.length > 0 ) {

config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css

@@ -0,0 +1,14 @@
+.venntooltip {
+    position: absolute;
+    text-align: center;
+    width: 128px;
+    height: 22px;
+    background: #333;
+    color: #ddd;
+    border: 0px;
+    border-radius: 8px;
+    opacity: 0;
+}
+.venn-area > .label {
+    font-size: 1em;
+}