Client libs: move backbone down into /libs (not backbone/backbone); Webpack: move to non-entry vendor bundling for libraries, clean up assoc.

client/galaxy/scripts/galaxy-app-base.js

@@ -1,16 +1,12 @@
 define([
     'libs/underscore',
-    'libs/backbone/backbone',
+    'libs/backbone',
     'mvc/base-mvc',
     'mvc/user/user-model',
     'utils/metrics-logger',
     'utils/add-logging',
     'utils/localization'
 ], function( _, Backbone, BASE_MVC, userModel, metricsLogger, addLogging, localize ){
-    console.debug( 'app-base id', jQuery.id );
-    if( !jQuery.id ){
-        jQuery.id = 'app-base';
-    }
 
 // TODO: move into a singleton pattern and have dependents import Galaxy
 // ============================================================================

client/galaxy/scripts/galaxy.base.js

@@ -569,8 +569,7 @@ function init_refresh_on_change () {
         .click( function() {
             return confirm( $(this).attr("confirm") );
         });
-};
-
+}
 
 // jQuery plugin to prevent double submission of forms
 // Ref: http://stackoverflow.com/questions/2830542/prevent-double-submission-of-forms-in-jquery
@@ -632,3 +631,15 @@ $(document).ready( function() {
     });
 
 });
+
+// globals from this file
+// TODO: move to not globals from this file
+window.obj_length = obj_length;
+window.make_popupmenu = make_popupmenu;
+window.make_popup_menus = make_popup_menus;
+window.replace_big_select_inputs = replace_big_select_inputs;
+window.async_save_text = async_save_text;
+window.commatize = commatize;
+window.reset_tool_search = reset_tool_search;
+window.GalaxyAsync = GalaxyAsync;
+window.init_refresh_on_change = init_refresh_on_change;

client/galaxy/scripts/galaxy.panels.js

@@ -1,4 +1,14 @@
-!function( exports, $ ){
+// HACK: add these to global scope until we stop asking for them there...
+// Via webpack: these are required here automatically by the provider plugin
+// Via script tag: these are redundant (identities) since they're already global
+window[ 'jQuery' ] = jQuery; // a weird form to prevent webpack from sub'ing 'window.jQuery' in the provider plugin
+window.$ = jQuery;
+window._ = _;
+window.Backbone = Backbone;
+window.Handlebars = Handlebars;
+console.debug('globals loaded:', window.jQuery, window.Backbone, '...');
+
+!function( exports ){
 
 "use strict"
 
@@ -86,7 +96,7 @@ $.extend( Panel.prototype, {
         }
     },
     force_panel: function( op ) {
-        if ( ( this.hidden && op == 'show' ) || ( ! this.hidden && op == 'hide' ) ) { 
+        if ( ( this.hidden && op == 'show' ) || ( ! this.hidden && op == 'hide' ) ) {
             this.do_toggle();
         }
     },
@@ -166,7 +176,7 @@ $.extend( Modal.prototype, {
         // Body
         var body = options.body;
         if ( body == "progress" ) {
-            body = $("<div class='progress progress-striped active'><div class='progress-bar' style='width: 100%'></div></div>"); 
+            body = $("<div class='progress progress-striped active'><div class='progress-bar' style='width: 100%'></div></div>");
         }
         this.$body.html( body );
     },
@@ -184,12 +194,12 @@ $.extend( Modal.prototype, {
             this.$body.css( "min-width", this.$body.width() );
             // Set max-height so that modal does not exceed window size and is in middle of page.
             // TODO: this could perhaps be handled better using CSS.
-            this.$body.css( "max-height", 
-                            $(window).height() - 
-                            this.$footer.outerHeight() - 
+            this.$body.css( "max-height",
+                            $(window).height() -
+                            this.$footer.outerHeight() -
                             this.$header.outerHeight() -
-                            parseInt( this.$dialog.css( "padding-top" ), 10 ) - 
-                            parseInt( this.$dialog.css( "padding-bottom" ), 10 ) 
+                            parseInt( this.$dialog.css( "padding-top" ), 10 ) -
+                            parseInt( this.$dialog.css( "padding-bottom" ), 10 )
                             );
         }
         // Callback on init
@@ -284,4 +294,4 @@ exports.show_message = show_message;
 exports.show_in_overlay = show_in_overlay;
 exports.user_changed = user_changed;
 
-}( window, window.jQuery );
+}( window );

client/galaxy/scripts/libs/common-libs.js

@@ -15,7 +15,7 @@ require( './bootstrap' );
 // MVC via backbone
 var _ = require( './underscore' );
 window._ = _;
-var Backbone = require( './backbone/backbone' );
+var Backbone = require( './backbone' );
 window.Backbone = Backbone;
 var Handlebars = require( './handlebars.runtime' );
 window.Handlebars = Handlebars;

client/galaxy/scripts/mvc/base-mvc.js

@@ -1,6 +1,6 @@
 define([
     'libs/underscore',
-    'libs/backbone/backbone',
+    'libs/backbone',
     'utils/add-logging',
     'utils/localization'
 ], function( _, Backbone, addLogging, _l ){

client/galaxy/scripts/mvc/user/user-model.js

@@ -1,6 +1,6 @@
 define([
     'libs/underscore',
-    'libs/backbone/backbone',
+    'libs/backbone',
     "mvc/base-mvc",
     "utils/localization"
 ], function( _, Backbone, baseMVC, _l ){

client/grunt-tasks/install-libs.js

@@ -16,7 +16,7 @@ module.exports = function( grunt ){
             'ravenjs':        [ 'dist/raven.js', 'raven.js' ],
             'underscore':     [ 'underscore.js', 'underscore.js' ],
             'handlebars':     [ 'handlebars.runtime.js', 'handlebars.runtime.js' ],
-            'backbone':       [ 'backbone.js', 'backbone/backbone.js' ],
+            'backbone':       [ 'backbone.js', 'backbone.js' ],
             'requirejs':      [ 'require.js', 'require.js' ],
             'd3':             [ 'd3.js', 'd3.js' ],
             'bib2json':       [ 'Parser.js', 'bibtex.js' ],

client/webpack.config.js

@@ -3,18 +3,35 @@ var webpack = require( 'webpack' ),
     path = require( 'path' ),
     scriptsBase = path.join( __dirname, 'galaxy/scripts' ),
     libsBase = path.join( scriptsBase, 'libs' ),
-    // chunks
-    CommonsChunkPlugin = new webpack.optimize.CommonsChunkPlugin( 'common.js' );
+    // libraries used on almost every page
+    // TODO: reduce
+    commonLibs = [
+        // jquery et al
+        'jquery',
+        'libs/jquery/jquery.migrate',
+        'libs/jquery/select2',
+        'libs/jquery/jquery.event.hover',
+        'libs/jquery/jquery.form',
+        'libs/jquery/jquery.rating',
+        'libs/jquery.sparklines',
+        'libs/bootstrap',
+        // // mvc
+        'libs/underscore',
+        'libs/backbone',
+        'libs/handlebars.runtime',
+        // // all pages get these
+        'galaxy.base',
+        'galaxy.panels',
+        'galaxy.autocom_tagging'
+    ];
 
 
 module.exports = {
     devtool : 'source-map',
     entry   : {
-        galaxy      : './galaxy/scripts/apps/galaxy.js',
-        // remove when these are no longer needed from any pages
-        libs        : './galaxy/scripts/apps/libs.js',
-        analysis    : './galaxy/scripts/apps/analysis.js',
-        history     : './galaxy/scripts/apps/history-app.js'
+        galaxy  : './galaxy/scripts/apps/galaxy.js',
+        analysis: './galaxy/scripts/apps/analysis.js',
+        vendor  : commonLibs
     },
     output  : {
         path        : '../static/scripts/bundled',
@@ -28,14 +45,26 @@ module.exports = {
             jquery      : path.join( libsBase, 'jquery/jquery' ),
             underscore  : path.join( libsBase, 'underscore.js' ),
             // we import these (for now) from the libs dir
-            'libs/underscore'       : path.join( libsBase, 'underscore.js' ),
-            'libs/backbone/backbone': path.join( libsBase, 'backbone/backbone.js' ),
+            // TODO:?? needed?
+            'libs/underscore'   : path.join( libsBase, 'underscore.js' ),
+            'libs/backbone'     : path.join( libsBase, 'backbone.js' ),
             // requirejs' i18n doesn't play well with webpack
             // note: strangely, order does matter here - this must come before utils below
             'utils/localization' : path.join( scriptsBase, 'utils/webpack-localization' ),
         }
     },
     plugins : [
-        CommonsChunkPlugin
+        new webpack.optimize.CommonsChunkPlugin( 'vendor', 'vendor.bundled.js' ),
+        // this plugin allows using the following keys/globals in scripts (w/o req'ing them first)
+        // and webpack will automagically require them in the bundle for you
+        new webpack.ProvidePlugin({
+            $:                  'jquery',
+            jQuery:             'jquery',
+            'window.jQuery':    'jquery',
+            _:                  "underscore",
+            Backbone:           'libs/backbone',
+            Handlebars:         'libs/handlebars.runtime'
+        }),
+        // new webpack.optimize.LimitChunkCountPlugin({ maxChunks: 1 })
     ]
 };

static/maps/galaxy-app-base.js.map

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@@ -1 +1 @@
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+{"version":3,"file":"user-model.js","sources":["../../../src/mvc/user/user-model.js"],"names":["define","_","Backbone","baseMVC","_l","logNamespace","User","Model","extend","LoggableMixin","_logNamespace","urlRoot","Galaxy","options","root","defaults","id","username","email","total_disk_usage","nice_total_disk_usage","quota_percent","is_admin","initialize","data","this","log","on","model","resp","changes","isAnonymous","get","isAdmin","loadFromApi","idOrCurrent","CURRENT_ID_STR","userFn","success","newModel","response","trigger","url","prototype","fetch","call","clearSessionStorage","key","sessionStorage","indexOf","removeItem","toString","userInfo","unshift","push","join","getCurrentUserFromApi","currentUser","Collection"],"mappings":"AAAAA,QACI,kBACA,gBACA,eACA,sBACD,SAAUC,EAAGC,EAAUC,EAASC,GAEnC,GAAIC,GAAe,OAKfC,EAAOJ,EAASK,MAAMC,OAAQL,EAAQM,eAAgBD,QAEtDE,cAAgBL,EAGhBM,QAAU,WAAY,MAAOC,QAAOC,QAAQC,KAAO,aAMnDC,UACIC,GAA0B,KAC1BC,SAA0B,IAAMb,EAAI,kBAAqB,IACzDc,MAA0B,GAC1BC,iBAA0B,EAC1BC,sBAA0B,GAC1BC,cAA0B,KAC1BC,UAA0B,GAM9BC,WAAa,SAAUC,GACnBC,KAAKC,IAAK,mBAAoBF,GAE9BC,KAAKE,GAAI,SAAU,SAAUC,EAAOC,GAAQJ,KAAKC,IAAKD,KAAO,eAAgBG,EAAOC,KACpFJ,KAAKE,GAAI,SAAU,SAAUC,EAAOJ,GAAQC,KAAKC,IAAKD,KAAO,gBAAiBG,EAAOJ,EAAKM,YAG9FC,YAAc,WACV,OAAUN,KAAKO,IAAK,UAGxBC,QAAU,WACN,MAASR,MAAKO,IAAK,aAUvBE,YAAc,SAAUC,EAAatB,GACjCsB,EAAcA,GAAe7B,EAAK8B,eAElCvB,EAAUA,KACV,IAAIe,GAAQH,KACRY,EAASxB,EAAQyB,OAYrB,OATAzB,GAAQyB,QAAU,SAAUC,EAAUC,GAClCZ,EAAMa,QAAS,SAAUF,EAAUC,GAC/BH,GAAUA,EAAQE,EAAUC,IAIhCL,IAAgB7B,EAAK8B,iBACrBvB,EAAQ6B,IAAMjB,KAAKd,QAAU,IAAML,EAAK8B,gBAErClC,EAASK,MAAMoC,UAAUC,MAAMC,KAAMpB,KAAMZ,IAKtDiC,oBAAsB,WAClB,IAAK,GAAIC,KAAOC,gBAGsB,IAA9BD,EAAIE,QAAS,YACbD,eAAeE,WAAYH,GAEZ,kBAARA,GACPC,eAAeE,WAAYH,IAMvCI,SAAW,WACP,GAAIC,IAAa3B,KAAKO,IAAK,YAK3B,OAJIP,MAAKO,IAAK,QACVoB,EAASC,QAAS5B,KAAKO,IAAK,OAC5BoB,EAASE,KAAM7B,KAAKO,IAAK,WAEtB,QAAUoB,EAASG,KAAM,KAAQ,MAKhDjD,GAAK8B,eAAiB,UAGtB9B,EAAKkD,sBAAwB,SAAU3C,GACnC,GAAI4C,GAAc,GAAInD,EAEtB,OADAmD,GAAYvB,YAAa5B,EAAK8B,eAAgBvB,GACvC4C,EAIUvD,GAASwD,WAAWlD,OAAQL,EAAQM,eAAgBD,QACrEoB,MAAUtB,EACVK,QAAU,WAAY,MAAOC,QAAOC,QAAQC,KAAO,cAMvD,QACIR,KAAOA"}

static/scripts/galaxy-app-base.js

@@ -1,2 +1,104 @@
-define(["libs/underscore","libs/backbone/backbone","mvc/base-mvc","mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(a,b,c,d,e,f,g){function h(a,b){console.debug("GalaxyApp:",a,b);var c=this;return c._init(a||{},b||{})}console.debug("app-base id",jQuery.id),jQuery.id||(jQuery.id="app-base"),f(h,"GalaxyApp");var i="galaxy:debug",j=i+":namespaces",k=!1;try{k="true"==localStorage.getItem(i)}catch(l){console.log(g("localStorage not available for debug flag retrieval"))}return h.prototype._init=function(c,d){var e=this;return a.extend(e,b.Events),k&&(e.logger=console),e._processOptions(c),e.debug("GalaxyApp.options: ",e.options),e.root=c.root||"/",e._initConfig(c.config||d.config||{}),e.debug("GalaxyApp.config: ",e.config),e._patchGalaxy(window.Galaxy),e._initLogger(e.options.loggerOptions||{}),e.debug("GalaxyApp.logger: ",e.logger),e._initLocale(),e.debug("GalaxyApp.localize: ",e.localize),e.config=c.config||{},e.debug("GalaxyApp.config: ",e.config),e._initUser(c.user||{}),e.debug("GalaxyApp.user: ",e.user),e._setUpListeners(),e.trigger("ready",e),e},h.prototype.defaultOptions={patchExisting:!0,root:"/"},h.prototype._processOptions=function(a){var b=this,c=b.defaultOptions;b.debug("_processOptions: ",a),b.options={};for(var d in c)c.hasOwnProperty(d)&&(b.options[d]=a.hasOwnProperty(d)?a[d]:c[d]);return b},h.prototype._initConfig=function(a){var b=this;return b.debug("_initConfig: ",a),b.config=a,b.config.debug=k||b.config.debug,b},h.prototype._patchGalaxy=function(a){var b=this;if(b.options.patchExisting&&a){b.debug("found existing Galaxy object:",a);for(var c in a)a.hasOwnProperty(c)&&(b.debug("	 patching in "+c+" to Galaxy"),b[c]=a[c])}},h.prototype._initLogger=function(a){var b=this;if(b.config.debug){a.consoleLogger=a.consoleLogger||console,a.consoleLevel=a.consoleLevel||e.MetricsLogger.ALL;try{a.consoleNamespaceWhitelist=localStorage.getItem(j).split(",")}catch(d){}}return b.debug("_initLogger:",a),b.logger=new e.MetricsLogger(a),b.config.debug&&(c.LoggableMixin.logger=b.logger),b},h.prototype._initLocale=function(a){var b=this;return b.debug("_initLocale:",a),b.localize=g,window._l=b.localize,b},h.prototype._initUser=function(a){var b=this;return b.debug("_initUser:",a),b.user=new d.User(a),b.user.logger=b.logger,b.currUser=b.user,b},h.prototype._setUpListeners=function(){var a=this;return a.lastAjax={},$(document).bind("ajaxSend",function(b,c,d){var e=d.data;try{e=JSON.parse(e)}catch(f){}a.lastAjax={url:location.href.slice(0,-1)+d.url,data:e}}),a},h.prototype.debugging=function(a){var b=this;try{if(void 0===a)return"true"===localStorage.getItem(i);if(a)return localStorage.setItem(i,!0),!0;localStorage.removeItem(i),b.debuggingNamespaces(null)}catch(c){console.log(g("localStorage not available for debug flag retrieval"))}return!1},h.prototype.debuggingNamespaces=function(a){var b=this;try{if(void 0===a){var c=localStorage.getItem(j);return"string"==typeof c?c.split(","):[]}null===a?localStorage.removeItem(j):localStorage.setItem(j,a);var d=b.debuggingNamespaces();return b.logger&&(b.logger.options.consoleNamespaceWhitelist=d),d}catch(e){console.log(g("localStorage not available for debug namespace retrieval"))}},h.prototype.toString=function(){var a=this.user?this.user.get("email")||"(anonymous)":"uninitialized";return"GalaxyApp("+a+")"},{GalaxyApp:h}});
-//# sourceMappingURL=../maps/galaxy-app-base.js.map
+define([ "libs/underscore", "libs/backbone", "mvc/base-mvc", "mvc/user/user-model", "utils/metrics-logger", "utils/add-logging", "utils/localization" ], function(_, Backbone, BASE_MVC, userModel, metricsLogger, addLogging, localize) {
+    function GalaxyApp(options, bootstrapped) {
+        console.debug("GalaxyApp:", options, bootstrapped);
+        var self = this;
+        return self._init(options || {}, bootstrapped || {});
+    }
+    addLogging(GalaxyApp, "GalaxyApp");
+    var DEBUGGING_KEY = "galaxy:debug", NAMESPACE_KEY = DEBUGGING_KEY + ":namespaces", localDebugging = !1;
+    try {
+        localDebugging = "true" == localStorage.getItem(DEBUGGING_KEY);
+    } catch (storageErr) {
+        console.log(localize("localStorage not available for debug flag retrieval"));
+    }
+    return GalaxyApp.prototype._init = function(options, bootstrapped) {
+        var self = this;
+        return _.extend(self, Backbone.Events), localDebugging && (self.logger = console), 
+        self._processOptions(options), self.debug("GalaxyApp.options: ", self.options), 
+        self.root = options.root || "/", self._initConfig(options.config || bootstrapped.config || {}), 
+        self.debug("GalaxyApp.config: ", self.config), self._patchGalaxy(window.Galaxy), 
+        self._initLogger(self.options.loggerOptions || {}), self.debug("GalaxyApp.logger: ", self.logger), 
+        self._initLocale(), self.debug("GalaxyApp.localize: ", self.localize), self.config = options.config || {}, 
+        self.debug("GalaxyApp.config: ", self.config), self._initUser(options.user || {}), 
+        self.debug("GalaxyApp.user: ", self.user), self._setUpListeners(), self.trigger("ready", self), 
+        self;
+    }, GalaxyApp.prototype.defaultOptions = {
+        patchExisting: !0,
+        root: "/"
+    }, GalaxyApp.prototype._processOptions = function(options) {
+        var self = this, defaults = self.defaultOptions;
+        self.debug("_processOptions: ", options), self.options = {};
+        for (var k in defaults) defaults.hasOwnProperty(k) && (self.options[k] = options.hasOwnProperty(k) ? options[k] : defaults[k]);
+        return self;
+    }, GalaxyApp.prototype._initConfig = function(config) {
+        var self = this;
+        return self.debug("_initConfig: ", config), self.config = config, self.config.debug = localDebugging || self.config.debug, 
+        self;
+    }, GalaxyApp.prototype._patchGalaxy = function(patchWith) {
+        var self = this;
+        if (self.options.patchExisting && patchWith) {
+            self.debug("found existing Galaxy object:", patchWith);
+            for (var k in patchWith) patchWith.hasOwnProperty(k) && (self.debug("	 patching in " + k + " to Galaxy"), 
+            self[k] = patchWith[k]);
+        }
+    }, GalaxyApp.prototype._initLogger = function(loggerOptions) {
+        var self = this;
+        if (self.config.debug) {
+            loggerOptions.consoleLogger = loggerOptions.consoleLogger || console, loggerOptions.consoleLevel = loggerOptions.consoleLevel || metricsLogger.MetricsLogger.ALL;
+            try {
+                loggerOptions.consoleNamespaceWhitelist = localStorage.getItem(NAMESPACE_KEY).split(",");
+            } catch (storageErr) {}
+        }
+        return self.debug("_initLogger:", loggerOptions), self.logger = new metricsLogger.MetricsLogger(loggerOptions), 
+        self.config.debug && (BASE_MVC.LoggableMixin.logger = self.logger), self;
+    }, GalaxyApp.prototype._initLocale = function(options) {
+        var self = this;
+        return self.debug("_initLocale:", options), self.localize = localize, window._l = self.localize, 
+        self;
+    }, GalaxyApp.prototype._initUser = function(userJSON) {
+        var self = this;
+        return self.debug("_initUser:", userJSON), self.user = new userModel.User(userJSON), 
+        self.user.logger = self.logger, self.currUser = self.user, self;
+    }, GalaxyApp.prototype._setUpListeners = function() {
+        var self = this;
+        return self.lastAjax = {}, $(document).bind("ajaxSend", function(ev, xhr, options) {
+            var data = options.data;
+            try {
+                data = JSON.parse(data);
+            } catch (err) {}
+            self.lastAjax = {
+                url: location.href.slice(0, -1) + options.url,
+                data: data
+            };
+        }), self;
+    }, GalaxyApp.prototype.debugging = function(setting) {
+        var self = this;
+        try {
+            if (void 0 === setting) return "true" === localStorage.getItem(DEBUGGING_KEY);
+            if (setting) return localStorage.setItem(DEBUGGING_KEY, !0), !0;
+            localStorage.removeItem(DEBUGGING_KEY), self.debuggingNamespaces(null);
+        } catch (storageErr) {
+            console.log(localize("localStorage not available for debug flag retrieval"));
+        }
+        return !1;
+    }, GalaxyApp.prototype.debuggingNamespaces = function(namespaces) {
+        var self = this;
+        try {
+            if (void 0 === namespaces) {
+                var csv = localStorage.getItem(NAMESPACE_KEY);
+                return "string" == typeof csv ? csv.split(",") : [];
+            }
+            null === namespaces ? localStorage.removeItem(NAMESPACE_KEY) : localStorage.setItem(NAMESPACE_KEY, namespaces);
+            var newSettings = self.debuggingNamespaces();
+            return self.logger && (self.logger.options.consoleNamespaceWhitelist = newSettings), 
+            newSettings;
+        } catch (storageErr) {
+            console.log(localize("localStorage not available for debug namespace retrieval"));
+        }
+    }, GalaxyApp.prototype.toString = function() {
+        var userEmail = this.user ? this.user.get("email") || "(anonymous)" : "uninitialized";
+        return "GalaxyApp(" + userEmail + ")";
+    }, {
+        GalaxyApp: GalaxyApp
+    };
+});

static/scripts/libs/common-libs.js

@@ -1,2 +1,2 @@
-var jquery=require("jquery");window.jQuery=window.$=jquery,require("./jquery/jquery.migrate"),require("./jquery/select2"),require("./jquery/jquery.event.hover"),require("./jquery/jquery.form"),require("./jquery/jquery.rating"),require("./jquery.sparklines"),require("./bootstrap");var _=require("./underscore");window._=_;var Backbone=require("./backbone/backbone");window.Backbone=Backbone;var Handlebars=require("./handlebars.runtime");window.Handlebars=Handlebars,require("../galaxy.base"),require("../galaxy.panels"),require("../galaxy.autocom_tagging"),exports.jquery=jquery,exports._=_,exports.Backbone=Backbone,exports.Handlebars=Handlebars;
+var jquery=require("jquery");window.jQuery=window.$=jquery,require("./jquery/jquery.migrate"),require("./jquery/select2"),require("./jquery/jquery.event.hover"),require("./jquery/jquery.form"),require("./jquery/jquery.rating"),require("./jquery.sparklines"),require("./bootstrap");var _=require("./underscore");window._=_;var Backbone=require("./backbone");window.Backbone=Backbone;var Handlebars=require("./handlebars.runtime");window.Handlebars=Handlebars,require("../galaxy.base"),require("../galaxy.panels"),require("../galaxy.autocom_tagging"),exports.jquery=jquery,exports._=_,exports.Backbone=Backbone,exports.Handlebars=Handlebars;
 //# sourceMappingURL=../../maps/libs/common-libs.js.map

static/scripts/mvc/user/user-model.js

@@ -1,2 +1,2 @@
-define(["libs/underscore","libs/backbone/backbone","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e="user",f=b.Model.extend(c.LoggableMixin).extend({_logNamespace:e,urlRoot:function(){return Galaxy.options.root+"api/users"},defaults:{id:null,username:"("+d("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null,is_admin:!1},initialize:function(a){this.log("User.initialize:",a),this.on("loaded",function(a,b){this.log(this+" has loaded:",a,b)}),this.on("change",function(a,b){this.log(this+" has changed:",a,b.changes)})},isAnonymous:function(){return!this.get("email")},isAdmin:function(){return this.get("is_admin")},loadFromApi:function(a,c){a=a||f.CURRENT_ID_STR,c=c||{};var d=this,e=c.success;return c.success=function(a,b){d.trigger("loaded",a,b),e&&e(a,b)},a===f.CURRENT_ID_STR&&(c.url=this.urlRoot+"/"+f.CURRENT_ID_STR),b.Model.prototype.fetch.call(this,c)},clearSessionStorage:function(){for(var a in sessionStorage)0===a.indexOf("history:")?sessionStorage.removeItem(a):"history-panel"===a&&sessionStorage.removeItem(a)},toString:function(){var a=[this.get("username")];return this.get("id")&&(a.unshift(this.get("id")),a.push(this.get("email"))),"User("+a.join(":")+")"}});f.CURRENT_ID_STR="current",f.getCurrentUserFromApi=function(a){var b=new f;return b.loadFromApi(f.CURRENT_ID_STR,a),b};b.Collection.extend(c.LoggableMixin).extend({model:f,urlRoot:function(){return Galaxy.options.root+"api/users"}});return{User:f}});
+define(["libs/underscore","libs/backbone","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e="user",f=b.Model.extend(c.LoggableMixin).extend({_logNamespace:e,urlRoot:function(){return Galaxy.options.root+"api/users"},defaults:{id:null,username:"("+d("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null,is_admin:!1},initialize:function(a){this.log("User.initialize:",a),this.on("loaded",function(a,b){this.log(this+" has loaded:",a,b)}),this.on("change",function(a,b){this.log(this+" has changed:",a,b.changes)})},isAnonymous:function(){return!this.get("email")},isAdmin:function(){return this.get("is_admin")},loadFromApi:function(a,c){a=a||f.CURRENT_ID_STR,c=c||{};var d=this,e=c.success;return c.success=function(a,b){d.trigger("loaded",a,b),e&&e(a,b)},a===f.CURRENT_ID_STR&&(c.url=this.urlRoot+"/"+f.CURRENT_ID_STR),b.Model.prototype.fetch.call(this,c)},clearSessionStorage:function(){for(var a in sessionStorage)0===a.indexOf("history:")?sessionStorage.removeItem(a):"history-panel"===a&&sessionStorage.removeItem(a)},toString:function(){var a=[this.get("username")];return this.get("id")&&(a.unshift(this.get("id")),a.push(this.get("email"))),"User("+a.join(":")+")"}});f.CURRENT_ID_STR="current",f.getCurrentUserFromApi=function(a){var b=new f;return b.loadFromApi(f.CURRENT_ID_STR,a),b};b.Collection.extend(c.LoggableMixin).extend({model:f,urlRoot:function(){return Galaxy.options.root+"api/users"}});return{User:f}});
 //# sourceMappingURL=../../../maps/mvc/user/user-model.js.map

templates/base.mako

@@ -46,9 +46,8 @@
 
     ${h.js(
         'libs/require',
-        'bundled/common',
         ## TODO: remove when all libs are required directly in modules
-        'bundled/libs.bundled'
+        'bundled/vendor.bundled',
     )}
 
     <script type="text/javascript">
@@ -83,9 +82,8 @@
                 "libs/underscore": {
                     exports: "_"
                 },
-                "libs/backbone/backbone": {
+                "libs/backbone": {
                     deps: [ 'jquery', 'libs/underscore' ],
-                    // deps: [ 'libs/underscore' ],
                     exports: "Backbone"
                 }
             },

templates/base/base_panels.mako

@@ -52,9 +52,8 @@
 
     ${h.js(
         'libs/require',
-        'bundled/common',
         ## TODO: remove when all libs are required directly in modules
-        'bundled/libs.bundled'
+        'bundled/vendor.bundled'
     )}
 
     <script type="text/javascript">
@@ -91,9 +90,8 @@
                 "libs/underscore": {
                     exports: "_"
                 },
-                "libs/backbone/backbone": {
+                "libs/backbone": {
                     deps: [ 'jquery', 'libs/underscore' ],
-                    // deps: [ 'libs/underscore' ],
                     exports: "Backbone"
                 }
             },

templates/js-app.mako

@@ -29,9 +29,7 @@
     </head>
 
     <body>
-        <script type="text/javascript" src="/static/scripts/bundled/common.js"></script>
-        ## TODO: remove when all libs are required directly in modules
-        <script type="text/javascript" src="/static/scripts/bundled/libs.bundled.js"></script>
+        <script type="text/javascript" src="/static/scripts/bundled/vendor.bundled.js"></script>
         <script type="text/javascript" src="/static/scripts/bundled/galaxy.bundled.js"></script>
         <script type="text/javascript">
             window.Galaxy = new GalaxyApp(

templates/webapps/galaxy/dataset/display.mako

@@ -12,7 +12,7 @@
         require.config({
             baseUrl: "${h.url_for('/static/scripts')}",
             shim: {
-                "libs/backbone/backbone": { exports: "Backbone" },
+                "libs/backbone": { exports: "Backbone" },
             },
             urlArgs: 'v=${app.server_starttime}'
         });

templates/webapps/galaxy/dataset/tabular_chunked.mako

@@ -11,7 +11,7 @@
         require.config({
             baseUrl: "${h.url_for('/static/scripts')}",
             shim: {
-                "libs/backbone/backbone": { exports: "Backbone" },
+                "libs/backbone": { exports: "Backbone" },
             },
             urlArgs: 'v=${app.server_starttime}'
         });

templates/webapps/galaxy/galaxy.panels.mako

@@ -25,16 +25,46 @@
     self.galaxy_config.update(config)
 %>
 
+<%def name="stylesheets()">
+   ## load default style
+   ${h.css("base")}
+
+   ## modify default style
+    <style type="text/css">
+    #center {
+        %if not self.galaxy_config['left_panel']:
+            left: 0 !important;
+        %endif
+        %if not self.galaxy_config['right_panel']:
+            right: 0 !important;
+        %endif
+    }
+    </style>
+
+    <style type="text/css">
+        %if self.galaxy_config['message_box']:
+            #left, #left-border, #center, #right-border, #right {
+                top: 64px;
+            }
+        %endif
+    </style>
+
+</%def>
+
 <%def name="javascripts()">
 
     ## load jscript libraries
     ${h.js(
-        'libs/jquery/jquery-ui',
-        'libs/d3',
-        'libs/require',
-        'bundled/common',
         ## TODO: remove when all libs are required directly in modules
-        'bundled/libs.bundled'
+        'bundled/vendor.bundled',
+    )}
+    <script type="text/javascript">
+        console.debug( 'jQuery:', jQuery )
+    </script>
+    ${h.js(
+       'libs/jquery/jquery-ui',
+       'libs/d3',
+       'libs/require',
     )}
 
     ## send errors to Sntry server if configured
@@ -62,27 +92,6 @@
         };
     </script>
 
-    ## load default style
-    ${h.css("base")}
-
-    ## modify default style
-    <style type="text/css">
-    #center {
-        %if not self.galaxy_config['left_panel']:
-            left: 0 !important;
-        %endif
-            %if not self.galaxy_config['right_panel']:
-            right: 0 !important;
-        %endif
-    }
-    %if self.galaxy_config['message_box']:
-        #left, #left-border, #center, #right-border, #right
-        {
-            top: 64px;
-        }
-    %endif
-    </style>
-
     ## default script wrapper
     <script type="text/javascript">
         ## configure require
@@ -92,14 +101,18 @@
             baseUrl: "${h.url_for('/static/scripts') }",
             shim: {
                 "libs/underscore": { exports: "_" },
+                "libs/backbone": {
+                    deps: [ 'jquery', 'libs/underscore' ],
+                    exports: "Backbone"
+                },
                 "libs/d3": { exports: "d3" },
-                "libs/backbone/backbone": { exports: "Backbone" },
             },
             urlArgs: 'v=${app.server_starttime}'
         });
         var galaxy_config = ${ h.dumps( self.galaxy_config ) };
 
     </script>
+
 </%def>
 
 <%def name="javascript_app()">
@@ -170,7 +183,7 @@
         ## force IE to standards mode, and prefer Google Chrome Frame if the user has already installed it
         <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1">
 
-        ## load scripts
+        ${self.stylesheets()}
         ${self.javascripts()}
         ${self.javascript_app()}
     </head>

templates/webapps/galaxy/visualization/display.mako

@@ -7,13 +7,13 @@
     <script type='text/javascript'>
         $(function() {
             // HACK: add bookmarks container and header.
-            $('#right > .unified-panel-body > div').append( 
+            $('#right > .unified-panel-body > div').append(
                 $('<div/>').attr('id', 'bookmarks-container')
                 .append( $('<h4/>').text('Bookmarks') )
             );
         });
     </script>
-    
+
     <!--[if lt IE 9]>
       <script type='text/javascript' src="${h.url_for('/static/scripts/libs/IE/excanvas.js')}"></script>
     <![endif]-->
@@ -21,7 +21,7 @@
 
 <%def name="stylesheets()">
     ${parent.stylesheets()}
-    
+
     ## Style changes needed for display.
     <style type="text/css">
         .page-body {
@@ -41,7 +41,7 @@
 </%def>
 
 <%def name="render_item_links( visualization )">
-    <a 
+    <a
         href="${h.url_for( controller='/visualization', action='imp', id=trans.security.encode_id( visualization.id ) )}"
         class="icon-button import"
         ## Needed to overwide initial width so that link is floated left appropriately.
@@ -53,11 +53,11 @@
     <div id="${trans.security.encode_id( visualization.id )}" class="unified-panel-body" style="overflow:none;top:0px;"></div>
 
     <script type="text/javascript">
-        require.config({ 
+        require.config({
             baseUrl: "${h.url_for('/static/scripts') }",
             shim: {
                 "libs/underscore": { exports: "_" },
-                "libs/backbone/backbone": { exports: "Backbone" },
+                "libs/backbone": { exports: "Backbone" },
             },
             urlArgs: 'v=${app.server_starttime}'
         });
@@ -65,13 +65,13 @@
 
             // FIXME: deliberate global required for now due to requireJS integration.
             view = null;
-            
+
             var ui = new (trackster.TracksterUI)( "${h.url_for('/')}" )
                 container_element = $("#${trans.security.encode_id( visualization.id )}");
 
             $(function() {
                 var is_embedded = (container_element.parents(".item-content").length > 0);
-                
+
                 // HTML setup.
                 if (is_embedded) {
                     container_element.css( { "position": "relative" } );
@@ -87,17 +87,17 @@
                 view = ui.create_visualization( {
                                                 container: container_element,
                                                 name: "${config.get('title') | h}",
-                                                vis_id: "${config.get('vis_id')}", 
+                                                vis_id: "${config.get('vis_id')}",
                                                 dbkey: "${config.get('dbkey')}"
-                                             }, 
+                                             },
                                              ${ h.dumps( config.get( 'viewport', dict() ) ) },
                                              ${ h.dumps( config['tracks'] ) },
                                              ${ h.dumps( config.get('bookmarks') ) }
                                              );
-                
+
                 // Set up keyboard navigation.
                 ui.init_keyboard_nav(view);
-                
+
                 // HACK: set viewport height because it cannot be set automatically. Currently, max height for embedded
                 // elts is 25em, so use 20em.
                 view.viewport_container.height("20em");

templates/webapps/galaxy/visualization/sweepster.mako

@@ -108,14 +108,14 @@
 
     ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form" )}
     ${h.js( "libs/require", "libs/jquery/jquery-ui" )}
-    
+
     <script type="text/javascript">
-        require.config({ 
+        require.config({
                 baseUrl: "${h.url_for('/static/scripts')}",
                 shim: {
                     "libs/underscore": { exports: "_" },
                     "libs/d3": { exports: "d3" },
-                    "libs/backbone/backbone": { exports: "Backbone" },
+                    "libs/backbone": { exports: "Backbone" },
                 },
                 urlArgs: 'v=${app.server_starttime}'
         });
@@ -123,8 +123,8 @@
         require(["libs/d3", "viz/sweepster"], function(d3, sweepster) {
 
             var viz;
-            $(function() {            
-                // -- Viz set up. --    
+            $(function() {
+                // -- Viz set up. --
                 var viz = new sweepster.SweepsterVisualization(
                     ${ h.dumps( config )}
                 );