Replace Backbone-relational usage with manually model chaining and remove backbone-relational scripts. Fix default colors bug in Trackster. Pack scripts.

2026-09-24 16:30:27 +08:00 · 2013-11-26 14:50:41 -05:00
parent 0aa108206e
commit b675432a2c
33 changed files with 93 additions and 2056 deletions
@@ -3,7 +3,7 @@
 */

 // dependencies
-define(["galaxy.masthead", "libs/backbone/backbone-relational"], function(mod_masthead) {
+define(["galaxy.masthead"], function(mod_masthead) {

 // frame manager
 var GalaxyFrame = Backbone.View.extend(
@@ -3,7 +3,7 @@
 */

 // dependencies
-define(["utils/galaxy.utils", "libs/backbone/backbone-relational"], function(mod_utils) {
+define(["utils/galaxy.utils"], function(mod_utils) {

 // masthead
 var GalaxyMasthead = Backbone.View.extend(
@@ -3,7 +3,7 @@
 */

 // dependencies
-define(["galaxy.masthead", "libs/backbone/backbone-relational"], function(mod_masthead) {
+define(["galaxy.masthead"], function(mod_masthead) {

 // frame manager
 var GalaxyMenu = Backbone.Model.extend(
@@ -3,7 +3,7 @@
 */

 // dependencies
-define(["libs/backbone/backbone-relational"], function() {
+define([], function() {

 // frame manager
 var GalaxyModal = Backbone.View.extend(
@@ -3,7 +3,7 @@
 */

 // dependencies
-define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils", "utils/galaxy.uploadbox", "libs/backbone/backbone-relational"], function(mod_modal, mod_masthead, mod_utils) {
+define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils", "utils/galaxy.uploadbox"], function(mod_modal, mod_masthead, mod_utils) {

 // galaxy upload
 var GalaxyUpload = Backbone.View.extend(
@@ -2,7 +2,7 @@
 * Simple base model for any visible element. Includes useful attributes and ability
 * to set and track visibility.
 */
-var BaseModel = Backbone.RelationalModel.extend({
+var BaseModel = Backbone.Model.extend({
    defaults: {
        name: null,
        hidden: false
@@ -1,16 +1,16 @@
 // Additional dependencies: jQuery, underscore.
-define(["libs/backbone/backbone-relational"], function() {
+define([], function() {

 /**
 * Dataset metedata.
 */
-var DatasetMetadata = Backbone.RelationalModel.extend({});
+var DatasetMetadata = Backbone.Model.extend({});

 /**
 * A dataset. In Galaxy, datasets are associated with a history, so
 * this object is also known as a HistoryDatasetAssociation.
 */
-var Dataset = Backbone.RelationalModel.extend({
+var Dataset = Backbone.Model.extend({
    defaults: {
        id: '',
        type: '',
@@ -20,8 +20,8 @@ var Dataset = Backbone.RelationalModel.extend({
    },

    initialize: function() {
-        // FIXME: pass back a metadata dict and then Backbone-relational
-        // can be used unpack metadata automatically.
+        this._set_metadata();
+        
        // Update metadata on change.
        this.on('change', this._set_metadata, this);
    },
@@ -2,7 +2,7 @@
 * Model, view, and controller objects for Galaxy tools and tool panel.
 */

- define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/backbone/backbone-relational" ], 
+ define( ["libs/underscore", "viz/trackster/util", "mvc/data" ], 
         function(_, util, data) {

 /**
@@ -32,7 +32,7 @@ var VisibilityMixin = {
 /**
 * A tool parameter.
 */
-var ToolParameter = Backbone.RelationalModel.extend({
+var ToolParameter = Backbone.Model.extend({
    defaults: {
        name: null,
        label: null,
@@ -42,13 +42,6 @@ var ToolParameter = Backbone.RelationalModel.extend({
        num_samples: 5
    },

-    subModelTypes: {
-        'integer': 'IntegerToolParameter',
-        'float': 'FloatToolParameter',
-        'data': 'DataToolParameter',
-        'select': 'SelectToolParameter'
-    },
-    
    initialize: function() {
        this.attributes.html = unescape(this.attributes.html);
    },
@@ -62,20 +55,19 @@ var ToolParameter = Backbone.RelationalModel.extend({
    }
 });

-// In order to resolve subModelTypes for tool parameters, use a custom scope here rather
-// than polluting the global scope.
-var tools_scope = {};
-Backbone.Relational.store.addModelScope(tools_scope);
+var ToolParameterCollection = Backbone.Collection.extend({
+    model: ToolParameter
+});

 /**
 * A data tool parameter.
 */
-var DataToolParameter = tools_scope.DataToolParameter = ToolParameter.extend({});
+var DataToolParameter = ToolParameter.extend({});

 /**
 * An integer tool parameter.
 */
-var IntegerToolParameter = tools_scope.IntegerToolParameter = ToolParameter.extend({
+var IntegerToolParameter = ToolParameter.extend({
    set_value: function(value) {
        this.set('value', parseInt(value, 10));
    },
@@ -90,7 +82,7 @@ var IntegerToolParameter = tools_scope.IntegerToolParameter = ToolParameter.exte
    }
 });

-var FloatToolParameter = tools_scope.FloatToolParameter = IntegerToolParameter.extend({
+var FloatToolParameter = IntegerToolParameter.extend({
    set_value: function(value) {
        this.set('value', parseFloat(value));
    }
@@ -99,7 +91,7 @@ var FloatToolParameter = tools_scope.FloatToolParameter = IntegerToolParameter.e
 /** 
 * A select tool parameter.
 */
-var SelectToolParameter = tools_scope.SelectToolParameter = ToolParameter.extend({
+var SelectToolParameter = ToolParameter.extend({
    /**
     * Returns tool options.
     */
@@ -110,10 +102,18 @@ var SelectToolParameter = tools_scope.SelectToolParameter = ToolParameter.extend
    }
 });

+// Set up dictionary of parameter types.
+ToolParameter.subModelTypes = {
+    'integer': IntegerToolParameter,
+    'float': FloatToolParameter,
+    'data': DataToolParameter,
+    'select': SelectToolParameter
+};
+
 /**
 * A Galaxy tool.
 */
-var Tool = Backbone.RelationalModel.extend({
+var Tool = Backbone.Model.extend({
    // Default attributes.
    defaults: {
        id: null,
@@ -124,13 +124,14 @@ var Tool = Backbone.RelationalModel.extend({
        outputs: []
    },

-    relations: [
-        {
-            type: Backbone.HasMany,
-            key: 'inputs',
-            relatedModel: ToolParameter
-        }
-    ],
+    initialize: function(options) {
+
+        // Set parameters.
+        this.set('inputs', new ToolParameterCollection(_.map(options.inputs, function(p) {
+            var p_class = ToolParameter.subModelTypes[p.type] || ToolParameter;
+            return new p_class(p);
+        })));
+    },

    urlRoot: galaxy_config.root + 'api/tools',

@@ -1 +1 @@
-define(["galaxy.masthead","libs/backbone/backbone-relational"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({title:"Shared Data",content:"library/index"});g.addMenu({title:"Data Libraries",content:"library/index",divider:true});g.addMenu({title:"Published Histories",content:"history/list_published"});g.addMenu({title:"Published Workflows",content:"workflow/list_published"});g.addMenu({title:"Published Visualizations",content:"visualization/list_published"});g.addMenu({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({title:"Lab"});h.addMenu({title:"Sequencing Requests",content:"requests/index"});h.addMenu({title:"Find Samples",content:"requests/find_samples_index"});h.addMenu({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({title:"Visualization",content:"visualization/list"});k.addMenu({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.addMenu({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({title:"Cloud",content:"cloudlaunch/index"});e.addMenu({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({title:"Help"});if(this.options.biostar_url){j.addMenu({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.addMenu({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.addMenu({title:"Support",content:this.options.support_url,target:"_blank"});j.addMenu({title:"Search",content:this.options.search_url,target:"_blank"});j.addMenu({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.addMenu({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.addMenu({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.addMenu({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.addMenu({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedout-only"});if(this.options.allow_user_creation){i.addMenu({title:"Login",content:"user/login",target:"galaxy_main"})}if(this.options.allow_user_creation){i.addMenu({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedin-only"});i.addMenu({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.addMenu({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.addMenu({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.addMenu({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.addMenu({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.addMenu({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.addMenu({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.addMenu({title:"Saved Pages",content:"page/list",target:"_top"});i.addMenu({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.addMenu({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}}});return{GalaxyMenu:a}});
+define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({title:"Shared Data",content:"library/index"});g.addMenu({title:"Data Libraries",content:"library/index",divider:true});g.addMenu({title:"Published Histories",content:"history/list_published"});g.addMenu({title:"Published Workflows",content:"workflow/list_published"});g.addMenu({title:"Published Visualizations",content:"visualization/list_published"});g.addMenu({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({title:"Lab"});h.addMenu({title:"Sequencing Requests",content:"requests/index"});h.addMenu({title:"Find Samples",content:"requests/find_samples_index"});h.addMenu({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({title:"Visualization",content:"visualization/list"});k.addMenu({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.addMenu({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({title:"Cloud",content:"cloudlaunch/index"});e.addMenu({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({title:"Help"});if(this.options.biostar_url){j.addMenu({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.addMenu({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.addMenu({title:"Support",content:this.options.support_url,target:"_blank"});j.addMenu({title:"Search",content:this.options.search_url,target:"_blank"});j.addMenu({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.addMenu({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.addMenu({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.addMenu({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.addMenu({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedout-only"});if(this.options.allow_user_creation){i.addMenu({title:"Login",content:"user/login",target:"galaxy_main"})}if(this.options.allow_user_creation){i.addMenu({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedin-only"});i.addMenu({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.addMenu({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.addMenu({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.addMenu({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.addMenu({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.addMenu({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.addMenu({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.addMenu({title:"Saved Pages",content:"page/list",target:"_top"});i.addMenu({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.addMenu({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}}});return{GalaxyMenu:a}});
@@ -1 +1 @@
-define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{},initialize:function(b){if(b){this.create(b)}},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">&times;</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}});
+define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{},initialize:function(b){if(b){this.create(b)}},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">&times;</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}});
@@ -1 +1 @@
-var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null,"  ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},toggle:function(){if(this.HUAVOptions.$elementShown.is(":hidden")){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}else{if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this)}}}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}};
+var BaseModel=Backbone.Model.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null,"  ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},toggle:function(){if(this.HUAVOptions.$elementShown.is(":hidden")){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}else{if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this)}}}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}};
@@ -1 +1 @@
-var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey").val(galaxy_config.app.default_dbkey)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f=0;f<e.length;f++){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.prefs.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}});
+var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["viz/visualization","viz/trackster_ui"],function(a,b){var c=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(d){browser_router=new a.TrackBrowserRouter(d);Backbone.history.start()},view_existing:function(){var d=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:d.title,vis_id:d.vis_id,dbkey:d.dbkey},d.viewport,d.tracks,d.bookmarks,true);this.init_editor()},view_new:function(){var d=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:d.template_view_new(e),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){d.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey").val(galaxy_config.app.default_dbkey)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(d){var f='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var e=0;e<d.length;e++){f+='<option value="'+d[e][1]+'">'+d[e][0]+"</option>"}f+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return f},create_browser:function(e,d){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e,dbkey:d},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.prefs.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(d){view.add_drawable(b.object_from_template(d,view,view))}})}$("#add-bookmark-button").click(function(){var e=view.chrom+":"+view.low+"-"+view.high,d="Bookmark description";return ui.add_bookmark(e,d,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:c}});
@@ -20,7 +20,7 @@ var ToolInputsSettings = Backbone.Model.extend({
 /**
 * Tree for a tool's parameters.
 */
-var ToolParameterTree = Backbone.RelationalModel.extend({
+var ToolParameterTree = Backbone.Model.extend({
    defaults: {
        tool: null,
        tree_data: null
@@ -248,23 +248,16 @@ var ToolParameterTree = Backbone.RelationalModel.extend({
    }
 });

-var SweepsterTrack = Backbone.RelationalModel.extend({
+var SweepsterTrack = Backbone.Model.extend({
    defaults: {
        track: null,
        mode: 'Pack',
        settings: null,
        regions: null
    },
-
-    relations: [
-        {
-            type: Backbone.HasMany,
-            key: 'regions',
-            relatedModel: visualization.GenomeRegion
-        }
-    ],
-
+    
    initialize: function(options) {
+        this.set('regions', new visualization.GenomeRegionCollection(options.regions));
        if (options.track) {
            // FIXME: find a better way to deal with needed URLs:
            var track_config = _.extend({
@@ -313,31 +306,12 @@ var SweepsterVisualization = visualization.Visualization.extend({
        default_mode: 'Pack'
    }),

-    relations: [
-        {
-            type: Backbone.HasOne,
-            key: 'dataset',
-            relatedModel: data.Dataset
-        },
-        {
-            type: Backbone.HasOne,
-            key: 'tool',
-            relatedModel: tools.Tool
-        },
-        {
-            type: Backbone.HasMany,
-            key: 'regions',
-            relatedModel: visualization.GenomeRegion
-        },
-        {
-            type: Backbone.HasMany,
-            key: 'tracks',
-            relatedModel: SweepsterTrack
-        }
-        // NOTE: cannot use relationship for parameter tree because creating tree is complex.
-    ],
-    
    initialize: function(options) {
+        this.set('dataset', new data.Dataset(options.dataset));
+        this.set('tool', new tools.Tool(options.tool));
+        this.set('regions', new visualization.GenomeRegionCollection(options.regions));
+        this.set('tracks', new SweepsterTrackCollection(options.tracks));
+
        var tool_with_samplable_inputs = this.get('tool');
        this.set('tool_with_samplable_inputs', tool_with_samplable_inputs);
        // Remove complex parameters for now.
@@ -354,7 +328,6 @@ var SweepsterVisualization = visualization.Visualization.extend({
    },

    toJSON: function() {
-        // TODO: could this be easier by using relational models?
        return {
            id: this.get('id'),
            title: 'Parameter exploration for dataset \''  + this.get('dataset').get('name') + '\'',
@@ -29,8 +29,8 @@ require(
 });

 // trackster viewer
-define( ["libs/backbone/backbone-relational", "viz/visualization", "viz/trackster_ui"],
-        function(backbone, visualization, trackster_ui)
+define( ["viz/visualization", "viz/trackster_ui"],
+        function(visualization, trackster_ui)
 {

 var TracksterView = Backbone.View.extend(
@@ -1618,6 +1618,8 @@ var TracksterTool = tools_mod.Tool.extend({
    },

    initialize: function(options) {
+        tools_mod.Tool.prototype.initialize.call(this, options);
+
        // Restore tool visibility from state; default to hidden.
        var hidden = true;
        if (options.tool_state !== undefined && options.tool_state.hidden !== undefined) {
@@ -1787,7 +1789,7 @@ var TracksterToolView = Backbone.View.extend({
            },
            current_track = track,
            // Set name of track to include tool name, parameters, and region used.
-            track_name = url_params.tool_id +
+            track_name = tool.get('name') +
                         current_track.tool_region_and_parameters_str(region),
            container;
            
@@ -1909,7 +1911,9 @@ var Config = Backbone.Model.extend({

        // Set default values.
        _.each(options.params, function(p) {
-            values[p.key] = p.default_value;
+            // For color parameters without a default value, assign a random color.
+            values[p.key] = (p.type === 'color' && !p.default_value ? util.get_random_color() : p.default_value );
+
        });

        // Restore saved values.
@@ -2341,7 +2345,7 @@ var Track = function(view, container, obj_dict) {
    this.dataset = null;
    if (obj_dict.dataset) {
        // Dataset can be a Backbone model or a dict that can be used to create a model.
-        this.dataset = (obj_dict.dataset instanceof Backbone.Model ? obj_dict.dataset : data.Dataset.findOrCreate(obj_dict.dataset) );
+        this.dataset = (obj_dict.dataset instanceof Backbone.Model ? obj_dict.dataset : new data.Dataset(obj_dict.dataset) );
    }
    this.dataset_check_type = 'converted_datasets_state';
    this.data_url_extra_params = {};
@@ -2430,7 +2434,7 @@ extend(Track.prototype, Drawable.prototype, {

                // Update track name.
                if (track.tool.is_visible()) {
-                    track.set_name(track.name + track.tool_region_and_parameters_str());
+                    track.set_name(track.prefs.name + track.tool_region_and_parameters_str());
                }
                else {
                    track.revert_name();
@@ -2446,8 +2450,8 @@ extend(Track.prototype, Drawable.prototype, {
            css_class: "arrow-split",
            on_click_fn: function(track) {
                var template =
-                    '<strong>Tool</strong>: <%= track.tool.name %><br/>' + 
-                    '<strong>Dataset</strong>: <%= track.name %><br/>' +
+                    '<strong>Tool</strong>: <%= track.tool.get("name") %><br/>' + 
+                    '<strong>Dataset</strong>: <%= track.prefs.name %><br/>' +
                    '<strong>Region(s)</strong>: <select name="regions">' +
                    '<option value="cur">current viewing area</option>' +
                    '<option value="bookmarks">bookmarks</option>' +
@@ -3821,7 +3825,7 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
    display_modes: CONTINUOUS_DATA_MODES,

    config_params: _.union( Drawable.prototype.config_params, [
-            { key: 'color', label: 'Color', type: 'color', default_value: util.get_random_color() },
+            { key: 'color', label: 'Color', type: 'color' },
            { key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined },
            { key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined },
            { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
@@ -3919,8 +3923,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
    display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],

    config_params: _.union( Drawable.prototype.config_params, [
-        { key: 'block_color', label: 'Block color', type: 'color', default_value: util.get_random_color() },
-        { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: util.get_random_color() },
+        { key: 'block_color', label: 'Block color', type: 'color' },
+        { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color' },
        { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
        { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true, 
          help: 'Show the number of items in each bin when drawing summary histogram' },
@@ -4217,7 +4221,7 @@ extend(VariantTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
    display_modes: ["Auto", "Coverage", "Dense", "Squish", "Pack"],

    config_params: _.union( Drawable.prototype.config_params, [
-        { key: 'color', label: 'Histogram color', type: 'color', default_value: util.get_random_color() },
+        { key: 'color', label: 'Histogram color', type: 'color' },
        { key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true },
        { key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true },
        { key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 },
@@ -4361,8 +4365,8 @@ var ReadTrack = function (view, container, obj_dict) {

 extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, {
    config_params: _.union( Drawable.prototype.config_params, [
-        { key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: util.get_random_color() },
-        { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: util.get_random_color() },
+        { key: 'block_color', label: 'Block and sense strand color', type: 'color' },
+        { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color' },
        { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
        { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
        { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true },
@@ -681,7 +681,7 @@ var Genome = Backbone.Model.extend({
 /**
 * A genomic region.
 */
-var GenomeRegion = Backbone.RelationalModel.extend({
+var GenomeRegion = Backbone.Model.extend({
    defaults: {
        chrom: null,
        start: 0,
@@ -850,19 +850,15 @@ var GenomeRegionCollection = Backbone.Collection.extend({
 /**
 * A genome browser bookmark.
 */
-var BrowserBookmark = Backbone.RelationalModel.extend({
+var BrowserBookmark = Backbone.Model.extend({
    defaults: {
        region: null,
        note: ''
    },

-    relations: [
-        {
-            type: Backbone.HasOne,
-            key: 'region',
-            relatedModel: GenomeRegion
-        }
-    ]
+    initialize: function(options) {
+        this.set('region', new GenomeRegion(options.region));
+    }
 });

 /**
@@ -876,17 +872,10 @@ var BrowserBookmarkCollection = Backbone.Collection.extend({
 * A track of data in a genome visualization.
 */
 // TODO: rename to Track and merge with Trackster's Track object.
-var BackboneTrack = Backbone.RelationalModel.extend({
-
-    relations: [
-        {
-            type: Backbone.HasOne,
-            key: 'dataset',
-            relatedModel: data_mod.Dataset
-        }
-    ],
+var BackboneTrack = Backbone.Model.extend({

    initialize: function(options) {
+        this.set('dataset', new data_mod.Dataset('dataset'));

        // -- Set up config settings. -- 

@@ -913,10 +902,14 @@ var BackboneTrack = Backbone.RelationalModel.extend({
    }
 });

+var BackboneTrackCollection = new Backbone.Collection.extend({
+    model: BackboneTrack
+});
+
 /**
 * A visualization.
 */
-var Visualization = Backbone.RelationalModel.extend({
+var Visualization = Backbone.Model.extend({
    defaults: {
        title: '',
        type: ''
@@ -953,13 +946,9 @@ var GenomeVisualization = Visualization.extend({
        viewport: null
    }),

-    relations: [
-        {
-            type: Backbone.HasMany,
-            key: 'tracks',
-            relatedModel: BackboneTrack
-        }
-    ],
+    initialize: function(options) {
+        this.set('tracks', new BackboneTrackCollection(options.tracks));
+    },

    /**
     * Add a track or array of tracks to the visualization.
@@ -47,7 +47,6 @@
        "libs/bootstrap",
        "libs/underscore",
        "libs/backbone/backbone",
-        "libs/backbone/backbone-relational",
        "libs/handlebars.runtime",
        "galaxy.base",
        "mvc/ui",
@@ -76,8 +75,7 @@
            baseUrl: "${h.url_for('/static/scripts') }",
            shim: {
                "libs/underscore": { exports: "_" },
-                "libs/backbone/backbone": { exports: "Backbone" },
-                "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
+                "libs/backbone/backbone": { exports: "Backbone" }
            }
        });
    </script>
@@ -53,7 +53,6 @@
        'libs/bootstrap',
        'libs/underscore',
        'libs/backbone/backbone',
-        'libs/backbone/backbone-relational',
        'libs/handlebars.runtime',
        'galaxy.base',
        'libs/require',
@@ -89,8 +88,7 @@
            baseUrl: "${h.url_for('/static/scripts') }",
            shim: {
                "libs/underscore": { exports: "_" },
-                "libs/backbone/backbone": { exports: "Backbone" },
-                "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
+                "libs/backbone/backbone": { exports: "Backbone" }
            }
        });
    </script>
@@ -13,7 +13,6 @@
            baseUrl: "${h.url_for('/static/scripts')}",
            shim: {
                "libs/backbone/backbone": { exports: "Backbone" },
-                "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
            }
        });

@@ -13,7 +13,6 @@
            baseUrl: "${h.url_for('/static/scripts')}",
            shim: {
                "libs/backbone/backbone": { exports: "Backbone" },
-                "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
            }
        });

@@ -33,7 +33,6 @@
        'libs/bootstrap',
        'libs/underscore',
        'libs/backbone/backbone',
-        'libs/backbone/backbone-relational',
        'libs/require',
        'libs/d3',
        'galaxy.base',
@@ -103,7 +102,6 @@
                "libs/underscore": { exports: "_" },
                "libs/d3": { exports: "d3" },
                "libs/backbone/backbone": { exports: "Backbone" },
-                "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
            }
        });

@@ -58,7 +58,6 @@
            shim: {
                "libs/underscore": { exports: "_" },
                "libs/backbone/backbone": { exports: "Backbone" },
-                "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
            }
        });
        require( ["base", "viz/visualization", "viz/trackster_ui", "viz/trackster/tracks"], 
@@ -116,7 +116,6 @@
                    "libs/underscore": { exports: "_" },
                    "libs/d3": { exports: "d3" },
                    "libs/backbone/backbone": { exports: "Backbone" },
-                    "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
                }
        });