Explicit vars from multi-declarations.

client/galaxy/scripts/galaxy.js

@@ -24,9 +24,10 @@ function GalaxyApp(options, bootstrapped) {
 addLogging(GalaxyApp, "GalaxyApp");
 
 // a debug flag can be set via local storage and made available during script/page loading
-var DEBUGGING_KEY = "galaxy:debug",
-    NAMESPACE_KEY = DEBUGGING_KEY + ":namespaces",
-    localDebugging = false;
+var DEBUGGING_KEY = "galaxy:debug";
+
+var NAMESPACE_KEY = DEBUGGING_KEY + ":namespaces";
+var localDebugging = false;
 try {
     localDebugging = localStorage.getItem(DEBUGGING_KEY) == "true";
 } catch (storageErr) {
@@ -92,8 +93,8 @@ GalaxyApp.prototype.defaultOptions = {
 
 /** filter to options present in defaultOptions (and default to them) */
 GalaxyApp.prototype._processOptions = function _processOptions(options) {
-    var self = this,
-        defaults = self.defaultOptions;
+    var self = this;
+    var defaults = self.defaultOptions;
 
     self.options = {};
     for (var k in defaults) {

client/galaxy/scripts/galaxy.pages.js

@@ -45,7 +45,10 @@ function init_galaxy_elts(wym) {
 
 // Based on the dialog type, return a dictionary of information about an item
 function get_item_info(dialog_type) {
-    var item_singular, item_plural, item_controller, item_class;
+    var item_singular;
+    var item_plural;
+    var item_controller;
+    var item_class;
     switch (dialog_type) {
         case CONTROLS.ITEM_HISTORY:
             item_singular = "History";
@@ -147,8 +150,11 @@ WYMeditor.editor.prototype.dialog = function(
             );
             $(wym._options.altSelector).val($(selected).attr(WYMeditor.ALT));
         }
+
         // Get current URL, title.
-        var curURL, curTitle;
+        var curURL;
+
+        var curTitle;
         if (selected) {
             curURL = $(selected).attr("href");
             if (curURL == undefined) curURL = "";
@@ -166,9 +172,10 @@ WYMeditor.editor.prototype.dialog = function(
             {
                 "Make link": function() {
                     // Get URL, name/title.
-                    var sUrl = $(wym._options.hrefSelector).val() || "",
-                        sId = $(".wym_id").val() || "",
-                        sName = $(wym._options.titleSelector).val() || "";
+                    var sUrl = $(wym._options.hrefSelector).val() || "";
+
+                    var sId = $(".wym_id").val() || "";
+                    var sName = $(wym._options.titleSelector).val() || "";
 
                     if (sUrl || sId) {
                         // Create link.

client/galaxy/scripts/layout/generic-nav-view.js

@@ -8,31 +8,38 @@ var GenericNavView = Backbone.View.extend({
     /** makes bootstrap modal and iframe inside it */
     makeModalIframe: function(e) {
         // make modal
-        var host = window.Galaxy.config.communication_server_host,
-            port = window.Galaxy.config.communication_server_port,
-            username = escape(window.Galaxy.user.attributes.username),
-            persistent_communication_rooms = escape(
-                window.Galaxy.config.persistent_communication_rooms
-            ),
-            query_string =
-                "?username=" +
-                username +
-                "&persistent_communication_rooms=" +
-                persistent_communication_rooms,
-            src = host + ":" + port + query_string,
-            $el_chat_modal_header = null,
-            $el_chat_modal_body = null,
-            iframe_template =
-                '<iframe class="f-iframe fade in communication-iframe" src="' +
-                src +
-                '"> </iframe>',
-            header_template =
-                '<i class="fa fa-comment" aria-hidden="true" title="Communicate with other users"></i>' +
-                '<i class="fa fa-expand expand-compress-modal" aria-hidden="true" title="Maximize"></i>' +
-                '<i class="fa fa-times close-modal" aria-hidden="true" title="Close"></i>',
-            frame_height = 350,
-            frame_width = 600,
-            class_names = "ui-modal chat-modal";
+        var host = window.Galaxy.config.communication_server_host;
+
+        var port = window.Galaxy.config.communication_server_port;
+        var username = escape(window.Galaxy.user.attributes.username);
+
+        var persistent_communication_rooms = escape(
+            window.Galaxy.config.persistent_communication_rooms
+        );
+
+        var query_string =
+            "?username=" +
+            username +
+            "&persistent_communication_rooms=" +
+            persistent_communication_rooms;
+
+        var src = host + ":" + port + query_string;
+        var $el_chat_modal_header = null;
+        var $el_chat_modal_body = null;
+
+        var iframe_template =
+            '<iframe class="f-iframe fade in communication-iframe" src="' +
+            src +
+            '"> </iframe>';
+
+        var header_template =
+            '<i class="fa fa-comment" aria-hidden="true" title="Communicate with other users"></i>' +
+            '<i class="fa fa-expand expand-compress-modal" aria-hidden="true" title="Maximize"></i>' +
+            '<i class="fa fa-times close-modal" aria-hidden="true" title="Close"></i>';
+
+        var frame_height = 350;
+        var frame_width = 600;
+        var class_names = "ui-modal chat-modal";
 
         // deletes the chat modal if already present and create one
         if ($(".chat-modal").length > 0) {
@@ -87,8 +94,8 @@ var GenericNavView = Backbone.View.extend({
 
     /**renders the chat icon as a nav item*/
     render: function() {
-        var self = this,
-            navItem = {};
+        var self = this;
+        var navItem = {};
         navItem = {
             id: "show-chat-online",
             icon: "fa-comment-o",

client/galaxy/scripts/layout/page.js

@@ -156,10 +156,10 @@ var View = Backbone.View.extend({
 
     /** Check if the communication server is online and show the icon otherwise hide the icon */
     _checkCommunicationServerOnline: function() {
-        var host = window.Galaxy.config.communication_server_host,
-            port = window.Galaxy.config.communication_server_port,
-            preferences = window.Galaxy.user.attributes.preferences,
-            $chat_icon_element = $("#show-chat-online");
+        var host = window.Galaxy.config.communication_server_host;
+        var port = window.Galaxy.config.communication_server_port;
+        var preferences = window.Galaxy.user.attributes.preferences;
+        var $chat_icon_element = $("#show-chat-online");
         /** Check if the user has deactivated the communication in it's personal settings */
         if (
             preferences &&

client/galaxy/scripts/layout/panel.js

@@ -2,8 +2,8 @@ import $ from "jquery";
 import * as _ from "libs/underscore";
 import * as Backbone from "libs/backbone";
 
-var MIN_PANEL_WIDTH = 160,
-    MAX_PANEL_WIDTH = 800;
+var MIN_PANEL_WIDTH = 160;
+var MAX_PANEL_WIDTH = 800;
 
 /** View for left/right panels used by Page view */
 var SidePanel = Backbone.View.extend({
@@ -80,15 +80,15 @@ var SidePanel = Backbone.View.extend({
     },
 
     _mousedownDragHandler: function(ev) {
-        var self = this,
-            draggingLeft = this.id === "left",
-            prevX = ev.pageX;
+        var self = this;
+        var draggingLeft = this.id === "left";
+        var prevX = ev.pageX;
 
         function move(e) {
             var delta = e.pageX - prevX;
             prevX = e.pageX;
-            var oldWidth = self.$el.width(),
-                newWidth = draggingLeft ? oldWidth + delta : oldWidth - delta;
+            var oldWidth = self.$el.width();
+            var newWidth = draggingLeft ? oldWidth + delta : oldWidth - delta;
             // Limit range
             newWidth = Math.min(
                 MAX_PANEL_WIDTH,
@@ -121,9 +121,9 @@ var SidePanel = Backbone.View.extend({
         if (!this.hidden) {
             return;
         }
-        var self = this,
-            animation = {},
-            whichSide = this.id;
+        var self = this;
+        var animation = {};
+        var whichSide = this.id;
         animation[whichSide] = 0;
         self.$el
             .css(whichSide, -this.saved_size)
@@ -140,8 +140,8 @@ var SidePanel = Backbone.View.extend({
         if (this.hidden) {
             return;
         }
-        var animation = {},
-            whichSide = this.id;
+        var animation = {};
+        var whichSide = this.id;
         this.saved_size = this.$el.width();
         animation[whichSide] = -this.saved_size;
         this.$el.animate(animation, "fast");

client/galaxy/scripts/layout/scratchbook.js

@@ -204,15 +204,16 @@ export default Backbone.View.extend({
                 content: function(parent_elt) {
                     // Create view config.
                     var view_config = {
-                            container: parent_elt,
-                            name: viz.get("title"),
-                            id: viz.id,
-                            // FIXME: this will not work with custom builds b/c the dbkey needed to be encoded.
-                            dbkey: viz.get("dbkey"),
-                            stand_alone: false
-                        },
-                        latest_revision = viz.get("latest_revision"),
-                        drawables = latest_revision.config.view.drawables;
+                        container: parent_elt,
+                        name: viz.get("title"),
+                        id: viz.id,
+                        // FIXME: this will not work with custom builds b/c the dbkey needed to be encoded.
+                        dbkey: viz.get("dbkey"),
+                        stand_alone: false
+                    };
+
+                    var latest_revision = viz.get("latest_revision");
+                    var drawables = latest_revision.config.view.drawables;
 
                     // Set up datasets in drawables.
                     _.each(drawables, function(d) {

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

@@ -111,8 +111,8 @@ var SessionStorageModel = Backbone.Model.extend({
     /** set storage to the stringified item */
     _create: function(model) {
         try {
-            var json = model.toJSON(),
-                set = sessionStorage.setItem(model.id, JSON.stringify(json));
+            var json = model.toJSON();
+            var set = sessionStorage.setItem(model.id, JSON.stringify(json));
             return set === null ? set : json;
             // DOMException is thrown in Safari if in private browsing mode and sessionStorage is attempted:
             // http://stackoverflow.com/questions/14555347
@@ -175,8 +175,8 @@ var SessionStorageModel = Backbone.Model.extend({
  *  NOTE: this does not combine any hashes (like events, etc.) and you're expected to handle that
  */
 function mixin(mixinHash1, /* mixinHash2, etc: ... variadic */ propsHash) {
-    var args = Array.prototype.slice.call(arguments, 0),
-        lastArg = args.pop();
+    var args = Array.prototype.slice.call(arguments, 0);
+    var lastArg = args.pop();
     args.unshift(lastArg);
     return _.defaults.apply(_, args);
 }
@@ -259,8 +259,8 @@ var SearchableModelMixin = {
      *  @returns {Boolean} was term found in (any) attribute(s)
      */
     matches: function(term) {
-        var ATTR_SPECIFIER = "=",
-            split = term.split(ATTR_SPECIFIER);
+        var ATTR_SPECIFIER = "=";
+        var split = term.split(ATTR_SPECIFIER);
         // attribute is specified - search only that
         if (split.length >= 2) {
             var attrKey = split[0];

client/galaxy/scripts/mvc/collection/collection-li.js

@@ -4,8 +4,9 @@ import BASE_MVC from "mvc/base-mvc";
 import _l from "utils/localization";
 
 //==============================================================================
-var FoldoutListItemView = LIST_ITEM.FoldoutListItemView,
-    ListItemView = LIST_ITEM.ListItemView;
+var FoldoutListItemView = LIST_ITEM.FoldoutListItemView;
+
+var ListItemView = LIST_ITEM.ListItemView;
 /** @class Read only view for DatasetCollection.
  */
 var DCListItemView = FoldoutListItemView.extend(

client/galaxy/scripts/mvc/collection/collection-view-edit.js

@@ -51,8 +51,9 @@ var CollectionViewEdit = _super.extend(
             this.tagsEditorShown = true;
 
             //TODO: extract
-            var panel = this,
-                nameSelector = "> .controls .name";
+            var panel = this;
+
+            var nameSelector = "> .controls .name";
             $where
                 .find(nameSelector)
                 .attr("title", _l("Click to rename collection"))

client/galaxy/scripts/mvc/collection/list-collection-creator.js

@@ -72,8 +72,8 @@ var DatasetCollectionElementView = Backbone.View
 
         /** animate the removal of this element and pub */
         discard: function() {
-            var view = this,
-                parentWidth = this.$el.parent().width();
+            var view = this;
+            var parentWidth = this.$el.parent().width();
             this.$el.animate(
                 { "margin-right": parentWidth },
                 "fast",
@@ -113,18 +113,21 @@ var DatasetCollectionElementView = Backbone.View
         _clickName: function(ev) {
             ev.stopPropagation();
             ev.preventDefault();
+
             var promptString = [
-                    _l("Enter a new name for the element"),
-                    ":\n(",
-                    _l(
-                        "Note that changing the name here will not rename the dataset"
-                    ),
-                    ")"
-                ].join(""),
-                response = prompt(
-                    _l("Enter a new name for the element") + ":",
-                    this.element.name
-                );
+                _l("Enter a new name for the element"),
+                ":\n(",
+                _l(
+                    "Note that changing the name here will not rename the dataset"
+                ),
+                ")"
+            ].join("");
+
+            var response = prompt(
+                _l("Enter a new name for the element") + ":",
+                this.element.name
+            );
+
             if (response) {
                 this.element.name = response;
                 this.render();
@@ -266,8 +269,8 @@ var ListCollectionCreator = Backbone.View
 
         /** separate working list into valid and invalid elements for this collection */
         _validateElements: function() {
-            var creator = this,
-                existingNames = {};
+            var creator = this;
+            var existingNames = {};
             creator.invalidElements = [];
 
             this.workingElements = this.workingElements.filter(function(
@@ -304,9 +307,9 @@ var ListCollectionCreator = Backbone.View
 
         /** mangle duplicate names using a mac-like '(counter)' addition to any duplicates */
         _mangleDuplicateNames: function() {
-            var SAFETY = 900,
-                counter = 1,
-                existingNames = {};
+            var SAFETY = 900;
+            var counter = 1;
+            var existingNames = {};
             this.workingElements.forEach(function(element) {
                 var currName = element.name;
                 while (existingNames.hasOwnProperty(currName)) {
@@ -439,9 +442,10 @@ var ListCollectionCreator = Backbone.View
         /** render the elements in order (or a warning if no elements found) */
         _renderList: function(speed, callback) {
             //this.debug( '-- _renderList' );
-            var creator = this,
-                $tmp = jQuery("<div/>"),
-                $list = creator.$list();
+            var creator = this;
+
+            var $tmp = jQuery("<div/>");
+            var $list = creator.$list();
 
             _.each(this.elementViews, function(view) {
                 view.destroy();
@@ -558,10 +562,11 @@ var ListCollectionCreator = Backbone.View
                 return;
             }
 
-            var creator = this,
-                elements = this.workingElements.map(function(element) {
-                    return creator._elementToJSON(element);
-                });
+            var creator = this;
+
+            var elements = this.workingElements.map(function(element) {
+                return creator._elementToJSON(element);
+            });
 
             creator.blocking = true;
             return creator
@@ -625,11 +630,11 @@ var ListCollectionCreator = Backbone.View
         _errorHandler: function(data) {
             this.error(data);
 
-            var creator = this,
-                content = data.message || _l("An error occurred");
+            var creator = this;
+            var content = data.message || _l("An error occurred");
             if (data.xhr) {
-                var xhr = data.xhr,
-                    message = data.message;
+                var xhr = data.xhr;
+                var message = data.message;
                 if (xhr.readyState === 0 && xhr.status === 0) {
                     content +=
                         ": " +
@@ -727,11 +732,11 @@ var ListCollectionCreator = Backbone.View
 
         /** If the mouse is near enough to the list's top or bottom, scroll the list */
         _checkForAutoscroll: function($element, y) {
-            var AUTOSCROLL_SPEED = 2,
-                offset = $element.offset(),
-                scrollTop = $element.scrollTop(),
-                upperDist = y - offset.top,
-                lowerDist = offset.top + $element.outerHeight() - y;
+            var AUTOSCROLL_SPEED = 2;
+            var offset = $element.offset();
+            var scrollTop = $element.scrollTop();
+            var upperDist = y - offset.top;
+            var lowerDist = offset.top + $element.outerHeight() - y;
             if (upperDist >= 0 && upperDist < this.autoscrollDist) {
                 $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);
             } else if (lowerDist >= 0 && lowerDist < this.autoscrollDist) {
@@ -743,14 +748,16 @@ var ListCollectionCreator = Backbone.View
      *  If the y is at the end of the list, return an empty jQuery object.
      */
         _getNearestElement: function(y) {
-            var WIGGLE = 4,
-                lis = this.$(
-                    ".collection-elements li.collection-element"
-                ).toArray();
+            var WIGGLE = 4;
+
+            var lis = this.$(
+                ".collection-elements li.collection-element"
+            ).toArray();
+
             for (var i = 0; i < lis.length; i++) {
-                var $li = $(lis[i]),
-                    top = $li.offset().top,
-                    halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;
+                var $li = $(lis[i]);
+                var top = $li.offset().top;
+                var halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;
                 if (top + halfHeight > y && top - halfHeight < y) {
                     return $li;
                 }
@@ -784,14 +791,16 @@ var ListCollectionCreator = Backbone.View
 
         /** resync the creator's list of elements based on the DOM order */
         _syncOrderToDom: function() {
-            var creator = this,
-                newElements = [];
+            var creator = this;
+            var newElements = [];
             //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?
             this.$(".collection-elements .collection-element").each(function() {
-                var id = $(this).attr("data-element-id"),
-                    element = _.findWhere(creator.workingElements, {
-                        id: id
-                    });
+                var id = $(this).attr("data-element-id");
+
+                var element = _.findWhere(creator.workingElements, {
+                    id: id
+                });
+
                 if (element) {
                     newElements.push(element);
                 } else {
@@ -1075,9 +1084,9 @@ var collectionCreatorModal = function _collectionCreatorModal(
     options,
     CreatorClass
 ) {
-    var deferred = jQuery.Deferred(),
-        modal = Galaxy.modal || new UI_MODAL.View(),
-        creator;
+    var deferred = jQuery.Deferred();
+    var modal = Galaxy.modal || new UI_MODAL.View();
+    var creator;
 
     options = _.defaults(options || {}, {
         elements: elements,
@@ -1121,29 +1130,26 @@ var listCollectionCreatorModal = function _listCollectionCreatorModal(
  *  @returns {Deferred} resolved when the collection is added to the history.
  */
 function createListCollection(contents, defaultHideSourceItems) {
-    var elements = contents.toJSON(),
-        promise = listCollectionCreatorModal(elements, {
-            defaultHideSourceItems: defaultHideSourceItems,
-            creationFn: function(elements, name, hideSourceItems) {
-                elements = elements.map(function(element) {
-                    return {
-                        id: element.id,
-                        name: element.name,
-                        //TODO: this allows for list:list even if the filter above does not - reconcile
-                        src:
-                            element.history_content_type === "dataset"
-                                ? "hda"
-                                : "hdca"
-                    };
-                });
-                return contents.createHDCA(
-                    elements,
-                    "list",
-                    name,
-                    hideSourceItems
-                );
-            }
-        });
+    var elements = contents.toJSON();
+
+    var promise = listCollectionCreatorModal(elements, {
+        defaultHideSourceItems: defaultHideSourceItems,
+        creationFn: function(elements, name, hideSourceItems) {
+            elements = elements.map(function(element) {
+                return {
+                    id: element.id,
+                    name: element.name,
+                    //TODO: this allows for list:list even if the filter above does not - reconcile
+                    src:
+                        element.history_content_type === "dataset"
+                            ? "hda"
+                            : "hdca"
+                };
+            });
+            return contents.createHDCA(elements, "list", name, hideSourceItems);
+        }
+    });
+
     return promise;
 }
 

client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js

@@ -94,10 +94,10 @@ function autoPairFnBuilder(options) {
         options.createPair ||
         function _defaultCreatePair(params) {
             params = params || {};
-            var a = params.listA.splice(params.indexA, 1)[0],
-                b = params.listB.splice(params.indexB, 1)[0],
-                aInBIndex = params.listB.indexOf(a),
-                bInAIndex = params.listA.indexOf(b);
+            var a = params.listA.splice(params.indexA, 1)[0];
+            var b = params.listB.splice(params.indexB, 1)[0];
+            var aInBIndex = params.listB.indexOf(a);
+            var bInAIndex = params.listA.indexOf(b);
             if (aInBIndex !== -1) {
                 params.listB.splice(aInBIndex, 1);
             }
@@ -131,15 +131,17 @@ function autoPairFnBuilder(options) {
     return function _strategy(params) {
         this.debug("autopair _strategy ---------------------------");
         params = params || {};
-        var listA = params.listA,
-            listB = params.listB,
-            indexA = 0,
-            indexB,
-            bestMatch = {
-                score: 0.0,
-                index: null
-            },
-            paired = [];
+        var listA = params.listA;
+        var listB = params.listB;
+        var indexA = 0;
+        var indexB;
+
+        var bestMatch = {
+            score: 0.0,
+            index: null
+        };
+
+        var paired = [];
         //console.debug( 'params:', JSON.stringify( params, null, '  ' ) );
         this.debug("starting list lens:", listA.length, listB.length);
         this.debug(
@@ -358,9 +360,10 @@ var PairedCollectionCreator = Backbone.View
         /** split initial list into two lists, those that pass forward filters & those passing reverse */
         _splitByFilters: function() {
             var regexFilters = this.filters.map(function(stringFilter) {
-                    return new RegExp(stringFilter);
-                }),
-                split = [[], []];
+                return new RegExp(stringFilter);
+            });
+
+            var split = [[], []];
 
             function _filter(unpaired, filter) {
                 return filter.test(unpaired.name);
@@ -387,11 +390,12 @@ var PairedCollectionCreator = Backbone.View
                     return low;
                 }
 
-                var mid = Math.floor((hi - low) / 2) + low,
-                    compared = naturalSort(
-                        dataset.name,
-                        this.unpaired[mid].name
-                    );
+                var mid = Math.floor((hi - low) / 2) + low;
+
+                var compared = naturalSort(
+                    dataset.name,
+                    this.unpaired[mid].name
+                );
 
                 if (compared < 0) {
                     return binSearchSortedIndex(low, mid);
@@ -421,8 +425,9 @@ var PairedCollectionCreator = Backbone.View
      */
         autoPair: function(strategy) {
             // split first using exact matching
-            var split = this._splitByFilters(),
-                paired = [];
+            var split = this._splitByFilters();
+
+            var paired = [];
             if (this.twoPassAutopairing) {
                 paired = this.autopairSimple({
                     listA: split[0],
@@ -470,17 +475,17 @@ var PairedCollectionCreator = Backbone.View
             },
             match: function _matches(params) {
                 params = params || {};
+
                 var distance = levenshteinDistance(
-                        params.matchTo,
-                        params.possible
-                    ),
-                    score =
-                        1.0 -
-                        distance /
-                            Math.max(
-                                params.matchTo.length,
-                                params.possible.length
-                            );
+                    params.matchTo,
+                    params.possible
+                );
+
+                var score =
+                    1.0 -
+                    distance /
+                        Math.max(params.matchTo.length, params.possible.length);
+
                 if (score > params.bestMatch.score) {
                     return {
                         index: params.index,
@@ -498,13 +503,16 @@ var PairedCollectionCreator = Backbone.View
             },
             match: function _matches(params) {
                 params = params || {};
+
                 var match = this._naiveStartingAndEndingLCS(
-                        params.matchTo,
-                        params.possible
-                    ).length,
-                    score =
-                        match /
-                        Math.max(params.matchTo.length, params.possible.length);
+                    params.matchTo,
+                    params.possible
+                ).length;
+
+                var score =
+                    match /
+                    Math.max(params.matchTo.length, params.possible.length);
+
                 if (score > params.bestMatch.score) {
                     return {
                         index: params.index,
@@ -517,10 +525,10 @@ var PairedCollectionCreator = Backbone.View
 
         /** return the concat'd longest common prefix and suffix from two strings */
         _naiveStartingAndEndingLCS: function(s1, s2) {
-            var fwdLCS = "",
-                revLCS = "",
-                i = 0,
-                j = 0;
+            var fwdLCS = "";
+            var revLCS = "";
+            var i = 0;
+            var j = 0;
             while (i < s1.length && i < s2.length) {
                 if (s1[i] !== s2[i]) {
                     break;
@@ -580,12 +588,14 @@ var PairedCollectionCreator = Backbone.View
                 removeExtensions !== undefined
                     ? removeExtensions
                     : this.removeExtensions;
-            var fwdName = fwd.name,
-                revName = rev.name,
-                lcs = this._naiveStartingAndEndingLCS(
-                    fwdName.replace(new RegExp(this.filters[0]), ""),
-                    revName.replace(new RegExp(this.filters[1]), "")
-                );
+            var fwdName = fwd.name;
+            var revName = rev.name;
+
+            var lcs = this._naiveStartingAndEndingLCS(
+                fwdName.replace(new RegExp(this.filters[0]), ""),
+                revName.replace(new RegExp(this.filters[1]), "")
+            );
+
             if (removeExtensions) {
                 var lastDotIndex = lcs.lastIndexOf(".");
                 if (lastDotIndex > 0) {
@@ -651,12 +661,13 @@ var PairedCollectionCreator = Backbone.View
      *  @returns {jQuery.xhr Object}    the jquery ajax request
      */
         createList: function(name) {
-            var creator = this,
-                url =
-                    Galaxy.root +
-                    "api/histories/" +
-                    this.historyId +
-                    "/contents/dataset_collections";
+            var creator = this;
+
+            var url =
+                Galaxy.root +
+                "api/histories/" +
+                this.historyId +
+                "/contents/dataset_collections";
 
             //TODO: use ListPairedCollection.create()
             var ajaxData = {
@@ -779,11 +790,12 @@ var PairedCollectionCreator = Backbone.View
         /** render the unpaired section, showing datasets accrd. to filters, update the unpaired counts */
         _renderUnpaired: function(speed, callback) {
             //this.debug( '-- _renderUnpaired' );
-            var creator = this,
-                $fwd,
-                $rev,
-                $prd = [],
-                split = this._splitByFilters();
+            var creator = this;
+
+            var $fwd;
+            var $rev;
+            var $prd = [];
+            var split = this._splitByFilters();
             // update unpaired counts
             this.$(".forward-column .title").text(
                 [split[0].length, _l("unpaired forward")].join(" ")
@@ -903,19 +915,23 @@ var PairedCollectionCreator = Backbone.View
         },
         /** try to detect if the unpaired section has a scrollbar and adjust left column for better centering of all */
         _adjUnpairedOnScrollbar: function() {
-            var $unpairedColumns = this.$(".unpaired-columns").last(),
-                $firstDataset = this.$(
-                    ".unpaired-columns .reverse-column .dataset"
-                ).first();
+            var $unpairedColumns = this.$(".unpaired-columns").last();
+
+            var $firstDataset = this.$(
+                ".unpaired-columns .reverse-column .dataset"
+            ).first();
+
             if (!$firstDataset.length) {
                 return;
             }
+
             var ucRight =
-                    $unpairedColumns.offset().left +
-                    $unpairedColumns.outerWidth(),
-                dsRight =
-                    $firstDataset.offset().left + $firstDataset.outerWidth(),
-                rightDiff = Math.floor(ucRight) - Math.floor(dsRight);
+                $unpairedColumns.offset().left + $unpairedColumns.outerWidth();
+
+            var dsRight =
+                $firstDataset.offset().left + $firstDataset.outerWidth();
+
+            var rightDiff = Math.floor(ucRight) - Math.floor(dsRight);
             //this.debug( 'rightDiff:', ucRight, '-', dsRight, '=', rightDiff );
             this.$(".unpaired-columns .forward-column").css(
                 "margin-left",
@@ -1092,8 +1108,8 @@ var PairedCollectionCreator = Backbone.View
                 this._renderUnpaired();
                 this._renderPaired();
 
-                var message,
-                    msgClass = null;
+                var message;
+                var msgClass = null;
                 if (this.paired.length) {
                     msgClass = "alert-success";
                     message = this.paired.length + " " + _l("pairs created");
@@ -1274,11 +1290,13 @@ var PairedCollectionCreator = Backbone.View
      */
         toggleSelectUnpaired: function($dataset, options) {
             options = options || {};
-            var dataset = $dataset.data("dataset"),
-                select =
-                    options.force !== undefined
-                        ? options.force
-                        : !$dataset.hasClass("selected");
+            var dataset = $dataset.data("dataset");
+
+            var select =
+                options.force !== undefined
+                    ? options.force
+                    : !$dataset.hasClass("selected");
+
             //this.debug( id, options.force, $dataset, dataset );
             if (!$dataset.length || dataset === undefined) {
                 return $dataset;
@@ -1299,10 +1317,10 @@ var PairedCollectionCreator = Backbone.View
         /** pair all the currently selected unpaired datasets */
         pairAllSelected: function(options) {
             options = options || {};
-            var creator = this,
-                fwds = [],
-                revs = [],
-                pairs = [];
+            var creator = this;
+            var fwds = [];
+            var revs = [];
+            var pairs = [];
             creator
                 .$(".unpaired-columns .forward-column .dataset.selected")
                 .each(function() {
@@ -1341,14 +1359,16 @@ var PairedCollectionCreator = Backbone.View
         /** when holding down the shift key on a click, 'paint' the moused over datasets as selected */
         _mousedownUnpaired: function(ev) {
             if (ev.shiftKey) {
-                var creator = this,
-                    $startTarget = $(ev.target).addClass("selected"),
-                    moveListener = function(ev) {
-                        creator
-                            .$(ev.target)
-                            .filter(".dataset")
-                            .addClass("selected");
-                    };
+                var creator = this;
+                var $startTarget = $(ev.target).addClass("selected");
+
+                var moveListener = function(ev) {
+                    creator
+                        .$(ev.target)
+                        .filter(".dataset")
+                        .addClass("selected");
+                };
+
                 $startTarget.parent().on("mousemove", moveListener);
 
                 // on any mouseup, stop listening to the move and try to pair any selected
@@ -1362,13 +1382,16 @@ var PairedCollectionCreator = Backbone.View
         /** attempt to pair two datasets directly across from one another */
         _clickPairRow: function(ev) {
             //if( !ev.currentTarget ){ return true; }
-            var rowIndex = $(ev.currentTarget).index(),
-                fwd = $(".unpaired-columns .forward-column .dataset")
-                    .eq(rowIndex)
-                    .data("dataset"),
-                rev = $(".unpaired-columns .reverse-column .dataset")
-                    .eq(rowIndex)
-                    .data("dataset");
+            var rowIndex = $(ev.currentTarget).index();
+
+            var fwd = $(".unpaired-columns .forward-column .dataset")
+                .eq(rowIndex)
+                .data("dataset");
+
+            var rev = $(".unpaired-columns .reverse-column .dataset")
+                .eq(rowIndex)
+                .data("dataset");
+
             //this.debug( 'row:', rowIndex, fwd, rev );
             this._pair(fwd, rev);
         },
@@ -1376,8 +1399,8 @@ var PairedCollectionCreator = Backbone.View
         // ........................................................................ divider/partition
         /** start dragging the visible divider/partition between unpaired and paired panes */
         _startPartitionDrag: function(ev) {
-            var creator = this,
-                startingY = ev.pageY;
+            var creator = this;
+            var startingY = ev.pageY;
             //this.debug( 'partition drag START:', ev );
             $("body").css("cursor", "ns-resize");
             creator.$(".flexible-partition-drag").css("color", "black");
@@ -1406,10 +1429,10 @@ var PairedCollectionCreator = Backbone.View
 
         /** adjust the parition up/down +/-adj pixels */
         adjPartition: function(adj) {
-            var $unpaired = this.$(".unpaired-columns"),
-                $paired = this.$(".paired-columns"),
-                unpairedHi = parseInt($unpaired.css("height"), 10),
-                pairedHi = parseInt($paired.css("height"), 10);
+            var $unpaired = this.$(".unpaired-columns");
+            var $paired = this.$(".paired-columns");
+            var unpairedHi = parseInt($unpaired.css("height"), 10);
+            var pairedHi = parseInt($paired.css("height"), 10);
             //this.debug( adj, 'hi\'s:', unpairedHi, pairedHi, unpairedHi + adj, pairedHi - adj );
 
             unpairedHi = Math.max(10, unpairedHi + adj);
@@ -1468,11 +1491,11 @@ var PairedCollectionCreator = Backbone.View
         /** rename a pair when the pair name is clicked */
         _clickPairName: function(ev) {
             ev.stopPropagation();
-            var $name = $(ev.currentTarget),
-                $pair = $name.parent().parent(),
-                index = $pair.index(".dataset.paired"),
-                pair = this.paired[index],
-                response = prompt("Enter a new name for the pair:", pair.name);
+            var $name = $(ev.currentTarget);
+            var $pair = $name.parent().parent();
+            var index = $pair.index(".dataset.paired");
+            var pair = this.paired[index];
+            var response = prompt("Enter a new name for the pair:", pair.name);
             if (response) {
                 pair.name = response;
                 // set a flag (which won't be passed in json creation) for manual naming so we don't overwrite these
@@ -1526,10 +1549,10 @@ var PairedCollectionCreator = Backbone.View
         /** If the mouse is near enough to the list's top or bottom, scroll the list */
         _checkForAutoscroll: function($element, y) {
             var AUTOSCROLL_SPEED = 2;
-            var offset = $element.offset(),
-                scrollTop = $element.scrollTop(),
-                upperDist = y - offset.top,
-                lowerDist = offset.top + $element.outerHeight() - y;
+            var offset = $element.offset();
+            var scrollTop = $element.scrollTop();
+            var upperDist = y - offset.top;
+            var lowerDist = offset.top + $element.outerHeight() - y;
             //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist );
             if (upperDist >= 0 && upperDist < this.autoscrollDist) {
                 $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);
@@ -1542,12 +1565,12 @@ var PairedCollectionCreator = Backbone.View
      *      If the y is at the end of the list, return an empty jQuery object.
      */
         _getNearestPairedDatasetLi: function(y) {
-            var WIGGLE = 4,
-                lis = this.$(".paired-columns .column-datasets li").toArray();
+            var WIGGLE = 4;
+            var lis = this.$(".paired-columns .column-datasets li").toArray();
             for (var i = 0; i < lis.length; i++) {
-                var $li = $(lis[i]),
-                    top = $li.offset().top,
-                    halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;
+                var $li = $(lis[i]);
+                var top = $li.offset().top;
+                var halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;
                 if (top + halfHeight > y && top - halfHeight < y) {
                     //this.debug( y, top + halfHeight, top - halfHeight )
                     return $li;
@@ -1907,8 +1930,8 @@ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal(
     datasets,
     options
 ) {
-    var deferred = jQuery.Deferred(),
-        creator;
+    var deferred = jQuery.Deferred();
+    var creator;
 
     options = _.defaults(options || {}, {
         datasets: datasets,

client/galaxy/scripts/mvc/collection/pair-collection-creator.js

@@ -88,9 +88,10 @@ var PairCollectionCreator = _super.extend({
     _renderList: function(speed, callback) {
         //this.debug( '-- _renderList' );
         //precondition: there are two valid elements in workingElements
-        var creator = this,
-            $tmp = jQuery("<div/>"),
-            $list = creator.$list();
+        var creator = this;
+
+        var $tmp = jQuery("<div/>");
+        var $list = creator.$list();
 
         // lose the original views, create the new, append all at once, then call their renders
         _.each(this.elementViews, function(view) {
@@ -279,22 +280,24 @@ var pairCollectionCreatorModal = function _pairCollectionCreatorModal(
  *  @returns {Deferred} resolved when the collection is added to the history.
  */
 function createPairCollection(contents, defaultHideSourceItems) {
-    var elements = contents.toJSON(),
-        promise = pairCollectionCreatorModal(elements, {
-            defaultHideSourceItems: defaultHideSourceItems,
-            creationFn: function(elements, name, hideSourceItems) {
-                elements = [
-                    { name: "forward", src: "hda", id: elements[0].id },
-                    { name: "reverse", src: "hda", id: elements[1].id }
-                ];
-                return contents.createHDCA(
-                    elements,
-                    "paired",
-                    name,
-                    hideSourceItems
-                );
-            }
-        });
+    var elements = contents.toJSON();
+
+    var promise = pairCollectionCreatorModal(elements, {
+        defaultHideSourceItems: defaultHideSourceItems,
+        creationFn: function(elements, name, hideSourceItems) {
+            elements = [
+                { name: "forward", src: "hda", id: elements[0].id },
+                { name: "reverse", src: "hda", id: elements[1].id }
+            ];
+            return contents.createHDCA(
+                elements,
+                "paired",
+                name,
+                hideSourceItems
+            );
+        }
+    });
+
     return promise;
 }
 

client/galaxy/scripts/mvc/dataset/data.js

@@ -95,8 +95,9 @@ var TabularDataset = Dataset.extend({
         }
 
         // Get next chunk.
-        var self = this,
-            next_chunk = $.Deferred();
+        var self = this;
+
+        var next_chunk = $.Deferred();
         $.getJSON(this.attributes.chunk_url, {
             offset: self.attributes.offset
         }).success(function(chunk) {
@@ -175,9 +176,9 @@ var TabularDatasetChunkedView = Backbone.View.extend({
             cellpadding: 0
         });
         this.$el.append(data_table);
-        var column_names = this.model.get_metadata("column_names"),
-            header_container = $("<thead/>").appendTo(data_table),
-            header_row = $("<tr/>").appendTo(header_container);
+        var column_names = this.model.get_metadata("column_names");
+        var header_container = $("<thead/>").appendTo(data_table);
+        var header_row = $("<tr/>").appendTo(header_container);
         if (column_names) {
             header_row.append(
                 "<th>" + column_names.join("</th><th>") + "</th>"
@@ -189,8 +190,9 @@ var TabularDatasetChunkedView = Backbone.View.extend({
         }
 
         // Render first chunk.
-        var self = this,
-            first_chunk = this.model.get("first_data_chunk");
+        var self = this;
+
+        var first_chunk = this.model.get("first_data_chunk");
         if (first_chunk) {
             // First chunk is bootstrapped, so render now.
             this._renderChunk(first_chunk);
@@ -239,9 +241,10 @@ var TabularDatasetChunkedView = Backbone.View.extend({
 
     _renderRow: function(line) {
         // Check length of cells to ensure this is a complete row.
-        var cells = line.split("\t"),
-            row = $("<tr>"),
-            num_columns = this.model.get_metadata("columns");
+        var cells = line.split("\t");
+
+        var row = $("<tr>");
+        var num_columns = this.model.get_metadata("columns");
 
         if (this.row_count % 2 !== 0) {
             row.addClass("dark_row");

client/galaxy/scripts/mvc/dataset/dataset-choice.js

@@ -100,11 +100,11 @@ var DatasetChoiceModal = function(datasetJSON, options) {
             ? _l("Choose datasets:")
             : _l("Choose a dataset:"));
 
-    var modal,
-        list,
-        buttons,
-        promise = jQuery.Deferred(),
-        filterFn = options.filter || _filterDatasetJSON;
+    var modal;
+    var list;
+    var buttons;
+    var promise = jQuery.Deferred();
+    var filterFn = options.filter || _filterDatasetJSON;
 
     // filter the given datasets and if none left return a rejected promise for use with fail()
     datasetJSON = filterFn(datasetJSON, options.where, options.datasetsOnly);

client/galaxy/scripts/mvc/dataset/dataset-error.js

@@ -14,8 +14,9 @@ var View = Backbone.View.extend({
     // Fetch data for the selected dataset and
     render: function() {
         var data_url =
-                Galaxy.root + "api/datasets/" + this.model.get("dataset_id"),
-            self = this;
+            Galaxy.root + "api/datasets/" + this.model.get("dataset_id");
+
+        var self = this;
 
         Utils.get({
             url: data_url,

client/galaxy/scripts/mvc/dataset/dataset-li-edit.js

@@ -54,25 +54,27 @@ var DatasetListItemEdit = _super.extend(
             ) {
                 return null;
             }
-            var purged = this.model.get("purged"),
-                deleted = this.model.get("deleted"),
-                editBtnData = {
-                    title: _l("Edit attributes"),
-                    href:
-                        Galaxy.root +
-                        "datasets/edit?dataset_id=" +
-                        this.model.attributes.id,
-                    faIcon: "fa-pencil",
-                    classes: "edit-btn",
-                    onclick: function(ev) {
-                        if (Galaxy.router) {
-                            ev.preventDefault();
-                            Galaxy.router.push("datasets/edit", {
-                                dataset_id: self.model.attributes.id
-                            });
-                        }
+            var purged = this.model.get("purged");
+            var deleted = this.model.get("deleted");
+
+            var editBtnData = {
+                title: _l("Edit attributes"),
+                href:
+                    Galaxy.root +
+                    "datasets/edit?dataset_id=" +
+                    this.model.attributes.id,
+                faIcon: "fa-pencil",
+                classes: "edit-btn",
+                onclick: function(ev) {
+                    if (Galaxy.router) {
+                        ev.preventDefault();
+                        Galaxy.router.push("datasets/edit", {
+                            dataset_id: self.model.attributes.id
+                        });
                     }
-                };
+                }
+            };
+
             // disable if purged or deleted and explain why in the tooltip
             if (deleted || purged) {
                 editBtnData.disabled = true;
@@ -103,8 +105,8 @@ var DatasetListItemEdit = _super.extend(
                 return null;
             }
 
-            var self = this,
-                deletedAlready = this.model.isDeletedOrPurged();
+            var self = this;
+            var deletedAlready = this.model.isDeletedOrPurged();
             return faIconButton({
                 title: !deletedAlready
                     ? _l("Delete")
@@ -124,8 +126,9 @@ var DatasetListItemEdit = _super.extend(
         /** In this override, add tags and annotations controls, make the ? dbkey a link to editing page */
         _renderDetails: function() {
             //TODO: generalize to be allow different details for each state
-            var $details = _super.prototype._renderDetails.call(this),
-                state = this.model.get("state");
+            var $details = _super.prototype._renderDetails.call(this);
+
+            var state = this.model.get("state");
 
             if (
                 !this.model.isDeletedOrPurged() &&

client/galaxy/scripts/mvc/dataset/dataset-li.js

@@ -215,8 +215,8 @@ var DatasetListItemView = _super.extend(
 
         /** Defer to the appropo summary rendering fn based on state */
         _renderSummary: function() {
-            var json = this.model.toJSON(),
-                summaryRenderFn = this.templates.summaries[json.state];
+            var json = this.model.toJSON();
+            var summaryRenderFn = this.templates.summaries[json.state];
             summaryRenderFn =
                 summaryRenderFn || this.templates.summaries.unknown;
             return summaryRenderFn(json, this);
@@ -224,9 +224,9 @@ var DatasetListItemView = _super.extend(
 
         /** Render messages to be displayed only when the details are shown */
         _renderDetailMessages: function() {
-            var view = this,
-                $warnings = $('<div class="detail-messages"></div>'),
-                json = view.model.toJSON();
+            var view = this;
+            var $warnings = $('<div class="detail-messages"></div>');
+            var json = view.model.toJSON();
             //TODO:! unordered (map)
             _.each(view.templates.detailMessages, function(templateFn) {
                 $warnings.append($(templateFn(json, view)));

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

@@ -211,8 +211,9 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
 
                 //TODO: ideally this would be a DELETE call to the api
                 //  using purge async for now
-                var hda = this,
-                    xhr = jQuery.ajax(options);
+                var hda = this;
+
+                var xhr = jQuery.ajax(options);
                 xhr.done(function(message, status, responseObj) {
                     hda.set({ deleted: true, purged: true });
                 });
@@ -327,9 +328,9 @@ var DatasetAssociationCollection = Backbone.Collection
             // ........................................................................ ajax
             /** using a queue, perform ajaxFn on each of the models in this collection */
             ajaxQueue: function(ajaxFn, options) {
-                var deferred = jQuery.Deferred(),
-                    startingLength = this.length,
-                    responses = [];
+                var deferred = jQuery.Deferred();
+                var startingLength = this.length;
+                var responses = [];
 
                 if (!startingLength) {
                     deferred.resolve([]);

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

@@ -31,8 +31,9 @@ export default Backbone.Model.extend({
         // Update URL arg with new condition.
         if (append) {
             // Update or append value.
-            var cur_val = this.attributes.filters[key],
-                new_val;
+            var cur_val = this.attributes.filters[key];
+
+            var new_val;
             if (cur_val === null || cur_val === undefined) {
                 new_val = value;
             } else if (typeof cur_val == "string") {

client/galaxy/scripts/mvc/grid/grid-view.js

@@ -378,8 +378,9 @@ export default Backbone.View.extend({
     // Set new value for categorical filter.
     set_categorical_filter: function(name, new_value) {
         // Update filter hyperlinks to reflect new filter value.
-        var category_filter = this.grid.get("categorical_filters")[name],
-            cur_value = this.grid.get("filters")[name];
+        var category_filter = this.grid.get("categorical_filters")[name];
+
+        var cur_value = this.grid.get("filters")[name];
         var self = this;
         this.$el.find("." + name + "-filter").each(function() {
             var text = $.trim($(this).text());
@@ -415,10 +416,13 @@ export default Backbone.View.extend({
         // Update page hyperlink to reflect new page.
         var self = this;
         this.$el.find(".page-link").each(function() {
-            var id = $(this).attr("id"),
-                page_num = parseInt(id.split("-")[2], 10), // Id has form 'page-link-<page_num>
-                cur_page = self.grid.get("cur_page"),
-                text;
+            var id = $(this).attr("id");
+
+            var // Id has form 'page-link-<page_num>
+            page_num = parseInt(id.split("-")[2], 10);
+
+            var cur_page = self.grid.get("cur_page");
+            var text;
             if (page_num === new_page) {
                 // Remove link to page since grid will be on this page. It is assumed that
                 // this element has a single child, a hyperlink/anchor with text.

client/galaxy/scripts/mvc/history/copy-dialog.js

@@ -89,23 +89,26 @@ var CopyDialog = {
     dialog: function _dialog(modal, history, options) {
         options = options || {};
 
-        var dialog = this,
-            deferred = jQuery.Deferred(),
-            // TODO: getting a little byzantine here
-            defaultCopyNameFn = options.nameFn || this.defaultName,
-            defaultCopyName = defaultCopyNameFn({
-                name: history.get("name")
-            }),
-            // TODO: these two might be simpler as one 3 state option (all,active,no-choice)
-            defaultCopyWhat = options.allDatasets
-                ? "copy-all"
-                : "copy-non-deleted",
-            allowAll = !_.isUndefined(options.allowAll)
-                ? options.allowAll
-                : true,
-            autoClose = !_.isUndefined(options.autoClose)
-                ? options.autoClose
-                : true;
+        var dialog = this;
+        var deferred = jQuery.Deferred();
+
+        var // TODO: getting a little byzantine here
+        defaultCopyNameFn = options.nameFn || this.defaultName;
+
+        var defaultCopyName = defaultCopyNameFn({
+            name: history.get("name")
+        });
+
+        var // TODO: these two might be simpler as one 3 state option (all,active,no-choice)
+        defaultCopyWhat = options.allDatasets ? "copy-all" : "copy-non-deleted";
+
+        var allowAll = !_.isUndefined(options.allowAll)
+            ? options.allowAll
+            : true;
+
+        var autoClose = !_.isUndefined(options.autoClose)
+            ? options.autoClose
+            : true;
 
         this.modal = modal;
 

client/galaxy/scripts/mvc/history/hda-model.js

@@ -4,8 +4,9 @@ import BASE_MVC from "mvc/base-mvc";
 import _l from "utils/localization";
 
 //==============================================================================
-var _super = DATASET.DatasetAssociation,
-    hcontentMixin = HISTORY_CONTENT.HistoryContentMixin;
+var _super = DATASET.DatasetAssociation;
+
+var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin;
 /** @class (HDA) model for a Galaxy dataset contained in and related to a history.
  */
 var HistoryDatasetAssociation = _super.extend(

client/galaxy/scripts/mvc/history/hdca-li-edit.js

@@ -41,8 +41,8 @@ var HDCAListItemEdit = _super.extend(
 
         /** Render icon-button to delete this collection. */
         _renderDeleteButton: function() {
-            var self = this,
-                deleted = this.model.get("deleted");
+            var self = this;
+            var deleted = this.model.get("deleted");
             return faIconButton({
                 title: deleted
                     ? _l("Dataset collection is already deleted")

client/galaxy/scripts/mvc/history/hdca-model.js

@@ -11,11 +11,12 @@ TODO:
     collection-model is used.
 
 ==============================================================================*/
-var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin,
-    ListDC = DC_MODEL.ListDatasetCollection,
-    PairDC = DC_MODEL.PairDatasetCollection,
-    ListPairedDC = DC_MODEL.ListPairedDatasetCollection,
-    ListOfListsDC = DC_MODEL.ListOfListsDatasetCollection;
+var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin;
+
+var ListDC = DC_MODEL.ListDatasetCollection;
+var PairDC = DC_MODEL.PairDatasetCollection;
+var ListPairedDC = DC_MODEL.ListPairedDatasetCollection;
+var ListOfListsDC = DC_MODEL.ListOfListsDatasetCollection;
 
 //==============================================================================
 /** Override to post to contents route w/o id. */

client/galaxy/scripts/mvc/history/history-contents.js

@@ -432,7 +432,10 @@ var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
     /** copy an existing, accessible hda into this collection */
     copy: function(json) {
         // TODO: somehow showhorn all this into 'save'
-        var id, type, contentType;
+        var id;
+
+        var type;
+        var contentType;
         if (_.isString(json)) {
             id = json;
             contentType = "hda";
@@ -447,30 +450,32 @@ var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
                 }[json.model_class] || "hda";
             type = contentType === "hdca" ? "dataset_collection" : "dataset";
         }
-        var collection = this,
-            xhr = jQuery
-                .ajax(this.url(), {
-                    method: "POST",
-                    contentType: "application/json",
-                    data: JSON.stringify({
-                        content: id,
-                        source: contentType,
-                        type: type
-                    })
+        var collection = this;
+
+        var xhr = jQuery
+            .ajax(this.url(), {
+                method: "POST",
+                contentType: "application/json",
+                data: JSON.stringify({
+                    content: id,
+                    source: contentType,
+                    type: type
                 })
-                .done(function(response) {
-                    collection.add([response], { parse: true });
-                })
-                .fail(function(error, status, message) {
-                    collection.trigger(
-                        "error",
-                        collection,
-                        xhr,
-                        {},
-                        "Error copying contents",
-                        { type: type, id: id, source: contentType }
-                    );
-                });
+            })
+            .done(function(response) {
+                collection.add([response], { parse: true });
+            })
+            .fail(function(error, status, message) {
+                collection.trigger(
+                    "error",
+                    collection,
+                    xhr,
+                    {},
+                    "Error copying contents",
+                    { type: type, id: id, source: contentType }
+                );
+            });
+
         return xhr;
     },
 

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

@@ -372,10 +372,11 @@ var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
             },
 
             setAsCurrent: function() {
-                var history = this,
-                    xhr = jQuery.getJSON(
-                        Galaxy.root + "history/set_as_current?id=" + this.id
-                    );
+                var history = this;
+
+                var xhr = jQuery.getJSON(
+                    Galaxy.root + "history/set_as_current?id=" + this.id
+                );
 
                 xhr.done(function() {
                     history.trigger("set-as-current", history);
@@ -546,8 +547,9 @@ var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).extend({
     /** create a new history and by default set it to be the current history */
     create: function create(data, hdas, historyOptions, xhrOptions) {
         //TODO: .create is actually a collection function that's overridden here
-        var collection = this,
-            xhr = jQuery.getJSON(Galaxy.root + "history/create_new_current");
+        var collection = this;
+
+        var xhr = jQuery.getJSON(Galaxy.root + "history/create_new_current");
         return xhr.done(function(newData) {
             collection.setCurrent(
                 new History(newData, [], historyOptions || {})

client/galaxy/scripts/mvc/history/history-structure-view.js

@@ -126,8 +126,9 @@ var HistoryStructureComponent = Backbone.View
             var view = this;
             view.component.eachVertex(function(vertex) {
                 //TODO: hack
-                var type = vertex.data.job ? "job" : "copy",
-                    li;
+                var type = vertex.data.job ? "job" : "copy";
+
+                var li;
                 if (type === "job") {
                     li = view._createJobListItem(vertex);
                 } else if (type === "copy") {
@@ -140,9 +141,9 @@ var HistoryStructureComponent = Backbone.View
 
         _createJobListItem: function(vertex) {
             this.debug("_createJobListItem:", vertex);
-            var view = this,
-                jobData = vertex.data,
-                job = new JOB.Job(jobData.job);
+            var view = this;
+            var jobData = vertex.data;
+            var job = new JOB.Job(jobData.job);
 
             // get the models of the outputs for this job from the history
             var outputModels = _.map(job.get("outputs"), function(output) {
@@ -201,13 +202,14 @@ var HistoryStructureComponent = Backbone.View
 
         _createLayout: function(options) {
             options = _.defaults(_.clone(options || {}), this.layoutDefaults);
-            var view = this,
-                vertices = _.values(view.component.vertices),
-                layout = _.extend(options, {
-                    nodeMap: {},
-                    links: [],
-                    svg: { width: 0, height: 0 }
-                });
+            var view = this;
+            var vertices = _.values(view.component.vertices);
+
+            var layout = _.extend(options, {
+                nodeMap: {},
+                links: [],
+                svg: { width: 0, height: 0 }
+            });
 
             vertices.forEach(function(v, j) {
                 var node = { name: v.name, x: 0, y: 0 };
@@ -280,8 +282,9 @@ var HistoryStructureComponent = Backbone.View
                 // position the job views accrd. to the layout
                 view.component.eachVertex(function(v) {
                     //TODO:?? liMap needed - can't we attach to vertex?
-                    var li = view._liMap[v.name],
-                        position = view.layout.nodeMap[v.name];
+                    var li = view._liMap[v.name];
+
+                    var position = view.layout.nodeMap[v.name];
                     //this.debug( position );
                     li.$el.css({ top: position.y, left: position.x });
                 });
@@ -297,8 +300,8 @@ var HistoryStructureComponent = Backbone.View
 
         _updateLayout: function() {
             this.debug(this + "._updateLayout:");
-            var view = this,
-                layout = view.layout;
+            var view = this;
+            var layout = view.layout;
 
             layout.linkHeight = layout.linkSpacing * _.size(layout.nodeMap);
             layout.svg.height = layout.linkHeight + layout.jobHeight;
@@ -308,8 +311,9 @@ var HistoryStructureComponent = Backbone.View
 
             //TODO:?? can't we just alter the component v and e's directly?
             // layout the job views putting jobSpacing btwn each
-            var x = 0,
-                y = layout.linkHeight;
+            var x = 0;
+
+            var y = layout.linkHeight;
             _.each(layout.nodeMap, function(node, jobId) {
                 //this.debug( node, jobId );
                 node.x = x;
@@ -321,8 +325,8 @@ var HistoryStructureComponent = Backbone.View
             // layout the links - connecting each job by it's main coords (currently)
             //TODO: somehow adjust the svg height based on the largest distance the longest connection needs
             layout.links.forEach(function(link) {
-                var source = layout.nodeMap[link.source],
-                    target = layout.nodeMap[link.target];
+                var source = layout.nodeMap[link.source];
+                var target = layout.nodeMap[link.target];
                 link.x1 = source.x + layout.linkAdjX;
                 link.y1 = source.y + layout.linkAdjY;
                 link.x2 = target.x + layout.linkAdjX;
@@ -335,8 +339,8 @@ var HistoryStructureComponent = Backbone.View
 
         renderSVG: function() {
             this.debug(this + ".renderSVG:");
-            var view = this,
-                layout = view.layout;
+            var view = this;
+            var layout = view.layout;
 
             var svg = d3.select(this.$graph().get(0)).select("svg");
             if (svg.empty()) {
@@ -379,11 +383,11 @@ var HistoryStructureComponent = Backbone.View
         },
 
         _connectionPath: function(d) {
-            var CURVE_X = 0,
-                controlY =
-                    (d.x2 - d.x1) /
-                    this.layout.svg.width *
-                    this.layout.linkHeight;
+            var CURVE_X = 0;
+
+            var controlY =
+                (d.x2 - d.x1) / this.layout.svg.width * this.layout.linkHeight;
+
             return [
                 "M",
                 d.x1,
@@ -418,23 +422,26 @@ var HistoryStructureComponent = Backbone.View
             this.debug("highlightConnected", jobElement, highlight);
             highlight = highlight !== undefined ? highlight : true;
 
-            var view = this,
-                component = view.component,
-                jobClassFn = highlight
-                    ? jQuery.prototype.addClass
-                    : jQuery.prototype.removeClass,
-                connectionClass = highlight
-                    ? "connection highlighted"
-                    : "connection";
+            var view = this;
+            var component = view.component;
+
+            var jobClassFn = highlight
+                ? jQuery.prototype.addClass
+                : jQuery.prototype.removeClass;
+
+            var connectionClass = highlight
+                ? "connection highlighted"
+                : "connection";
 
             //console.debug( 'mouseover', this );
-            var $hoverTarget = jobClassFn.call($(jobElement), "highlighted"),
-                id = $hoverTarget.data(view._VERTEX_NAME_DATA_KEY);
+            var $hoverTarget = jobClassFn.call($(jobElement), "highlighted");
+
+            var id = $hoverTarget.data(view._VERTEX_NAME_DATA_KEY);
 
             // immed. ancestors
             component.edges({ target: id }).forEach(function(edge) {
-                var ancestorId = edge.source,
-                    ancestorLi = view._liMap[ancestorId];
+                var ancestorId = edge.source;
+                var ancestorLi = view._liMap[ancestorId];
                 //view.debug( '\t ancestor:', ancestorId, ancestorLi );
                 jobClassFn.call(ancestorLi.$el, "highlighted");
                 view
@@ -443,8 +450,8 @@ var HistoryStructureComponent = Backbone.View
             });
             // descendants
             component.vertices[id].eachEdge(function(edge) {
-                var descendantId = edge.target,
-                    descendantLi = view._liMap[descendantId];
+                var descendantId = edge.target;
+                var descendantLi = view._liMap[descendantId];
                 //view.debug( '\t descendant:', descendantId, descendantLi );
                 jobClassFn.call(descendantLi.$el, "highlighted");
                 view
@@ -486,8 +493,8 @@ var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({
     //TODO: how can we use the dom height of the job li's - they're not visible when this is called?
     _updateLayout: function() {
         this.debug(this + "._updateLayout:");
-        var view = this,
-            layout = view.layout;
+        var view = this;
+        var layout = view.layout;
         //this.info( this.cid, '_updateLayout' )
 
         layout.linkWidth = layout.linkSpacing * _.size(layout.nodeMap);
@@ -497,8 +504,9 @@ var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({
         layout.svg.height = 0;
 
         //TODO:?? can't we just alter the component v and e's directly?
-        var x = layout.linkWidth,
-            y = 0;
+        var x = layout.linkWidth;
+
+        var y = 0;
         _.each(layout.nodeMap, function(node, nodeId) {
             node.x = x;
             node.y = y;
@@ -509,8 +517,8 @@ var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({
 
         // layout the links - connecting each job by it's main coords (currently)
         layout.links.forEach(function(link) {
-            var source = layout.nodeMap[link.source],
-                target = layout.nodeMap[link.target];
+            var source = layout.nodeMap[link.source];
+            var target = layout.nodeMap[link.target];
             link.x1 = source.x + layout.linkAdjX;
             link.y1 = source.y + layout.linkAdjY;
             link.x2 = target.x + layout.linkAdjX;
@@ -523,9 +531,11 @@ var VerticalHistoryStructureComponent = HistoryStructureComponent.extend({
     },
 
     _connectionPath: function(d) {
-        var CURVE_Y = 0,
-            controlX =
-                (d.y2 - d.y1) / this.layout.svg.height * this.layout.linkWidth;
+        var CURVE_Y = 0;
+
+        var controlX =
+            (d.y2 - d.y1) / this.layout.svg.height * this.layout.linkWidth;
+
         return [
             "M",
             d.x1,

client/galaxy/scripts/mvc/history/history-view-edit.js

@@ -229,8 +229,8 @@ var HistoryViewEdit = _super.extend(
                 return;
             }
 
-            var panel = this,
-                nameSelector = "> .controls .name";
+            var panel = this;
+            var nameSelector = "> .controls .name";
             $where
                 .find(nameSelector)
                 .attr("title", _l("Click to rename history"))
@@ -258,46 +258,47 @@ var HistoryViewEdit = _super.extend(
      *  ajax calls made for multiple datasets are queued
      */
         multiselectActions: function() {
-            var panel = this,
-                actions = [
-                    {
-                        html: _l("Hide datasets"),
-                        func: function() {
-                            var action =
-                                HDA_MODEL.HistoryDatasetAssociation.prototype
-                                    .hide;
-                            panel.getSelectedModels().ajaxQueue(action);
-                        }
-                    },
-                    {
-                        html: _l("Unhide datasets"),
-                        func: function() {
-                            var action =
-                                HDA_MODEL.HistoryDatasetAssociation.prototype
-                                    .unhide;
-                            panel.getSelectedModels().ajaxQueue(action);
-                        }
-                    },
-                    {
-                        html: _l("Delete datasets"),
-                        func: function() {
-                            var action =
-                                HDA_MODEL.HistoryDatasetAssociation.prototype[
-                                    "delete"
-                                ];
-                            panel.getSelectedModels().ajaxQueue(action);
-                        }
-                    },
-                    {
-                        html: _l("Undelete datasets"),
-                        func: function() {
-                            var action =
-                                HDA_MODEL.HistoryDatasetAssociation.prototype
-                                    .undelete;
-                            panel.getSelectedModels().ajaxQueue(action);
-                        }
+            var panel = this;
+
+            var actions = [
+                {
+                    html: _l("Hide datasets"),
+                    func: function() {
+                        var action =
+                            HDA_MODEL.HistoryDatasetAssociation.prototype.hide;
+                        panel.getSelectedModels().ajaxQueue(action);
                     }
-                ];
+                },
+                {
+                    html: _l("Unhide datasets"),
+                    func: function() {
+                        var action =
+                            HDA_MODEL.HistoryDatasetAssociation.prototype
+                                .unhide;
+                        panel.getSelectedModels().ajaxQueue(action);
+                    }
+                },
+                {
+                    html: _l("Delete datasets"),
+                    func: function() {
+                        var action =
+                            HDA_MODEL.HistoryDatasetAssociation.prototype[
+                                "delete"
+                            ];
+                        panel.getSelectedModels().ajaxQueue(action);
+                    }
+                },
+                {
+                    html: _l("Undelete datasets"),
+                    func: function() {
+                        var action =
+                            HDA_MODEL.HistoryDatasetAssociation.prototype
+                                .undelete;
+                        panel.getSelectedModels().ajaxQueue(action);
+                    }
+                }
+            ];
+
             if (panel.purgeAllowed) {
                 actions.push({
                     html: _l("Permanently delete datasets"),

client/galaxy/scripts/mvc/history/job-dag.js

@@ -59,8 +59,8 @@ JobDAG.prototype.init = function _init(options) {
 
 /** add job filters based on options */
 JobDAG.prototype._initFilters = function __initFilters() {
-    var self = this,
-        filters = [];
+    var self = this;
+    var filters = [];
 
     if (self.options.excludeSetMetadata) {
         self.filteredSetMetadata = [];
@@ -173,8 +173,9 @@ JobDAG.prototype.sort = function _sort(jobs) {
 /** decorate with input/output datasets and tool */
 JobDAG.prototype.preprocessJob = function _preprocessJob(job, index) {
     //this.info( 'preprocessJob', job, index );
-    var self = this,
-        jobData = { job: job };
+    var self = this;
+
+    var jobData = { job: job };
 
     jobData.inputs = self._processInputs(job);
     if (_.size(jobData.inputs) === 0) {
@@ -194,9 +195,9 @@ JobDAG.prototype.preprocessJob = function _preprocessJob(job, index) {
 /**
  */
 JobDAG.prototype._processInputs = function __processInputs(job) {
-    var self = this,
-        inputs = job.inputs,
-        inputMap = {};
+    var self = this;
+    var inputs = job.inputs;
+    var inputMap = {};
     _.each(inputs, function(input, nameInJob) {
         input = _.clone(self._validateInputOutput(input));
         input.name = nameInJob;
@@ -233,9 +234,9 @@ JobDAG.prototype._validateInputOutput = function __validateInputOutput(
 /**
  */
 JobDAG.prototype._processOutputs = function __processOutputs(job) {
-    var self = this,
-        outputs = job.outputs,
-        outputMap = {};
+    var self = this;
+    var outputs = job.outputs;
+    var outputMap = {};
     _.each(outputs, function(output, nameInJob) {
         output = _.clone(self._validateInputOutput(output));
         output.name = nameInJob;
@@ -321,8 +322,9 @@ JobDAG.prototype.createJobLessVertex = function _createJobLessVertex(
 ) {
     // currently, copied contents are the only history contents without jobs (that I know of)
     //note: following needed to prevent id collision btwn content and jobs in vertex map
-    var JOBLESS_ID_MANGLER = "copy-",
-        mangledId = JOBLESS_ID_MANGLER + contentId;
+    var JOBLESS_ID_MANGLER = "copy-";
+
+    var mangledId = JOBLESS_ID_MANGLER + contentId;
     return this.createVertex(mangledId, this._historyContentsMap[contentId]);
 };
 
@@ -335,11 +337,13 @@ JobDAG.prototype.weakComponentGraphArray = function() {
         //  since update_time for jobless/copied datasets is changes more often
         component.vertices.sort(function cmpCreate(a, b) {
             var aCreateTime = a.data.job
-                    ? a.data.job.create_time
-                    : a.data.create_time,
-                bCreateTime = b.data.job
-                    ? b.data.job.create_time
-                    : b.data.create_time;
+                ? a.data.job.create_time
+                : a.data.create_time;
+
+            var bCreateTime = b.data.job
+                ? b.data.job.create_time
+                : b.data.create_time;
+
             if (aCreateTime > bCreateTime) {
                 return 1;
             }

client/galaxy/scripts/mvc/history/multi-panel.js

@@ -88,8 +88,8 @@ var HistoryViewColumn = Backbone.View.extend(baseMVC.LoggableMixin).extend({
 
     /** do the dimensions of this column overlap the given (horizontal) browser coords? */
     inView: function(viewLeft, viewRight) {
-        var columnLeft = this.$el.offset().left,
-            columnRight = columnLeft + this.$el.width();
+        var columnLeft = this.$el.offset().left;
+        var columnRight = columnLeft + this.$el.width();
         if (columnRight < viewLeft) {
             return false;
         }
@@ -429,8 +429,8 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
                 this.collection.includeDeleted,
                 history
             );
-            var multipanel = this,
-                column = multipanel.columnMap[history.id];
+            var multipanel = this;
+            var column = multipanel.columnMap[history.id];
             if (!column) {
                 return;
             }
@@ -538,8 +538,9 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     /** add a new column for history and make it the current history/column */
     addAsCurrentColumn: function add(history, collection, options) {
         //this.log( 'adding current column for:', history );
-        var multipanel = this,
-            newColumn = this.addColumn(history, false);
+        var multipanel = this;
+
+        var newColumn = this.addColumn(history, false);
         this.setCurrentHistory(history);
         newColumn.once("rendered", function() {
             multipanel.queueHdaFetch(newColumn);
@@ -554,8 +555,8 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
         if (!column) {
             return;
         }
-        var multipanel = this,
-            widthToRemove = this.options.columnWidth + this.options.columnGap;
+        var multipanel = this;
+        var widthToRemove = this.options.columnWidth + this.options.columnGap;
         column.$el.fadeOut("fast", function() {
             if (render) {
                 $(this).remove();
@@ -863,9 +864,9 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
 
     /** change the collection order and re-fetch when the drop down in the options menu is changed */
     _chooseOrder: function(ev) {
-        var multipanel = this,
-            collection = multipanel.collection,
-            orderKey = $(ev.currentTarget).data("order");
+        var multipanel = this;
+        var collection = multipanel.collection;
+        var orderKey = $(ev.currentTarget).data("order");
         // set the sort order text also
         multipanel
             .$(".current-order")
@@ -1010,9 +1011,9 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
 
     /** Adjust the height of the first, current column since flex-boxes won't work with fixed postiion elements */
     _recalcFirstColumnHeight: function() {
-        var $firstColumn = this.$(".history-column").first(),
-            middleHeight = this.$(".middle").height(),
-            controlHeight = $firstColumn.find(".panel-controls").height();
+        var $firstColumn = this.$(".history-column").first();
+        var middleHeight = this.$(".middle").height();
+        var controlHeight = $firstColumn.find(".panel-controls").height();
         $firstColumn
             .height(middleHeight)
             .find(".inner")
@@ -1021,9 +1022,9 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
 
     /** Get the left and right pixel coords of the middle element */
     _viewport: function() {
-        var $outerMiddle = this.$(".middle").parent(),
-            viewLeft = $outerMiddle.offset().left,
-            width = $outerMiddle.width();
+        var $outerMiddle = this.$(".middle").parent();
+        var viewLeft = $outerMiddle.offset().left;
+        var width = $outerMiddle.width();
         return {
             left: viewLeft,
             right: viewLeft + width
@@ -1052,9 +1053,9 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
     /** is the middle, horizontally scrolling section scrolled fully to the right? */
     checkForEndOfScroll: function(viewport) {
         viewport = viewport || this._viewport();
-        var END_PADDING = 16,
-            $middle = this.$(".middle"),
-            scrollRight = $middle.parent().scrollLeft() + viewport.right;
+        var END_PADDING = 16;
+        var $middle = this.$(".middle");
+        var scrollRight = $middle.parent().scrollLeft() + viewport.right;
         if (scrollRight >= $middle.width() - END_PADDING) {
             this.trigger("end-of-scroll");
         }

client/galaxy/scripts/mvc/history/options-menu.js

@@ -254,9 +254,9 @@ function buildMenu(isAnon, purgeAllowed, urlRoot) {
 
 var create = function($button, options) {
     options = options || {};
-    var isAnon = options.anonymous === undefined ? true : options.anonymous,
-        purgeAllowed = options.purgeAllowed || false,
-        menu = buildMenu(isAnon, purgeAllowed, Galaxy.root);
+    var isAnon = options.anonymous === undefined ? true : options.anonymous;
+    var purgeAllowed = options.purgeAllowed || false;
+    var menu = buildMenu(isAnon, purgeAllowed, Galaxy.root);
     //console.debug( 'menu:', menu );
     return new PopupMenu($button, menu);
 };

client/galaxy/scripts/mvc/job/job-li.js

@@ -59,8 +59,9 @@ var JobListItemView = _super.extend(
         /** Return tool.inputs that should/can be safely displayed */
         _labelParamMap: function() {
             //ADAPTER
-            var params = this.model.get("params"),
-                labelParamMap = {};
+            var params = this.model.get("params");
+
+            var labelParamMap = {};
             _.each(this.tool.inputs, function(i) {
                 //console.debug( i.label, i.model_class );
                 if (i.label && i.model_class !== "DataToolParameter") {
@@ -72,8 +73,9 @@ var JobListItemView = _super.extend(
 
         _labelInputMap: function() {
             //ADAPTER
-            var view = this,
-                labelInputMap = {};
+            var view = this;
+
+            var labelInputMap = {};
             _.each(this.jobData.inputs, function(input) {
                 var toolInput = view._findToolInput(input.name);
                 if (toolInput) {
@@ -86,8 +88,9 @@ var JobListItemView = _super.extend(
         /** Return a tool.inputs object that matches (or partially matches) the given (job input) name */
         _findToolInput: function(name) {
             //ADAPTER
-            var toolInputs = this.tool.inputs,
-                exactMatch = _.findWhere(toolInputs, { name: name });
+            var toolInputs = this.tool.inputs;
+
+            var exactMatch = _.findWhere(toolInputs, { name: name });
             if (exactMatch) {
                 return exactMatch;
             }

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

@@ -166,14 +166,16 @@ var JobCollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(
         // ........................................................................ ajax
         /** fetches all details for each job in the collection using a queue */
         queueDetailFetching: function() {
-            var collection = this,
-                queue = new AJAX_QUEUE.AjaxQueue(
-                    this.map(function(job) {
-                        return function() {
-                            return job.fetch({ silent: true });
-                        };
-                    })
-                );
+            var collection = this;
+
+            var queue = new AJAX_QUEUE.AjaxQueue(
+                this.map(function(job) {
+                    return function() {
+                        return job.fetch({ silent: true });
+                    };
+                })
+            );
+
             queue.done(function() {
                 collection.trigger("details-loaded");
             });
@@ -204,8 +206,8 @@ var JobCollection = Backbone.Collection.extend(BASE_MVC.LoggableMixin).extend(
         /** class level fn for fetching the job details for all jobs in a history */
         fromHistory: function(historyId) {
             console.debug(this);
-            var Collection = this,
-                collection = new Collection([]);
+            var Collection = this;
+            var collection = new Collection([]);
             collection
                 .fetch({ data: { history_id: historyId } })
                 .done(function() {

client/galaxy/scripts/mvc/job/job-params.js

@@ -2,9 +2,9 @@
 import Utils from "utils/utils";
 /** Build messages after user action */
 function build_messages(self) {
-    var $el_message = self.$el.find(".response-message"),
-        status = Utils.getQueryString("status"),
-        message = Utils.getQueryString("message");
+    var $el_message = self.$el.find(".response-message");
+    var status = Utils.getQueryString("status");
+    var message = Utils.getQueryString("message");
 
     if (message && message !== "") {
         $el_message.addClass(status + "message");

client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js

@@ -168,8 +168,8 @@ var FolderToolbarView = Backbone.View.extend({
         var folderDetails = this.serialize_new_folder();
         if (this.validate_new_folder(folderDetails)) {
             var folder = new mod_library_model.FolderAsModel();
-            var url_items = Backbone.history.fragment.split("/"),
-                current_folder_id;
+            var url_items = Backbone.history.fragment.split("/");
+            var current_folder_id;
             if (url_items.indexOf("page") > -1) {
                 current_folder_id = url_items[url_items.length - 3];
             } else {

client/galaxy/scripts/mvc/list/list-item.js

@@ -153,8 +153,8 @@ var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({
 
     /** Inner fn called when expand (public) has fetched the details */
     _expand: function() {
-        var view = this,
-            $newDetails = view._renderDetails();
+        var view = this;
+        var $newDetails = view._renderDetails();
         view.$details().replaceWith($newDetails);
         // needs to be set after the above or the slide will not show
         view.expanded = true;
@@ -253,9 +253,9 @@ var ListItemView = ExpandableView.extend(
 
         /** Render any warnings the item may need to show (e.g. "I'm deleted") */
         _renderWarnings: function() {
-            var view = this,
-                $warnings = $('<div class="warnings"></div>'),
-                json = view.model.toJSON();
+            var view = this;
+            var $warnings = $('<div class="warnings"></div>');
+            var json = view.model.toJSON();
             //TODO:! unordered (map)
             _.each(view.templates.warnings, function(templateFn) {
                 $warnings.append($(templateFn(json, view)));
@@ -304,8 +304,9 @@ var ListItemView = ExpandableView.extend(
         /** expand when the title bar is in focus and enter or space is pressed */
         _keyDownTitleBar: function(event) {
             // bail (with propagation) if keydown and not space or enter
-            var KEYCODE_SPACE = 32,
-                KEYCODE_RETURN = 13;
+            var KEYCODE_SPACE = 32;
+
+            var KEYCODE_RETURN = 13;
             if (
                 event &&
                 event.type === "keydown" &&
@@ -433,13 +434,15 @@ var FoldoutListItemView = ListItemView.extend({
     /** In this override, handle collection expansion. */
     _createFoldoutPanel: function() {
         var model = this.model;
-        var FoldoutClass = this._getFoldoutPanelClass(model),
-            options = this._getFoldoutPanelOptions(model),
-            foldout = new FoldoutClass(
-                _.extend(options, {
-                    model: model
-                })
-            );
+        var FoldoutClass = this._getFoldoutPanelClass(model);
+        var options = this._getFoldoutPanelOptions(model);
+
+        var foldout = new FoldoutClass(
+            _.extend(options, {
+                model: model
+            })
+        );
+
         return foldout;
     },
 

client/galaxy/scripts/mvc/list/list-view.js

@@ -312,8 +312,8 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
         /** render a menu containing the actions available to sets of selected items */
         _renderMultiselectActionMenu: function($where) {
             $where = $where || this.$el;
-            var $menu = $where.find(".list-action-menu"),
-                actions = this.multiselectActions();
+            var $menu = $where.find(".list-action-menu");
+            var actions = this.multiselectActions();
             if (!actions.length) {
                 return $menu.empty();
             }
@@ -499,8 +499,9 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
                 "draggable:dragstart",
                 function(ev, v) {
                     //TODO: set multiple drag data here
-                    var json = {},
-                        selected = this.getSelectedModels();
+                    var json = {};
+
+                    var selected = this.getSelectedModels();
                     if (selected.length) {
                         json = selected.toJSON();
                     } else {
@@ -684,8 +685,8 @@ var ListPanel = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(
                 return viewA ? [viewA] : [];
             }
 
-            var indexA = this.views.indexOf(viewA),
-                indexB = this.views.indexOf(viewB);
+            var indexA = this.views.indexOf(viewA);
+            var indexB = this.views.indexOf(viewB);
 
             // handle not found
             if (indexA === -1 || indexB === -1) {
@@ -1068,8 +1069,8 @@ var ModelListPanel = ListPanel.extend({
      */
     _renderControls: function($newRender) {
         this.debug(this + "(ModelListPanel)._renderControls");
-        var json = this.model ? this.model.toJSON() : {},
-            $controls = $(this.templates.controls(json, this));
+        var json = this.model ? this.model.toJSON() : {};
+        var $controls = $(this.templates.controls(json, this));
         $newRender.find(".controls").replaceWith($controls);
         return $controls;
     },

client/galaxy/scripts/mvc/tool/tool-form-composite.js

@@ -146,8 +146,8 @@ var View = Backbone.View.extend({
         var wp_count = 0;
         this.wp_inputs = {};
         function _handleWorkflowParameter(value, callback) {
-            var re = /\$\{(.+?)\}/g,
-                match;
+            var re = /\$\{(.+?)\}/g;
+            var match;
             while ((match = re.exec(String(value)))) {
                 var wp_name = match[1];
                 callback(
@@ -509,8 +509,8 @@ var View = Backbone.View.extend({
                             }
                         } else if (input.wp_linked) {
                             new_value = input.value;
-                            var re = /\$\{(.+?)\}/g,
-                                match;
+                            var re = /\$\{(.+?)\}/g;
+                            var match;
                             while ((match = re.exec(input.value))) {
                                 var wp_field =
                                     self.wp_form.field_list[

client/galaxy/scripts/mvc/tool/tools.js

@@ -160,10 +160,12 @@ var Tool = Backbone.Model.extend({
      * client and server yet.
      */
     remove_inputs: function(types) {
-        var tool = this,
-            incompatible_inputs = tool.get("inputs").filter(function(input) {
-                return types.indexOf(input.get("type")) !== -1;
-            });
+        var tool = this;
+
+        var incompatible_inputs = tool.get("inputs").filter(function(input) {
+            return types.indexOf(input.get("type")) !== -1;
+        });
+
         tool.get("inputs").remove(incompatible_inputs);
     },
 
@@ -261,20 +263,21 @@ var Tool = Backbone.Model.extend({
         // Because job may require indexing datasets, use server-side
         // deferred to ensure that job is run. Also use deferred that
         // resolves to outputs from tool.
-        var run_deferred = $.Deferred(),
-            ss_deferred = new util.ServerStateDeferred({
-                ajax_settings: {
-                    url: this.urlRoot,
-                    data: JSON.stringify(payload),
-                    dataType: "json",
-                    contentType: "application/json",
-                    type: "POST"
-                },
-                interval: 2000,
-                success_fn: function(response) {
-                    return response !== "pending";
-                }
-            });
+        var run_deferred = $.Deferred();
+
+        var ss_deferred = new util.ServerStateDeferred({
+            ajax_settings: {
+                url: this.urlRoot,
+                data: JSON.stringify(payload),
+                dataType: "json",
+                contentType: "application/json",
+                type: "POST"
+            },
+            interval: 2000,
+            success_fn: function(response) {
+                return response !== "pending";
+            }
+        });
 
         // Run job and resolve run_deferred to tool outputs.
         $.when(ss_deferred.go()).then(function(result) {
@@ -321,8 +324,8 @@ var ToolSection = Backbone.Model.extend({
     },
 
     apply_search_results: function(results) {
-        var all_hidden = true,
-            cur_label;
+        var all_hidden = true;
+        var cur_label;
         _.each(this.attributes.elems, function(elt) {
             if (elt instanceof ToolSectionLabel) {
                 cur_label = elt;
@@ -439,23 +442,24 @@ var ToolPanel = Backbone.Model.extend({
      */
     parse: function(response) {
         // Recursive function to parse tool panel elements.
-        var self = this,
-            // Helper to recursively parse tool panel.
-            parse_elt = function(elt_dict) {
-                var type = elt_dict.model_class;
-                // There are many types of tools; for now, anything that ends in 'Tool'
-                // is treated as a generic tool.
-                if (type.indexOf("Tool") === type.length - 4) {
-                    return self.attributes.tools.get(elt_dict.id);
-                } else if (type === "ToolSection") {
-                    // Parse elements.
-                    var elems = _.map(elt_dict.elems, parse_elt);
-                    elt_dict.elems = elems;
-                    return new ToolSection(elt_dict);
-                } else if (type === "ToolSectionLabel") {
-                    return new ToolSectionLabel(elt_dict);
-                }
-            };
+        var self = this;
+
+        var // Helper to recursively parse tool panel.
+        parse_elt = function(elt_dict) {
+            var type = elt_dict.model_class;
+            // There are many types of tools; for now, anything that ends in 'Tool'
+            // is treated as a generic tool.
+            if (type.indexOf("Tool") === type.length - 4) {
+                return self.attributes.tools.get(elt_dict.id);
+            } else if (type === "ToolSection") {
+                // Parse elements.
+                var elems = _.map(elt_dict.elems, parse_elt);
+                elt_dict.elems = elems;
+                return new ToolSection(elt_dict);
+            } else if (type === "ToolSectionLabel") {
+                return new ToolSectionLabel(elt_dict);
+            }
+        };
 
         return _.map(response, parse_elt);
     },
@@ -737,9 +741,10 @@ var ToolPanelView = Backbone.View.extend({
         self.$el.find("a.tool-link").click(function(e) {
             // Tool id is always the first class.
             var tool_id = $(this)
-                    .attr("class")
-                    .split(/\s+/)[0],
-                tool = self.model.get("tools").get(tool_id);
+                .attr("class")
+                .split(/\s+/)[0];
+
+            var tool = self.model.get("tools").get(tool_id);
 
             self.trigger("tool_link_click", e, tool);
         });

client/galaxy/scripts/mvc/toolshed/workflows-view.js

@@ -29,8 +29,8 @@ var View = Backbone.View.extend({
     },
 
     bindEvents: function() {
-        var that = this,
-            repository_id;
+        var that = this;
+        var repository_id;
         $(".show_wf_repo").on("click", function() {
             var tool_ids = $(this).attr("data-toolids");
             var toolshed = $(this).attr("data-shed");

client/galaxy/scripts/mvc/ui/popup-menu.js

@@ -95,11 +95,13 @@ var PopupMenu = Backbone.View.extend({
                     "</a></li>"
                 ].join("");
             }
-            var href = option.href || "javascript:void(0);",
-                target = option.target ? ' target="' + option.target + '"' : "",
-                check = option.checked
-                    ? '<span class="fa fa-check"></span>'
-                    : "";
+            var href = option.href || "javascript:void(0);";
+            var target = option.target ? ' target="' + option.target + '"' : "";
+
+            var check = option.checked
+                ? '<span class="fa fa-check"></span>'
+                : "";
+
             return [
                 '<li><a class="popupmenu-option" href="',
                 href,
@@ -257,15 +259,15 @@ PopupMenu.convertLinksToOptions = function($parent, selector) {
     selector = selector || "a";
     var options = [];
     $parent.find(selector).each(function(elem, i) {
-        var option = {},
-            $link = $(elem);
+        var option = {};
+        var $link = $(elem);
 
         // convert link text to the option text (html) and the href into the option func
         option.html = $link.text();
         if ($link.attr("href")) {
-            var linkHref = $link.attr("href"),
-                linkTarget = $link.attr("target"),
-                confirmText = $link.attr("confirm");
+            var linkHref = $link.attr("href");
+            var linkTarget = $link.attr("target");
+            var confirmText = $link.attr("confirm");
 
             option.func = function() {
                 // if there's a "confirm" attribute, throw up a confirmation dialog, and
@@ -348,10 +350,12 @@ PopupMenu.make_popup_menus = function(
     $(parent)
         .find(menuSelector)
         .each(function() {
-            var $menuElement = $(this),
-                $buttonElement = $(parent).find(
-                    buttonSelectorBuildFn($menuElement, parent)
-                );
+            var $menuElement = $(this);
+
+            var $buttonElement = $(parent).find(
+                buttonSelectorBuildFn($menuElement, parent)
+            );
+
             popupMenusCreated.push(
                 PopupMenu.fromDom($buttonElement, $menuElement)
             );

client/galaxy/scripts/mvc/ui/ui-popover.js

@@ -126,7 +126,9 @@ var View = Backbone.View.extend({
         var container_position = $container.position();
 
         // get position
-        var top, left;
+        var top;
+
+        var left;
         top = left = 0;
         if (["top", "bottom"].indexOf(placement) != -1) {
             left =

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

@@ -64,8 +64,8 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
             idOrCurrent = idOrCurrent || User.CURRENT_ID_STR;
 
             options = options || {};
-            var model = this,
-                userFn = options.success;
+            var model = this;
+            var userFn = options.success;
 
             /** @ignore */
             options.success = function(newModel, response) {

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

@@ -58,12 +58,15 @@ var UserQuotaMeter = Backbone.View.extend(baseMVC.LoggableMixin).extend(
      *  @returns {jQuery} the rendered meter
      */
         _render_quota: function() {
-            var modelJson = this.model.toJSON(),
-                //prevPercent = this.model.previous( 'quota_percent' ),
-                percent = modelJson.quota_percent,
-                //meter = $( UserQuotaMeter.templates.quota( modelJson ) );
-                $meter = $(this._templateQuotaMeter(modelJson)),
-                $bar = $meter.find(".progress-bar");
+            var modelJson = this.model.toJSON();
+
+            var //prevPercent = this.model.previous( 'quota_percent' ),
+            percent = modelJson.quota_percent;
+
+            var //meter = $( UserQuotaMeter.templates.quota( modelJson ) );
+            $meter = $(this._templateQuotaMeter(modelJson));
+
+            var $bar = $meter.find(".progress-bar");
             //this.log( this + '.rendering quota, percent:', percent, 'meter:', meter );
 
             // OVER QUOTA: color the quota bar and show the quota error message

client/galaxy/scripts/mvc/workflow/workflow-canvas.js

@@ -30,7 +30,8 @@ $.extend(CanvasManager.prototype, {
         this.cc.each(function() {
             this.scroll_panel = new ScrollPanel(this);
         });
-        var x_adjust, y_adjust;
+        var x_adjust;
+        var y_adjust;
         this.cv
             .bind("dragstart", function() {
                 var o = $(this).offset();
@@ -49,14 +50,17 @@ $.extend(CanvasManager.prototype, {
             if (self.overview.hasClass("blockaclick")) {
                 self.overview.removeClass("blockaclick");
             } else {
-                var in_w = self.cc.width(),
-                    in_h = self.cc.height(),
-                    o_w = self.oc.width(),
-                    o_h = self.oc.height(),
-                    new_x_offset =
-                        e.pageX - self.oc.offset().left - self.ov.width() / 2,
-                    new_y_offset =
-                        e.pageY - self.oc.offset().top - self.ov.height() / 2;
+                var in_w = self.cc.width();
+                var in_h = self.cc.height();
+                var o_w = self.oc.width();
+                var o_h = self.oc.height();
+
+                var new_x_offset =
+                    e.pageX - self.oc.offset().left - self.ov.width() / 2;
+
+                var new_y_offset =
+                    e.pageY - self.oc.offset().top - self.ov.height() / 2;
+
                 move(
                     -(new_x_offset / o_w * in_w),
                     -(new_y_offset / o_h * in_h)
@@ -68,12 +72,12 @@ $.extend(CanvasManager.prototype, {
         // Dragging for overview pane
         this.ov
             .bind("drag", function(e, d) {
-                var in_w = self.cc.width(),
-                    in_h = self.cc.height(),
-                    o_w = self.oc.width(),
-                    o_h = self.oc.height(),
-                    new_x_offset = d.offsetX - self.overview.offset().left,
-                    new_y_offset = d.offsetY - self.overview.offset().top;
+                var in_w = self.cc.width();
+                var in_h = self.cc.height();
+                var o_w = self.oc.width();
+                var o_h = self.oc.height();
+                var new_x_offset = d.offsetX - self.overview.offset().left;
+                var new_y_offset = d.offsetY - self.overview.offset().top;
                 move(
                     -(new_x_offset / o_w * in_w),
                     -(new_y_offset / o_h * in_h)
@@ -104,15 +108,15 @@ $.extend(CanvasManager.prototype, {
         $("#overview-border div").bind("drag", function() {});
     },
     update_viewport_overlay: function() {
-        var cc = this.cc,
-            cv = this.cv,
-            oc = this.oc,
-            ov = this.ov,
-            in_w = cc.width(),
-            in_h = cc.height(),
-            o_w = oc.width(),
-            o_h = oc.height(),
-            cc_pos = cc.position();
+        var cc = this.cc;
+        var cv = this.cv;
+        var oc = this.oc;
+        var ov = this.ov;
+        var in_w = cc.width();
+        var in_h = cc.height();
+        var o_w = oc.width();
+        var o_h = oc.height();
+        var cc_pos = cc.position();
         ov.css({
             left: -(cc_pos.left / in_w * o_w),
             top: -(cc_pos.top / in_h * o_h),
@@ -122,15 +126,20 @@ $.extend(CanvasManager.prototype, {
         });
     },
     draw_overview: function() {
-        var canvas_el = $("#overview-canvas"),
-            size = canvas_el
-                .parent()
-                .parent()
-                .width(),
-            c = canvas_el.get(0).getContext("2d"),
-            in_w = $("#canvas-container").width(),
-            in_h = $("#canvas-container").height();
-        var o_h, shift_h, o_w, shift_w;
+        var canvas_el = $("#overview-canvas");
+
+        var size = canvas_el
+            .parent()
+            .parent()
+            .width();
+
+        var c = canvas_el.get(0).getContext("2d");
+        var in_w = $("#canvas-container").width();
+        var in_h = $("#canvas-container").height();
+        var o_h;
+        var shift_h;
+        var o_w;
+        var shift_w;
         // Fit canvas into overview area
         var cv_w = this.cv.width();
         var cv_h = this.cv.height();
@@ -166,12 +175,12 @@ $.extend(CanvasManager.prototype, {
             c.fillStyle = "#D2C099";
             c.strokeStyle = "#D8B365";
             c.lineWidth = 1;
-            var node_element = $(node.element),
-                position = node_element.position(),
-                x = position.left / in_w * o_w,
-                y = position.top / in_h * o_h,
-                w = node_element.width() / in_w * o_w,
-                h = node_element.height() / in_h * o_h;
+            var node_element = $(node.element);
+            var position = node_element.position();
+            var x = position.left / in_w * o_w;
+            var y = position.top / in_h * o_h;
+            var w = node_element.width() / in_w * o_w;
+            var h = node_element.height() / in_h * o_h;
             if (node.errors) {
                 c.fillStyle = "#FFCCCC";
                 c.strokeStyle = "#AA6666";
@@ -196,33 +205,44 @@ function ScrollPanel(panel) {
 $.extend(ScrollPanel.prototype, {
     test: function(e, onmove) {
         clearTimeout(this.timeout);
-        var x = e.pageX,
-            y = e.pageY,
-            // Panel size and position
-            panel = $(this.panel),
-            panel_pos = panel.position(),
-            panel_w = panel.width(),
-            panel_h = panel.height(),
-            // Viewport size and offset
-            viewport = panel.parent(),
-            viewport_w = viewport.width(),
-            viewport_h = viewport.height(),
-            viewport_offset = viewport.offset(),
-            // Edges of viewport (in page coordinates)
-            min_x = viewport_offset.left,
-            min_y = viewport_offset.top,
-            max_x = min_x + viewport.width(),
-            max_y = min_y + viewport.height(),
-            // Legal panel range
-            p_min_x = -(panel_w - viewport_w / 2),
-            p_min_y = -(panel_h - viewport_h / 2),
-            p_max_x = viewport_w / 2,
-            p_max_y = viewport_h / 2,
-            // Did the panel move?
-            moved = false,
-            // Constants
-            close_dist = 5,
-            nudge = 23;
+        var x = e.pageX;
+        var y = e.pageY;
+
+        var // Panel size and position
+        panel = $(this.panel);
+
+        var panel_pos = panel.position();
+        var panel_w = panel.width();
+        var panel_h = panel.height();
+
+        var // Viewport size and offset
+        viewport = panel.parent();
+
+        var viewport_w = viewport.width();
+        var viewport_h = viewport.height();
+        var viewport_offset = viewport.offset();
+
+        var // Edges of viewport (in page coordinates)
+        min_x = viewport_offset.left;
+
+        var min_y = viewport_offset.top;
+        var max_x = min_x + viewport.width();
+        var max_y = min_y + viewport.height();
+
+        var // Legal panel range
+        p_min_x = -(panel_w - viewport_w / 2);
+
+        var p_min_y = -(panel_h - viewport_h / 2);
+        var p_max_x = viewport_w / 2;
+        var p_max_y = viewport_h / 2;
+
+        var // Did the panel move?
+        moved = false;
+
+        var // Constants
+        close_dist = 5;
+
+        var nudge = 23;
         if (x - close_dist < min_x) {
             if (panel_pos.left < p_max_x) {
                 var t = Math.min(nudge, p_max_x - panel_pos.left);

client/galaxy/scripts/mvc/workflow/workflow-connector.js

@@ -83,11 +83,13 @@ $.extend(Connector.prototype, {
         start_y -= canvas_top;
         end_x -= canvas_left;
         end_y -= canvas_top;
+
         // Draw the line
 
-        var c = this.canvas.getContext("2d"),
-            start_offsets = null,
-            end_offsets = null;
+        var c = this.canvas.getContext("2d");
+
+        var start_offsets = null;
+        var end_offsets = null;
         var num_offsets = 1;
         if (this.handle1 && this.handle1.isMappedOver()) {
             var start_offsets = [-6, -3, 0, 3, 6];
@@ -103,8 +105,8 @@ $.extend(Connector.prototype, {
         }
         var connector = this;
         for (var i = 0; i < num_offsets; i++) {
-            var inner_width = 5,
-                outer_width = 7;
+            var inner_width = 5;
+            var outer_width = 7;
             if (start_offsets.length > 1 || end_offsets.length > 1) {
                 // We have a multi-run, using many lines, make them small.
                 inner_width = 1;

client/galaxy/scripts/mvc/workflow/workflow-manager.js

@@ -434,11 +434,11 @@ $.extend(Workflow.prototype, {
         });
     },
     bounds_for_all_nodes: function() {
-        var xmin = Infinity,
-            xmax = -Infinity,
-            ymin = Infinity,
-            ymax = -Infinity,
-            p;
+        var xmin = Infinity;
+        var xmax = -Infinity;
+        var ymin = Infinity;
+        var ymax = -Infinity;
+        var p;
         $.each(this.nodes, function(id, node) {
             var e = $(node.element);
             p = e.position();

client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js

@@ -192,10 +192,11 @@ var BaseOutputTerminalView = TerminalView.extend({
     onDrag: function(e, d) {
         var onmove = function() {
             var po = $(d.proxy)
-                    .offsetParent()
-                    .offset(),
-                x = d.offsetX - po.left,
-                y = d.offsetY - po.top;
+                .offsetParent()
+                .offset();
+
+            var x = d.offsetX - po.left;
+            var y = d.offsetY - po.top;
             $(d.proxy).css({ left: x, top: y });
             d.proxy.terminal.redraw();
             // FIXME: global

client/galaxy/scripts/mvc/workflow/workflow-view.js

@@ -644,7 +644,8 @@ export default Backbone.View.extend({
     scroll_to_nodes: function() {
         var cv = $("#canvas-viewport");
         var cc = $("#canvas-container");
-        var top, left;
+        var top;
+        var left;
         if (cc.width() < cv.width()) {
             left = (cv.width() - cc.width()) / 2;
         } else {
@@ -923,10 +924,11 @@ export default Backbone.View.extend({
             .bind("drag", function(e, d) {
                 // Move
                 var po = $(this)
-                        .offsetParent()
-                        .offset(),
-                    x = d.offsetX - po.left,
-                    y = d.offsetY - po.top;
+                    .offsetParent()
+                    .offset();
+
+                var x = d.offsetX - po.left;
+                var y = d.offsetY - po.top;
                 $(this).css({ left: x, top: y });
                 // Redraw
                 $(this)

client/galaxy/scripts/onload.js

@@ -87,12 +87,14 @@ function init_refresh_on_change() {
     $("select[refresh_on_change='true']")
         .off("change")
         .change(function() {
-            var select_field = $(this),
-                select_val = select_field.val(),
-                refresh = false,
-                ref_on_change_vals = select_field.attr(
-                    "refresh_on_change_values"
-                );
+            var select_field = $(this);
+            var select_val = select_field.val();
+            var refresh = false;
+
+            var ref_on_change_vals = select_field.attr(
+                "refresh_on_change_values"
+            );
+
             if (ref_on_change_vals) {
                 ref_on_change_vals = ref_on_change_vals.split(",");
                 var last_selected_value = select_field.attr(
@@ -114,12 +116,14 @@ function init_refresh_on_change() {
     $(":checkbox[refresh_on_change='true']")
         .off("click")
         .click(function() {
-            var select_field = $(this),
-                select_val = select_field.val(),
-                refresh = false,
-                ref_on_change_vals = select_field.attr(
-                    "refresh_on_change_values"
-                );
+            var select_field = $(this);
+            var select_val = select_field.val();
+            var refresh = false;
+
+            var ref_on_change_vals = select_field.attr(
+                "refresh_on_change_values"
+            );
+
             if (ref_on_change_vals) {
                 ref_on_change_vals = ref_on_change_vals.split(",");
                 var last_selected_value = select_field.attr(

client/galaxy/scripts/reports_webapp/run_stats.js

@@ -578,8 +578,8 @@ function create_histogram(inp_data, name, title) {
 
     // Formatter for x axis times (converting minutes to HH:MM).
     var formatMinutes = function(d) {
-        var hours = Math.floor(d / 60),
-            minutes = Math.floor(d - hours * 60);
+        var hours = Math.floor(d / 60);
+        var minutes = Math.floor(d - hours * 60);
 
         if (hours < 10) {
             hours = "0" + hours;
@@ -628,8 +628,9 @@ function create_histogram(inp_data, name, title) {
         })
         .on("mouseenter", function(d) {
             // Show tool tip
-            var i = 0,
-                size = d.length;
+            var i = 0;
+
+            var size = d.length;
 
             while (size >= 1) {
                 size = size / 10;

client/galaxy/scripts/ui/editable-text.js

@@ -11,12 +11,15 @@ var $ = jQuery;
  */
 $.fn.make_text_editable = function(config_dict) {
     // Get config options.
-    var num_cols = "num_cols" in config_dict ? config_dict.num_cols : 30,
-        num_rows = "num_rows" in config_dict ? config_dict.num_rows : 4,
-        use_textarea =
-            "use_textarea" in config_dict ? config_dict.use_textarea : false,
-        on_finish = "on_finish" in config_dict ? config_dict.on_finish : null,
-        help_text = "help_text" in config_dict ? config_dict.help_text : null;
+    var num_cols = "num_cols" in config_dict ? config_dict.num_cols : 30;
+
+    var num_rows = "num_rows" in config_dict ? config_dict.num_rows : 4;
+
+    var use_textarea =
+        "use_textarea" in config_dict ? config_dict.use_textarea : false;
+
+    var on_finish = "on_finish" in config_dict ? config_dict.on_finish : null;
+    var help_text = "help_text" in config_dict ? config_dict.help_text : null;
 
     // Add element behavior.
     var container = $(this);
@@ -47,11 +50,10 @@ $.fn.make_text_editable = function(config_dict) {
 
         // Create input element(s) for editing.
         var cur_text =
-                "cur_text" in config_dict
-                    ? config_dict.cur_text
-                    : container.text(),
-            input_elt,
-            button_elt;
+            "cur_text" in config_dict ? config_dict.cur_text : container.text();
+
+        var input_elt;
+        var button_elt;
 
         if (use_textarea) {
             input_elt = $("<textarea/>")

client/galaxy/scripts/ui/filter-control.js

@@ -53,9 +53,9 @@ function dropDownSelect(options, selected) {
 
     // trigger 'change.dropdown-select' when a new selection is made using the dropdown
     function selectThis(event) {
-        var $this = $(this),
-            $select = $this.parents(".dropdown-select"),
-            newSelection = $this.text();
+        var $this = $(this);
+        var $select = $this.parents(".dropdown-select");
+        var newSelection = $this.text();
         $select.find(".dropdown-select-selected").text(newSelection);
         $select.trigger("change.dropdown-select", newSelection);
     }
@@ -140,8 +140,8 @@ FilterControl.prototype._renderKeySelect = function __renderKeySelect() {
 
 /** render the op dropDownSelect, bind a change event to it, and return it */
 FilterControl.prototype._renderOpSelect = function __renderOpSelect() {
-    var filterControl = this,
-        ops = this.currFilter.ops;
+    var filterControl = this;
+    var ops = this.currFilter.ops;
     //TODO: search for currOp in avail. ops: use that for selected if there; otherwise: first op
     this.$opSelect = dropDownSelect(ops, ops[0])
         .addClass("filter-control-op")
@@ -177,16 +177,20 @@ FilterControl.prototype._renderValueInput = function __renderValueInput() {
 /** return the current state/setting for the filter as a three key object: key, op, value */
 FilterControl.prototype.val = function _val() {
     var key = this.$element
-            .find(".filter-control-key .dropdown-select-selected")
-            .text(),
-        op = this.$element
-            .find(".filter-control-op .dropdown-select-selected")
-            .text(),
-        // handle either a dropdown or plain input
-        $value = this.$element.find(".filter-control-value"),
-        value = $value.hasClass("dropdown-select")
-            ? $value.find(".dropdown-select-selected").text()
-            : $value.val();
+        .find(".filter-control-key .dropdown-select-selected")
+        .text();
+
+    var op = this.$element
+        .find(".filter-control-op .dropdown-select-selected")
+        .text();
+
+    var // handle either a dropdown or plain input
+    $value = this.$element.find(".filter-control-value");
+
+    var value = $value.hasClass("dropdown-select")
+        ? $value.find(".dropdown-select-selected").text()
+        : $value.val();
+
     return { key: key, op: op, value: value };
 };
 
@@ -200,8 +204,8 @@ jQuery.fn.extend({
     filterControl: function $filterControl(options) {
         var nonOptionsArgs = jQuery.makeArray(arguments).slice(1);
         return this.map(function() {
-            var $this = $(this),
-                data = $this.data(FilterControl.prototype.DATA_KEY);
+            var $this = $(this);
+            var data = $this.data(FilterControl.prototype.DATA_KEY);
 
             if (jQuery.type(options) === "object") {
                 data = new FilterControl($this, options);

client/galaxy/scripts/ui/hoverhighlight.js

@@ -12,8 +12,8 @@ jQuery.fn.extend({
         }
 
         $(this).each(function() {
-            var $this = $(this),
-                targetSelector = $this.data("target");
+            var $this = $(this);
+            var targetSelector = $this.data("target");
 
             if (targetSelector) {
                 $this

client/galaxy/scripts/ui/loading-indicator.js

@@ -24,13 +24,14 @@ function LoadingIndicator($where, options) {
         ].join("\n");
 
         var $indicator = $(html)
-                .hide()
-                .css(
-                    options.css || {
-                        position: "fixed"
-                    }
-                ),
-            $text = $indicator.children(".loading-indicator-text");
+            .hide()
+            .css(
+                options.css || {
+                    position: "fixed"
+                }
+            );
+
+        var $text = $indicator.children(".loading-indicator-text");
 
         if (options.cover) {
             $indicator.css({

client/galaxy/scripts/ui/mode-button.js

@@ -170,8 +170,8 @@ $.fn.modeButton = function $modeButton(options) {
         });
     }
 
-    var $first = $(this[0]),
-        button = $first.data("mode-button");
+    var $first = $(this[0]);
+    var button = $first.data("mode-button");
 
     if (!button) {
         throw new Error(

client/galaxy/scripts/ui/pagination.js

@@ -91,12 +91,13 @@ Pagination.prototype._render = function __render() {
 
 /** render previous and next pagination buttons */
 Pagination.prototype._renderPrevNext = function __renderPrevNext() {
-    var pagination = this,
-        $prev = _make$Li("Prev"),
-        $next = _make$Li("Next"),
-        $paginationContainer = $("<ul/>").addClass(
-            "pagination pagination-prev-next"
-        );
+    var pagination = this;
+    var $prev = _make$Li("Prev");
+    var $next = _make$Li("Next");
+
+    var $paginationContainer = $("<ul/>").addClass(
+        "pagination pagination-prev-next"
+    );
 
     // disable if it either end
     if (this.currPage === 0) {
@@ -127,16 +128,19 @@ Pagination.prototype._renderPrevNext = function __renderPrevNext() {
 Pagination.prototype._renderPages = function __renderPages() {
     // it's better to scroll the control and let the user see all pages
     //  than to force her/him to change pages in order to find the one they want (as traditional << >> does)
-    var pagination = this,
-        $scrollingContainer = $("<div>").addClass(
-            "pagination-scroll-container"
-        ),
-        $paginationContainer = $("<ul/>").addClass(
-            "pagination pagination-page-list"
-        ),
-        page$LiClick = function(ev) {
-            pagination.goToPage($(this).data("page"));
-        };
+    var pagination = this;
+
+    var $scrollingContainer = $("<div>").addClass(
+        "pagination-scroll-container"
+    );
+
+    var $paginationContainer = $("<ul/>").addClass(
+        "pagination pagination-page-list"
+    );
+
+    var page$LiClick = function(ev) {
+        pagination.goToPage($(this).data("page"));
+    };
 
     for (var i = 0; i < this.numPages; i += 1) {
         // add html5 data tag 'page' for later click event handler use
@@ -162,8 +166,8 @@ Pagination.prototype._scrollToActivePage = function __scrollToActivePage() {
         return this;
     }
 
-    var $activePage = this.$element.find("li.active"),
-        midpoint = $container.width() / 2;
+    var $activePage = this.$element.find("li.active");
+    var midpoint = $container.width() / 2;
     //console.debug( $container, $activePage, midpoint );
     $container.scrollLeft(
         $container.scrollLeft() + $activePage.position().left - midpoint
@@ -225,8 +229,9 @@ jQuery.fn.extend({
         }
 
         // (other invocations only work on the first element in selected)
-        var $firstElement = $(this[0]),
-            previousControl = $firstElement.data(Pagination.prototype.DATA_KEY);
+        var $firstElement = $(this[0]);
+
+        var previousControl = $firstElement.data(Pagination.prototype.DATA_KEY);
         // if a pagination control was found for this element, either...
         if (previousControl) {
             // invoke a function on the pagination object if passed a string (the function name)

client/galaxy/scripts/ui/peek-column-selector.js

@@ -2,6 +2,7 @@
 // Uses AMD or browser globals to create a jQuery plugin.
 import jQuery from "jquery";
 var $ = jQuery;
+
 //==============================================================================
 /** Column selection using the peek display as the control.
      *  Adds rows to the bottom of the peek with clickable areas in each cell
@@ -48,41 +49,52 @@ var $ = jQuery;
 
 /** option defaults */
 var defaults = {
-        /** does this control allow renaming headers? */
-        renameColumns: false,
-        /** does this control allow renaming headers? */
-        columnNames: [],
-        /** the comment character used by the peek's datatype */
-        commentChar: "#",
-        /** should comment rows be shown or hidden in the peek */
-        hideCommentRows: false,
-        /** should a column of row control prompts be used */
-        includePrompts: true,
-        /** what is the content of the top left cell (often a title) */
-        topLeftContent: "Columns:"
-    },
-    /** class added to the pre.peek element (to allow css on just the control) */
-    PEEKCONTROL_CLASS = "peek-column-selector",
-    /** the string of the event fired when a control row changes */
-    CHANGE_EVENT = "peek-column-selector.change",
-    /** the string of the event fired when a column is renamed */
-    RENAME_EVENT = "peek-column-selector.rename",
-    /** class added to the control rows */
-    ROW_CLASS = "control",
-    /** class added to the left-hand cells that serve as row prompts */
-    PROMPT_CLASS = "control-prompt",
-    /** class added to selected _cells_/tds */
-    SELECTED_CLASS = "selected",
-    /** class added to disabled/un-clickable cells/tds */
-    DISABLED_CLASS = "disabled",
-    /** class added to the clickable surface within a cell to select it */
-    BUTTON_CLASS = "button",
-    /** class added to peek table header (th) cells to indicate they can be clicked and are renamable */
-    RENAMABLE_HEADER_CLASS = "renamable-header",
-    /** the data key used for each cell to store the column index ('data-...') */
-    COLUMN_INDEX_DATA_KEY = "column-index",
-    /** renamable header data key used to store the column name (w/o the number and dot: '1.Bler') */
-    COLUMN_NAME_DATA_KEY = "column-name";
+    /** does this control allow renaming headers? */
+    renameColumns: false,
+    /** does this control allow renaming headers? */
+    columnNames: [],
+    /** the comment character used by the peek's datatype */
+    commentChar: "#",
+    /** should comment rows be shown or hidden in the peek */
+    hideCommentRows: false,
+    /** should a column of row control prompts be used */
+    includePrompts: true,
+    /** what is the content of the top left cell (often a title) */
+    topLeftContent: "Columns:"
+};
+
+var /** class added to the pre.peek element (to allow css on just the control) */
+PEEKCONTROL_CLASS = "peek-column-selector";
+
+var /** the string of the event fired when a control row changes */
+CHANGE_EVENT = "peek-column-selector.change";
+
+var /** the string of the event fired when a column is renamed */
+RENAME_EVENT = "peek-column-selector.rename";
+
+var /** class added to the control rows */
+ROW_CLASS = "control";
+
+var /** class added to the left-hand cells that serve as row prompts */
+PROMPT_CLASS = "control-prompt";
+
+var /** class added to selected _cells_/tds */
+SELECTED_CLASS = "selected";
+
+var /** class added to disabled/un-clickable cells/tds */
+DISABLED_CLASS = "disabled";
+
+var /** class added to the clickable surface within a cell to select it */
+BUTTON_CLASS = "button";
+
+var /** class added to peek table header (th) cells to indicate they can be clicked and are renamable */
+RENAMABLE_HEADER_CLASS = "renamable-header";
+
+var /** the data key used for each cell to store the column index ('data-...') */
+COLUMN_INDEX_DATA_KEY = "column-index";
+
+var /** renamable header data key used to store the column name (w/o the number and dot: '1.Bler') */
+COLUMN_NAME_DATA_KEY = "column-name";
 
 //TODO: not happy with pure functional here - rows should polymorph (multi, single, etc.)
 //TODO: needs clean up, move handlers to outer scope
@@ -187,9 +199,10 @@ function buildSingleSelectCell(control, columnIndex) {
                 setSelectedText($cell, control, columnIndex);
 
                 // fire the event from the table itself, passing the id and index of selected
-                var eventData = {},
-                    key = $cell.parent().attr("id"),
-                    val = $cell.data(COLUMN_INDEX_DATA_KEY);
+                var eventData = {};
+
+                var key = $cell.parent().attr("id");
+                var val = $cell.data(COLUMN_INDEX_DATA_KEY);
                 eventData[key] = val;
                 $cell.parents(".peek").trigger(CHANGE_EVENT, eventData);
             }
@@ -220,10 +233,12 @@ function buildMultiSelectCell(control, columnIndex) {
                 .map(function(i, e) {
                     return $(e).data(COLUMN_INDEX_DATA_KEY);
                 });
+
             // fire the event from the table itself, passing the id and index of selected
-            var eventData = {},
-                key = $cell.parent().attr("id"),
-                val = jQuery.makeArray(selectedColumnIndeces);
+            var eventData = {};
+
+            var key = $cell.parent().attr("id");
+            var val = jQuery.makeArray(selectedColumnIndeces);
             eventData[key] = val;
             $cell.parents(".peek").trigger(CHANGE_EVENT, eventData);
         });
@@ -265,25 +280,28 @@ function buildControlRow(cellCount, control, includePrompts) {
 function peekColumnSelector(options) {
     options = jQuery.extend(true, {}, defaults, options);
 
-    var $peek = $(this).addClass(PEEKCONTROL_CLASS),
-        $peektable = $peek.find("table"),
-        // get the size of the tables - width and height, number of comment rows
-        columnCount = $peektable.find("th").length,
-        rowCount = $peektable.find("tr").length,
-        // get the rows containing text starting with the comment char (also make them grey)
-        $commentRows = $peektable.find("td[colspan]").map(function(e, i) {
-            var $this = $(this);
-            if (
-                $this.text() &&
-                $this.text().match(new RegExp("^" + options.commentChar))
-            ) {
-                return $(this)
-                    .css("color", "grey")
-                    .parent()
-                    .get(0);
-            }
-            return null;
-        });
+    var $peek = $(this).addClass(PEEKCONTROL_CLASS);
+    var $peektable = $peek.find("table");
+
+    var // get the size of the tables - width and height, number of comment rows
+    columnCount = $peektable.find("th").length;
+
+    var rowCount = $peektable.find("tr").length;
+
+    var // get the rows containing text starting with the comment char (also make them grey)
+    $commentRows = $peektable.find("td[colspan]").map(function(e, i) {
+        var $this = $(this);
+        if (
+            $this.text() &&
+            $this.text().match(new RegExp("^" + options.commentChar))
+        ) {
+            return $(this)
+                .css("color", "grey")
+                .parent()
+                .get(0);
+        }
+        return null;
+    });
 
     // should comment rows in the peek be hidden?
     if (options.hideCommentRows) {
@@ -306,10 +324,12 @@ function peekColumnSelector(options) {
 
     // save either the options column name or the parsed text of each column header in html5 data attr and text
     var $headers = $peektable.find("th:not(.top-left)").each(function(i, e) {
-        var $this = $(this),
-            // can be '1.name' or '1'
-            text = $this.text().replace(/^\d+\.*/, ""),
-            name = options.columnNames[i] || text;
+        var $this = $(this);
+
+        var // can be '1.name' or '1'
+        text = $this.text().replace(/^\d+\.*/, "");
+
+        var name = options.columnNames[i] || text;
         $this
             .attr("data-" + COLUMN_NAME_DATA_KEY, name)
             .text(i + 1 + (name ? "." + name : ""));
@@ -321,10 +341,11 @@ function peekColumnSelector(options) {
             .addClass(RENAMABLE_HEADER_CLASS)
             .click(function renameColumn() {
                 // prompt for new name
-                var $this = $(this),
-                    index = $this.index() + (options.includePrompts ? 0 : 1),
-                    prevName = $this.data(COLUMN_NAME_DATA_KEY),
-                    newColumnName = prompt("New column name:", prevName);
+                var $this = $(this);
+
+                var index = $this.index() + (options.includePrompts ? 0 : 1);
+                var prevName = $this.data(COLUMN_NAME_DATA_KEY);
+                var newColumnName = prompt("New column name:", prevName);
                 if (newColumnName !== null && newColumnName !== prevName) {
                     // set the new text and data
                     $this

client/galaxy/scripts/ui/popupmenu.js

@@ -126,11 +126,11 @@ function make_popup_menus(parent) {
 
             // find each anchor in the menu, convert them into an options map: { a.text : click_function }
             menu.find("a").each(function() {
-                var link = $(this),
-                    link_dom = link.get(0),
-                    confirmtext = link_dom.getAttribute("confirm"),
-                    href = link_dom.getAttribute("href"),
-                    target = link_dom.getAttribute("target");
+                var link = $(this);
+                var link_dom = link.get(0);
+                var confirmtext = link_dom.getAttribute("confirm");
+                var href = link_dom.getAttribute("href");
+                var target = link_dom.getAttribute("target");
 
                 // no href - no function (gen. a label)
                 if (!href) {

client/galaxy/scripts/ui/scroll-panel.js

@@ -6,32 +6,38 @@ $.ui.plugin.add("draggable", "scrollPanel", {
     drag: function(e, ui) {
         var instance = $(this).data("draggable");
         clearTimeout(instance.timeout);
-        var o = ui.options,
-            element = instance.element,
-            panel = o.panel,
-            panel_pos = panel.position(),
-            panel_w = panel.width(),
-            panel_h = panel.height(),
-            viewport = panel.parent(),
-            viewport_w = viewport.width(),
-            viewport_h = viewport.height(),
-            element_w = element.width(),
-            element_h = element.height(),
-            moved = false,
-            close_dist = 5,
-            nudge = 23,
-            // Legal panel range
-            p_min_x = -(panel_w - viewport_w),
-            p_min_y = -(panel_h - viewport_h),
-            p_max_x = 0,
-            p_max_y = 0,
-            // Visible
-            min_vis_x = -panel_pos.left,
-            max_vis_x = min_vis_x + viewport_w,
-            min_vis_y = -panel_pos.top,
-            max_vis_y = min_vis_y + viewport_h,
-            // Mouse
-            mouse_x = ui.position.left + instance.offset.click.left;
+        var o = ui.options;
+        var element = instance.element;
+        var panel = o.panel;
+        var panel_pos = panel.position();
+        var panel_w = panel.width();
+        var panel_h = panel.height();
+        var viewport = panel.parent();
+        var viewport_w = viewport.width();
+        var viewport_h = viewport.height();
+        var element_w = element.width();
+        var element_h = element.height();
+        var moved = false;
+        var close_dist = 5;
+        var nudge = 23;
+
+        var // Legal panel range
+        p_min_x = -(panel_w - viewport_w);
+
+        var p_min_y = -(panel_h - viewport_h);
+        var p_max_x = 0;
+        var p_max_y = 0;
+
+        var // Visible
+        min_vis_x = -panel_pos.left;
+
+        var max_vis_x = min_vis_x + viewport_w;
+        var min_vis_y = -panel_pos.top;
+        var max_vis_y = min_vis_y + viewport_h;
+
+        var // Mouse
+        mouse_x = ui.position.left + instance.offset.click.left;
+
         mouse_y = ui.position.top + instance.offset.click.top;
         // Move it
         if (panel_pos.left < p_max_x && mouse_x - close_dist < min_vis_x) {

client/galaxy/scripts/ui/search-input.js

@@ -19,22 +19,23 @@ var _l =
      *      is focused will clear the input and call a separate callback.
      */
 function searchInput(parentNode, options) {
-    var KEYCODE_ESC = 27,
-        KEYCODE_RETURN = 13,
-        $parentNode = $(parentNode),
-        firstSearch = true,
-        defaults = {
-            initialVal: "",
-            name: "search",
-            placeholder: "search",
-            classes: "",
-            onclear: function() {},
-            onfirstsearch: null,
-            onsearch: function(inputVal) {},
-            minSearchLen: 0,
-            escWillClear: true,
-            oninit: function() {}
-        };
+    var KEYCODE_ESC = 27;
+    var KEYCODE_RETURN = 13;
+    var $parentNode = $(parentNode);
+    var firstSearch = true;
+
+    var defaults = {
+        initialVal: "",
+        name: "search",
+        placeholder: "search",
+        classes: "",
+        onclear: function() {},
+        onfirstsearch: null,
+        onsearch: function(inputVal) {},
+        minSearchLen: 0,
+        escWillClear: true,
+        oninit: function() {}
+    };
 
     // .................................................................... input rendering and events
     // visually clear the search, trigger an event, and call the callback

client/galaxy/scripts/utils/ajax-queue.js

@@ -39,13 +39,14 @@ AjaxQueue.prototype.init = function init(initialFunctions) {
 /** add a fn to the queue */
 AjaxQueue.prototype.add = function add(fn) {
     //console.debug( 'AjaxQueue.prototype.add:', fn );
-    var self = this,
-        index = this.queue.length;
+    var self = this;
+
+    var index = this.queue.length;
     this.numToProcess += 1;
 
     this.queue.push(function() {
-        var fnIndex = index,
-            xhr = fn();
+        var fnIndex = index;
+        var xhr = fn();
         // if successful, notify using the deferred to allow tracking progress
         xhr.done(function(response) {
             self.deferred.notify({

client/galaxy/scripts/utils/async-save-text.js

@@ -31,9 +31,9 @@ function async_save_text(
         if ($("#renaming-active").length > 0) {
             return;
         }
-        var text_elt = $("#" + text_elt_id),
-            old_text = text_elt.text(),
-            t;
+        var text_elt = $("#" + text_elt_id);
+        var old_text = text_elt.text();
+        var t;
 
         if (use_textarea) {
             t = $("<textarea></textarea>")

client/galaxy/scripts/utils/config.js

@@ -232,9 +232,10 @@ var ConfigSettingCollectionView = Backbone.View.extend({
             }
 
             // Build row for param.
-            var id = "param_" + index,
-                type = param.get("type"),
-                value = param.get("value");
+            var id = "param_" + index;
+
+            var type = param.get("type");
+            var value = param.get("value");
             var row = $("<div class='form-row' />").appendTo(container);
             row.append(
                 $("<label />")
@@ -272,78 +273,84 @@ var ConfigSettingCollectionView = Backbone.View.extend({
                 row.append(select);
             } else if (type === "color") {
                 // Draw parameter as color picker
-                var container_div = $("<div/>").appendTo(row),
-                    input = $("<input />")
-                        .attr("id", id)
-                        .attr("name", id)
-                        .val(value)
-                        .css("float", "left")
-                        .appendTo(container_div)
-                        .click(function(e) {
-                            // Hide other pickers.
-                            $(".tooltip").removeClass("in");
+                var container_div = $("<div/>").appendTo(row);
 
-                            // Show input's color picker.
-                            var tip = $(this)
-                                .siblings(".tooltip")
-                                .addClass("in");
-                            tip
-                                .css({
-                                    // left: $(this).position().left + ( $(input).width() / 2 ) - 60,
-                                    // top: $(this).position().top + $(this.height)
-                                    left:
-                                        $(this).position().left +
-                                        $(this).width() +
-                                        5,
-                                    top:
-                                        $(this).position().top -
-                                        $(tip).height() / 2 +
-                                        $(this).height() / 2
-                                })
-                                .show();
+                var input = $("<input />")
+                    .attr("id", id)
+                    .attr("name", id)
+                    .val(value)
+                    .css("float", "left")
+                    .appendTo(container_div)
+                    .click(function(e) {
+                        // Hide other pickers.
+                        $(".tooltip").removeClass("in");
 
-                            // Click management:
-
-                            // Keep showing tip if clicking in tip.
-                            tip.click(function(e) {
-                                e.stopPropagation();
-                            });
-
-                            // Hide tip if clicking outside of tip.
-                            $(document).bind("click.color-picker", function() {
-                                tip.hide();
-                                $(document).unbind("click.color-picker");
-                            });
-
-                            // No propagation to avoid triggering document click (and tip hiding) above.
-                            e.stopPropagation();
-                        }),
-                    // Icon for setting a new random color; behavior set below.
-                    new_color_icon = $("<a href='javascript:void(0)'/>")
-                        .addClass("icon-button arrow-circle")
-                        .appendTo(container_div)
-                        .attr("title", "Set new random color")
-                        .tooltip(),
-                    // Color picker in tool tip style.
-                    tip = $(
-                        "<div class='tooltip right' style='position: absolute;' />"
-                    )
-                        .appendTo(container_div)
-                        .hide(),
-                    // Inner div for padding purposes
-                    tip_inner = $(
-                        "<div class='tooltip-inner' style='text-align: inherit'></div>"
-                    ).appendTo(tip),
-                    tip_arrow = $("<div class='tooltip-arrow'></div>").appendTo(
+                        // Show input's color picker.
+                        var tip = $(this)
+                            .siblings(".tooltip")
+                            .addClass("in");
                         tip
-                    ),
-                    farb_obj = $.farbtastic(tip_inner, {
-                        width: 100,
-                        height: 100,
-                        callback: input,
-                        color: value
+                            .css({
+                                // left: $(this).position().left + ( $(input).width() / 2 ) - 60,
+                                // top: $(this).position().top + $(this.height)
+                                left:
+                                    $(this).position().left +
+                                    $(this).width() +
+                                    5,
+                                top:
+                                    $(this).position().top -
+                                    $(tip).height() / 2 +
+                                    $(this).height() / 2
+                            })
+                            .show();
+
+                        // Click management:
+
+                        // Keep showing tip if clicking in tip.
+                        tip.click(function(e) {
+                            e.stopPropagation();
+                        });
+
+                        // Hide tip if clicking outside of tip.
+                        $(document).bind("click.color-picker", function() {
+                            tip.hide();
+                            $(document).unbind("click.color-picker");
+                        });
+
+                        // No propagation to avoid triggering document click (and tip hiding) above.
+                        e.stopPropagation();
                     });
 
+                var // Icon for setting a new random color; behavior set below.
+                new_color_icon = $("<a href='javascript:void(0)'/>")
+                    .addClass("icon-button arrow-circle")
+                    .appendTo(container_div)
+                    .attr("title", "Set new random color")
+                    .tooltip();
+
+                var // Color picker in tool tip style.
+                tip = $(
+                    "<div class='tooltip right' style='position: absolute;' />"
+                )
+                    .appendTo(container_div)
+                    .hide();
+
+                var // Inner div for padding purposes
+                tip_inner = $(
+                    "<div class='tooltip-inner' style='text-align: inherit'></div>"
+                ).appendTo(tip);
+
+                var tip_arrow = $("<div class='tooltip-arrow'></div>").appendTo(
+                    tip
+                );
+
+                var farb_obj = $.farbtastic(tip_inner, {
+                    width: 100,
+                    height: 100,
+                    callback: input,
+                    color: value
+                });
+
                 // Clear floating.
                 container_div.append($("<div/>").css("clear", "both"));
 
@@ -375,25 +382,28 @@ var ConfigSettingCollectionView = Backbone.View.extend({
      */
     render_in_modal: function(title) {
         // Set up handlers for cancel, ok button and for handling esc key.
-        var self = this,
-            cancel_fn = function() {
-                Galaxy.modal.hide();
-                $(window).unbind("keypress.check_enter_esc");
-            },
-            ok_fn = function() {
-                Galaxy.modal.hide();
-                $(window).unbind("keypress.check_enter_esc");
-                self.update_from_form();
-            },
-            check_enter_esc = function(e) {
-                if ((e.keyCode || e.which) === 27) {
-                    // Escape key
-                    cancel_fn();
-                } else if ((e.keyCode || e.which) === 13) {
-                    // Enter key
-                    ok_fn();
-                }
-            };
+        var self = this;
+
+        var cancel_fn = function() {
+            Galaxy.modal.hide();
+            $(window).unbind("keypress.check_enter_esc");
+        };
+
+        var ok_fn = function() {
+            Galaxy.modal.hide();
+            $(window).unbind("keypress.check_enter_esc");
+            self.update_from_form();
+        };
+
+        var check_enter_esc = function(e) {
+            if ((e.keyCode || e.which) === 27) {
+                // Escape key
+                cancel_fn();
+            } else if ((e.keyCode || e.which) === 13) {
+                // Enter key
+                ok_fn();
+            }
+        };
 
         // Set keypress handler.
         $(window).bind("keypress.check_enter_esc", check_enter_esc);

client/galaxy/scripts/utils/graph.js

@@ -39,10 +39,10 @@ function matches(d, d2) {
  *      if propsOrFn is function, call the fn and returned the mapped values from it
  */
 function iterate(obj, propsOrFn) {
-    var fn = typeof propsOrFn === "function" ? propsOrFn : undefined,
-        props = typeof propsOrFn === "object" ? propsOrFn : undefined,
-        returned = [],
-        index = 0;
+    var fn = typeof propsOrFn === "function" ? propsOrFn : undefined;
+    var props = typeof propsOrFn === "object" ? propsOrFn : undefined;
+    var returned = [];
+    var index = 0;
     for (var key in obj) {
         if (obj.hasOwnProperty(key)) {
             var value = obj[key];
@@ -211,8 +211,8 @@ BreadthFirstSearch.prototype._search = function __search(start, search) {
         edges: []
     };
 
-    var self = this,
-        queue = [];
+    var self = this;
+    var queue = [];
 
     function discoverAdjacent(adj, edge) {
         var source = this;
@@ -268,8 +268,8 @@ DepthFirstSearch.prototype._search = function(start, search) {
         entryTimes: {},
         exitTimes: {}
     };
-    var self = this,
-        time = 0;
+    var self = this;
+    var time = 0;
 
     // discover verts adjacent to the source (this):
     //  processing each edge, saving the edge to the tree, and caching the reverse path with parents
@@ -363,8 +363,8 @@ Graph.prototype.readNodesAndLinks = function(data) {
     //console.debug( JSON.stringify( self.vertices, null, '  ' ) );
 
     (data.links || []).forEach(function(edge, i) {
-        var sourceName = data.nodes[edge.source].name,
-            targetName = data.nodes[edge.target].name;
+        var sourceName = data.nodes[edge.source].name;
+        var targetName = data.nodes[edge.target].name;
         self.createEdge(sourceName, targetName, self.directed);
     });
     //self.print();
@@ -421,8 +421,9 @@ Graph.prototype.createEdge = function(sourceName, targetName, directed, data) {
     }
 
     //TODO: prob. move to vertex
-    var self = this,
-        edge = new Edge(sourceName, targetName, data);
+    var self = this;
+
+    var edge = new Edge(sourceName, targetName, data);
     sourceVertex.edges[targetName] = edge;
     sourceVertex.degree += 1;
     self.numEdges += 1;
@@ -485,8 +486,8 @@ Graph.prototype.print = function() {
 
 /** Return a DOT format string of this graph */
 Graph.prototype.toDOT = function() {
-    var self = this,
-        strings = [];
+    var self = this;
+    var strings = [];
     strings.push("graph bler {");
     self.edges(function(edge) {
         strings.push("\t" + edge.from + " -- " + edge.to + ";");
@@ -497,8 +498,8 @@ Graph.prototype.toDOT = function() {
 
 /** Return vertices and edges of this graph in d3 node/link format */
 Graph.prototype.toNodesAndLinks = function() {
-    var self = this,
-        indeces = {};
+    var self = this;
+    var indeces = {};
     return {
         nodes: self.eachVertex(function(vertex, key, i) {
             indeces[vertex.name] = i;
@@ -562,10 +563,11 @@ Graph.prototype.depthFirstSearchTree = function(start, processFns) {
 Graph.prototype.weakComponents = function() {
     //TODO: alternately, instead of returning graph-like objects:
     //  - could simply decorate the vertices (vertex.component = componentIndex), or clone the graph and do that
-    var self = this,
-        searchGraph = this,
-        undiscovered,
-        components = [];
+    var self = this;
+
+    var searchGraph = this;
+    var undiscovered;
+    var components = [];
 
     function getComponent(undiscoveredVertex) {
         //TODO: better interface on dfs (search v. searchTree)

client/galaxy/scripts/utils/metrics-logger.js

@@ -247,16 +247,20 @@ MetricsLogger.prototype._postCache = function _postCache(options) {
         return jQuery.when({});
     }
 
-    var self = this,
-        postSize = options.count || self._postSize,
-        // do not splice - remove after *successful* post
-        entries = self.cache.get(postSize),
-        entriesLength = entries.length,
-        // use the optional getPingData to add any extra info we may want to send
-        postData =
-            typeof self.options.getPingData === "function"
-                ? self.options.getPingData()
-                : {};
+    var self = this;
+    var postSize = options.count || self._postSize;
+
+    var // do not splice - remove after *successful* post
+    entries = self.cache.get(postSize);
+
+    var entriesLength = entries.length;
+
+    var // use the optional getPingData to add any extra info we may want to send
+    postData =
+        typeof self.options.getPingData === "function"
+            ? self.options.getPingData()
+            : {};
+
     //console.debug( postSize, entriesLength );
 
     // add the metrics and send
@@ -312,8 +316,9 @@ MetricsLogger.prototype._emitToConsole = function _emitToConsole(
     logArguments
 ) {
     //console.debug( '_emitToConsole:', level, namespace, logArguments );
-    var self = this,
-        whitelist = self.options.consoleNamespaceWhitelist;
+    var self = this;
+
+    var whitelist = self.options.consoleNamespaceWhitelist;
     if (!self.consoleLogger) {
         return self;
     }
@@ -474,9 +479,9 @@ LoggingCache.prototype._initStorage = function _initStorage() {
 
 /** add an entry to the cache, removing the oldest beforehand if size >= maxSize */
 LoggingCache.prototype.add = function add(entry) {
-    var self = this,
-        _cache = self._fetchAndParse(),
-        overage = _cache.length + 1 - self.maxSize;
+    var self = this;
+    var _cache = self._fetchAndParse();
+    var overage = _cache.length + 1 - self.maxSize;
     if (overage > 0) {
         _cache.splice(0, overage);
     }
@@ -514,8 +519,8 @@ LoggingCache.prototype.get = function get(count) {
 
 /** remove count number of entries starting with the oldest */
 LoggingCache.prototype.remove = function remove(count) {
-    var _cache = this._fetchAndParse(),
-        removed = _cache.splice(0, count);
+    var _cache = this._fetchAndParse();
+    var removed = _cache.splice(0, count);
     this._unparseAndStore(_cache);
     return removed;
 };

client/galaxy/scripts/utils/natural-sort.js

@@ -1,14 +1,15 @@
 // Alphanumeric/natural sort fn
 function naturalSort(a, b) {
     // setup temp-scope variables for comparison evauluation
-    var re = /(-?[0-9\.]+)/g,
-        x = a.toString().toLowerCase() || "",
-        y = b.toString().toLowerCase() || "",
-        nC = String.fromCharCode(0),
-        xN = x.replace(re, nC + "$1" + nC).split(nC),
-        yN = y.replace(re, nC + "$1" + nC).split(nC),
-        xD = new Date(x).getTime(),
-        yD = xD ? new Date(y).getTime() : null;
+    var re = /(-?[0-9\.]+)/g;
+
+    var x = a.toString().toLowerCase() || "";
+    var y = b.toString().toLowerCase() || "";
+    var nC = String.fromCharCode(0);
+    var xN = x.replace(re, nC + "$1" + nC).split(nC);
+    var yN = y.replace(re, nC + "$1" + nC).split(nC);
+    var xD = new Date(x).getTime();
+    var yD = xD ? new Date(y).getTime() : null;
     // natural sorting of dates
     if (yD) {
         if (xD < yD) {
@@ -17,8 +18,11 @@ function naturalSort(a, b) {
             return 1;
         }
     }
+
     // natural sorting through split numeric strings and default strings
-    var oFxNcL, oFyNcL;
+    var oFxNcL;
+
+    var oFyNcL;
     for (
         var cLoc = 0, numS = Math.max(xN.length, yN.length);
         cLoc < numS;

client/galaxy/scripts/utils/query-string-parsing.js

@@ -21,8 +21,8 @@ function parse(queryString) {
     if (!queryString) {
         return {};
     }
-    var parsed = {},
-        split = queryString.split("&");
+    var parsed = {};
+    var split = queryString.split("&");
     split.forEach(function(pairString) {
         var pair = pairString.split("=");
         parsed[pair[0]] = decodeURI(pair[1]);

client/galaxy/scripts/utils/utils.js

@@ -26,7 +26,10 @@ function deepeach(dict, callback) {
 
 /** Identifies urls and replaces them with anchors */
 function linkify(inputText) {
-    var replacedText, replacePattern1, replacePattern2, replacePattern3;
+    var replacedText;
+    var replacePattern1;
+    var replacePattern2;
+    var replacePattern3;
 
     // URLs starting with http://, https://, or ftp://
     replacePattern1 = /(\b(https?|ftp):\/\/[-A-Z0-9+&@#\/%?=~_|!:,.;]*[-A-Z0-9+&@#\/%=~_|])/gim;
@@ -260,10 +263,11 @@ function roundToDecimalPlaces(number, numPlaces) {
 }
 
 // calculate on import
-var kb = 1024,
-    mb = kb * kb,
-    gb = mb * kb,
-    tb = gb * kb;
+var kb = 1024;
+
+var mb = kb * kb;
+var gb = mb * kb;
+var tb = gb * kb;
 /**
      * Format byte size to string with units
      * @param{Integer}   size           - Size in bytes

client/galaxy/scripts/viz/bbi-data-manager.js

@@ -14,8 +14,9 @@ var BBIDataManager = visualization.GenomeDataManager.extend({
         this.set_data(region, deferred);
 
         var url =
-                Galaxy.root + "datasets/" + this.get("dataset").id + "/display",
-            self = this;
+            Galaxy.root + "datasets/" + this.get("dataset").id + "/display";
+
+        var self = this;
         var promise = new $.Deferred();
         $.when(bigwig.makeBwg(url)).then(function(bb, err) {
             $.when(
@@ -27,8 +28,9 @@ var BBIDataManager = visualization.GenomeDataManager.extend({
             ).then(function(data) {
                 // Transform data into "bigwig" format for LinePainter. "bigwig" format is an array of 2-element arrays
                 // where each element is [position, score]; unlike real bigwig format, no gaps are allowed.
-                var result = [],
-                    prev = { max: Number.MIN_VALUE };
+                var result = [];
+
+                var prev = { max: Number.MIN_VALUE };
                 data.forEach(function(d) {
                     // If there is a gap between prev and d, fill it with an interval with score 0.
                     // This is necessary for LinePainter to draw correctly.

client/galaxy/scripts/viz/circster.js

@@ -16,8 +16,8 @@ var SVGUtils = Backbone.Model.extend({
      * Returns true if element is visible.
      */
     is_visible: function(svg_elt, svg) {
-        var eltBRect = svg_elt.getBoundingClientRect(),
-            svgBRect = $("svg")[0].getBoundingClientRect();
+        var eltBRect = svg_elt.getBoundingClientRect();
+        var svgBRect = $("svg")[0].getBoundingClientRect();
 
         if (
             // To the left of screen?
@@ -70,11 +70,14 @@ var UsesTicks = {
             });
 
         // Add line + text for ticks.
-        var tick_coords = [],
-            text_coords = [],
-            text_anchor = function(d) {
-                return d.angle > Math.PI ? "end" : null;
-            };
+        var tick_coords = [];
+
+        var text_coords = [];
+
+        var text_anchor = function(d) {
+            return d.angle > Math.PI ? "end" : null;
+        };
+
         if (horizontal) {
             tick_coords = [0, 0, 0, -4];
             text_coords = [4, 0, "", ".35em"];
@@ -201,27 +204,32 @@ var CircsterView = Backbone.View.extend({
      * Returns a list of circular tracks' radius bounds.
      */
     get_tracks_bounds: function() {
-        var circular_tracks = this.get_circular_tracks(),
-            dataset_arc_height = this.model
-                .get("config")
-                .get_value("arc_dataset_height"),
-            track_gap = this.model.get("config").get_value("track_gap"),
-            // Subtract 20 to make sure chrom labels are on screen.
-            min_dimension = Math.min(this.$el.width(), this.$el.height()) - 20,
-            // Compute radius start based on model, will be centered
-            // and fit entirely inside element by default.
-            radius_start =
-                min_dimension / 2 -
-                circular_tracks.length * (dataset_arc_height + track_gap) +
-                // Add track_gap back in because no gap is needed for last track.
-                track_gap -
-                this.label_arc_height,
-            // Compute range of track starting radii.
-            tracks_start_radii = d3.range(
-                radius_start,
-                min_dimension / 2,
-                dataset_arc_height + track_gap
-            );
+        var circular_tracks = this.get_circular_tracks();
+
+        var dataset_arc_height = this.model
+            .get("config")
+            .get_value("arc_dataset_height");
+
+        var track_gap = this.model.get("config").get_value("track_gap");
+
+        var // Subtract 20 to make sure chrom labels are on screen.
+        min_dimension = Math.min(this.$el.width(), this.$el.height()) - 20;
+
+        var // Compute radius start based on model, will be centered
+        // and fit entirely inside element by default.
+        radius_start =
+            min_dimension / 2 -
+            circular_tracks.length * (dataset_arc_height + track_gap) +
+            // Add track_gap back in because no gap is needed for last track.
+            track_gap -
+            this.label_arc_height;
+
+        var // Compute range of track starting radii.
+        tracks_start_radii = d3.range(
+            radius_start,
+            min_dimension / 2,
+            dataset_arc_height + track_gap
+        );
 
         // Map from track start to bounds.
         var self = this;
@@ -234,62 +242,63 @@ var CircsterView = Backbone.View.extend({
      * Renders circular tracks, chord tracks, and label tracks.
      */
     render: function() {
-        var self = this,
-            width = self.$el.width(),
-            height = self.$el.height(),
-            circular_tracks = this.get_circular_tracks(),
-            chords_tracks = this.get_chord_tracks(),
-            total_gap = self.model.get("config").get_value("total_gap"),
-            tracks_bounds = this.get_tracks_bounds(),
-            // Set up SVG element.
-            svg = d3
-                .select(self.$el[0])
-                .append("svg")
-                .attr("width", width)
-                .attr("height", height)
-                .attr("pointer-events", "all")
-                // Set up zooming, dragging.
-                .append("svg:g")
-                .call(
-                    d3.behavior.zoom().on("zoom", function() {
-                        // Do zoom, drag.
-                        var scale = d3.event.scale;
-                        svg.attr(
-                            "transform",
-                            "translate(" +
-                                d3.event.translate +
-                                ")" +
-                                " scale(" +
-                                scale +
-                                ")"
-                        );
+        var self = this;
+        var width = self.$el.width();
+        var height = self.$el.height();
+        var circular_tracks = this.get_circular_tracks();
+        var chords_tracks = this.get_chord_tracks();
+        var total_gap = self.model.get("config").get_value("total_gap");
+        var tracks_bounds = this.get_tracks_bounds();
 
-                        // Propagate scale changes to views.
-                        if (self.scale !== scale) {
-                            // Use timeout to wait for zooming/dragging to stop before rendering more detail.
-                            if (self.zoom_drag_timeout) {
-                                clearTimeout(self.zoom_drag_timeout);
-                            }
-                            self.zoom_drag_timeout = setTimeout(function() {
-                                // Render more detail in tracks' visible elements.
-                                // FIXME: do not do this right now; it is not fully implemented--e.g. data bounds
-                                // are not updated when new data is fetched--and fetching more detailed quantitative
-                                // data is not that useful.
-                                /*
-                            _.each(self.circular_views, function(view) {
-                                view.update_scale(scale);
-                            });
-                            */
-                            }, 400);
+        var // Set up SVG element.
+        svg = d3
+            .select(self.$el[0])
+            .append("svg")
+            .attr("width", width)
+            .attr("height", height)
+            .attr("pointer-events", "all")
+            // Set up zooming, dragging.
+            .append("svg:g")
+            .call(
+                d3.behavior.zoom().on("zoom", function() {
+                    // Do zoom, drag.
+                    var scale = d3.event.scale;
+                    svg.attr(
+                        "transform",
+                        "translate(" +
+                            d3.event.translate +
+                            ")" +
+                            " scale(" +
+                            scale +
+                            ")"
+                    );
+
+                    // Propagate scale changes to views.
+                    if (self.scale !== scale) {
+                        // Use timeout to wait for zooming/dragging to stop before rendering more detail.
+                        if (self.zoom_drag_timeout) {
+                            clearTimeout(self.zoom_drag_timeout);
                         }
-                    })
-                )
-                .attr(
-                    "transform",
-                    "translate(" + width / 2 + "," + height / 2 + ")"
-                )
-                .append("svg:g")
-                .attr("class", "tracks");
+                        self.zoom_drag_timeout = setTimeout(function() {
+                            // Render more detail in tracks' visible elements.
+                            // FIXME: do not do this right now; it is not fully implemented--e.g. data bounds
+                            // are not updated when new data is fetched--and fetching more detailed quantitative
+                            // data is not that useful.
+                            /*
+                        _.each(self.circular_views, function(view) {
+                            view.update_scale(scale);
+                        });
+                        */
+                        }, 400);
+                    }
+                })
+            )
+            .attr(
+                "transform",
+                "translate(" + width / 2 + "," + height / 2 + ")"
+            )
+            .append("svg:g")
+            .attr("class", "tracks");
 
         // -- Render circular tracks. --
 
@@ -330,12 +339,14 @@ var CircsterView = Backbone.View.extend({
         // (a) outer radius of last circular track;
         // (b)
         var outermost_radius = this.circular_views[
-                this.circular_views.length - 1
-            ].radius_bounds[1],
-            track_bounds = [
-                outermost_radius,
-                outermost_radius + this.label_arc_height
-            ];
+            this.circular_views.length - 1
+        ].radius_bounds[1];
+
+        var track_bounds = [
+            outermost_radius,
+            outermost_radius + this.label_arc_height
+        ];
+
         this.label_track_view = new CircsterChromLabelTrackView({
             el: svg.append("g")[0],
             track: new CircsterLabelTrack(),
@@ -355,14 +366,16 @@ var CircsterView = Backbone.View.extend({
 
         if (new_track.get("track_type") === "DiagonalHeatmapTrack") {
             // Added chords track.
-            var innermost_radius_bounds = this.circular_views[0].radius_bounds,
-                new_view = new CircsterChromInteractionsTrackView({
-                    el: d3.select("g.tracks").append("g")[0],
-                    track: new_track,
-                    radius_bounds: innermost_radius_bounds,
-                    genome: this.genome,
-                    total_gap: total_gap
-                });
+            var innermost_radius_bounds = this.circular_views[0].radius_bounds;
+
+            var new_view = new CircsterChromInteractionsTrackView({
+                el: d3.select("g.tracks").append("g")[0],
+                track: new_track,
+                radius_bounds: innermost_radius_bounds,
+                genome: this.genome,
+                total_gap: total_gap
+            });
+
             new_view.render();
             this.chords_views.push(new_view);
         } else {
@@ -380,14 +393,16 @@ var CircsterView = Backbone.View.extend({
             });
 
             // Render new track.
-            var track_index = this.circular_views.length,
-                track_view = new CircsterBigWigTrackView({
-                    el: d3.select("g.tracks").append("g")[0],
-                    track: new_track,
-                    radius_bounds: new_track_bounds[track_index],
-                    genome: this.genome,
-                    total_gap: total_gap
-                });
+            var track_index = this.circular_views.length;
+
+            var track_view = new CircsterBigWigTrackView({
+                el: d3.select("g.tracks").append("g")[0],
+                track: new_track,
+                radius_bounds: new_track_bounds[track_index],
+                genome: this.genome,
+                total_gap: total_gap
+            });
+
             track_view.render();
             this.circular_views.push(track_view);
 
@@ -475,24 +490,27 @@ var CircsterTrackView = Backbone.View.extend({
         var track_parent_elt = this.parent_elt;
 
         // -- Render background arcs. --
-        var genome_arcs = this.chroms_layout,
-            arc_gen = d3.svg
-                .arc()
-                .innerRadius(this.radius_bounds[0])
-                .outerRadius(this.radius_bounds[1]),
-            // Attach data to group element.
-            chroms_elts = track_parent_elt
-                .selectAll("g")
-                .data(genome_arcs)
-                .enter()
-                .append("svg:g"),
-            // Draw chrom arcs/paths.
-            chroms_paths = chroms_elts
-                .append("path")
-                .attr("d", arc_gen)
-                .attr("class", "chrom-background")
-                .style("stroke", this.bg_stroke)
-                .style("fill", this.loading_bg_fill);
+        var genome_arcs = this.chroms_layout;
+
+        var arc_gen = d3.svg
+            .arc()
+            .innerRadius(this.radius_bounds[0])
+            .outerRadius(this.radius_bounds[1]);
+
+        var // Attach data to group element.
+        chroms_elts = track_parent_elt
+            .selectAll("g")
+            .data(genome_arcs)
+            .enter()
+            .append("svg:g");
+
+        var // Draw chrom arcs/paths.
+        chroms_paths = chroms_elts
+            .append("path")
+            .attr("d", arc_gen)
+            .attr("class", "chrom-background")
+            .style("stroke", this.bg_stroke)
+            .style("fill", this.loading_bg_fill);
 
         // Append titles to paths.
         chroms_paths.append("title").text(function(d) {
@@ -501,12 +519,14 @@ var CircsterTrackView = Backbone.View.extend({
 
         // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. --
 
-        var self = this,
-            data_manager = self.track.get("data_manager"),
-            // If track has a data manager, get deferred that resolves when data is ready.
-            data_ready_deferred = data_manager
-                ? data_manager.data_is_ready()
-                : true;
+        var self = this;
+
+        var data_manager = self.track.get("data_manager");
+
+        var // If track has a data manager, get deferred that resolves when data is ready.
+        data_ready_deferred = data_manager
+            ? data_manager.data_is_ready()
+            : true;
 
         // When data is ready, render track.
         $.when(data_ready_deferred).then(function() {
@@ -562,8 +582,9 @@ var CircsterTrackView = Backbone.View.extend({
 
         // -- Scale increased, so render visible data with more detail. --
 
-        var self = this,
-            utils = new SVGUtils();
+        var self = this;
+
+        var utils = new SVGUtils();
 
         // Select all chrom data and filter to operate on those that are visible.
         this.parent_elt
@@ -574,11 +595,12 @@ var CircsterTrackView = Backbone.View.extend({
             .each(function(d, i) {
                 // -- Now operating on a single path element representing chromosome data. --
 
-                var path_elt = d3.select(this),
-                    chrom = path_elt.attr("chrom"),
-                    chrom_region = self.genome.get_chrom_region(chrom),
-                    data_manager = self.track.get("data_manager"),
-                    data_deferred;
+                var path_elt = d3.select(this);
+
+                var chrom = path_elt.attr("chrom");
+                var chrom_region = self.genome.get_chrom_region(chrom);
+                var data_manager = self.track.get("data_manager");
+                var data_deferred;
 
                 // If can't get more detailed data, return.
                 if (!data_manager.can_get_more_detailed_data(chrom_region)) {
@@ -628,10 +650,10 @@ var CircsterTrackView = Backbone.View.extend({
      * Transitions chrom data to new values (e.g new radius or data bounds).
      */
     _transition_chrom_data: function() {
-        var track = this.track,
-            chrom_arcs = this.chroms_layout,
-            chrom_data_paths = this.parent_elt.selectAll("g>path.chrom-data"),
-            num_paths = chrom_data_paths[0].length;
+        var track = this.track;
+        var chrom_arcs = this.chroms_layout;
+        var chrom_data_paths = this.parent_elt.selectAll("g>path.chrom-data");
+        var num_paths = chrom_data_paths[0].length;
 
         if (num_paths > 0) {
             var self = this;
@@ -641,11 +663,13 @@ var CircsterTrackView = Backbone.View.extend({
                 // Map chrom data to path data, filtering out null values.
                 var path_data = _.reject(
                     _.map(genome_wide_data, function(chrom_data, i) {
-                        var rval = null,
-                            path_fn = self._get_path_function(
-                                chrom_arcs[i],
-                                chrom_data
-                            );
+                        var rval = null;
+
+                        var path_fn = self._get_path_function(
+                            chrom_arcs[i],
+                            chrom_data
+                        );
+
                         if (path_fn) {
                             rval = path_fn(chrom_data.data);
                         }
@@ -694,10 +718,10 @@ var CircsterTrackView = Backbone.View.extend({
      * Render data as elements attached to svg.
      */
     _render_data: function(svg) {
-        var self = this,
-            chrom_arcs = this.chroms_layout,
-            track = this.track,
-            rendered_deferred = $.Deferred();
+        var self = this;
+        var chrom_arcs = this.chroms_layout;
+        var track = this.track;
+        var rendered_deferred = $.Deferred();
 
         // When genome-wide data is available, render data.
         $.when(
@@ -722,8 +746,8 @@ var CircsterTrackView = Backbone.View.extend({
 
             // Render each chromosome's data.
             _.each(layout_and_data, function(chrom_info) {
-                var chrom_arc = chrom_info[0],
-                    data = chrom_info[1];
+                var chrom_arc = chrom_info[0];
+                var data = chrom_info[1];
                 return self._render_chrom_data(svg, chrom_arc, data);
             });
 
@@ -756,24 +780,26 @@ var CircsterTrackView = Backbone.View.extend({
      */
     _chroms_layout: function() {
         // Setup chroms layout using pie.
-        var chroms_info = this.genome.get_chroms_info(),
-            pie_layout = d3.layout
-                .pie()
-                .value(function(d) {
-                    return d.len;
-                })
-                .sort(null),
-            init_arcs = pie_layout(chroms_info),
-            gap_per_chrom = 2 * Math.PI * this.total_gap / chroms_info.length,
-            chrom_arcs = _.map(init_arcs, function(arc, index) {
-                // For short chroms, endAngle === startAngle.
-                var new_endAngle = arc.endAngle - gap_per_chrom;
-                arc.endAngle =
-                    new_endAngle > arc.startAngle
-                        ? new_endAngle
-                        : arc.startAngle;
-                return arc;
-            });
+        var chroms_info = this.genome.get_chroms_info();
+
+        var pie_layout = d3.layout
+            .pie()
+            .value(function(d) {
+                return d.len;
+            })
+            .sort(null);
+
+        var init_arcs = pie_layout(chroms_info);
+        var gap_per_chrom = 2 * Math.PI * this.total_gap / chroms_info.length;
+
+        var chrom_arcs = _.map(init_arcs, function(arc, index) {
+            // For short chroms, endAngle === startAngle.
+            var new_endAngle = arc.endAngle - gap_per_chrom;
+            arc.endAngle =
+                new_endAngle > arc.startAngle ? new_endAngle : arc.startAngle;
+            return arc;
+        });
+
         return chrom_arcs;
     }
 });
@@ -800,8 +826,9 @@ var CircsterChromLabelTrackView = CircsterTrackView.extend({
     _render_data: function(svg) {
         // -- Add chromosome label where it will fit; an alternative labeling mechanism
         // would be nice for small chromosomes. --
-        var self = this,
-            chrom_arcs = svg.selectAll("g");
+        var self = this;
+
+        var chrom_arcs = svg.selectAll("g");
 
         chrom_arcs.selectAll("path").attr("id", function(d) {
             return "label-" + d.data.chrom;
@@ -827,14 +854,15 @@ var CircsterChromLabelTrackView = CircsterTrackView.extend({
 
         /** Returns an array of tick angles and labels, given a chrom arc. */
         var chromArcTicks = function(d) {
-            var k = (d.endAngle - d.startAngle) / d.value,
-                ticks = d3.range(0, d.value, 25000000).map(function(v, i) {
-                    return {
-                        radius: self.innerRadius,
-                        angle: v * k + d.startAngle,
-                        label: i === 0 ? 0 : i % 3 ? null : self.formatNum(v)
-                    };
-                });
+            var k = (d.endAngle - d.startAngle) / d.value;
+
+            var ticks = d3.range(0, d.value, 25000000).map(function(v, i) {
+                return {
+                    radius: self.innerRadius,
+                    angle: v * k + d.startAngle,
+                    label: i === 0 ? 0 : i % 3 ? null : self.formatNum(v)
+                };
+            });
 
             // If there are fewer that 4 ticks, label last tick so that at least one non-zero tick is labeled.
             if (ticks.length < 4) {
@@ -892,11 +920,13 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
      * Update track when min and/or max are changed.
      */
     _update_min_max: function() {
-        var track_config = this.track.get("config"),
-            new_bounds = [
-                track_config.get_value("min_value"),
-                track_config.get_value("max_value")
-            ];
+        var track_config = this.track.get("config");
+
+        var new_bounds = [
+            track_config.get_value("min_value"),
+            track_config.get_value("max_value")
+        ];
+
         this._update_data_bounds(new_bounds);
 
         // FIXME: this works to update tick/text bounds, but there's probably a better way to do this
@@ -926,12 +956,13 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
         }
 
         // There is path data, so render as path.
-        var parent = svg.datum(chrom_data.data),
-            path = parent
-                .append("path")
-                .attr("class", "chrom-data")
-                .attr("chrom", chrom_arc.data.chrom)
-                .attr("d", path_data);
+        var parent = svg.datum(chrom_data.data);
+
+        var path = parent
+            .append("path")
+            .attr("class", "chrom-data")
+            .attr("chrom", chrom_arc.data.chrom)
+            .attr("d", path_data);
 
         return path;
     },
@@ -985,11 +1016,12 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
      * Render track min, max using ticks.
      */
     render_labels: function() {
-        var self = this,
-            // Keep counter of visible chroms.
-            textTransform = function() {
-                return "rotate(90)";
-            };
+        var self = this;
+
+        var // Keep counter of visible chroms.
+        textTransform = function() {
+            return "rotate(90)";
+        };
 
         // FIXME:
         // (1) using min_max class below is needed for _update_min_max, which could be improved.
@@ -1036,18 +1068,22 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({
         }
 
         // Transition labels to new radius bounds.
-        var self = this,
-            visibleChroms = _.filter(this.chroms_layout, function(c) {
-                return c.endAngle - c.startAngle > 0.08;
-            }),
-            labeledChroms = _.filter(visibleChroms, function(c, i) {
-                return i % 3 === 0;
-            }),
-            new_data = _.flatten(
-                _.map(labeledChroms, function(c) {
-                    return self._data_bounds_ticks_fn()(c);
-                })
-            );
+        var self = this;
+
+        var visibleChroms = _.filter(this.chroms_layout, function(c) {
+            return c.endAngle - c.startAngle > 0.08;
+        });
+
+        var labeledChroms = _.filter(visibleChroms, function(c, i) {
+            return i % 3 === 0;
+        });
+
+        var new_data = _.flatten(
+            _.map(labeledChroms, function(c) {
+                return self._data_bounds_ticks_fn()(c);
+            })
+        );
+
         this.parent_elt
             .selectAll("g.tick")
             .data(new_data)
@@ -1138,8 +1174,8 @@ var CircsterChromInteractionsTrackView = CircsterTrackView.extend({
             $.when(
                 self.track.get("data_manager").get_genome_wide_data(self.genome)
             ).then(function(genome_wide_data) {
-                var chord_data = [],
-                    chroms_info = self.genome.get_chroms_info();
+                var chord_data = [];
+                var chroms_info = self.genome.get_chroms_info();
                 // Convert chromosome data into chord data.
                 _.each(genome_wide_data, function(chrom_data, index) {
                     // Map each interaction into chord data.
@@ -1149,13 +1185,15 @@ var CircsterChromInteractionsTrackView = CircsterTrackView.extend({
                     ) {
                         // Each datum is an interaction/chord.
                         var source_angle = self._get_region_angle(
-                                cur_chrom,
-                                datum[1]
-                            ),
-                            target_angle = self._get_region_angle(
-                                datum[3],
-                                datum[4]
-                            );
+                            cur_chrom,
+                            datum[1]
+                        );
+
+                        var target_angle = self._get_region_angle(
+                            datum[3],
+                            datum[4]
+                        );
+
                         return {
                             source: {
                                 startAngle: source_angle,
@@ -1218,10 +1256,11 @@ var CircsterChromInteractionsTrackView = CircsterTrackView.extend({
 var Circster = Backbone.View.extend({
     initialize: function() {
         // -- Configure visualization --
-        var genome = new visualization.Genome(galaxy_config.app.genome),
-            vis = new visualization.GenomeVisualization(
-                galaxy_config.app.viz_config
-            );
+        var genome = new visualization.Genome(galaxy_config.app.genome);
+
+        var vis = new visualization.GenomeVisualization(
+            galaxy_config.app.viz_config
+        );
 
         // Add Circster-specific config options.
         vis.get("config").add([

client/galaxy/scripts/viz/phyloviz.js

@@ -13,10 +13,11 @@ var UserMenuBase = Backbone.View.extend({
      */
     isAcceptableValue: function($inputKey, min, max) {
         //TODO: use better feedback than alert
-        var value = $inputKey.val(),
-            fieldName =
-                $inputKey.attr("displayLabel") ||
-                $inputKey.attr("id").replace("phyloViz", "");
+        var value = $inputKey.val();
+
+        var fieldName =
+            $inputKey.attr("displayLabel") ||
+            $inputKey.attr("id").replace("phyloViz", "");
 
         function isNumeric(n) {
             return !isNaN(parseFloat(n)) && isFinite(n);
@@ -58,18 +59,31 @@ var UserMenuBase = Backbone.View.extend({
  *                  2) Nodes must appear in other after they have expand and contracted
  */
 function PhyloTreeLayout() {
-    var self = this,
-        hierarchy = d3.layout
-            .hierarchy()
-            .sort(null)
-            .value(null),
-        height = 360, // ! represents both the layout angle and the height of the layout, in px
-        layoutMode = "Linear",
-        leafHeight = 18, // height of each individual leaf node
-        depthSeparation = 200, // separation between nodes of different depth, in px
-        leafIndex = 0, // change to recurssive call
-        defaultDist = 0.5, // tree defaults to 0.5 dist if no dist is specified
-        maxTextWidth = 50; // maximum length of the text labels
+    var self = this; // maximum length of the text labels
+
+    var hierarchy = d3.layout
+        .hierarchy()
+        .sort(null)
+        .value(null);
+
+    var // ! represents both the layout angle and the height of the layout, in px
+    height = 360;
+
+    var layoutMode = "Linear";
+
+    var // height of each individual leaf node
+    leafHeight = 18;
+
+    var // separation between nodes of different depth, in px
+    depthSeparation = 200;
+
+    var // change to recurssive call
+    leafIndex = 0;
+
+    var // tree defaults to 0.5 dist if no dist is specified
+    defaultDist = 0.5;
+
+    var maxTextWidth = 50;
 
     self.leafHeight = function(inputLeafHeight) {
         if (typeof inputLeafHeight === "undefined") {
@@ -125,11 +139,13 @@ function PhyloTreeLayout() {
             // if d is an array, replate with the first object (newick, phyloxml)
             d = d[0];
         }
+
         // self is to find the depth of all the nodes, assumes root is passed in
-        var _nodes = hierarchy.call(self, d, i),
-            nodes = [],
-            maxDepth = 0,
-            numLeaves = 0;
+        var _nodes = hierarchy.call(self, d, i);
+
+        var nodes = [];
+        var maxDepth = 0;
+        var numLeaves = 0;
         //console.debug( JSON.stringify( _nodes, null, 2 ) )
         window._d = d;
         window._nodes = _nodes;
@@ -168,8 +184,8 @@ function PhyloTreeLayout() {
      * -- The layout will first calculate the y0 field going towards the leaves, and x0 when returning
      */
     function layout(node, maxDepth, vertSeparation, parent) {
-        var children = node.children,
-            sumChildVertSeparation = 0;
+        var children = node.children;
+        var sumChildVertSeparation = 0;
 
         // calculation of node's dist from parents, going down.
         var dist = node.dist || defaultDist;
@@ -351,8 +367,8 @@ var PhylovizLayoutBase = Backbone.View.extend({
      *  AND possibly when the tree is edited.
      */
     updateAndRender: function(source) {
-        var vis = d3.select(".vis"),
-            self = this;
+        var vis = d3.select(".vis");
+        var self = this;
         source = source || self.model.root;
 
         self.renderNodes(source);
@@ -441,8 +457,8 @@ var PhylovizLayoutBase = Backbone.View.extend({
         $(".tooltip").remove(); //clean up tooltip, just in case its listeners are removed by d3
         $(".node")
             .attr("data-original-title", function() {
-                var d = this.__data__,
-                    annotation = d.annotation || "None";
+                var d = this.__data__;
+                var annotation = d.annotation || "None";
                 return d
                     ? (d.name ? d.name + "<br/>" : "") +
                           "Dist: " +
@@ -492,18 +508,19 @@ var PhylovizLinearView = PhylovizLayoutBase.extend({
      * Renders the nodes base on Linear layout.
      */
     renderNodes: function(source) {
-        var self = this,
-            fontSize = self.model.get("fontSize") + "px";
+        var self = this;
+        var fontSize = self.model.get("fontSize") + "px";
 
         // assigning properties from models
         self.tree
             .separation(self.model.get("separation"))
             .leafHeight(self.model.get("leafHeight"));
 
-        var duration = 500,
-            nodes = self.tree
-                .separation(self.model.get("separation"))
-                .nodes(self.model.root);
+        var duration = 500;
+
+        var nodes = self.tree
+            .separation(self.model.get("separation"))
+            .nodes(self.model.root);
 
         var node = self.vis.selectAll("g.node").data(nodes, function(d) {
             return d.name + d.id || (d.id = ++self.i);
@@ -706,17 +723,18 @@ var PhylovizView = Backbone.View.extend({
      * Uses d3.zoom events, and extend them to allow manual updates and keeping states in model
      */
     zoomAndPan: function(event) {
-        var zoomParams, translateParams;
+        var zoomParams;
+        var translateParams;
         if (typeof event !== "undefined") {
             zoomParams = event.zoom;
             translateParams = event.translate;
         }
 
-        var self = this,
-            scaleFactor = self.zoomFunc.scale(),
-            translationCoor = self.zoomFunc.translate(),
-            zoomStatement = "",
-            translateStatement = "";
+        var self = this;
+        var scaleFactor = self.zoomFunc.scale();
+        var translationCoor = self.zoomFunc.translate();
+        var zoomStatement = "";
+        var translateStatement = "";
 
         // Do manual scaling.
         switch (zoomParams) {
@@ -779,8 +797,8 @@ var PhylovizView = Backbone.View.extend({
      * Primes the Ajax URL to load another Nexus tree
      */
     reloadViz: function() {
-        var self = this,
-            treeIndex = $("#phylovizNexSelector :selected").val();
+        var self = this;
+        var treeIndex = $("#phylovizNexSelector :selected").val();
         $.getJSON(
             self.phyloTree.get("dataset").url(),
             {
@@ -872,37 +890,39 @@ var HeaderButtons = Backbone.View.extend({
     },
 
     initNavBtns: function() {
-        var self = this,
-            navMenu = mod_icon_btn.create_icon_buttons_menu(
-                [
-                    {
-                        icon_class: "zoom-in",
-                        title: "Zoom in",
-                        on_click: function() {
-                            self.phylovizView.zoomAndPan({ zoom: "+" });
-                        }
-                    },
-                    {
-                        icon_class: "zoom-out",
-                        title: "Zoom out",
-                        on_click: function() {
-                            self.phylovizView.zoomAndPan({ zoom: "-" });
-                        }
-                    },
-                    {
-                        icon_class: "arrow-circle",
-                        title: "Reset Zoom/Pan",
-                        on_click: function() {
-                            self.phylovizView.zoomAndPan({
-                                zoom: "reset"
-                            });
-                        }
-                    }
-                ],
+        var self = this;
+
+        var navMenu = mod_icon_btn.create_icon_buttons_menu(
+            [
                 {
-                    tooltip_config: { placement: "bottom" }
+                    icon_class: "zoom-in",
+                    title: "Zoom in",
+                    on_click: function() {
+                        self.phylovizView.zoomAndPan({ zoom: "+" });
+                    }
+                },
+                {
+                    icon_class: "zoom-out",
+                    title: "Zoom out",
+                    on_click: function() {
+                        self.phylovizView.zoomAndPan({ zoom: "-" });
+                    }
+                },
+                {
+                    icon_class: "arrow-circle",
+                    title: "Reset Zoom/Pan",
+                    on_click: function() {
+                        self.phylovizView.zoomAndPan({
+                            zoom: "reset"
+                        });
+                    }
                 }
-            );
+            ],
+            {
+                tooltip_config: { placement: "bottom" }
+            }
+        );
+
         $("#phyloVizNavBtns").append(navMenu.$el);
     }
 });
@@ -1041,8 +1061,8 @@ var NodeSelectionView = UserMenuBase.extend({
      * For turning on and off the child elements
      */
     toggleUI: function() {
-        var self = this,
-            checked = self.UI.enableEdit.is(":checked");
+        var self = this;
+        var checked = self.UI.enableEdit.is(":checked");
 
         if (!checked) {
             self.cancelChanges();
@@ -1064,8 +1084,8 @@ var NodeSelectionView = UserMenuBase.extend({
      * Reverting to previous values in case user change their minds
      */
     cancelChanges: function() {
-        var self = this,
-            node = self.phyloTree.get("selectedNode");
+        var self = this;
+        var node = self.phyloTree.get("selectedNode");
         if (node) {
             $.each(self.valuesOfConcern, function(key, value) {
                 self.UI[key].val(node[key]);
@@ -1077,8 +1097,8 @@ var NodeSelectionView = UserMenuBase.extend({
      * Changing the data in the underlying tree with user-specified values
      */
     updateNodes: function() {
-        var self = this,
-            node = self.phyloTree.get("selectedNode");
+        var self = this;
+        var node = self.phyloTree.get("selectedNode");
         if (node) {
             if (
                 !self.isAcceptableValue(self.UI.dist, 0, 1) ||
@@ -1106,12 +1126,14 @@ var PhyloVizSearch = UserMenuBase.extend({
         var self = this;
 
         $("#phyloVizSearchBtn").on("click", function() {
-            var searchTerm = $("#phyloVizSearchTerm"),
-                searchConditionVal = $("#phyloVizSearchCondition")
-                    .val()
-                    .split("-"),
-                attr = searchConditionVal[0],
-                condition = searchConditionVal[1];
+            var searchTerm = $("#phyloVizSearchTerm");
+
+            var searchConditionVal = $("#phyloVizSearchCondition")
+                .val()
+                .split("-");
+
+            var attr = searchConditionVal[0];
+            var condition = searchConditionVal[1];
             self.hasIllegalJsonCharacters(searchTerm);
 
             if (attr === "dist") {

client/galaxy/scripts/viz/sweepster.js

@@ -110,37 +110,38 @@ var ToolParameterTree = Backbone.Model.extend({
                 samples: param.get_samples()
             };
         });
-        var node_id = 0,
-            // Creates tree data recursively.
-            create_tree_data = function(params_samples, index) {
-                var param_samples = params_samples[index],
-                    param = param_samples.param,
-                    param_label = param.get("label"),
-                    settings = param_samples.samples;
+        var node_id = 0;
 
-                // Create leaves when last parameter setting is reached.
-                if (params_samples.length - 1 === index) {
-                    return _.map(settings, function(setting) {
-                        return {
-                            id: node_id++,
-                            name: setting,
-                            param: param,
-                            value: setting
-                        };
-                    });
-                }
+        var // Creates tree data recursively.
+        create_tree_data = function(params_samples, index) {
+            var param_samples = params_samples[index],
+                param = param_samples.param,
+                param_label = param.get("label"),
+                settings = param_samples.samples;
 
-                // Recurse to handle other parameters.
+            // Create leaves when last parameter setting is reached.
+            if (params_samples.length - 1 === index) {
                 return _.map(settings, function(setting) {
                     return {
                         id: node_id++,
                         name: setting,
                         param: param,
-                        value: setting,
-                        children: create_tree_data(params_samples, index + 1)
+                        value: setting
                     };
                 });
-            };
+            }
+
+            // Recurse to handle other parameters.
+            return _.map(settings, function(setting) {
+                return {
+                    id: node_id++,
+                    name: setting,
+                    param: param,
+                    value: setting,
+                    children: create_tree_data(params_samples, index + 1)
+                };
+            });
+        };
 
         this.set("tree_data", {
             name: "Root",
@@ -191,30 +192,32 @@ var ToolParameterTree = Backbone.Model.extend({
         }
 
         // Walk subtree starting at clicked node to get full list of settings.
-        var self = this,
-            get_settings = function(node, settings) {
-                // Add setting for this node. Root node does not have a param,
-                // however.
-                if (node.param) {
-                    settings[node.param.get("name")] = node.value;
-                }
+        var self = this;
 
-                if (!node.children) {
-                    // At leaf node, so return settings.
-                    return new ToolInputsSettings({
-                        inputs: self.get("tool").get("inputs"),
-                        values: settings
-                    });
-                } else {
-                    // At interior node: return list of subtree settings.
-                    return _.flatten(
-                        _.map(node.children, function(c) {
-                            return get_settings(c, _.clone(settings));
-                        })
-                    );
-                }
-            },
-            all_settings = get_settings(target_node, fixed_settings);
+        var get_settings = function(node, settings) {
+            // Add setting for this node. Root node does not have a param,
+            // however.
+            if (node.param) {
+                settings[node.param.get("name")] = node.value;
+            }
+
+            if (!node.children) {
+                // At leaf node, so return settings.
+                return new ToolInputsSettings({
+                    inputs: self.get("tool").get("inputs"),
+                    values: settings
+                });
+            } else {
+                // At interior node: return list of subtree settings.
+                return _.flatten(
+                    _.map(node.children, function(c) {
+                        return get_settings(c, _.clone(settings));
+                    })
+                );
+            }
+        };
+
+        var all_settings = get_settings(target_node, fixed_settings);
 
         // If user clicked on leaf, settings is a single dict. Convert to array for simplicity.
         if (!_.isArray(all_settings)) {
@@ -243,8 +246,9 @@ var ToolParameterTree = Backbone.Model.extend({
         };
 
         // Get node's parents.
-        var parents = [],
-            cur_parent = node.parent;
+        var parents = [];
+
+        var cur_parent = node.parent;
         while (cur_parent) {
             parents.push(cur_parent);
             cur_parent = cur_parent.parent;
@@ -257,12 +261,13 @@ var ToolParameterTree = Backbone.Model.extend({
      * Returns the leaf that corresponds to a settings collection.
      */
     get_leaf: function(settings) {
-        var cur_node = this.get("tree_data"),
-            find_child = function(children) {
-                return _.find(children, function(child) {
-                    return settings[child.param.get("name")] === child.value;
-                });
-            };
+        var cur_node = this.get("tree_data");
+
+        var find_child = function(children) {
+            return _.find(children, function(child) {
+                return settings[child.param.get("name")] === child.value;
+            });
+        };
 
         while (cur_node.children) {
             cur_node = find_child(cur_node.children);
@@ -314,8 +319,8 @@ var SweepsterTrack = Backbone.Model.extend({
     },
 
     same_settings: function(a_track) {
-        var this_settings = this.get("settings"),
-            other_settings = a_track.get("settings");
+        var this_settings = this.get("settings");
+        var other_settings = a_track.get("settings");
         for (var prop in this_settings) {
             if (
                 !other_settings[prop] ||
@@ -423,15 +428,19 @@ var SweepsterTrackView = Backbone.View.extend({
     render: function() {
         // Render settings icon and popup.
         // TODO: use template.
-        var settings = this.model.get("settings"),
-            values = settings.get("values"),
-            settings_td = $("<td/>")
-                .addClass("settings")
-                .appendTo(this.$el),
-            settings_div = $("<div/>")
-                .addClass("track-info")
-                .hide()
-                .appendTo(settings_td);
+        var settings = this.model.get("settings");
+
+        var values = settings.get("values");
+
+        var settings_td = $("<td/>")
+            .addClass("settings")
+            .appendTo(this.$el);
+
+        var settings_div = $("<div/>")
+            .addClass("track-info")
+            .hide()
+            .appendTo(settings_td);
+
         settings_div.append(
             $("<div/>")
                 .css("font-weight", "bold")
@@ -442,14 +451,16 @@ var SweepsterTrackView = Backbone.View.extend({
                 input.get("label") + ": " + values[input.get("name")] + "<br/>"
             );
         });
-        var self = this,
-            run_on_dataset_button = $("<button/>")
-                .appendTo(settings_div)
-                .text("Run on complete dataset")
-                .click(function() {
-                    settings_div.toggle();
-                    self.trigger("run_on_dataset", settings);
-                });
+        var self = this;
+
+        var run_on_dataset_button = $("<button/>")
+            .appendTo(settings_div)
+            .text("Run on complete dataset")
+            .click(function() {
+                settings_div.toggle();
+                self.trigger("run_on_dataset", settings);
+            });
+
         var icon_menu = mod_icon_btn.create_icon_buttons_menu([
             {
                 title: "Settings",
@@ -493,10 +504,10 @@ var SweepsterTrackView = Backbone.View.extend({
      * Draw tiles for regions.
      */
     draw_tiles: function() {
-        var self = this,
-            track = this.model.get("track"),
-            regions = this.model.get("regions"),
-            tile_containers = this.$el.find("td.tile");
+        var self = this;
+        var track = this.model.get("track");
+        var regions = this.model.get("regions");
+        var tile_containers = this.$el.find("td.tile");
 
         // Do nothing if track is not defined.
         if (!track) {
@@ -507,9 +518,9 @@ var SweepsterTrackView = Backbone.View.extend({
         $.when(track.data_manager.data_is_ready()).then(function(data_ok) {
             // Draw tile for each region.
             regions.each(function(region, index) {
-                var resolution = region.length() / self.TILE_LEN,
-                    w_scale = 1 / resolution,
-                    mode = self.model.get("mode");
+                var resolution = region.length() / self.TILE_LEN;
+                var w_scale = 1 / resolution;
+                var mode = self.model.get("mode");
                 $.when(
                     track.data_manager.get_data(region, mode, resolution, {})
                 ).then(function(tile_data) {
@@ -559,10 +570,10 @@ var ToolInputValOrSweepView = Backbone.View.extend({
     },
 
     render: function() {
-        var input = this.model,
-            type = input.get("type"),
-            single_input_row = this.$el.find(".form-row-input"),
-            sweep_inputs_row = null;
+        var input = this.model;
+        var type = input.get("type");
+        var single_input_row = this.$el.find(".form-row-input");
+        var sweep_inputs_row = null;
 
         // Update tool inputs as single input changes.
         single_input_row.find(":input").change(function() {
@@ -576,11 +587,12 @@ var ToolInputValOrSweepView = Backbone.View.extend({
             );
         } else if (input instanceof tools.SelectToolParameter) {
             var options = _.map(this.$el.find("select option"), function(
-                    option
-                ) {
-                    return $(option).val();
-                }),
-                options_text = options.join(", ");
+                option
+            ) {
+                return $(option).val();
+            });
+
+            var options_text = options.join(", ");
             sweep_inputs_row = $(
                 _.template(this.select_input_template)({
                     options: options_text
@@ -590,35 +602,37 @@ var ToolInputValOrSweepView = Backbone.View.extend({
         sweep_inputs_row.insertAfter(single_input_row);
 
         // Add buttons for adding/removing parameter.
-        var self = this,
-            menu = mod_icon_btn.create_icon_buttons_menu(
-                [
-                    {
-                        title: "Add parameter to tree",
-                        icon_class: "plus-button",
-                        on_click: function() {
-                            input.set("in_ptree", true);
-                            single_input_row.hide();
-                            sweep_inputs_row.show();
-                            $(this).hide();
-                            self.$el.find(".icon-button.toggle").show();
-                        }
-                    },
-                    {
-                        title: "Remove parameter from tree",
-                        icon_class: "toggle",
-                        on_click: function() {
-                            // Remove parameter from tree params where name matches clicked paramter.
-                            input.set("in_ptree", false);
-                            sweep_inputs_row.hide();
-                            single_input_row.show();
-                            $(this).hide();
-                            self.$el.find(".icon-button.plus-button").show();
-                        }
+        var self = this;
+
+        var menu = mod_icon_btn.create_icon_buttons_menu(
+            [
+                {
+                    title: "Add parameter to tree",
+                    icon_class: "plus-button",
+                    on_click: function() {
+                        input.set("in_ptree", true);
+                        single_input_row.hide();
+                        sweep_inputs_row.show();
+                        $(this).hide();
+                        self.$el.find(".icon-button.toggle").show();
                     }
-                ],
-                {}
-            );
+                },
+                {
+                    title: "Remove parameter from tree",
+                    icon_class: "toggle",
+                    on_click: function() {
+                        // Remove parameter from tree params where name matches clicked paramter.
+                        input.set("in_ptree", false);
+                        sweep_inputs_row.hide();
+                        single_input_row.show();
+                        $(this).hide();
+                        self.$el.find(".icon-button.plus-button").show();
+                    }
+                }
+            ],
+            {}
+        );
+
         this.$el.prepend(menu.$el);
 
         // Show/hide input rows and icons depending on whether parameter is in the tree.
@@ -655,8 +669,9 @@ var ToolParameterTreeDesignView = Backbone.View.extend({
         this.$el.append(tool_form_view.$el);
 
         // Set up views for each tool input.
-        var self = this,
-            inputs = self.model.get("tool").get("inputs");
+        var self = this;
+
+        var inputs = self.model.get("tool").get("inputs");
         this.$el
             .find(".form-row")
             .not(".form-actions")
@@ -708,8 +723,8 @@ var ToolParameterTreeView = Backbone.View.extend({
         // Setup and add labels for tree levels.
         var param_depths = _.uniq(_.pluck(nodes, "y"));
         _.each(tree_params, function(param, index) {
-            var x = param_depths[index + 1],
-                center_left = $("#center").position().left;
+            var x = param_depths[index + 1];
+            var center_left = $("#center").position().left;
             self.$el.append(
                 $("<div>")
                     .addClass("label")
@@ -879,9 +894,10 @@ var SweepsterVisualizationView = Backbone.View.extend({
         $("#left").append(tree_design_view.$el);
 
         // Render track collection container/view in right panel.
-        var self = this,
-            regions = self.model.get("regions"),
-            tr = $("<tr/>").appendTo(this.track_collection_container);
+        var self = this;
+
+        var regions = self.model.get("regions");
+        var tr = $("<tr/>").appendTo(this.track_collection_container);
 
         regions.each(function(region) {
             tr.append($("<th>").text(region.toString()));
@@ -901,17 +917,18 @@ var SweepsterVisualizationView = Backbone.View.extend({
         // -- Render help and tool parameter tree in center panel. --
 
         // Help includes text and a close button.
-        var help_div = $(this.helpText).addClass("help"),
-            close_button = mod_icon_btn.create_icon_buttons_menu([
-                {
-                    title: "Close",
-                    icon_class: "cross-circle",
-                    on_click: function() {
-                        $(".tooltip").remove();
-                        help_div.remove();
-                    }
+        var help_div = $(this.helpText).addClass("help");
+
+        var close_button = mod_icon_btn.create_icon_buttons_menu([
+            {
+                title: "Close",
+                icon_class: "cross-circle",
+                on_click: function() {
+                    $(".tooltip").remove();
+                    help_div.remove();
                 }
-            ]);
+            }
+        ]);
 
         help_div.prepend(close_button.$el.css("float", "right"));
         $("#center").append(help_div);
@@ -966,8 +983,9 @@ var SweepsterVisualizationView = Backbone.View.extend({
         );
 
         // Create mode selection popup. Mode selection changes default mode and mode for all tracks.
-        var modes = ["Squish", "Pack"],
-            mode_mapping = {};
+        var modes = ["Squish", "Pack"];
+
+        var mode_mapping = {};
         _.each(modes, function(mode) {
             mode_mapping[mode] = function() {
                 self.model.set("default_mode", mode);
@@ -991,9 +1009,9 @@ var SweepsterVisualizationView = Backbone.View.extend({
     },
 
     run_tool_on_dataset: function(settings) {
-        var tool = this.model.get("tool"),
-            tool_name = tool.get("name"),
-            dataset = this.model.get("dataset");
+        var tool = this.model.get("tool");
+        var tool_name = tool.get("name");
+        var dataset = this.model.get("dataset");
         tool.set_input_values(settings.get("values"));
         $.when(tool.rerun(dataset)).then(function(outputs) {
             // TODO.
@@ -1017,8 +1035,8 @@ var SweepsterVisualizationView = Backbone.View.extend({
      * Add track to model and view.
      */
     add_track: function(pm_track) {
-        var self = this,
-            param_tree = this.model.get("parameter_tree");
+        var self = this;
+        var param_tree = this.model.get("parameter_tree");
 
         // Add track to model.
         self.model.add_track(pm_track);
@@ -1068,18 +1086,22 @@ var SweepsterVisualizationView = Backbone.View.extend({
      */
     handle_node_clicks: function() {
         // When node clicked in tree, run tool and add tracks to model.
-        var self = this,
-            param_tree = this.model.get("parameter_tree"),
-            regions = this.model.get("regions"),
-            node = d3
-                .select(this.tool_param_tree_view.$el[0])
-                .selectAll("g.node");
+        var self = this;
+
+        var param_tree = this.model.get("parameter_tree");
+        var regions = this.model.get("regions");
+
+        var node = d3
+            .select(this.tool_param_tree_view.$el[0])
+            .selectAll("g.node");
+
         node.on("click", function(d, i) {
             // Get all settings corresponding to node.
-            var tool = self.model.get("tool"),
-                dataset = self.model.get("dataset"),
-                all_settings = param_tree.get_node_settings(d),
-                run_jobs_deferred = $.Deferred();
+            var tool = self.model.get("tool");
+
+            var dataset = self.model.get("dataset");
+            var all_settings = param_tree.get_node_settings(d);
+            var run_jobs_deferred = $.Deferred();
 
             // Do not allow 10+ jobs to be run.
             if (all_settings.length >= 10) {
@@ -1131,8 +1153,9 @@ var SweepsterVisualizationView = Backbone.View.extend({
                             // HACKish: output is an HDA with track config attribute. To create a track
                             // that works correctly with Backbone relational, it is necessary to
                             // use a modified version of the track config.
-                            var dataset = output.first(),
-                                track_config = dataset.get("track_config");
+                            var dataset = output.first();
+
+                            var track_config = dataset.get("track_config");
                             // Set dataset to be the tool's output.
                             track_config.dataset = dataset;
                             // Set tool to null so that it is not unpacked; unpacking it messes with

client/galaxy/scripts/viz/trackster.js

@@ -69,18 +69,19 @@ var TracksterUI = Base.extend({
 
         // FIXME: give unique IDs to Drawables and save overview as ID.
         var overview_track_name = view.overview_drawable
-                ? view.overview_drawable.config.get_value("name")
-                : null,
-            viz_config = {
-                view: view.to_dict(),
-                viewport: {
-                    chrom: view.chrom,
-                    start: view.low,
-                    end: view.high,
-                    overview: overview_track_name
-                },
-                bookmarks: bookmarks
-            };
+            ? view.overview_drawable.config.get_value("name")
+            : null;
+
+        var viz_config = {
+            view: view.to_dict(),
+            viewport: {
+                chrom: view.chrom,
+                start: view.low,
+                end: view.high,
+                overview: overview_track_name
+            },
+            bookmarks: bookmarks
+        };
 
         // Make call to save visualization.
         return $.ajax({
@@ -126,81 +127,83 @@ var TracksterUI = Base.extend({
      * Create button menu
      */
     createButtonMenu: function() {
-        var self = this,
-            menu = mod_icon_btn.create_icon_buttons_menu(
-                [
-                    {
-                        icon_class: "plus-button",
-                        title: "Add tracks",
-                        on_click: function() {
-                            visualization.select_datasets(
-                                { dbkey: view.dbkey },
-                                function(new_tracks) {
-                                    _.each(new_tracks, function(track) {
-                                        view.add_drawable(
-                                            tracks.object_from_template(
-                                                track,
-                                                view,
-                                                view
-                                            )
-                                        );
-                                    });
-                                }
-                            );
-                        }
-                    },
-                    {
-                        icon_class: "block--plus",
-                        title: "Add group",
-                        on_click: function() {
-                            view.add_drawable(
-                                new tracks.DrawableGroup(view, view, {
-                                    name: "New Group"
-                                })
-                            );
-                        }
-                    },
-                    {
-                        icon_class: "bookmarks",
-                        title: "Bookmarks",
-                        on_click: function() {
-                            // HACK -- use style to determine if panel is hidden and hide/show accordingly.
-                            force_right_panel(
-                                $("div#right").css("right") == "0px"
-                                    ? "hide"
-                                    : "show"
-                            );
-                        }
-                    },
-                    {
-                        icon_class: "globe",
-                        title: "Circster",
-                        on_click: function() {
-                            window.location =
-                                self.baseURL +
-                                "visualization/circster?id=" +
-                                view.vis_id;
-                        }
-                    },
-                    {
-                        icon_class: "disk--arrow",
-                        title: "Save",
-                        on_click: function() {
-                            self.save_viz();
-                        }
-                    },
-                    {
-                        icon_class: "cross-circle",
-                        title: "Close",
-                        on_click: function() {
-                            self.handle_unsaved_changes(view);
-                        }
-                    }
-                ],
+        var self = this;
+
+        var menu = mod_icon_btn.create_icon_buttons_menu(
+            [
                 {
-                    tooltip_config: { placement: "bottom" }
+                    icon_class: "plus-button",
+                    title: "Add tracks",
+                    on_click: function() {
+                        visualization.select_datasets(
+                            { dbkey: view.dbkey },
+                            function(new_tracks) {
+                                _.each(new_tracks, function(track) {
+                                    view.add_drawable(
+                                        tracks.object_from_template(
+                                            track,
+                                            view,
+                                            view
+                                        )
+                                    );
+                                });
+                            }
+                        );
+                    }
+                },
+                {
+                    icon_class: "block--plus",
+                    title: "Add group",
+                    on_click: function() {
+                        view.add_drawable(
+                            new tracks.DrawableGroup(view, view, {
+                                name: "New Group"
+                            })
+                        );
+                    }
+                },
+                {
+                    icon_class: "bookmarks",
+                    title: "Bookmarks",
+                    on_click: function() {
+                        // HACK -- use style to determine if panel is hidden and hide/show accordingly.
+                        force_right_panel(
+                            $("div#right").css("right") == "0px"
+                                ? "hide"
+                                : "show"
+                        );
+                    }
+                },
+                {
+                    icon_class: "globe",
+                    title: "Circster",
+                    on_click: function() {
+                        window.location =
+                            self.baseURL +
+                            "visualization/circster?id=" +
+                            view.vis_id;
+                    }
+                },
+                {
+                    icon_class: "disk--arrow",
+                    title: "Save",
+                    on_click: function() {
+                        self.save_viz();
+                    }
+                },
+                {
+                    icon_class: "cross-circle",
+                    title: "Close",
+                    on_click: function() {
+                        self.handle_unsaved_changes(view);
+                    }
                 }
-            );
+            ],
+            {
+                tooltip_config: { placement: "bottom" }
+            }
+        );
+
         this.buttonMenu = menu;
         return menu;
     },
@@ -210,40 +213,45 @@ var TracksterUI = Base.extend({
      */
     add_bookmark: function(position, annotation, editable) {
         // Create HTML.
-        var bookmarks_container = $("#right .unified-panel-body"),
-            new_bookmark = $("<div/>")
-                .addClass("bookmark")
-                .appendTo(bookmarks_container);
+        var bookmarks_container = $("#right .unified-panel-body");
+
+        var new_bookmark = $("<div/>")
+            .addClass("bookmark")
+            .appendTo(bookmarks_container);
 
         var position_div = $("<div/>")
-                .addClass("position")
-                .appendTo(new_bookmark),
-            position_link = $("<a href=''/>")
-                .text(position)
-                .appendTo(position_div)
-                .click(function() {
-                    view.go_to(position);
-                    return false;
-                }),
-            annotation_div = $("<div/>")
-                .text(annotation)
-                .appendTo(new_bookmark);
+            .addClass("position")
+            .appendTo(new_bookmark);
+
+        var position_link = $("<a href=''/>")
+            .text(position)
+            .appendTo(position_div)
+            .click(function() {
+                view.go_to(position);
+                return false;
+            });
+
+        var annotation_div = $("<div/>")
+            .text(annotation)
+            .appendTo(new_bookmark);
 
         // If editable, enable bookmark deletion and annotation editing.
         if (editable) {
             var delete_icon_container = $("<div/>")
-                    .addClass("delete-icon-container")
-                    .prependTo(new_bookmark)
-                    .click(function() {
-                        // Remove bookmark.
-                        new_bookmark.slideUp("fast");
-                        new_bookmark.remove();
-                        view.has_changes = true;
-                        return false;
-                    }),
-                delete_icon = $("<a href=''/>")
-                    .addClass("icon-button delete")
-                    .appendTo(delete_icon_container);
+                .addClass("delete-icon-container")
+                .prependTo(new_bookmark)
+                .click(function() {
+                    // Remove bookmark.
+                    new_bookmark.slideUp("fast");
+                    new_bookmark.remove();
+                    view.has_changes = true;
+                    return false;
+                });
+
+            var delete_icon = $("<a href=''/>")
+                .addClass("icon-button delete")
+                .appendTo(delete_icon_container);
+
             annotation_div
                 .make_text_editable({
                     num_rows: 3,
@@ -268,18 +276,20 @@ var TracksterUI = Base.extend({
         editable
     ) {
         // Create view.
-        var self = this,
-            view = new tracks.TracksterView(
-                _.extend(view_config, { header: false })
-            );
+        var self = this;
+
+        var view = new tracks.TracksterView(
+            _.extend(view_config, { header: false })
+        );
+
         view.editor = true;
         $.when(view.load_chroms_deferred).then(function(chrom_info) {
             // Viewport config.
             if (viewport_config) {
-                var chrom = viewport_config.chrom,
-                    start = viewport_config.start,
-                    end = viewport_config.end,
-                    overview_drawable_name = viewport_config.overview;
+                var chrom = viewport_config.chrom;
+                var start = viewport_config.start;
+                var end = viewport_config.end;
+                var overview_drawable_name = viewport_config.overview;
 
                 if (chrom && start !== undefined && end) {
                     view.change_chrom(chrom, start, end);
@@ -295,7 +305,10 @@ var TracksterUI = Base.extend({
             // Add drawables to view.
             if (drawables_config) {
                 // FIXME: can from_dict() be used to create view and add drawables?
-                var drawable_config, drawable_type, drawable;
+                var drawable_config;
+
+                var drawable_type;
+                var drawable;
                 for (var i = 0; i < drawables_config.length; i++) {
                     view.add_drawable(
                         tracks.object_from_template(
@@ -461,14 +474,16 @@ var TracksterView = Backbone.View.extend({
 
     choose_existing_or_new: function() {
         var self = this;
-        var dbkey = query_string.get("dbkey"),
-            listTracksParams = {},
-            dataset_params = {
-                dbkey: dbkey,
-                dataset_id: query_string.get("dataset_id"),
-                hda_ldda: query_string.get("hda_ldda"),
-                gene_region: query_string.get("gene_region")
-            };
+        var dbkey = query_string.get("dbkey");
+        var listTracksParams = {};
+
+        var dataset_params = {
+            dbkey: dbkey,
+            dataset_id: query_string.get("dataset_id"),
+            hda_ldda: query_string.get("hda_ldda"),
+            gene_region: query_string.get("gene_region")
+        };
+
         if (dbkey) {
             listTracksParams["f-dbkey"] = dbkey;
         }
@@ -697,8 +712,9 @@ var TracksterView = Backbone.View.extend({
         // initialize icons
         $("#add-bookmark-button").click(function() {
             // add new bookmark.
-            var position = view.chrom + ":" + view.low + "-" + view.high,
-                annotation = "Bookmark description";
+            var position = view.chrom + ":" + view.low + "-" + view.high;
+
+            var annotation = "Bookmark description";
             return ui.add_bookmark(position, annotation, true);
         });
 

client/galaxy/scripts/viz/trackster/filters.js

@@ -68,12 +68,14 @@ var NumberFilter = function(obj_dict) {
     // Enable users to edit parameter's value via a text box.
     var edit_slider_values = function(container, span, slider) {
         container.click(function() {
-            var cur_value = span.text(),
-                max = parseFloat(slider.slider("option", "max")),
-                input_size =
-                    max <= 1 ? 4 : max <= 1000000 ? max.toString().length : 6,
-                multi_value = false,
-                slider_row = $(this).parents(".slider-row");
+            var cur_value = span.text();
+            var max = parseFloat(slider.slider("option", "max"));
+
+            var input_size =
+                max <= 1 ? 4 : max <= 1000000 ? max.toString().length : 6;
+
+            var multi_value = false;
+            var slider_row = $(this).parents(".slider-row");
 
             // Row now has input.
             slider_row.addClass("input");
@@ -110,16 +112,19 @@ var NumberFilter = function(obj_dict) {
                         // Enter/return key initiates callback. If new value(s) are in slider range,
                         // change value (which calls slider's change() function).
                         //
-                        var slider_min = slider.slider("option", "min"),
-                            slider_max = slider.slider("option", "max"),
-                            invalid = function(a_val) {
-                                return (
-                                    isNaN(a_val) ||
-                                    a_val > slider_max ||
-                                    a_val < slider_min
-                                );
-                            },
-                            new_value = $(this).val();
+                        var slider_min = slider.slider("option", "min");
+
+                        var slider_max = slider.slider("option", "max");
+
+                        var invalid = function(a_val) {
+                            return (
+                                isNaN(a_val) ||
+                                a_val > slider_max ||
+                                a_val < slider_min
+                            );
+                        };
+
+                        var new_value = $(this).val();
                         if (!multi_value) {
                             new_value = parseFloat(new_value);
                             if (invalid(new_value)) {
@@ -171,19 +176,23 @@ var NumberFilter = function(obj_dict) {
 
     // Set up filter label (name, values).
     var filter_label = $("<div/>")
-            .addClass("elt-label")
-            .appendTo(filter.parent_div),
-        name_span = $("<span/>")
-            .addClass("slider-name")
-            .text(filter.name + "  ")
-            .appendTo(filter_label),
-        values_span = $("<span/>").text(this.low + "-" + this.high),
-        values_span_container = $("<span/>")
-            .addClass("slider-value")
-            .appendTo(filter_label)
-            .append("[")
-            .append(values_span)
-            .append("]");
+        .addClass("elt-label")
+        .appendTo(filter.parent_div);
+
+    var name_span = $("<span/>")
+        .addClass("slider-name")
+        .text(filter.name + "  ")
+        .appendTo(filter_label);
+
+    var values_span = $("<span/>").text(this.low + "-" + this.high);
+
+    var values_span_container = $("<span/>")
+        .addClass("slider-value")
+        .appendTo(filter_label)
+        .append("[")
+        .append(values_span)
+        .append("]");
+
     filter.values_span = values_span;
 
     // Set up slider for filter.
@@ -439,8 +448,8 @@ extend(NumberFilter.prototype, {
             this.parent_div.hide();
         }
 
-        var slider_min = this.slider.slider("option", "min"),
-            slider_max = this.slider.slider("option", "max");
+        var slider_min = this.slider.slider("option", "min");
+        var slider_max = this.slider.slider("option", "max");
         if (this.min < slider_min || this.max > slider_max) {
             // Update slider min, max, step.
             this.slider.slider("option", "min", this.min);
@@ -501,11 +510,13 @@ var FiltersManager = function(track, obj_dict) {
     if (obj_dict && "filters" in obj_dict) {
         // Second condition needed for backward compatibility.
         var alpha_filter_name =
-                "alpha_filter" in obj_dict ? obj_dict.alpha_filter : null,
-            height_filter_name =
-                "height_filter" in obj_dict ? obj_dict.height_filter : null,
-            filters_dict = obj_dict.filters,
-            filter;
+            "alpha_filter" in obj_dict ? obj_dict.alpha_filter : null;
+
+        var height_filter_name =
+            "height_filter" in obj_dict ? obj_dict.height_filter : null;
+
+        var filters_dict = obj_dict.filters;
+        var filter;
         for (var i = 0; i < filters_dict.length; i++) {
             if (filters_dict[i].type === "number") {
                 filter = new NumberFilter(filters_dict[i]);
@@ -561,9 +572,9 @@ extend(FiltersManager.prototype, {
      * Returns dictionary for manager.
      */
     to_dict: function() {
-        var obj_dict = {},
-            filter_dicts = [],
-            filter;
+        var obj_dict = {};
+        var filter_dicts = [];
+        var filter;
 
         // Include individual filter states.
         for (var i = 0; i < this.filters.length; i++) {
@@ -648,9 +659,10 @@ extend(FiltersManager.prototype, {
         // Find and group active filters. Active filters are those being used to hide data.
         // Filters with the same tool id are grouped.
         //
-        var active_filters = {},
-            filter,
-            tool_filter_conditions;
+        var active_filters = {};
+
+        var filter;
+        var tool_filter_conditions;
         for (var i = 0; i < this.filters.length; i++) {
             filter = this.filters[i];
             if (filter.tool_id) {
@@ -693,16 +705,18 @@ extend(FiltersManager.prototype, {
         // iteratively application.
         (function run_filter(input_dataset_id, filters) {
             var // Set up filtering info and params.
-                filter_tuple = filters[0],
-                tool_id = filter_tuple[0],
-                tool_filters = filter_tuple[1],
-                tool_filter_str = "(" + tool_filters.join(") and (") + ")",
-                url_params = {
-                    cond: tool_filter_str,
-                    input: input_dataset_id,
-                    target_dataset_id: input_dataset_id,
-                    tool_id: tool_id
-                };
+            filter_tuple = filters[0];
+
+            var tool_id = filter_tuple[0];
+            var tool_filters = filter_tuple[1];
+            var tool_filter_str = "(" + tool_filters.join(") and (") + ")";
+
+            var url_params = {
+                cond: tool_filter_str,
+                input: input_dataset_id,
+                target_dataset_id: input_dataset_id,
+                tool_id: tool_id
+            };
 
             // Remove current filter.
             filters = filters.slice(1);

client/galaxy/scripts/viz/trackster/painters.js

@@ -1,22 +1,24 @@
 import * as _ from "libs/underscore";
+
 /**
  * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig.
  * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first
  * region overlaps the start (but not the end) of the second region.
  * NOTE: Coordinates are assumed to be in BED format: half open (start is closed, end is open).
  */
-var BEFORE = 1001,
-    CONTAINS = 1002,
-    OVERLAP_START = 1003,
-    OVERLAP_END = 1004,
-    CONTAINED_BY = 1005,
-    AFTER = 1006;
+var BEFORE = 1001;
+
+var CONTAINS = 1002;
+var OVERLAP_START = 1003;
+var OVERLAP_END = 1004;
+var CONTAINED_BY = 1005;
+var AFTER = 1006;
 var compute_overlap = function(first_region, second_region) {
-    var first_start = first_region[0],
-        first_end = first_region[1],
-        second_start = second_region[0],
-        second_end = second_region[1],
-        overlap;
+    var first_start = first_region[0];
+    var first_end = first_region[1];
+    var second_start = second_region[0];
+    var second_end = second_region[1];
+    var overlap;
     if (first_start < second_start) {
         if (first_end <= second_start) {
             overlap = BEFORE;
@@ -83,9 +85,10 @@ var drawDownwardEquilateralTriangle = function(
     side_len
 ) {
     // Compute other two points of triangle.
-    var x1 = down_vertex_x - side_len / 2,
-        x2 = down_vertex_x + side_len / 2,
-        y = down_vertex_y - Math.sqrt(side_len * 3 / 2);
+    var x1 = down_vertex_x - side_len / 2;
+
+    var x2 = down_vertex_x + side_len / 2;
+    var y = down_vertex_y - Math.sqrt(side_len * 3 / 2);
 
     // Draw and fill.
     ctx.beginPath();
@@ -192,14 +195,14 @@ LinePainter.prototype.default_prefs = {
 };
 
 LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
-    var in_path = false,
-        min_value = this.prefs.min_value,
-        max_value = this.prefs.max_value,
-        vertical_range = max_value - min_value,
-        height_px = height,
-        view_start = this.view_start,
-        mode = this.mode,
-        data = this.data;
+    var in_path = false;
+    var min_value = this.prefs.min_value;
+    var max_value = this.prefs.max_value;
+    var vertical_range = max_value - min_value;
+    var height_px = height;
+    var view_start = this.view_start;
+    var mode = this.mode;
+    var data = this.data;
 
     ctx.save();
 
@@ -213,7 +216,9 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
     }
 
     ctx.beginPath();
-    var x_scaled, y, delta_x_pxs;
+    var x_scaled;
+    var y;
+    var delta_x_pxs;
     if (data.length > 1) {
         delta_x_pxs = _.map(data.slice(0, -1), function(d, i) {
             return Math.ceil((data[i + 1][0] - data[i][0]) * w_scale);
@@ -223,14 +228,16 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
     }
 
     // Painter color can be in either block_color (FeatureTrack) or color pref (LineTrack).
-    var painter_color = this.prefs.block_color || this.prefs.color,
-        // Extract RGB from preference color.
-        pref_color = parseInt(painter_color.slice(1), 16),
-        pref_r = (pref_color & 0xff0000) >> 16,
-        pref_g = (pref_color & 0x00ff00) >> 8,
-        pref_b = pref_color & 0x0000ff,
-        top_overflow = false,
-        bot_overflow = false;
+    var painter_color = this.prefs.block_color || this.prefs.color;
+
+    var // Extract RGB from preference color.
+    pref_color = parseInt(painter_color.slice(1), 16);
+
+    var pref_r = (pref_color & 0xff0000) >> 16;
+    var pref_g = (pref_color & 0x00ff00) >> 8;
+    var pref_b = pref_color & 0x0000ff;
+    var top_overflow = false;
+    var bot_overflow = false;
 
     // Paint track.
     var delta_x_px;
@@ -267,11 +274,13 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
             y = Math.round(y / vertical_range * height_px);
             ctx.fillRect(x_scaled, y_zero, delta_x_px, -y);
         } else if (mode === "Intensity") {
-            var saturation = (y - min_value) / vertical_range,
-                // Range is [pref_color, 255] where saturation = 0 --> 255 and saturation = 1 --> pref color
-                new_r = Math.round(pref_r + (255 - pref_r) * (1 - saturation)),
-                new_g = Math.round(pref_g + (255 - pref_g) * (1 - saturation)),
-                new_b = Math.round(pref_b + (255 - pref_b) * (1 - saturation));
+            var saturation = (y - min_value) / vertical_range;
+
+            var // Range is [pref_color, 255] where saturation = 0 --> 255 and saturation = 1 --> pref color
+            new_r = Math.round(pref_r + (255 - pref_r) * (1 - saturation));
+
+            var new_g = Math.round(pref_g + (255 - pref_g) * (1 - saturation));
+            var new_b = Math.round(pref_b + (255 - pref_b) * (1 - saturation));
             ctx.fillStyle = "rgb(" + new_r + "," + new_g + "," + new_b + ")";
             ctx.fillRect(x_scaled, 0, delta_x_px, height_px);
         } else {
@@ -365,8 +374,9 @@ FeaturePositionMapper.prototype.map_feature_data = function(
  */
 FeaturePositionMapper.prototype.get_feature_data = function(x, y) {
     // Find slot using Y.
-    var slot = Math.floor((y - this.y_translation) / this.slot_height),
-        feature_dict;
+    var slot = Math.floor((y - this.y_translation) / this.slot_height);
+
+    var feature_dict;
 
     // May not be over a slot due to padding, margin, etc.
     if (!this.feature_positions[slot]) {
@@ -411,9 +421,10 @@ FeaturePainter.prototype.default_prefs = {
 _.extend(FeaturePainter.prototype, {
     get_required_height: function(rows_required, width) {
         // y_scale is the height per row
-        var required_height = this.get_row_height(),
-            y_scale = required_height,
-            mode = this.mode;
+        var required_height = this.get_row_height();
+
+        var y_scale = required_height;
+        var mode = this.mode;
         // If using a packing mode, need to multiply by the number of slots used
         if (mode === "no_detail" || mode === "Squish" || mode === "Pack") {
             required_height = rows_required * y_scale;
@@ -431,31 +442,32 @@ _.extend(FeaturePainter.prototype, {
      * a FeaturePositionMapper object with information about where features were drawn.
      */
     draw: function(ctx, width, height, w_scale, slots) {
-        var data = this.data,
-            view_start = this.view_start,
-            view_end = this.view_end;
+        var data = this.data;
+        var view_start = this.view_start;
+        var view_end = this.view_end;
 
         ctx.save();
 
         ctx.fillStyle = this.prefs.block_color;
         ctx.textAlign = "right";
 
-        var y_scale = this.get_row_height(),
-            feature_mapper = new FeaturePositionMapper(y_scale),
-            x_draw_coords,
-            incomplete_features = [];
+        var y_scale = this.get_row_height();
+        var feature_mapper = new FeaturePositionMapper(y_scale);
+        var x_draw_coords;
+        var incomplete_features = [];
 
         for (var i = 0, len = data.length; i < len; i++) {
-            var feature = data[i],
-                feature_uid = feature[0],
-                feature_start = feature[1],
-                feature_end = feature[2],
-                // Slot valid only if features are slotted and this feature is slotted;
-                // feature may not be due to lack of space.
-                slot =
-                    slots && slots[feature_uid] !== undefined
-                        ? slots[feature_uid].slot
-                        : null;
+            var feature = data[i];
+            var feature_uid = feature[0];
+            var feature_start = feature[1];
+            var feature_end = feature[2];
+
+            var // Slot valid only if features are slotted and this feature is slotted;
+            // feature may not be due to lack of space.
+            slot =
+                slots && slots[feature_uid] !== undefined
+                    ? slots[feature_uid].slot
+                    : null;
 
             // Draw feature if (a) mode is dense or feature is slotted (as it must be for all non-dense modes) and
             // (b) there's overlap between the feature and drawing region.
@@ -517,16 +529,17 @@ _.extend(FeaturePainter.prototype, {
 
 // Constants specific to feature tracks moved here (HACKING, these should
 // basically all be configuration options)
-var DENSE_TRACK_HEIGHT = 10,
-    NO_DETAIL_TRACK_HEIGHT = 3,
-    SQUISH_TRACK_HEIGHT = 5,
-    PACK_TRACK_HEIGHT = 10,
-    NO_DETAIL_FEATURE_HEIGHT = 1,
-    DENSE_FEATURE_HEIGHT = 9,
-    SQUISH_FEATURE_HEIGHT = 3,
-    PACK_FEATURE_HEIGHT = 9,
-    LABEL_SPACING = 2,
-    CONNECTOR_COLOR = "#ccc";
+var DENSE_TRACK_HEIGHT = 10;
+
+var NO_DETAIL_TRACK_HEIGHT = 3;
+var SQUISH_TRACK_HEIGHT = 5;
+var PACK_TRACK_HEIGHT = 10;
+var NO_DETAIL_FEATURE_HEIGHT = 1;
+var DENSE_FEATURE_HEIGHT = 9;
+var SQUISH_FEATURE_HEIGHT = 3;
+var PACK_FEATURE_HEIGHT = 9;
+var LABEL_SPACING = 2;
+var CONNECTOR_COLOR = "#ccc";
 
 var LinkedFeaturePainter = function(
     data,
@@ -558,8 +571,8 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
      * Height of a single row, depends on mode
      */
     get_row_height: function() {
-        var mode = this.mode,
-            height;
+        var mode = this.mode;
+        var height;
         if (mode === "Dense") {
             height = DENSE_TRACK_HEIGHT;
         } else if (mode === "no_detail") {
@@ -587,39 +600,44 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
         y_scale,
         width
     ) {
-        var feature_uid = feature[0],
-            feature_start = feature[1],
-            feature_end = feature[2],
-            feature_name = feature[3],
-            feature_strand = feature[4],
-            // -0.5 to offset region between bases.
-            f_start = Math.floor(
-                Math.max(0, (feature_start - tile_low - 0.5) * w_scale)
-            ),
-            f_end = Math.ceil(
-                Math.min(
-                    width,
-                    Math.max(0, (feature_end - tile_low - 0.5) * w_scale)
-                )
-            ),
-            draw_start = f_start,
-            draw_end = f_end,
-            y_start =
-                (mode === "Dense" ? 0 : 0 + slot) * y_scale +
-                this.get_top_padding(width),
-            thickness,
-            y_start,
-            thick_start = null,
-            thick_end = null,
-            // TODO: is there any reason why block, label color cannot be set at the Painter level?
-            // For now, assume '.' === '+'
-            block_color =
-                !feature_strand ||
-                feature_strand === "+" ||
-                feature_strand === "."
-                    ? this.prefs.block_color
-                    : this.prefs.reverse_strand_color,
-            label_color = this.prefs.label_color;
+        var feature_uid = feature[0];
+        var feature_start = feature[1];
+        var feature_end = feature[2];
+        var feature_name = feature[3];
+        var feature_strand = feature[4];
+
+        var // -0.5 to offset region between bases.
+        f_start = Math.floor(
+            Math.max(0, (feature_start - tile_low - 0.5) * w_scale)
+        );
+
+        var f_end = Math.ceil(
+            Math.min(
+                width,
+                Math.max(0, (feature_end - tile_low - 0.5) * w_scale)
+            )
+        );
+
+        var draw_start = f_start;
+        var draw_end = f_end;
+
+        var y_start =
+            (mode === "Dense" ? 0 : 0 + slot) * y_scale +
+            this.get_top_padding(width);
+
+        var thickness;
+        var y_start;
+        var thick_start = null;
+        var thick_end = null;
+
+        var // TODO: is there any reason why block, label color cannot be set at the Painter level?
+        // For now, assume '.' === '+'
+        block_color =
+            !feature_strand || feature_strand === "+" || feature_strand === "."
+                ? this.prefs.block_color
+                : this.prefs.reverse_strand_color;
+
+        var label_color = this.prefs.label_color;
 
         // Set global alpha.
         ctx.globalAlpha = this.alpha_scaler.gen_val(feature);
@@ -641,11 +659,13 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
         } else {
             // Mode is either Squish or Pack:
             // Feature details.
-            var feature_ts = feature[5],
-                feature_te = feature[6],
-                feature_blocks = feature[7],
-                // Whether we are drawing full height or squished features
-                full_height = true;
+            var feature_ts = feature[5];
+
+            var feature_te = feature[6];
+            var feature_blocks = feature[7];
+
+            var // Whether we are drawing full height or squished features
+            full_height = true;
 
             if (feature_ts && feature_te) {
                 thick_start = Math.floor(
@@ -660,7 +680,9 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
             }
 
             // Set vars that depend on mode.
-            var thin_height, thick_height;
+            var thin_height;
+
+            var thick_height;
             if (mode === "Squish") {
                 thin_height = 1;
                 thick_height = SQUISH_FEATURE_HEIGHT;
@@ -712,7 +734,9 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                 //
 
                 // Compute y axis start position and height
-                var cur_y_start, cur_height;
+                var cur_y_start;
+
+                var cur_height;
                 if (mode === "Squish" || mode === "Dense") {
                     cur_y_start =
                         y_start + Math.floor(SQUISH_FEATURE_HEIGHT / 2) + 1;
@@ -759,19 +783,22 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                 // Draw blocks.
                 var start_and_height;
                 for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
-                    var block = feature_blocks[k],
-                        // -0.5 to offset block between bases.
-                        block_start = Math.floor(
-                            Math.max(0, (block[0] - tile_low - 0.5) * w_scale)
-                        ),
-                        block_end = Math.ceil(
-                            Math.min(
-                                width,
-                                Math.max((block[1] - tile_low - 0.5) * w_scale)
-                            )
-                        ),
-                        last_block_start,
-                        last_block_end;
+                    var block = feature_blocks[k];
+
+                    var // -0.5 to offset block between bases.
+                    block_start = Math.floor(
+                        Math.max(0, (block[0] - tile_low - 0.5) * w_scale)
+                    );
+
+                    var block_end = Math.ceil(
+                        Math.min(
+                            width,
+                            Math.max((block[1] - tile_low - 0.5) * w_scale)
+                        )
+                    );
+
+                    var last_block_start;
+                    var last_block_end;
 
                     // Skip drawing if block not on tile.
                     if (block_start > block_end) {
@@ -795,10 +822,11 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
                         !(block_start > thick_end || block_end < thick_start)
                     ) {
                         var block_thick_start = Math.max(
-                                block_start,
-                                thick_start
-                            ),
-                            block_thick_end = Math.min(block_end, thick_end);
+                            block_start,
+                            thick_start
+                        );
+
+                        var block_thick_end = Math.min(block_end, thick_end);
                         ctx.fillRect(
                             block_thick_start,
                             y_start + 1,
@@ -852,10 +880,12 @@ _.extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
 
                     // Height scaling: draw white lines to reduce height according to height scale factor.
                     ctx.fillStyle = "white"; // TODO: set this to background color.
-                    var hscale_factor = this.height_scaler.gen_val(feature),
-                        // Ceil ensures that min height is >= 1.
-                        new_height = Math.ceil(thick_height * hscale_factor),
-                        ws_height = Math.round((thick_height - new_height) / 2);
+                    var hscale_factor = this.height_scaler.gen_val(feature);
+
+                    var // Ceil ensures that min height is >= 1.
+                    new_height = Math.ceil(thick_height * hscale_factor);
+
+                    var ws_height = Math.round((thick_height - new_height) / 2);
                     if (hscale_factor !== 1) {
                         ctx.fillRect(
                             f_start,
@@ -945,8 +975,8 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
      * Returns height based on mode.
      */
     get_row_height: function() {
-        var height,
-            mode = this.mode;
+        var height;
+        var mode = this.mode;
         if (mode === "Dense") {
             height = DENSE_TRACK_HEIGHT;
         } else if (mode === "Squish") {
@@ -970,35 +1000,36 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
         var cigar_ops = "MIDNSHP=X";
 
         // Parse cigar.
-        var blocks = [[0, 0]],
-            cur_block = blocks[0],
-            base_pos = 0,
-            // Parse cigar operations out and update/create blocks as needed.
-            parsed_cigar = _.map(
-                cigar_str.match(/[0-9]+[MIDNSHP=X]/g),
-                function(op) {
-                    // Get operation length, character.
-                    var op_len = parseInt(op.slice(0, -1), 10),
-                        op_char = op.slice(-1);
+        var blocks = [[0, 0]];
 
-                    // Update drawing block.
-                    if (op_char === "N") {
-                        // At skip, so need to start new block if current block represents
-                        // drawing area.
-                        if (cur_block[1] !== 0) {
-                            cur_block = [base_pos + op_len, base_pos + op_len];
-                            blocks.push(cur_block);
-                        }
-                    } else if ("ISHP".indexOf(op_char) === -1) {
-                        // Operation is M,D,=,X.
-                        cur_block[1] += op_len;
-                        base_pos += op_len;
-                    }
+        var cur_block = blocks[0];
+        var base_pos = 0;
 
-                    // Return parsed cigar.
-                    return [cigar_ops.indexOf(op_char), op_len];
+        var // Parse cigar operations out and update/create blocks as needed.
+        parsed_cigar = _.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g), function(
+            op
+        ) {
+            // Get operation length, character.
+            var op_len = parseInt(op.slice(0, -1), 10),
+                op_char = op.slice(-1);
+
+            // Update drawing block.
+            if (op_char === "N") {
+                // At skip, so need to start new block if current block represents
+                // drawing area.
+                if (cur_block[1] !== 0) {
+                    cur_block = [base_pos + op_len, base_pos + op_len];
+                    blocks.push(cur_block);
                 }
-            );
+            } else if ("ISHP".indexOf(op_char) === -1) {
+                // Operation is M,D,=,X.
+                cur_block[1] += op_len;
+                base_pos += op_len;
+            }
+
+            // Return parsed cigar.
+            return [cigar_ops.indexOf(op_char), op_len];
+        });
 
         return {
             blocks: blocks,
@@ -1023,44 +1054,50 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
     ) {
         // Helper function to update base and sequnence offsets.
         var update_base_offset = function(offset, cig_op, cig_len) {
-                if ("M=NXD".indexOf(cig_op) !== -1) {
-                    offset += cig_len;
-                }
-                return offset;
-            },
-            update_seq_offset = function(offset, cig_op, cig_len) {
-                if ("IX".indexOf(cig_op) !== -1) {
-                    offset += cig_len;
-                }
-                return offset;
-            },
-            // Gets drawing coordinate for a sequence coordinate. Assumes closure variables w_scale and tile_low.
-            get_draw_coord = function(sequence_coord) {
-                // -0.5 to offset sequence between bases.
-                return Math.floor(
-                    Math.max(0, (sequence_coord - tile_low - 0.5) * w_scale)
-                );
-            };
+            if ("M=NXD".indexOf(cig_op) !== -1) {
+                offset += cig_len;
+            }
+            return offset;
+        };
+
+        var update_seq_offset = function(offset, cig_op, cig_len) {
+            if ("IX".indexOf(cig_op) !== -1) {
+                offset += cig_len;
+            }
+            return offset;
+        };
+
+        var // Gets drawing coordinate for a sequence coordinate. Assumes closure variables w_scale and tile_low.
+        get_draw_coord = function(sequence_coord) {
+            // -0.5 to offset sequence between bases.
+            return Math.floor(
+                Math.max(0, (sequence_coord - tile_low - 0.5) * w_scale)
+            );
+        };
 
         ctx.textAlign = "center";
-        var tile_region = [tile_low, tile_high],
-            base_offset = 0,
-            seq_offset = 0,
-            gap = Math.round(w_scale / 2),
-            char_width_px = ctx.canvas.manager.char_width_px,
-            block_color =
-                strand === "+"
-                    ? this.prefs.detail_block_color
-                    : this.prefs.reverse_strand_color,
-            pack_mode = mode === "Pack",
-            draw_height = pack_mode
-                ? PACK_FEATURE_HEIGHT
-                : SQUISH_FEATURE_HEIGHT,
-            rect_y = y_start + 1,
-            paint_utils = new ReadPainterUtils(ctx, draw_height, w_scale, mode),
-            drawing_blocks = [],
-            s_start,
-            s_end;
+        var tile_region = [tile_low, tile_high];
+        var base_offset = 0;
+        var seq_offset = 0;
+        var gap = Math.round(w_scale / 2);
+        var char_width_px = ctx.canvas.manager.char_width_px;
+
+        var block_color =
+            strand === "+"
+                ? this.prefs.detail_block_color
+                : this.prefs.reverse_strand_color;
+
+        var pack_mode = mode === "Pack";
+
+        var draw_height = pack_mode
+            ? PACK_FEATURE_HEIGHT
+            : SQUISH_FEATURE_HEIGHT;
+
+        var rect_y = y_start + 1;
+        var paint_utils = new ReadPainterUtils(ctx, draw_height, w_scale, mode);
+        var drawing_blocks = [];
+        var s_start;
+        var s_end;
 
         // Keep list of items that need to be drawn on top of initial drawing layer.
         var draw_last = [];
@@ -1099,9 +1136,9 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
 
         // Draw read features.
         for (var cig_id = 0, len = cigar.length; cig_id < len; cig_id++) {
-            var cig = cigar[cig_id],
-                cig_op = "MIDNSHP=X"[cig[0]],
-                cig_len = cig[1];
+            var cig = cigar[cig_id];
+            var cig_op = "MIDNSHP=X"[cig[0]];
+            var cig_len = cig[1];
 
             var seq_start = feature_start + base_offset;
             s_start = get_draw_coord(seq_start);
@@ -1342,7 +1379,9 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
         // Draw last items.
         //
         ctx.fillStyle = "yellow";
-        var item, type, data;
+        var item;
+        var type;
+        var data;
         for (var i = 0; i < draw_last.length; i++) {
             item = draw_last[i];
             type = item.type;
@@ -1373,27 +1412,30 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
         width
     ) {
         // All features need a start, end, and vertical center.
-        var feature_uid = feature[0],
-            feature_start = feature[1],
-            feature_end = feature[2],
-            feature_name = feature[3],
-            // -0.5 to put element between bases.
-            f_start = Math.floor(
-                Math.max(
-                    -0.5 * w_scale,
-                    (feature_start - tile_low - 0.5) * w_scale
-                )
-            ),
-            f_end = Math.ceil(
-                Math.min(
-                    width,
-                    Math.max(0, (feature_end - tile_low - 0.5) * w_scale)
-                )
-            ),
-            y_start = (mode === "Dense" ? 0 : 0 + slot) * y_scale,
-            draw_height =
-                mode === "Pack" ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT,
-            label_color = this.prefs.label_color;
+        var feature_uid = feature[0];
+
+        var feature_start = feature[1];
+        var feature_end = feature[2];
+        var feature_name = feature[3];
+
+        var // -0.5 to put element between bases.
+        f_start = Math.floor(
+            Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale)
+        );
+
+        var f_end = Math.ceil(
+            Math.min(
+                width,
+                Math.max(0, (feature_end - tile_low - 0.5) * w_scale)
+            )
+        );
+
+        var y_start = (mode === "Dense" ? 0 : 0 + slot) * y_scale;
+
+        var draw_height =
+            mode === "Pack" ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT;
+
+        var label_color = this.prefs.label_color;
 
         // Draw read.
         if (feature[5] instanceof Array) {
@@ -1450,20 +1492,22 @@ _.extend(ReadPainter.prototype, FeaturePainter.prototype, {
             // make it possible to put together more easily.
             // -0.5 to position connector correctly between reads.
             var b1_end = Math.ceil(
-                    Math.min(
-                        width,
-                        Math.max(
-                            -0.5 * w_scale,
-                            (feature[4][1] - tile_low - 0.5) * w_scale
-                        )
-                    )
-                ),
-                b2_start = Math.floor(
+                Math.min(
+                    width,
                     Math.max(
                         -0.5 * w_scale,
-                        (feature[5][0] - tile_low - 0.5) * w_scale
+                        (feature[4][1] - tile_low - 0.5) * w_scale
                     )
-                );
+                )
+            );
+
+            var b2_start = Math.floor(
+                Math.max(
+                    -0.5 * w_scale,
+                    (feature[5][0] - tile_low - 0.5) * w_scale
+                )
+            );
+
             if (connector && b2_start > b1_end) {
                 ctx.fillStyle = CONNECTOR_COLOR;
                 var line_height = y_start + 1 + (draw_height - 1) / 2;
@@ -1551,9 +1595,9 @@ _.extend(
         calculate_longest_feature_length: function() {
             var longest_feature_length = 0;
             for (var i = 0, len = this.data.length; i < len; i++) {
-                var feature = this.data[i],
-                    feature_start = feature[1],
-                    feature_end = feature[2];
+                var feature = this.data[i];
+                var feature_start = feature[1];
+                var feature_end = feature[2];
                 longest_feature_length = Math.max(
                     longest_feature_length,
                     feature_end - feature_start
@@ -1563,8 +1607,8 @@ _.extend(
         },
 
         get_top_padding: function(width) {
-            var view_range = this.view_end - this.view_start,
-                w_scale = width / view_range;
+            var view_range = this.view_end - this.view_start;
+            var w_scale = width / view_range;
             return Math.min(
                 128,
                 Math.ceil(this.longest_feature_length / 2 * w_scale)
@@ -1580,11 +1624,14 @@ _.extend(
             y_start
         ) {
             // Arc drawing -- from closest endpoints
-            var x_center = (block1_end + block2_start) / 2,
-                radius = block2_start - x_center;
+            var x_center = (block1_end + block2_start) / 2;
+
+            var radius = block2_start - x_center;
+
             // For full half circles
-            var angle1 = Math.PI,
-                angle2 = 0;
+            var angle1 = Math.PI;
+
+            var angle2 = 0;
             if (radius > 0) {
                 ctx.beginPath();
                 ctx.arc(x_center, y_start, block2_start - x_center, Math.PI, 0);
@@ -1661,17 +1708,16 @@ Color.prototype = {
     },
 
     toHSL: function() {
-        var r = this.rgb[0] / 255,
-            g = this.rgb[1] / 255,
-            b = this.rgb[2] / 255,
-            a = this.alpha;
-
-        var max = Math.max(r, g, b),
-            min = Math.min(r, g, b);
-        var h,
-            s,
-            l = (max + min) / 2,
-            d = max - min;
+        var r = this.rgb[0] / 255;
+        var g = this.rgb[1] / 255;
+        var b = this.rgb[2] / 255;
+        var a = this.alpha;
+        var max = Math.max(r, g, b);
+        var min = Math.min(r, g, b);
+        var h;
+        var s;
+        var l = (max + min) / 2;
+        var d = max - min;
 
         if (max === min) {
             h = s = 0;
@@ -1785,7 +1831,8 @@ SplitRamp.prototype.map_value = function(value) {
 
 var DiagonalHeatmapPainter = function(data, view_start, view_end, prefs, mode) {
     Painter.call(this, data, view_start, view_end, prefs, mode);
-    var i, len;
+    var i;
+    var len;
 
     if (this.prefs.min_value === undefined) {
         var min_value = Infinity;
@@ -1812,14 +1859,14 @@ DiagonalHeatmapPainter.prototype.default_prefs = {
 };
 
 DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
-    var min_value = this.prefs.min_value,
-        max_value = this.prefs.max_value,
-        value_range = max_value - min_value,
-        height_px = height,
-        view_start = this.view_start,
-        mode = this.mode,
-        data = this.data,
-        invsqrt2 = 1 / Math.sqrt(2);
+    var min_value = this.prefs.min_value;
+    var max_value = this.prefs.max_value;
+    var value_range = max_value - min_value;
+    var height_px = height;
+    var view_start = this.view_start;
+    var mode = this.mode;
+    var data = this.data;
+    var invsqrt2 = 1 / Math.sqrt(2);
 
     var ramp = new SplitRamp(
         this.prefs.neg_color,
@@ -1829,7 +1876,12 @@ DiagonalHeatmapPainter.prototype.draw = function(ctx, width, height, w_scale) {
         max_value
     );
 
-    var d, s1, e1, s2, e2, value;
+    var d;
+    var s1;
+    var e1;
+    var s2;
+    var e2;
+    var value;
 
     var scale = function(p) {
         return (p - view_start) * w_scale;
@@ -1907,8 +1959,8 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
      * Height of a single row, depends on mode
      */
     get_row_height: function() {
-        var mode = this.mode,
-            height;
+        var mode = this.mode;
+        var height;
         if (mode === "Dense") {
             height = DENSE_TRACK_HEIGHT;
         } else if (mode === "Squish") {
@@ -1949,11 +2001,11 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
          *    -len: how long the deletion is
          */
         get_indel_info = function(ref, alt) {
-            var ref_len = ref.length,
-                alt_len = alt.length,
-                start = 0,
-                len = 1,
-                type = null;
+            var ref_len = ref.length;
+            var alt_len = alt.length;
+            var start = 0;
+            var len = 1;
+            var type = null;
             if (alt === "-") {
                 type = "deletion";
                 len = ref.length;
@@ -1972,45 +2024,49 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
         };
 
         // Draw.
-        var locus_data,
-            pos,
-            id,
-            ref,
-            alt,
-            qual,
-            filter,
-            sample_gts,
-            allele_counts,
-            variant,
-            draw_x_start,
-            draw_y_start,
-            genotype,
-            // Always draw variants at least 1 pixel wide.
-            base_px = Math.max(1, Math.floor(w_scale)),
-            // Determine number of samples.
-            num_samples = this.data.length
-                ? this.data[0][7].split(",").length
-                : 0,
-            row_height =
-                this.mode === "Squish"
-                    ? SQUISH_TRACK_HEIGHT
-                    : PACK_TRACK_HEIGHT,
-            // If zoomed out, fill the whole row with feature to make it easier to read;
-            // when zoomed in, use feature height so that there are gaps in sample rows.
-            feature_height =
-                w_scale < 0.1
-                    ? row_height
-                    : this.mode === "Squish"
-                      ? SQUISH_FEATURE_HEIGHT
-                      : PACK_FEATURE_HEIGHT,
-            draw_summary = true,
-            paint_utils = new ReadPainterUtils(
-                ctx,
-                row_height,
-                w_scale,
-                this.mode
-            ),
-            j;
+        var locus_data;
+
+        var pos;
+        var id;
+        var ref;
+        var alt;
+        var qual;
+        var filter;
+        var sample_gts;
+        var allele_counts;
+        var variant;
+        var draw_x_start;
+        var draw_y_start;
+        var genotype;
+
+        var // Always draw variants at least 1 pixel wide.
+        base_px = Math.max(1, Math.floor(w_scale));
+
+        var // Determine number of samples.
+        num_samples = this.data.length ? this.data[0][7].split(",").length : 0;
+
+        var row_height =
+            this.mode === "Squish" ? SQUISH_TRACK_HEIGHT : PACK_TRACK_HEIGHT;
+
+        var // If zoomed out, fill the whole row with feature to make it easier to read;
+        // when zoomed in, use feature height so that there are gaps in sample rows.
+        feature_height =
+            w_scale < 0.1
+                ? row_height
+                : this.mode === "Squish"
+                  ? SQUISH_FEATURE_HEIGHT
+                  : PACK_FEATURE_HEIGHT;
+
+        var draw_summary = true;
+
+        var paint_utils = new ReadPainterUtils(
+            ctx,
+            row_height,
+            w_scale,
+            this.mode
+        );
+
+        var j;
 
         // If there's a single sample, update drawing variables.
         if (num_samples === 1) {
@@ -2049,11 +2105,12 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
             // Process alterate values to derive information about each alt.
             alt = _.map(_.flatten(alt), function(a) {
                 var alt_info = {
-                        type: "snp",
-                        value: a,
-                        start: 0
-                    },
-                    indel_info = get_indel_info(ref, a);
+                    type: "snp",
+                    value: a,
+                    start: 0
+                };
+
+                var indel_info = get_indel_info(ref, a);
 
                 return _.extend(alt_info, indel_info);
             });

client/galaxy/scripts/viz/trackster/slotting.js

@@ -2,8 +2,9 @@ import * as _ from "libs/underscore";
 var extend = _.extend;
 
 // HACK: LABEL_SPACING is currently duplicated between here and painters
-var LABEL_SPACING = 2,
-    PACK_SPACING = 5;
+var LABEL_SPACING = 2;
+
+var PACK_SPACING = 5;
 
 /**
  * Hold slotting information for a feature.
@@ -40,10 +41,11 @@ extend(FeatureSlotter.prototype, {
      */
     _get_draw_coords: function(feature) {
         // Get initial draw coordinates using w_scale.
-        var draw_start = Math.floor(feature[1] * this.w_scale),
-            draw_end = Math.ceil(feature[2] * this.w_scale),
-            f_name = feature[3],
-            text_align;
+        var draw_start = Math.floor(feature[1] * this.w_scale);
+
+        var draw_end = Math.ceil(feature[2] * this.w_scale);
+        var f_name = feature[3];
+        var text_align;
 
         // Update start, end drawing locations to include feature name.
         // Try to put the name on the left, if not, put on right.
@@ -92,11 +94,12 @@ extend(FeatureSlotter.prototype, {
      */
     _find_slot: function(draw_coords) {
         // TODO: Use a data structure for faster searching of available slots.
-        var draw_start = draw_coords[0],
-            draw_end = draw_coords[1];
+        var draw_start = draw_coords[0];
+
+        var draw_end = draw_coords[1];
         for (var slot_num = 0; slot_num <= this.max_rows; slot_num++) {
-            var has_overlap = false,
-                slot = this.start_end_dct[slot_num];
+            var has_overlap = false;
+            var slot = this.start_end_dct[slot_num];
             if (slot !== undefined) {
                 // Iterate through features already in slot to see if current feature will fit.
                 for (var k = 0, k_len = slot.length; k < k_len; k++) {
@@ -119,11 +122,11 @@ extend(FeatureSlotter.prototype, {
      * Slot features.
      */
     slot_features: function(features) {
-        var start_end_dct = this.start_end_dct,
-            undone = [],
-            highest_slot = 0,
-            feature,
-            feature_uid;
+        var start_end_dct = this.start_end_dct;
+        var undone = [];
+        var highest_slot = 0;
+        var feature;
+        var feature_uid;
 
         // Loop through features to (a) find those that are not yet slotted and (b) update
         // those that are slotted if new information is availabe. For (a), features already
@@ -144,10 +147,11 @@ extend(FeatureSlotter.prototype, {
                     // Feature has changed (e.g. a single read now has its pair), so recalculate its
                     // drawing coordinates.
                     var old_draw_coords = this._get_draw_coords(
-                            slotted_info.feature
-                        ),
-                        new_draw_coords = this._get_draw_coords(feature),
-                        slotted_coords = this.start_end_dct[slotted_info.slot];
+                        slotted_info.feature
+                    );
+
+                    var new_draw_coords = this._get_draw_coords(feature);
+                    var slotted_coords = this.start_end_dct[slotted_info.slot];
                     for (var k = 0; k < slotted_coords.length; k++) {
                         var dc = slotted_coords[k];
                         if (

client/galaxy/scripts/viz/trackster/util.js

@@ -34,22 +34,24 @@ var ServerStateDeferred = Backbone.Model.extend({
      * Returns a deferred that resolves when success function returns true.
      */
     go: function() {
-        var deferred = $.Deferred(),
-            self = this,
-            ajax_settings = self.get("ajax_settings"),
-            success_fn = self.get("success_fn"),
-            interval = self.get("interval"),
-            _go = function() {
-                $.ajax(ajax_settings).success(function(result) {
-                    if (success_fn(result)) {
-                        // Result is good, so resolve.
-                        deferred.resolve(result);
-                    } else {
-                        // Result not good, try again.
-                        setTimeout(_go, interval);
-                    }
-                });
-            };
+        var deferred = $.Deferred();
+        var self = this;
+        var ajax_settings = self.get("ajax_settings");
+        var success_fn = self.get("success_fn");
+        var interval = self.get("interval");
+
+        var _go = function() {
+            $.ajax(ajax_settings).success(function(result) {
+                if (success_fn(result)) {
+                    // Result is good, so resolve.
+                    deferred.resolve(result);
+                } else {
+                    // Result not good, try again.
+                    setTimeout(_go, interval);
+                }
+            });
+        };
+
         _go();
         return deferred;
     }
@@ -95,19 +97,20 @@ var get_random_color = function(colors) {
     };
 
     // Create new random color.
-    var new_color,
-        nr,
-        ng,
-        nb,
-        other_color,
-        or,
-        og,
-        ob,
-        n_brightness,
-        o_brightness,
-        diff,
-        ok = false,
-        num_tries = 0;
+    var new_color;
+
+    var nr;
+    var ng;
+    var nb;
+    var other_color;
+    var or;
+    var og;
+    var ob;
+    var n_brightness;
+    var o_brightness;
+    var diff;
+    var ok = false;
+    var num_tries = 0;
     do {
         // New color is never white b/c random in [0,1)
         new_color = Math.round(Math.random() * 0xffffff);

client/galaxy/scripts/viz/visualization.js

@@ -14,8 +14,8 @@ var CustomToJSON = {
      * Returns JSON representation of object using to_json_keys and to_json_mappers.
      */
     toJSON: function() {
-        var self = this,
-            json = {};
+        var self = this;
+        var json = {};
         _.each(self.constructor.to_json_keys, function(k) {
             var val = self.get(k);
             if (k in self.constructor.to_json_mappers) {
@@ -147,9 +147,9 @@ var CanvasManager = function(default_font) {
 
 _.extend(CanvasManager.prototype, {
     load_pattern: function(key, path) {
-        var patterns = this.patterns,
-            dummy_context = this.dummy_context,
-            image = new Image();
+        var patterns = this.patterns;
+        var dummy_context = this.dummy_context;
+        var image = new Image();
         image.src = Galaxy.root + "static/images" + path;
         image.onload = function() {
             patterns[key] = dummy_context.createPattern(image, "repeat");
@@ -187,12 +187,13 @@ var Cache = Backbone.Model.extend({
      * Get an element from the cache using its key.
      */
     get_elt: function(key) {
-        var obj_cache = this.attributes.obj_cache,
-            key_ary = this.attributes.key_ary,
-            key_str = key.toString(),
-            index = _.indexOf(key_ary, function(k) {
-                return k.toString() === key_str;
-            });
+        var obj_cache = this.attributes.obj_cache;
+        var key_ary = this.attributes.key_ary;
+        var key_str = key.toString();
+
+        var index = _.indexOf(key_ary, function(k) {
+            return k.toString() === key_str;
+        });
 
         // Update cache.
         if (index !== -1) {
@@ -214,10 +215,10 @@ var Cache = Backbone.Model.extend({
      * Put an element into the cache.
      */
     set_elt: function(key, value) {
-        var obj_cache = this.attributes.obj_cache,
-            key_ary = this.attributes.key_ary,
-            key_str = key.toString(),
-            num_elements = this.attributes.num_elements;
+        var obj_cache = this.attributes.obj_cache;
+        var key_ary = this.attributes.key_ary;
+        var key_str = key.toString();
+        var num_elements = this.attributes.num_elements;
 
         // Update keys, objects.
         if (!obj_cache[key_str]) {
@@ -323,30 +324,32 @@ var GenomeDataManager = Cache.extend({
      * cannot be used).
      */
     data_is_ready: function() {
-        var dataset = this.get("dataset"),
-            ready_deferred = $.Deferred(),
-            // If requesting raw data, query dataset state; if requesting (converted) data,
-            // need to query converted datasets state.
-            query_type =
-                this.get("data_type") === "raw_data"
-                    ? "state"
-                    : this.get("data_type") === "data"
-                      ? "converted_datasets_state"
-                      : "error",
-            ss_deferred = new util_mod.ServerStateDeferred({
-                ajax_settings: {
-                    url: this.get("dataset").url(),
-                    data: {
-                        hda_ldda: dataset.get("hda_ldda"),
-                        data_type: query_type
-                    },
-                    dataType: "json"
+        var dataset = this.get("dataset");
+        var ready_deferred = $.Deferred();
+
+        var // If requesting raw data, query dataset state; if requesting (converted) data,
+        // need to query converted datasets state.
+        query_type =
+            this.get("data_type") === "raw_data"
+                ? "state"
+                : this.get("data_type") === "data"
+                  ? "converted_datasets_state"
+                  : "error";
+
+        var ss_deferred = new util_mod.ServerStateDeferred({
+            ajax_settings: {
+                url: this.get("dataset").url(),
+                data: {
+                    hda_ldda: dataset.get("hda_ldda"),
+                    data_type: query_type
                 },
-                interval: 5000,
-                success_fn: function(response) {
-                    return response !== "pending";
-                }
-            });
+                dataType: "json"
+            },
+            interval: 5000,
+            success_fn: function(response) {
+                return response !== "pending";
+            }
+        });
 
         $.when(ss_deferred.go()).then(function(response) {
             ready_deferred.resolve(response === "ok" || response === "data");
@@ -358,12 +361,14 @@ var GenomeDataManager = Cache.extend({
      * Perform a feature search from server; returns Deferred object that resolves when data is available.
      */
     search_features: function(query) {
-        var dataset = this.get("dataset"),
-            params = {
-                query: query,
-                hda_ldda: dataset.get("hda_ldda"),
-                data_type: "features"
-            };
+        var dataset = this.get("dataset");
+
+        var params = {
+            query: query,
+            hda_ldda: dataset.get("hda_ldda"),
+            data_type: "features"
+        };
+
         return $.getJSON(dataset.url(), params);
     },
 
@@ -374,16 +379,17 @@ var GenomeDataManager = Cache.extend({
      */
     load_data: function(region, mode, resolution, extra_params) {
         // Setup data request params.
-        var dataset = this.get("dataset"),
-            params = {
-                data_type: this.get("data_type"),
-                chrom: region.get("chrom"),
-                low: region.get("start"),
-                high: region.get("end"),
-                mode: mode,
-                resolution: resolution,
-                hda_ldda: dataset.get("hda_ldda")
-            };
+        var dataset = this.get("dataset");
+
+        var params = {
+            data_type: this.get("data_type"),
+            chrom: region.get("chrom"),
+            low: region.get("start"),
+            high: region.get("end"),
+            mode: mode,
+            resolution: resolution,
+            hda_ldda: dataset.get("hda_ldda")
+        };
 
         $.extend(params, extra_params);
 
@@ -399,12 +405,13 @@ var GenomeDataManager = Cache.extend({
         }
 
         // Do request.
-        var manager = this,
-            entry = $.getJSON(dataset.url(), params, function(result) {
-                // Add region to the result.
-                result.region = region;
-                manager.set_data(region, result);
-            });
+        var manager = this;
+
+        var entry = $.getJSON(dataset.url(), params, function(result) {
+            // Add region to the result.
+            result.region = region;
+            manager.set_data(region, result);
+        });
 
         this.set_data(region, entry);
         return entry;
@@ -429,10 +436,11 @@ var GenomeDataManager = Cache.extend({
         // TODO: this logic could be improved if the visualization knew whether
         // the data was "index" or "data."
         //
-        var key_ary = this.get("key_ary"),
-            obj_cache = this.get("obj_cache"),
-            entry_region,
-            is_subregion;
+        var key_ary = this.get("key_ary");
+
+        var obj_cache = this.get("obj_cache");
+        var entry_region;
+        var is_subregion;
         for (var i = 0; i < key_ary.length; i++) {
             entry_region = key_ary[i];
 
@@ -551,14 +559,16 @@ var GenomeDataManager = Cache.extend({
         // Get additional data, append to current data, and set new data. Use a custom deferred object
         // to signal when new data is available.
         //
-        var data_manager = this,
-            new_data_request = this.load_data(
-                query_region,
-                mode,
-                resolution,
-                extra_params
-            ),
-            new_data_available = $.Deferred();
+        var data_manager = this;
+
+        var new_data_request = this.load_data(
+            query_region,
+            mode,
+            resolution,
+            extra_params
+        );
+
+        var new_data_available = $.Deferred();
         // load_data sets cache to new_data_request, but use custom deferred object so that signal and data
         // is all data, not just new data.
         this.set_data(region, new_data_available);
@@ -650,27 +660,29 @@ var GenomeDataManager = Cache.extend({
     get_genome_wide_data: function(genome) {
         // -- Get all data. --
 
-        var self = this,
-            all_data_available = true,
-            //  Map chromosome info into genome data.
-            gw_data = _.map(genome.get("chroms_info").chrom_info, function(
-                chrom_info
-            ) {
-                var chrom_data = self.get_elt(
-                    new GenomeRegion({
-                        chrom: chrom_info.chrom,
-                        start: 0,
-                        end: chrom_info.len
-                    })
-                );
+        var self = this;
 
-                // Set flag if data is not available.
-                if (!chrom_data) {
-                    all_data_available = false;
-                }
+        var all_data_available = true;
 
-                return chrom_data;
-            });
+        var //  Map chromosome info into genome data.
+        gw_data = _.map(genome.get("chroms_info").chrom_info, function(
+            chrom_info
+        ) {
+            var chrom_data = self.get_elt(
+                new GenomeRegion({
+                    chrom: chrom_info.chrom,
+                    start: 0,
+                    end: chrom_info.len
+                })
+            );
+
+            // Set flag if data is not available.
+            if (!chrom_data) {
+                all_data_available = false;
+            }
+
+            return chrom_data;
+        });
 
         // -- If all data is available, return it. --
         if (all_data_available) {
@@ -830,9 +842,9 @@ var GenomeRegion = Backbone.Model.extend(
      */
         initialize: function(options) {
             if (options.from_str) {
-                var pieces = options.from_str.split(":"),
-                    chrom = pieces[0],
-                    start_end = pieces[1].split("-");
+                var pieces = options.from_str.split(":");
+                var chrom = pieces[0];
+                var start_end = pieces[1].split("-");
                 this.set({
                     chrom: chrom,
                     start: parseInt(start_end[0], 10),
@@ -893,13 +905,13 @@ var GenomeRegion = Backbone.Model.extend(
      * hence, OVERLAP_START indicates that the first region overlaps the start (but not the end) of the second region.
      */
         compute_overlap: function(a_region) {
-            var first_chrom = this.get("chrom"),
-                second_chrom = a_region.get("chrom"),
-                first_start = this.get("start"),
-                second_start = a_region.get("start"),
-                first_end = this.get("end"),
-                second_end = a_region.get("end"),
-                overlap;
+            var first_chrom = this.get("chrom");
+            var second_chrom = a_region.get("chrom");
+            var first_start = this.get("start");
+            var second_start = a_region.get("start");
+            var first_end = this.get("end");
+            var second_end = a_region.get("end");
+            var overlap;
 
             // Compare chroms.
             if (first_chrom && second_chrom && first_chrom !== second_chrom) {

client/galaxy/scripts/viz/viz_views.js

@@ -108,9 +108,10 @@ var TrackHeaderView = Backbone.View.extend({
         );
 
         // Setup popup menu for changing modes.
-        var self = this,
-            track = this.model,
-            mode_mapping = {};
+        var self = this;
+
+        var track = this.model;
+        var mode_mapping = {};
         for (var i = 0, len = track.display_modes.length; i < len; i++) {
             var mode = track.display_modes[i];
             mode_mapping[mode] = (function(mode) {