Cleanup in galaxy/scripts/viz, lints cleanly with one exception that …

…I do not understand.

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

@@ -19,7 +19,6 @@ var BBIDataManager = visualization.GenomeDataManager.extend({
         var url = `${getAppRoot()}datasets/${this.get("dataset").id}/display`;
 
         var self = this;
-        var promise = new $.Deferred();
         $.when(bigwig.makeBwg(url)).then((bb, err) => {
             $.when(bb.readWigData(region.get("chrom"), region.get("start"), region.get("end"))).then(data => {
                 // Transform data into "bigwig" format for LinePainter. "bigwig" format is an array of 2-element arrays

client/galaxy/scripts/viz/phyloviz.js

@@ -5,6 +5,8 @@ import * as d3 from "libs/d3";
 import visualization_mod from "viz/visualization";
 import { Dataset } from "mvc/dataset/data";
 import mod_icon_btn from "mvc/ui/icon-button";
+import { show_message, hide_modal } from "layout/modal";
+
 /**
  * Base class of any menus that takes in user interaction. Contains checking methods.
  */
@@ -271,7 +273,7 @@ var PhyloTree = visualization_mod.Visualization.extend({
     toggleAll: function(d) {
         if (d.children && d.children.length !== 0) {
             d.children.forEach(this.toggleAll);
-            toggle(d);
+            this.toggle(d);
         }
     },
 
@@ -361,7 +363,6 @@ var PhylovizLayoutBase = Backbone.View.extend({
      *  AND possibly when the tree is edited.
      */
     updateAndRender: function(source) {
-        var vis = d3.select(".vis");
         var self = this;
         source = source || self.model.root;
 
@@ -375,9 +376,6 @@ var PhylovizLayoutBase = Backbone.View.extend({
      */
     renderLinks: function(source) {
         var self = this;
-        var diagonal = self.diagonal;
-        var duration = self.duration;
-        var layoutMode = self.layoutMode;
         var link = self.vis.selectAll("g.completeLink").data(self.tree.links(self.nodes), d => d.target.id);
 
         var calcalateLinePos = d => {
@@ -409,7 +407,7 @@ var PhylovizLayoutBase = Backbone.View.extend({
             return `M ${d.pos0} L ${d.pos1} L ${d.pos2}`;
         });
 
-        var linkExit = link.exit().remove();
+        link.exit().remove();
     },
 
     // User Interaction methods below
@@ -671,7 +669,7 @@ export var PhylovizView = Backbone.View.extend({
         $("#title").text(`Phylogenetic Tree from ${self.phyloTree.get("title")}:`);
 
         // -- Create Linear view instance --
-        var linearView = new PhylovizLinearView(self.layoutOptions);
+        new PhylovizLinearView(self.layoutOptions);
     },
 
     /**

client/galaxy/scripts/viz/sweepster.js

@@ -15,6 +15,8 @@ import tools from "mvc/tool/tools";
 import { Dataset } from "mvc/dataset/data";
 import config from "utils/config";
 import mod_icon_btn from "mvc/ui/icon-button";
+import { make_popupmenu } from "ui/popupmenu";
+import { show_modal, hide_modal } from "layout/modal";
 
 /**
  * A collection of tool input settings. Object is useful for keeping a list of settings
@@ -116,7 +118,6 @@ var ToolParameterTree = Backbone.Model.extend({
         create_tree_data = (params_samples, index) => {
             var param_samples = params_samples[index],
                 param = param_samples.param,
-                param_label = param.get("label"),
                 settings = param_samples.samples;
 
             // Create leaves when last parameter setting is reached.
@@ -408,7 +409,7 @@ var SweepsterTrackView = Backbone.View.extend({
         });
         var self = this;
 
-        var run_on_dataset_button = $("<button/>")
+        $("<button/>")
             .appendTo(settings_div)
             .text("Run on complete dataset")
             .click(() => {
@@ -507,7 +508,6 @@ var ToolInputValOrSweepView = Backbone.View.extend({
 
     render: function() {
         var input = this.model;
-        var type = input.get("type");
         var single_input_row = this.$el.find(".form-row-input");
         var sweep_inputs_row = null;
 
@@ -606,7 +606,7 @@ var ToolParameterTreeDesignView = Backbone.View.extend({
             .find(".form-row")
             .not(".form-actions")
             .each(function(i) {
-                var input_view = new ToolInputValOrSweepView({
+                new ToolInputValOrSweepView({
                     model: inputs.at(i),
                     tool_row: $(this)
                 });
@@ -671,7 +671,7 @@ var ToolParameterTreeView = Backbone.View.extend({
             .attr("transform", "translate(40, 20)");
 
         // Draw links.
-        var link = vis
+        vis
             .selectAll("path.link")
             .data(cluster.links(nodes))
             .enter()

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

@@ -1,6 +1,7 @@
+import $ from "jquery";
 import _l from "utils/localization";
 import _ from "libs/underscore";
-var extend = _.extend;
+import { getGalaxyInstance } from "app";
 
 /**
  * Filters that enable users to show/hide data points dynamically.
@@ -15,7 +16,7 @@ var Filter = function(obj_dict) {
     this.tool_exp_name = obj_dict.tool_exp_name;
 };
 
-extend(Filter.prototype, {
+_.extend(Filter.prototype, {
     /**
      * Convert filter to dictionary.
      */
@@ -259,13 +260,14 @@ var NumberFilter = function(obj_dict) {
     // Add to clear floating layout.
     $("<div style='clear: both;'/>").appendTo(filter.parent_div);
 };
-extend(NumberFilter.prototype, {
+
+_.extend(NumberFilter.prototype, {
     /**
      * Convert filter to dictionary.
      */
     to_dict: function() {
         var obj_dict = Filter.prototype.to_dict.call(this);
-        return extend(obj_dict, {
+        return _.extend(obj_dict, {
             type: "number",
             min: this.min,
             max: this.max,
@@ -503,7 +505,7 @@ var FiltersManager = function(track, obj_dict) {
     }
 };
 
-extend(FiltersManager.prototype, {
+_.extend(FiltersManager.prototype, {
     // HTML manipulation and inspection.
     show: function() {
         this.parent_div.show();
@@ -655,6 +657,7 @@ extend(FiltersManager.prototype, {
 
             // DBTODO: This will never work, run_tool_url doesn't exist?
             $.getJSON(run_tool_url, url_params, response => {
+                let Galaxy = getGalaxyInstance();
                 if (response.error) {
                     // General error.
                     Galaxy.modal.show({

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

@@ -1,3 +1,6 @@
+import $ from "jquery";
+import Backbone from "backbone";
+
 /**
  * Stringifies a number adding commas for digit grouping as per North America.
  */

client/galaxy/scripts/viz/visualization.js

@@ -8,6 +8,7 @@ import util_mod from "viz/trackster/util";
 import config_mod from "utils/config";
 import GridView from "mvc/grid/grid-view";
 import Tabs from "mvc/ui/ui-tabs";
+import { getGalaxyInstance } from "app";
 
 /**
  * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes
@@ -72,6 +73,7 @@ var select_datasets = (filters, success_fn) => {
     });
 
     // modal
+    let Galaxy = getGalaxyInstance();
     Galaxy.modal.show({
         title: _l("Select datasets for new tracks"),
         body: tabs.$el,