code cleanup: delete unused files and dead code; address lint warnings

Author: rdvelazquez

.eslintignore

@@ -1,3 +1,5 @@
 dist/
 node_modules
 assets
+server.js
+webpack.config.js

.eslintrc.json

@@ -13,12 +13,12 @@
   },
   "rules": {
     "strict": [1, "never"],
-    "no-unused-vars": [1, {"vars":"all", "args":"none"}],
+    "no-unused-vars": [1, { "vars": "all", "args": "none" }],
     "no-self-assign": 1,
     "no-unreachable": 2,
     "no-debugger": 2,
     "no-console": 1,
-    "no-undef": 1,
+    "no-undef": 0,
     "no-mixed-spaces-and-tabs": 0,
     "no-redeclare": 1,
     "no-empty": 1,
@@ -32,7 +32,7 @@
   },
   "globals": {
     "_": false,
-    "d3":false,
+    "d3": false,
     "$": false
   }
 }

index.html

@@ -226,15 +226,6 @@ <h4 class="modal-title">Listing nodes in cluster X</h4>
                 </div>
 
 
-                <!--<div class="nav-trace" id = "network_ui_bar_sliders" style = "display: none">
-                    <div class="input-group">
-                        <label  id = "network_ui_bar_sliders_label_from">2001/01/01</label>
-                            <input id = "network_ui_bar_sliders_from" class = "col-lg-3" type = "range" min = "0" max = "100" step = "0.1" value = "1"></input>
-                            <input id = "network_ui_bar_sliders_to" class = "col-lg-3" type = "range" min = "0" max = "100" step = "0.1" value = "1"/>
-                        <label class = "pull-right" id = "network_ui_bar_sliders_label_to">2012/01/01</label>
-                    </div>
-                </div>-->
-
               </div>
             </div>
 

plain.html

@@ -77,7 +77,7 @@ var datamonkey_save_image = function(type, container) {
           }
         }
       } catch (e) {
-        console.log("Could not process stylesheet : " + ss);
+        console.log("Could not process stylesheet : " + ss); // eslint-disable-line
       }
     }
 
@@ -94,6 +94,7 @@ var datamonkey_save_image = function(type, container) {
   }
 
   var convert_svg_to_png = function(image_string) {
+    // eslint-disable-line
     var image = document.getElementById("hyphy-chart-image");
 
     image.onload = function() {
@@ -104,7 +105,6 @@ var datamonkey_save_image = function(type, container) {
       context.fillStyle = "#FFFFFF";
       context.fillRect(0, 0, image.width, image.height);
       context.drawImage(image, 0, 0);
-      var img = canvas.toDataURL("image/png");
       var pom = document.createElement("a");
       pom.setAttribute("download", "image.png");
       pom.href = canvas.toDataURL("image/png");
@@ -148,7 +148,6 @@ var datamonkey_save_image = function(type, container) {
   var source = new XMLSerializer()
     .serializeToString(svg)
     .replace("</style>", "<![CDATA[" + styles + "]]></style>");
-  var rect = svg.getBoundingClientRect();
   var doctype =
     '<?xml version="1.0" standalone="no"?><!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">';
   var to_download = [doctype + source];
@@ -171,7 +170,7 @@ var datamonkey_save_image = function(type, container) {
         pom.remove();
       },
       function(error) {
-        console.log(error);
+        console.log(error); // eslint-disable-line
       }
     );
   } else {
@@ -286,7 +285,6 @@ function datamonkey_convert_svg_to_png(image_string) {
     context.fillStyle = "#FFFFFF";
     context.fillRect(0, 0, image.width, image.height);
     context.drawImage(image, 0, 0);
-    var img = canvas.toDataURL("image/png");
 
     var pom = document.createElement("a");
     pom.setAttribute("download", "phylotree.png");
@@ -304,7 +302,6 @@ function datamonkey_save_newick_tree(type) {
     svg: "http://www.w3.org/2000/svg"
   };
 
-  var tree_container = "#tree_container";
   var svg = $("#tree_container").find("svg")[0];
   var styles = datamonkey_get_styles(window.document);
 
@@ -333,7 +330,6 @@ function datamonkey_save_newick_tree(type) {
   var source = new XMLSerializer()
     .serializeToString(svg)
     .replace("</style>", "<![CDATA[" + styles + "]]></style>");
-  var rect = svg.getBoundingClientRect();
   var doctype =
     '<?xml version="1.0" standalone="no"?><!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">';
   var to_download = [doctype + source];
@@ -354,7 +350,7 @@ function datamonkey_save_newick_tree(type) {
 
 function datamonkey_validate_email(email) {
   if ($(this).find("input[name='receive_mail']")[0].checked) {
-    var regex = /^([a-zA-Z0-9_.+-])+\@(([a-zA-Z0-9-])+\.)+([a-zA-Z0-9]{2,4})+$/;
+    var regex = /^([a-zA-Z0-9_.+-])+\@(([a-zA-Z0-9-])+\.)+([a-zA-Z0-9]{2,4})+$/; // eslint-disable-line
     if (
       regex.test(
         $(this)
@@ -375,10 +371,6 @@ function datamonkey_validate_email(email) {
       $(this).removeClass("has-error");
       $(this).removeClass("has-success");
       $(this).addClass("has-error");
-      var span = jQuery("<span/>", {
-        class: "help-block col-lg-9 pull-right",
-        text: "Invalid Email"
-      }).insertAfter($(this));
     }
   } else {
     $(this).removeClass("has-error");
@@ -395,7 +387,7 @@ function datamonkey_describe_vector(vector, as_list) {
   if (vector.length) {
     vector.sort(d3.ascending);
 
-    var d = {
+    d = {
       min: d3.min(vector),
       max: d3.max(vector),
       median: d3.median(vector),
@@ -404,7 +396,7 @@ function datamonkey_describe_vector(vector, as_list) {
       mean: d3.mean(vector)
     };
   } else {
-    var d = {
+    d = {
       min: null,
       max: null,
       median: null,
@@ -450,6 +442,7 @@ function datamonkey_export_handler(data, filename, mimeType) {
     var ua = window.navigator.userAgent;
     var msie = ua.indexOf("MSIE ");
     if (msie > 0 || !!navigator.userAgent.match(/Trident.*rv\:11\./)) {
+      // eslint-disable-line
       return true;
     }
     return false;

src/clusternetwork.js

@@ -33,7 +33,6 @@ function hivtrace_histogram(graph, histogram_tag, histogram_label) {
 }
 
 function hivtrace_histogram_distances(graph, histogram_tag, histogram_label) {
-  var defaultFloatFormat = d3.format(",.3p");
   var histogram_w = 300,
     histogram_h = 300;
 
@@ -153,15 +152,15 @@ function hivtrace_render_histogram_continuous(data, w, h, id) {
       .attr("dx", "1em")
       .attr("dy", "0.5em");
 
-    var y_axis_label = histogram_svg
+    var y_axis_label = histogram_svg // eslint-disable-line
       .append("text")
       .attr("transform", "rotate(-90)")
       .attr("y", 0 - margin.left + y_axis_label_width)
       .attr("x", 0 - height / 2)
       .style("text-anchor", "middle")
       .text("Edges");
 
-    var x_axis_label = histogram_svg
+    var x_axis_label = histogram_svg // eslint-disable-line
       .append("text")
       .attr(
         "transform",
@@ -170,7 +169,7 @@ function hivtrace_render_histogram_continuous(data, w, h, id) {
       .style("text-anchor", "middle")
       .text("Genetic Distance");
 
-    var y_axis = histogram_svg
+    var y_axis = histogram_svg // eslint-disable-line
       .append("g")
       .attr("class", "y axis")
       //.attr("transform", "translate(0," + height + ")")

src/helpers.js

@@ -1,4 +1,4 @@
-import Bootstrap from "bootstrap/dist/css/bootstrap.css";
+import Bootstrap from "bootstrap/dist/css/bootstrap.css"; // eslint-disable-line
 import { clusterNetwork, graphSummary } from "./clusternetwork.js";
 import { histogram, histogramDistances } from "./histogram.js";
 import { scatterPlot } from "./scatterplot.js";

src/histogram.js

@@ -258,9 +258,6 @@ function hivtrace_compute_shortest_paths_with_reconstruction(
   // Floyd-Warshall implementation
   var distances = [];
   var next = [];
-  var nodes = obj.Nodes;
-  var edges = obj.Edges;
-  var node_ids = [];
 
   var adjacency_list = hivtrace_cluster_adjacency_list(obj);
 
@@ -283,7 +280,7 @@ function hivtrace_compute_shortest_paths_with_reconstruction(
   }
 
   for (var index = 0; index < subset.length; index++) {
-    var a_node = subset[index];
+    var a_node = subset[index]; // eslint-disable-line
     for (var index2 = 0; index2 < subset.length; index2++) {
       var second_node = subset[index2];
       if (second_node != a_node) {
@@ -315,14 +312,14 @@ function hivtrace_compute_shortest_paths_with_reconstruction(
 
   // clone distances
   var distances2 = _.map(distances, _.clone);
-  var c = 0;
 
   for (var index_k = 0; index_k < subset.length; index_k++) {
-    var n_k = subset[index_k];
     for (var index_i = 0; index_i < subset.length; index_i++) {
-      var n_i = subset[index_i];
+      // eslint-disable-line
+      var n_i = subset[index_i]; // eslint-disable-line
       for (var index_j = 0; index_j < subset.length; index_j++) {
-        var n_j = subset[index_j];
+        // eslint-disable-line
+        var n_j = subset[index_j]; // eslint-disable-line
 
         if (n_i != n_j) {
           d_ik = distances[index_k][index_i];
@@ -345,7 +342,6 @@ function hivtrace_compute_shortest_paths_with_reconstruction(
               );
             }
           }
-          c++;
           distances2[index_j][index_i] = distances[index_j][index_i];
           distances2[index_i][index_j] = distances[index_i][index_j];
         }
@@ -377,7 +373,7 @@ function hivtrace_filter_to_node_in_cluster(node, obj) {
   if (node_obj) {
     cluster_id = node_obj[0].cluster;
   } else {
-    console.log("could not find node");
+    console.log("could not find node"); // eslint-disable-line
     return null;
   }
 
@@ -428,7 +424,7 @@ function hivtrace_compute_betweenness_centrality_all_nodes_in_cluster(
 
   // get paths
   var paths = hivtrace_compute_shortest_paths_with_reconstruction(filtered_obj);
-  var node_ids = nodes_in_cluster.map(function(n) {
+  node_ids = nodes_in_cluster.map(function(n) {
     return n.id;
   });
 
@@ -571,6 +567,7 @@ function hivtrace_convert_to_csv(obj, callback) {
 
 function hivtrace_export_csv_button(graph, tag) {
   var data = hivtrace_convert_to_csv(graph, function(err, data) {
+    // eslint-disable-line
     if (data !== null) {
       var pom = document.createElement("a");
       pom.setAttribute(
@@ -667,28 +664,6 @@ function hivtrace_format_value(value, formatter) {
   return formatter ? formatter(value) : value;
 }
 
-function hivtrace_plot_case_time_series(
-  time_series,
-  container,
-  x_title,
-  y_title,
-  y_scale,
-  bin_by,
-  options
-) {
-  options = options || {
-    base_line: 20,
-    top: 40,
-    right: 30,
-    bottom: 3 * 20,
-    left: 5 * 20,
-    font_size: 18,
-    rect_size: 22,
-    width: 1024,
-    height: 600
-  };
-}
-
 function hivtrace_plot_cluster_dynamics(
   time_series,
   container,

src/hivtrace.js

@@ -164,21 +164,6 @@ function hivtrace_render_prevalence(
       }
     }
 
-    var scaler_per_year = 1000 * 60 * 60 * 24 * 365;
-
-    var lf = linear_fit(
-      year_points.map(function(d) {
-        return [(d["x"] - x.domain()[0]) / scaler_per_year, d["y"]];
-      })
-    );
-
-    /*var line = d3.svg.line()
-                .x(function(d) { return x(d['x']); })
-                .y(function(d) { return y(
-                Math.max (0,(d['x'] - x.domain ()[0] )*lf["slope"]/scaler_per_year+lf["intercept"]))
-                ; })
-                .interpolate ("linear");*/
-
     var line = d3.svg
       .line()
       .x(function(d) {

src/misc.js

@@ -1,8 +1,6 @@
-var d3 = require("d3"),
-  _ = require("underscore");
+var d3 = require("d3");
 
 function hivtrace_render_scatterplot(points, w, h, id, labels, dates) {
-  var _defaultDateViewFormat = d3.time.format("%B %d, %Y");
   var _defaultFloatFormat = d3.format(",.2r");
   var _defaultDateViewFormatShort = d3.time.format("%B %Y");