Merge branch 'release/0.10.0-beta.1'

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2017 University of Michigan Center for Statistical Genetics
+Copyright (c) 2019 University of Michigan Center for Statistical Genetics
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -19,8 +19,9 @@ and [statgen.github.io/locuszoom/#examples](http://statgen.github.io/locuszoom/#
 The page you build that embeds the LocusZoom plugin must include the following resources, found in the `dist` directory:
 
 * `locuszoom.vendor.min.js`  
-  This file contains the concatenated vendor libraries. You can alternatively include [d3](http://d3js.org/) and 
-  [Q](https://github.com/kriskowal/q) from other sources, so long as they are included **before including LocusZoom files**.  
+  This file contains the concatenated vendor libraries. You can alternatively include [d3](http://d3js.org/)
+  from other sources, so long as it is included **before including LocusZoom files**. This bundle also contains a 
+  polyfill for ES6 `Promise`, which you may need if your site supports certain older browsers such as Internet Explorer.
 
 * `locuszoom.app.js` OR `locuszoom.app.min.js`  
   This is the primary application logic. It should only be included *after* the vendor dependencies have been included.  
@@ -227,7 +228,6 @@ LocusZoom is an entirely client-side application designed to plug into arbitrary
  or something else entirely. It has the following vendor dependencies:
 
 * [d3](http://d3js.org/) for a data visualization framework
-* [Q](https://github.com/kriskowal/q) for a promises framework
 
 ### Build System and Automated Testing
 
@@ -244,7 +244,7 @@ following files (in the `dist` folder):
 * `locuszoom.app.js` - A concatenated app file suitable for use in development
 * `locuszoom.app.min.js` - A concatenated and minified app file suitable for use in production
 * `locuszoom.vendor.min.js` - A concatenated vendor file suitable for use as a single vendor include in either 
-development or production (contains d3 and Q)
+development or production (contains d3)
 * `locuszoom.css` - A generated CSS file for all LocusZoom styles
 
 This build process will also write sourcemaps, to help with debugging code even in production environments.

assets/js/app/.eslintrc

@@ -1,7 +1,7 @@
 {
   "globals": {
     "d3": false,
-    "Q": false
+    "Promise": false
   },
   "env": {
     "browser": true

assets/js/app/Dashboard.js

@@ -856,9 +856,11 @@ LocusZoom.Dashboard.Components.add('download', function(layout) {
                 this.button.selector
                     .classed('lz-dashboard-button-gray-disabled', true)
                     .html('Preparing Image');
-                this.generateBase64SVG().then(function(base64_string) {
+                this.generateBase64SVG().then(function(url) {
+                    var old = this.button.selector.attr('href');
+                    if (old) { URL.revokeObjectURL(old); }  // Clean up old url instance to prevent memory leaks
                     this.button.selector
-                        .attr('href', 'data:image/svg+xml;base64,\n' + base64_string)
+                        .attr('href', url)
                         .classed('lz-dashboard-button-gray-disabled', false)
                         .classed('lz-dashboard-button-gray-highlighted', true)
                         .html('Download Image');
@@ -887,7 +889,7 @@ LocusZoom.Dashboard.Components.add('download', function(layout) {
         }
     }
     this.generateBase64SVG = function() {
-        return Q.fcall(function () {
+        return new Promise(function (resolve, reject) {
             // Insert a hidden div, clone the node into that so we can modify it with d3
             var container = this.parent.selector.append('div').style('display', 'none')
                 .html(this.parent_plot.svg.node().outerHTML);
@@ -907,10 +909,9 @@ LocusZoom.Dashboard.Components.add('download', function(layout) {
             initial_html = initial_html.slice(0,insert_at) + style_def + initial_html.slice(insert_at);
             // Delete the container node
             container.remove();
-            // Base64-encode the string and return it
-            return btoa(encodeURIComponent(initial_html).replace(/%([0-9A-F]{2})/g, function(match, p1) {
-                return String.fromCharCode('0x' + p1);
-            }));
+            // Create an object URL based on the rendered markup
+            var content = new Blob([initial_html], { type: 'image/svg+xml' });
+            resolve(URL.createObjectURL(content));
         }.bind(this));
     };
 });

assets/js/app/Data.js

@@ -242,7 +242,7 @@ LocusZoom.Data.Requester = function(sources) {
         });
         //assume the fields are requested in dependent order
         //TODO: better manage dependencies
-        var ret = Q.when({header:{}, body: [], discrete: {}});
+        var ret = Promise.resolve({header:{}, body: [], discrete: {}});
         for(var i = 0; i < request_handles.length; i++) {
             // If a single datalayer uses multiple sources, perform the next request when the previous one completes
             ret = ret.then(request_handles[i]);
@@ -331,7 +331,7 @@ LocusZoom.Data.Source.prototype.getRequest = function(state, chain, fields) {
     var req;
     var cacheKey = this.getCacheKey(state, chain, fields);
     if (this.enableCache && typeof(cacheKey) !== 'undefined' && cacheKey === this._cachedKey) {
-        req = Q.when(this._cachedResponse);  // Resolve to the value of the current promise
+        req = Promise.resolve(this._cachedResponse);  // Resolve to the value of the current promise
     } else {
         req = this.fetchRequest(state, chain, fields);
         if (this.enableCache) {
@@ -371,7 +371,7 @@ LocusZoom.Data.Source.prototype.getData = function(state, fields, outnames, tran
         if (self.dependentSource && chain && chain.body && !chain.body.length) {
             // A "dependent" source should not attempt to fire a request if there is no data for it to act on.
             // Therefore, it should simply return the previous data chain.
-            return Q.when(chain);
+            return Promise.resolve(chain);
         }
 
         return self.getRequest(state, chain, fields).then(function(resp) {
@@ -537,24 +537,24 @@ LocusZoom.Data.Source.prototype.parseResponse = function(resp, chain, fields, ou
         // to occur for annotation sources (such as from ExAC). If empty response is received, skip parsing and log.
         // FIXME: Throw an error after pending, eg https://github.com/konradjk/exac_browser/issues/345
         console.error("No usable response was returned for source: '" + source_id + "'. Parsing will be skipped.");
-        return Q.when(chain);
+        return Promise.resolve(chain);
     }
 
     var json = typeof resp == 'string' ? JSON.parse(resp) : resp;
 
     var self = this;
     // Perform the 4 steps of parsing the payload and return a combined chain object
-    return Q.when(self.normalizeResponse(json.data || json))
+    return Promise.resolve(self.normalizeResponse(json.data || json))
         .then(function(standardized) {
             // Perform calculations on the data from just this source
-            return Q.when(self.annotateData(standardized, chain));
+            return Promise.resolve(self.annotateData(standardized, chain));
         }).then(function (data) {
-            return Q.when(self.extractFields(data, fields, outnames, trans));
+            return Promise.resolve(self.extractFields(data, fields, outnames, trans));
         }).then(function (one_source_body) {
             // Store a copy of the data that would be returned by parsing this source in isolation (and taking the
             //   fields array into account). This is useful when we want to re-use the source output in many ways.
             chain.discrete[source_id] = one_source_body;
-            return Q.when(self.combineChainBody(one_source_body, chain, fields, outnames, trans));
+            return Promise.resolve(self.combineChainBody(one_source_body, chain, fields, outnames, trans));
         }).then(function (new_body) {
             return { header: chain.header || {}, discrete: chain.discrete, body: new_body };
         });
@@ -1143,7 +1143,7 @@ LocusZoom.Data.StaticSource = LocusZoom.Data.Source.extend(function(data) {
 },'StaticJSON');
 
 LocusZoom.Data.StaticSource.prototype.getRequest = function(state, chain, fields) {
-    return Q.fcall(function() {return this._data;}.bind(this));
+    return Promise.resolve(this._data);
 };
 
 LocusZoom.Data.StaticSource.prototype.toJSON = function() {
@@ -1233,7 +1233,7 @@ LocusZoom.Data.ConnectorSource.prototype.getRequest = function(state, chain, fie
             throw new Error(self.constructor.SOURCE_NAME + ' cannot be used before loading required data for: ' + chain_source_id);
         }
     });
-    return Q.when(chain.body || []);
+    return Promise.resolve(chain.body || []);
 };
 
 LocusZoom.Data.ConnectorSource.prototype.parseResponse = function(data, chain, fields, outnames, trans) {
@@ -1242,7 +1242,7 @@ LocusZoom.Data.ConnectorSource.prototype.parseResponse = function(data, chain, f
 
     // Because of how the chain works, connectors are not very good at applying new transformations or namespacing.
     // Typically connectors are called with `connector_name:all` in the fields array.
-    return Q.when(this.combineChainBody(data, chain, fields, outnames, trans))
+    return Promise.resolve(this.combineChainBody(data, chain, fields, outnames, trans))
         .then(function(new_body) {
             return {header: chain.header || {}, discrete: chain.discrete || {}, body: new_body};
         });