Babel 7 upgrade

package.json

@@ -32,6 +32,7 @@
   },
   "license": "(LGPL-2.1 OR Artistic-2.0)",
   "dependencies": {
+    "@babel/runtime": "^7.4.5",
     "express": "^4.15.4",
     "fs-extra": "^4.0.1",
     "node-fetch": "^2.2.0",
@@ -40,23 +41,22 @@
     "shelljs": "^0.7.8"
   },
   "devDependencies": {
+    "@babel/core": "^7.4.5",
+    "@babel/plugin-transform-runtime": "^7.4.4",
+    "@babel/polyfill": "^7.4.4",
+    "@babel/preset-env": "^7.4.5",
     "@gmod/bam": "^1.0.15",
-    "@gmod/cram": "^1.5.1",
+    "@gmod/cram": "^1.5.3",
     "@gmod/gff": "^1.1.1",
     "@gmod/indexedfasta": "^1.0.11",
     "@gmod/tabix": "^1.1.5",
-    "@gmod/tribble-index": "^2.0.3",
-    "@gmod/twobit": "^1.1.2",
+    "@gmod/tribble-index": "^2.0.4",
+    "@gmod/twobit": "^1.1.9",
     "@gmod/vcf": "^2.0.2",
     "ajv": "^6.2.1",
     "ava": "^0.25.0",
-    "babel-core": "^6.26.0",
     "babel-eslint": "^8.2.2",
-    "babel-loader": "^7.1.4",
-    "babel-plugin-transform-async-to-generator": "^6.24.1",
-    "babel-plugin-transform-es2015-classes": "^6.24.1",
-    "babel-polyfill": "^6.26.0",
-    "babel-preset-es2015-without-strict": "^0.0.4",
+    "babel-loader": "^8.0.6",
     "buffer-crc32": "^0.2.13",
     "clean-webpack-plugin": "^0.1.18",
     "copy-webpack-plugin": "^4.6.0",
@@ -66,7 +66,7 @@
     "dojo": "^1.14.2",
     "dojo-dstore": "^1.1.1",
     "dojo-util": "^1.14.2",
-    "dojo-webpack-plugin": "^2.8.5",
+    "dojo-webpack-plugin": "^2.8.8",
     "dojox": "^1.14.2",
     "electron": "^3.0.12",
     "electron-packager": "^12.0.1",
@@ -89,11 +89,11 @@
     "style-loader": "^0.20.2",
     "tenacious-fetch": "^2.1.0",
     "tmp": "^0.0.33",
-    "uglifyjs-webpack-plugin": "^1.2.2",
+    "uglifyjs-webpack-plugin": "^2.1.3",
     "url-loader": "0.5.7",
     "util-deprecate": "^1.0.2",
-    "webpack": "^4.26.1",
-    "webpack-cli": "^3.1.2",
+    "webpack": "^4.32.2",
+    "webpack-cli": "^3.3.2",
     "whatwg-fetch": "^2.0.4",
     "yarn": "^1.12.3"
   }

src/JBrowse/Store/SeqFeature/IndexedStatsEstimationMixin.js

@@ -14,9 +14,12 @@ return declare( GlobalStats, {
      * estimate the feature density of the store.
      * @private
      */
-    async _estimateGlobalStats(refseq) {
-        refseq = refseq || this.refSeq
+    _estimateGlobalStats: async function _estimateGlobalStats(query) {
+        const refseq = query || this.refSeq || {}
         let featCount
+        if(!refseq.name || !refseq.name.length) {
+            featCount = -1
+        }
         if (this.indexedData) {
             featCount = await this.indexedData.lineCount(this.browser.regularizeReferenceName(refseq.name))
         } else if (this.bam) {
@@ -25,7 +28,7 @@ return declare( GlobalStats, {
             featCount = await this.bam.index.lineCount(chrId, true)
         }
         if (featCount == -1) {
-            return this.inherited('_estimateGlobalStats', arguments)
+            return this.inherited(_estimateGlobalStats, arguments)
         }
         const correctionFactor = (this.getConf('topLevelFeaturesPercent') || 100) / 100
         const featureDensity = featCount / (refseq.end - refseq.start) * correctionFactor

src/JBrowse/View/Export/GFF3.js

@@ -81,10 +81,10 @@ return declare( ExportBase,
         return this._gff3_reserved_attributes_by_lcname[ fieldname.toLowerCase() ];
     },
 
-    exportRegion(region, callback) {
+    exportRegion: function exportRegion(region, callback) {
         this.print( "##gff-version 3\n");
         this.print( `##sequence-region ${region.ref} ${region.start+1} ${region.end}\n` );
-        this.inherited(arguments)
+        this.inherited(exportRegion, arguments)
     },
 
     /**

src/JBrowse/main.js

@@ -1,4 +1,5 @@
-import 'babel-polyfill'
+import "@babel/polyfill";
+
 
 require([
     'JBrowse/Browser',

src/JBrowse/standalone.js

@@ -1,4 +1,4 @@
-import 'babel-polyfill'
+import '@babel/polyfill'
 
 require([
     'JBrowse/Browser',

tests/js_tests/main.js

@@ -1,6 +1,6 @@
 __webpack_public_path__ = '../../dist/'
 
-import 'babel-polyfill'
+import '@babel/polyfill'
 
 var jasmine = window.jasmine;
 var jasmineEnv = jasmine.getEnv();

webpack.config.js

@@ -1,5 +1,5 @@
 /* eslint-env node */
-require('babel-polyfill')
+require('@babel/polyfill')
 
 const DojoWebpackPlugin = require("dojo-webpack-plugin")
 const CopyWebpackPlugin = require("copy-webpack-plugin")
@@ -10,6 +10,8 @@ const path = require("path")
 const glob = require('glob')
 const webpack = require("webpack")
 
+
+
 // if JBROWSE_BUILD_MIN env var is 1 or true, then we also minimize the JS
 // and forego generating source maps
 const DEBUG = ! [1,'1','true'].includes(process.env.JBROWSE_BUILD_MIN)
@@ -56,17 +58,18 @@ var webpackConf = {
         ),
     ],
     module: {
+        // the order of these rules does matter
         rules: [
             {
                 test: /\.js$/,
-                exclude: /node_modules\/(?!(quick-lru|@gmod\/cram|@gmod\/bam|@gmod\/indexedfasta|@gmod\/tabix|@gmod\/tribble-index|@gmod\/binary-parser|@gmod\/bgzf-filehandle))/,
+                exclude: /node_modules\/(?!quick-lru)/,
                 use: {
-                  loader: 'babel-loader',
-                  options: {
-                    presets: ['es2015-without-strict'],
-                    plugins: ['transform-async-to-generator','transform-es2015-classes'],
-                    cacheDirectory: true
-                  }
+                    loader: 'babel-loader',
+                    options: {
+                        sourceType: 'unambiguous', // this bypasses some things with using module.exports and export es6
+                        presets: ['@babel/preset-env'],
+                        //plugins: ['@babel/plugin-transform-runtime']
+                    }
                 }
             },
             {
@@ -111,6 +114,7 @@ if (DEBUG) {
     webpackConf.mode = 'development'
     webpackConf.entry.run_jasmine = 'tests/js_tests/main.js'
     webpackConf.plugins.push( new webpack.optimize.AggressiveMergingPlugin() )
+
 } else {
     webpackConf.mode = 'production'
     webpackConf.plugins.push( new UglifyJsPlugin())