Move jszlib dependency to util directory (#1580)

* Move jszlib code into util * Eliminate jszlib references
GMOD · Mar 11, 2021 · 351f951 · 351f951
1 parent 848ca08
commit 351f951
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Showing 7 changed files with 4,248 additions and 46 deletions.
diff --git a/build/dojo-loader-config.js b/build/dojo-loader-config.js
@@ -1,56 +1,44 @@
+const { findPlugins } = require("./plugin-util");
 
-const {findPlugins} = require('./plugin-util')
-
-module.exports = function(env) {
-
+module.exports = function (env) {
     dojoConfig = {
-        baseUrl: '.',
+        baseUrl: ".",
         packages: [
             {
-                name: 'dojo',
-                location: env.dojoRoot + 'dojo',
+                name: "dojo",
+                location: env.dojoRoot + "dojo",
             },
             {
-                name: 'dijit',
-                location: env.dojoRoot + 'dijit',
+                name: "dijit",
+                location: env.dojoRoot + "dijit",
             },
             {
-                name: 'dojox',
-                location: env.dojoRoot + 'dojox',
+                name: "dojox",
+                location: env.dojoRoot + "dojox",
             },
             {
-                name: 'JBrowse',
-                location: 'src/JBrowse',
-                lib: '.'
+                name: "JBrowse",
+                location: "src/JBrowse",
+                lib: ".",
             },
             {
-                name: 'dgrid',
-                location: env.dojoRoot + 'dgrid',
-                lib: '.'
+                name: "dgrid",
+                location: env.dojoRoot + "dgrid",
+                lib: ".",
             },
             {
-                name: 'dstore',
-                location: env.dojoRoot + 'dojo-dstore',
-                lib: '.'
+                name: "dstore",
+                location: env.dojoRoot + "dojo-dstore",
+                lib: ".",
             },
             {
-                name: 'jszlib',
-                location: env.dojoRoot + 'jszlib',
-                lib: '.'
+                name: "FileSaver",
+                location: env.dojoRoot + "filesaver.js",
+                lib: ".",
             },
-            {
-                name: 'FileSaver',
-                location: env.dojoRoot + 'filesaver.js',
-                lib: '.'
-            }
-        ]
-        .concat(
-            findPlugins('.')
-        )
-        ,
-
-        async: true
-    }
+        ].concat(findPlugins(".")),
+        async: true,
+    };
 
-    return dojoConfig
+    return dojoConfig;
 };
diff --git a/package.json b/package.json
@@ -78,7 +78,6 @@
     "http-range-fetcher": "^1.2.1",
     "imports-loader": "^0.8.0",
     "jasmine-node": "^3.0.0",
-    "jszlib": "git+https://github.com/cmdcolin/jszlib.git#c966ceac3b283d2248764c09e07a4b268edd5032",
     "node-sass": "^4.12.0",
     "puppeteer": "^1.0.0",
     "quick-lru": "^2.0.0",

diff --git a/src/JBrowse/Model/BGZip/BGZBlob.js b/src/JBrowse/Model/BGZip/BGZBlob.js
@@ -3,8 +3,8 @@
  */
 define( [
             'dojo/_base/declare',
-            'jszlib/inflate',
-            'jszlib/arrayCopy'
+            'JBrowse/Util/jszlib',
+            'JBrowse/Util/arrayCopy',
         ],
         function(
             declare,

diff --git a/src/JBrowse/Store/SeqFeature/BigWig/RequestWorker.js b/src/JBrowse/Store/SeqFeature/BigWig/RequestWorker.js
@@ -9,8 +9,8 @@ define( [
             'dojo/promise/all',
             'JBrowse/Model/Range',
             'JBrowse/Model/SimpleFeature',
-            'jszlib/inflate',
-            'jszlib/arrayCopy'
+            'JBrowse/Util/jszlib',
+            'JBrowse/Util/arrayCopy'
         ],
         function(
             declare,

diff --git a/src/JBrowse/Util/arrayCopy.js b/src/JBrowse/Util/arrayCopy.js
@@ -0,0 +1,50 @@
+define([], function () {
+    var testArray;
+    try {
+        testArray = new Uint8Array(1);
+    } catch (x) {}
+    var hasSlice = false; /* (typeof testArray.slice === 'function'); */ // Chrome slice performance is so dire that we're currently not using it...
+
+    function arrayCopy(src, srcOffset, dest, destOffset, count) {
+        if (count == 0) {
+            return;
+        }
+        if (!src) {
+            throw "Undef src";
+        } else if (!dest) {
+            throw "Undef dest";
+        }
+
+        if (srcOffset == 0 && count == src.length) {
+            arrayCopy_fast(src, dest, destOffset);
+        } else if (src.subarray) {
+            arrayCopy_fast(
+                src.subarray(srcOffset, srcOffset + count),
+                dest,
+                destOffset
+            );
+        } else if (src.BYTES_PER_ELEMENT == 1 && count > 100) {
+            arrayCopy_fast(
+                new Uint8Array(src.buffer, src.byteOffset + srcOffset, count),
+                dest,
+                destOffset
+            );
+        } else {
+            arrayCopy_slow(src, srcOffset, dest, destOffset, count);
+        }
+    }
+
+    function arrayCopy_slow(src, srcOffset, dest, destOffset, count) {
+        // dlog('_slow call: srcOffset=' + srcOffset + '; destOffset=' + destOffset + '; count=' + count);
+
+        for (var i = 0; i < count; ++i) {
+            dest[destOffset + i] = src[srcOffset + i];
+        }
+    }
+
+    function arrayCopy_fast(src, dest, destOffset) {
+        dest.set(src, destOffset);
+    }
+
+    return arrayCopy;
+});