igv 2.15.4 → 2.15.5

package/dist/igv.js

@@ -18584,6 +18584,7 @@
             });
             this.RANGE_WARNING_GIVEN = false;
             this.oauth = new Oauth();
+            this.contentLengthMap = new Map();
         }
 
         setApiKey(key) {
@@ -18661,6 +18662,18 @@
             }
         }
 
+        async getContentLength(url, options) {
+            if (!this.contentLengthMap.has(url)) {
+                options = options || {};
+                options.method = 'HEAD';
+                options.GET_CONTENT_LENGTH = true;
+                const contentLengthString = await this._loadURL(url, options);
+                const contentLength = contentLengthString ? Number.parseInt(contentLengthString) : -1;
+                this.contentLengthMap.set(url, contentLength);
+            }
+            return this.contentLengthMap.get(url)
+        }
+
         async _loadURL(url, options) {
 
             const self = this;
@@ -18675,6 +18688,11 @@
                 oauthToken = await (typeof oauthToken === 'function' ? oauthToken() : oauthToken);
             }
 
+            let contentLength = -1;
+            if (options.range && !isAmazonV4Signed(url) && !isGoogleStorageSigned(url)) {
+                contentLength = await this.getContentLength(url);
+            }
+
             return new Promise(function (resolve, reject) {
 
                 // Various Google tansformations
@@ -18700,13 +18718,6 @@
                 }
                 const range = options.range;
 
-                // const isChrome = navigator.userAgent.indexOf('Chrome') > -1
-                // const isSafari = navigator.vendor.indexOf("Apple") === 0 && /\sSafari\//.test(navigator.userAgent)
-                // if (range && isChrome && !isAmazonV4Signed(url) && !isGoogleStorageSigned(url)) {
-                //     // Hack to prevent caching for byte-ranges. Attempt to fix net:err-cache errors in Chrome
-                //     url += url.includes("?") ? "&" : "?"
-                //     url += "someRandomSeed=" + Math.random().toString(36)
-                // }
 
                 const xhr = new XMLHttpRequest();
                 const sendData = options.sendData || options.body;
@@ -18722,7 +18733,13 @@
                 }
 
                 if (range) {
-                    var rangeEnd = range.size ? range.start + range.size - 1 : "";
+                    let rangeEnd = "";
+                    if (range.size) {
+                        rangeEnd = range.start + range.size - 1;
+                        if (contentLength > 0) {
+                            rangeEnd = Math.min(rangeEnd, contentLength - 1);
+                        }
+                    }
                     xhr.setRequestHeader("Range", "bytes=" + range.start + "-" + rangeEnd);
                     //      xhr.setRequestHeader("Cache-Control", "no-cache");    <= This can cause CORS issues, disabled for now
                 }
@@ -18748,6 +18765,11 @@
                 }
 
                 xhr.onload = async function (event) {
+
+                    if (options.GET_CONTENT_LENGTH) {
+                        resolve(xhr.getResponseHeader('content-length'));
+                    }
+
                     // when the url points to a local file, the status is 0 but that is not an error
                     if (xhr.status === 0 || (xhr.status >= 200 && xhr.status <= 300)) {
                         if (range && xhr.status !== 206 && range.start !== 0) {
@@ -18780,6 +18802,7 @@
                     }
                 };
 
+
                 xhr.onerror = function (event) {
                     if (isGoogleURL(url) && !options.retries) {
                         tryGoogleAuth();
@@ -18911,7 +18934,6 @@
     }
 
 
-
     /**
      * Return a Google oAuth token, triggering a sign in if required.   This method should not be called until we know
      * a token is required, that is until we've tried the url and received a 401, 403, or 404.
@@ -19070,6 +19092,11 @@
         }
     }
 
+    function isAmazonV4Signed(url) {
+        return url.indexOf("X-Amz-Signature") > -1
+    }
+
+
     const igvxhr = new IGVXhr();
 
     /*
@@ -23950,7 +23977,7 @@
         }
     };
 
-    const _version = "2.15.4";
+    const _version = "2.15.5";
     function version() {
         return _version
     }
@@ -30285,7 +30312,8 @@
             this.config = config || {};
             this.genome = genome;
             this.indexURL = config.indexURL;
-            this.indexed = config.indexed;
+            this.indexed = config.indexed || this.indexURL !== undefined;
+            this.queryable = this.indexed;
 
             if (isFile(this.config.url)) {
                 this.filename = this.config.url.name;
@@ -31945,7 +31973,7 @@
 
             const queryableFormats = new Set(["bigwig", "bw", "bigbed", "bb", "biginteract", "biggenepred", "bignarrowpeak", "tdf"]);
 
-            this.queryable = config.queryable === true;   // False by default, unless explicitly set
+            this.queryable = config.indexURL || config.queryable === true;   // False by default, unless explicitly set
             if (config.reader) {
                 // Explicit reader implementation
                 this.reader = config.reader;
@@ -32043,6 +32071,7 @@
             //   * view is "whole genome" but no features are loaded
             //   * cache is disabled
             //   * cache does not contain requested range
+           // const containsRange = this.featureCache.containsRange(new GenomicInterval(queryChr, start, end))
             if ((isWholeGenome && !this.wgFeatures && this.supportsWholeGenome()) ||
                 this.config.disableCache ||
                 !this.featureCache ||
@@ -40883,7 +40912,7 @@
 
         function onDragEnd() {
             if (track.trackView && track.displayMode !== "SQUISHED") {
-                track.trackView.repaintViews();      // TODO -- refine this to the viewport that was dragged after DOM refactor
+                track.trackView.updateViews();      // TODO -- refine this to the viewport that was dragged after DOM refactor
             }
         }