igv 3.2.4 → 3.2.5

package/dist/igv.esm.js

@@ -8623,6 +8623,7 @@ function getCurrentAccessToken() {
 }
 
 
+let promise;
 /**
  * Return a promise for an access token for the given scope.  If the user hasn't authorized the scope request it
  *
@@ -8641,22 +8642,27 @@ async function getAccessToken(scope) {
         return google.igv.tokenResponse.access_token
     } else {
         const tokenClient = google.igv.tokenClient;
-        return new Promise((resolve, reject) => {
-            try {
-                // Settle this promise in the response callback for requestAccessToken()
-                tokenClient.callback = (tokenResponse) => {
-                    if (tokenResponse.error !== undefined) {
-                        reject(tokenResponse);
-                    }
-                    google.igv.tokenResponse = tokenResponse;
-                    google.igv.tokenExpiresAt = Date.now() + tokenResponse.expires_in * 1000;
-                    resolve(tokenResponse.access_token);
-                };
-                tokenClient.requestAccessToken({scope});
-            } catch (err) {
-                console.log(err);
-            }
-        })
+        if(!promise) {
+            promise = new Promise((resolve, reject) => {
+                try {
+                    // Settle this promise in the response callback for requestAccessToken()
+                    tokenClient.callback = (tokenResponse) => {
+                        if (tokenResponse.error !== undefined) {
+                            reject(tokenResponse);
+                        }
+                        google.igv.tokenResponse = tokenResponse;
+                        google.igv.tokenExpiresAt = Date.now() + tokenResponse.expires_in * 1000;
+                        console.log("Access token expires at " + new Date(google.igv.tokenExpiresAt));
+                        resolve(tokenResponse.access_token);
+                    };
+                    console.log("Requesting access token");
+                    tokenClient.requestAccessToken({scope});
+                } catch (err) {
+                    console.log(err);
+                }
+            });
+        }
+        return promise
     }
 }
 
@@ -30846,6 +30852,7 @@ function indentLevel(str) {
 }
 
 const DEFAULT_GENOMES_URL = "https://igv.org/genomes/genomes.json";
+const BACKUP_GENOMES_URL = "https://raw.githubusercontent.com/igvteam/igv.js/main/packages/igv/src/genomes/genomes.json";
 
 const GenomeUtils = {
 
@@ -30853,34 +30860,41 @@ const GenomeUtils = {
 
         if (!GenomeUtils.KNOWN_GENOMES) {
 
-            const table = {};
+            GenomeUtils.KNOWN_GENOMES = {};
+
+            const processJson = (jsonArray, table) => {
+                jsonArray.forEach(function (json) {
+                    table[json.id] = json;
+                });
+                return table
+            };
 
             // Get default genomes
             if (config.loadDefaultGenomes !== false) {
-                const url = DEFAULT_GENOMES_URL;
-                const jsonArray = await igvxhr.loadJson(url, {timeout: 5000});
-                processJson(jsonArray);
+                try {
+                    const jsonArray = await igvxhr.loadJson(DEFAULT_GENOMES_URL, {timeout: 2000});
+                    processJson(jsonArray, GenomeUtils.KNOWN_GENOMES);
+                } catch (error) {
+                    try {
+                        console.error("Error initializing default genomes:", error);
+                        const jsonArray = await igvxhr.loadJson(BACKUP_GENOMES_URL, {timeout: 2000});
+                        processJson(jsonArray, GenomeUtils.KNOWN_GENOMES);
+                    } catch (e) {
+                        console.error("Error initializing backup genomes:", error);
+                    }
+                }
             }
 
-            // Add user-defined genomes
+            // Append user-defined genomes, which might override defaults
             const genomeList = config.genomeList || config.genomes;
             if (genomeList) {
                 if (typeof genomeList === 'string') {
                     const jsonArray = await igvxhr.loadJson(genomeList, {});
-                    processJson(jsonArray);
+                     processJson(jsonArray, GenomeUtils.KNOWN_GENOMES);
                 } else {
-                    processJson(genomeList);
+                     processJson(genomeList, GenomeUtils.KNOWN_GENOMES);
                 }
             }
-
-            GenomeUtils.KNOWN_GENOMES = table;
-
-            function processJson(jsonArray) {
-                jsonArray.forEach(function (json) {
-                    table[json.id] = json;
-                });
-                return table
-            }
         }
     },
 
@@ -30906,7 +30920,7 @@ const GenomeUtils = {
         } else if (idOrConfig.genome) {
             genomeID = idOrConfig.genome;
         } else if (idOrConfig.id !== undefined && !(idOrConfig.fastaURL || idOrConfig.twobitURL)) {
-            // Backward compatibilityz
+            // Backward compatibility
             genomeID = idOrConfig.id;
         }
 
@@ -68819,6 +68833,115 @@ function prettyPrint(number) {
     }
 }
 
+/**
+ * Configurable properties
+ * Locus {chr, start, end}
+ * url - url to image.   Later url to webservice to fetch image
+ */
+
+class ImageTrack extends TrackBase {
+
+    static defaults = {}
+
+    constructor(config, browser) {
+        super(config, browser);
+    }
+
+    init(config) {
+
+        super.init(config);
+
+        if (!config.images) {
+            throw Error("images are required")
+        }
+
+        this.locus = config.locus;
+        this.type = "image";
+        this.resolutionAware = true;
+    }
+
+
+    async postInit() {
+
+        this._images = [];
+
+        for (let i of this.config.images) {
+            const img = new Image();
+            img.onload = () => {
+                i.img = img;
+                i.bpPerPixel = (i.end - i.start) / img.width;
+                this._images.push(i);
+            };
+            img.onerror = (err) => {
+                console.error(err);
+            };
+            //if (img.complete) {   //cached image
+            //    img.onload()
+           // }
+            img.src = i.src;
+        }
+
+    }
+
+    computePixelHeight(features) {
+        return features ? features.height : 0
+    }
+
+
+    menuItemList() {
+
+        const menuItems = [];
+
+        return menuItems
+    }
+
+
+    async getFeatures(chr, start, end, bpPerPixel) {
+        // Return  image.  Scaled or not?
+        return this.selectImage(chr, start, end, bpPerPixel)
+    }
+
+    selectImage(chr, start, end, bpPerPixel) {
+
+        // Select the highest resolution image containing the interval.  If no image contains the interval return
+        // the lowest resolution image if it overlaps
+        if(this._images.length == 0) {
+            return null
+        }
+        this._images.sort((a, b) => a.bpPerPixel < b.bpPerPixel ? -1 : 1);
+        for(let i of this._images) {
+            if(i.bpPerPixel > bpPerPixel) {
+                return i
+            }
+        }
+        const lowRes = this._images[this._images.length-1];
+        if(lowRes.chr === chr) {
+            return lowRes
+        } else {
+            return null
+        }
+    }
+
+    draw({context, pixelTop, pixelWidth, pixelHeight, features, bpPerPixel, bpStart}) {
+
+        const image = features.img;
+        if (image) {
+            const nw = image.width;
+            const nh = image.height;
+            const imageBpPerPixel = (features.end - features.start) / nw;
+            const scale = imageBpPerPixel / bpPerPixel;
+            const x = (features.start - bpStart) / bpPerPixel;
+            context.drawImage(image, x, 0, scale * nw, nh);
+        }
+
+    }
+
+    get supportsWholeGenome() {
+        return false
+    }
+
+}
+
 //import CNVPytorTrack from "./CNVpytor/cnvpytorTrack.js"
 
 
@@ -68844,7 +68967,8 @@ const trackFunctions =
         ['gcnv', (config, browser) => new GCNVTrack(config, browser)],
         ['junction', (config, browser) => new SpliceJunctionTrack(config, browser)],
         ['blat', (config, browser) => new BlatTrack(config, browser)],
-        ['cnvpytor', (config, browser) => new CNVPytorTrack(config, browser)]
+        ['cnvpytor', (config, browser) => new CNVPytorTrack(config, browser)],
+        ['image', (config, browser) => new ImageTrack(config, browser)]
     ]);
 
 
@@ -69322,7 +69446,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.2.4";
+const _version = "3.2.5";
 function version() {
     return _version
 }
@@ -73865,7 +73989,7 @@ class Browser {
     async loadTrackList(configList) {
 
         // Impose an order if not specified
-        let order = 0;
+        let order = this.trackViews.length + 1;
         for (let c of configList) {
             if (c.order === undefined) {
                 c.order = order++;