Hub track configs (#1724)

* Add method to genome to get track configurations for menu. * Add genome change event
igvteam · Oct 27, 2023 · 948f8d4 · 948f8d4
1 parent f330ef4
commit 948f8d4
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Showing 9 changed files with 60 additions and 59 deletions.
diff --git a/dev/ucsc/hub.html b/dev/ucsc/hub.html
@@ -39,27 +39,27 @@
     }
 
     const hub = await Hub.loadHub("https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt", hubOptions)
-    const ref = hub.getGenomeConfig()
 
     const igvConfig = {
-        reference: ref
+        reference: hub.getGenomeConfig()
     }
 
-    // for(let tc of hub.getTrackConfigurations()) {
-    //     for(let t of tc.tracks) {
-    //         if(t.url.endsWith("undefined")) console.log(`${tc.label}  ${t.name}  ${t.url}`)
-    //     }
-    // }
-
     const browser = await igv.createBrowser(document.getElementById('igvDiv'), igvConfig)
 
+    browser.on('genomechange', (genome) => {
+        console.log(genome.getTrackConfigurations())
+    })
+
     const selector = document.getElementById("select")
     selector.addEventListener("change", () => document.getElementById("hub-input").value = selector.value)
 
     document.getElementById("hub-input").value = "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"
 
-    document.getElementById("load-genome").addEventListener("click", () =>
-        browser.loadGenome({url: document.getElementById("hub-input").value}))
+    document.getElementById("load-genome").addEventListener("click", async () => {
+        await browser.loadGenome({url: document.getElementById("hub-input").value})
+        console.log(browser.genome.getTrackConfigurations())
+    })
+
 
     document.getElementById("load-session").addEventListener("click", () =>
         browser.loadSession({url: document.getElementById("hub-input").value}))

diff --git a/js/browser.js b/js/browser.js
@@ -682,7 +682,7 @@ class Browser {
      */
     async loadReference(genomeConfig, initialLocus) {
 
-        const genome = await Genome.loadGenome(genomeConfig)
+        const genome = await Genome.createGenome(genomeConfig)
 
         const genomeChange = undefined === this.genome || (this.genome.id !== genome.id)
 
@@ -702,6 +702,10 @@ class Browser {
             throw new Error(`Cannot set initial locus ${locus}`)
         }
 
+        if(genomeChange) {
+            this.fireEvent('genomechange', [genome])
+        }
+
         if (genomeChange && this.circularView) {
             this.circularView.setAssembly({
                 name: this.genome.id,

diff --git a/js/genome/genome.js b/js/genome/genome.js
@@ -18,7 +18,7 @@ import {loadChromSizes} from "./chromSizes.js"
 
 class Genome {
 
-    static async loadGenome(options) {
+    static async createGenome(options) {
 
         const genome = new Genome(options)
         await genome.init()
@@ -30,9 +30,9 @@ class Genome {
         this.id = config.id || generateGenomeID(config)
         this.name = config.name
         this.nameSet = config.nameSet
-
     }
 
+
     async init() {
 
         const config = this.config
@@ -278,6 +278,10 @@ class Genome {
         const l = this.wgChromosomeNames.reduce((accumulator, currentValue) => accumulator += this.chromosomes.get(currentValue).bpLength, 0)
         this.chromosomes.set("all", new Chromosome("all", 0, l))
     }
+
+    getTrackConfigurations() {
+        return this.config.trackConfigurations
+    }
 }
 
 /**

diff --git a/js/index.js b/js/index.js
@@ -12,6 +12,7 @@ import {igvxhr} from "../node_modules/igv-utils/src/index.js"
 import {registerTrackClass, registerTrackCreatorFunction} from "./trackFactory.js"
 import TrackBase from "./trackBase.js"
 import Hub from "./ucsc/ucscHub.js"
+import Browser from "./browser.js"
 
 const setApiKey = igvxhr.setApiKey
 
@@ -47,6 +48,7 @@ export default {
     registerTrackClass,
     registerTrackCreatorFunction,
     registerFileFormats,
-    Hub
+    Hub,
+    uncompressSession: Browser.uncompressSession
 }
 
diff --git a/js/ucsc/ucscHub.js b/js/ucsc/ucscHub.js
@@ -89,33 +89,6 @@ class Hub {
         return this.genomeStanza.getProperty("defaultPos")
     }
 
-    getTrackConfigurations() {
-
-        // Organize track configs by group
-        const trackConfigMap = new Map()
-        for (let c of this.#getTracksConfigs()) {
-            const groupName = c.group || "other"
-            if (trackConfigMap.has(groupName)) {
-                trackConfigMap.get(groupName).push(c)
-            } else {
-                trackConfigMap.set(groupName, [c])
-            }
-        }
-
-        // Build group structure
-        const groupStanazMap = this.groupStanzas ?
-            new Map(this.groupStanzas.map(groupStanza => [groupStanza.getProperty("name"), groupStanza])) :
-            new Map()
-
-        return Array.from(trackConfigMap.keys()).map(groupName => {
-            return {
-                label: groupStanazMap.has(groupName) ? groupStanazMap.get(groupName).getProperty("label") : groupName,
-                tracks: trackConfigMap.get(groupName)
-            }
-        })
-
-    }
-
     /*  Example genome stanza
 genome GCF_000186305.1
 taxId 176946
@@ -205,11 +178,40 @@ isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
             config.tracks = this.#getTracksConfigs(filter)
         }
 
+        config.trackConfigurations = this.#getGroupedTrackConfigurations()
+
         return config
     }
 
+    #getGroupedTrackConfigurations() {
+
+        // Organize track configs by group
+        const trackConfigMap = new Map()
+        for (let c of this.#getTracksConfigs()) {
+            const groupName = c.group || "other"
+            if (trackConfigMap.has(groupName)) {
+                trackConfigMap.get(groupName).push(c)
+            } else {
+                trackConfigMap.set(groupName, [c])
+            }
+        }
+
+        // Build group structure
+        const groupStanazMap = this.groupStanzas ?
+            new Map(this.groupStanzas.map(groupStanza => [groupStanza.getProperty("name"), groupStanza])) :
+            new Map()
+
+        return Array.from(trackConfigMap.keys()).map(groupName => {
+            return {
+                label: groupStanazMap.has(groupName) ? groupStanazMap.get(groupName).getProperty("label") : groupName,
+                tracks: trackConfigMap.get(groupName)
+            }
+        })
+
+    }
+
     /**
-     * Return collection of igv track config object, organized by "group*
+     * Return an array of igv track config objects that satisfy the filter
      */
     #getTracksConfigs(filter) {
         return this.trackStanzas.filter(t => {

diff --git a/test/testBED.js b/test/testBED.js
@@ -325,7 +325,7 @@ suite("testBed", function () {
         this.timeout(20000)
 
         // Need an actual genome object for this test, not a mock object
-        const genome = await Genome.loadGenome({
+        const genome = await Genome.createGenome({
             id: "hg38",
             name: "Human (GRCh38/hg38)",
             fastaURL: "https://s3.dualstack.us-east-1.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",

diff --git a/test/testGenome.js b/test/testGenome.js
@@ -17,7 +17,7 @@ suite("testGenome", function () {
             wholeGenomeView: true
         }
 
-        const genome = await Genome.loadGenome(reference)
+        const genome = await Genome.createGenome(reference)
         assert.ok(genome)
         assert.equal(86, genome.chromosomeNames.length)
         assert.equal(genome.getCumulativeOffset("2"), 249250621)
@@ -35,7 +35,7 @@ suite("testGenome", function () {
             chromSizes: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt"
         }
 
-        const genome = await Genome.loadGenome(reference)
+        const genome = await Genome.createGenome(reference)
         assert.ok(genome.chromosomes.size > 0)
         assert.ok(genome.chromosomeNames.length > 0)
 

diff --git a/test/testHubs.js b/test/testHubs.js
@@ -10,7 +10,7 @@ import {isString} from "../node_modules/igv-utils/src/stringUtils.js"
 suite("hub.txt", function () {
 
 
-    test("genome", async function () {
+    test("genome config", async function () {
 
         const hub = await Hub.loadHub("test/data/hubs/hub.txt")
         assert.ok(hub.hub)
@@ -27,20 +27,9 @@ suite("hub.txt", function () {
         assert.ok(genomeConfig.twoBitURL)
         assert.ok(genomeConfig.chromAliasBbURL)
         assert.ok(genomeConfig.cytobandBbURL)
+        assert.ok(genomeConfig.trackConfigurations.length > 0)
     })
 
-    test("track configs", async function () {
-
-        const hub = await Hub.loadHub("test/data/hubs/hub.txt")
-        assert.ok(hub.hub)
-        assert.ok(hub.genomeStanza)
-        assert.equal(22, hub.trackStanzas.length)
-
-        const trackConfigs = hub.getTrackConfigurations()
-
-        assert.ok(trackConfigs.length > 0)
-
-    })
 
 
 })

diff --git a/test/testSeg.js b/test/testSeg.js
@@ -41,7 +41,7 @@ suite("testSeg", function () {
             cytobandURL: "https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/b37/b37_cytoband.txt"
         }
 
-        const genome = await Genome.loadGenome(reference)
+        const genome = await Genome.createGenome(reference)
         const url = "https://www.dropbox.com/s/h1rotg4xgn1bq8a/segmented_data_080520.seg.gz?dl=0"
         const featureSource = FeatureSource({
             format: 'seg',