Hubs 2 (#1721)

* Export ucsc HUB class
* Add method to extract all loadable track configurations for web-app menu

Author: jrobinso

dev/ucsc/hub.html

@@ -35,12 +35,10 @@
 
 
     const hubOptions = {
-        url: "https://hgdownload.soe.ucsc.edu/hubs/GCA/018/471/515/GCA_018471515.1/hub.txt",
-        includeTracks: "all"
+        includeTracks: true
     }
 
-
-    const hub = await Hub.loadHub(hubOptions)
+    const hub = await Hub.loadHub("https://hgdownload.soe.ucsc.edu/hubs/GCA/018/471/515/GCA_018471515.1/hub.txt", hubOptions)
     const ref = hub.getGenomeConfig()
 
     const igvConfig = {

dev/ucsc/slowHub.html

@@ -16,12 +16,11 @@
 
 
     const hubOptions = {
-        url: "https://hgdownload.soe.ucsc.edu/hubs/GCA/004/027/145/GCA_004027145.1/hub.txt",
-        includeTracks: "all"
+        includeTracks: true
     }
 
+    const hub = await Hub.loadHub("https://hgdownload.soe.ucsc.edu/hubs/GCA/004/027/145/GCA_004027145.1/hub.txt", hubOptions)
 
-    const hub = await Hub.loadHub(hubOptions)
 
     const igvConfig = {
         showChromosomeWidget: false,

js/browser.js

@@ -493,7 +493,9 @@ class Browser {
                     return new XMLSession(string, knownGenomes)
 
                 } else if (filename.endsWith("hub.txt")) {
-                    const hub = await Hub.loadHub(options)
+
+                    const hub = await Hub.loadHub(urlOrFile, options)
+
                     if(chromosomeSelectWidget) {
                         chromosomeSelectWidget.hide()
                     }
@@ -763,7 +765,7 @@ class Browser {
 
         let genomeConfig
         if (idOrConfig.url && StringUtils.isString(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt")) {
-            const hub = await Hub.loadHub(idOrConfig)
+            const hub = await Hub.loadHub(idOrConfig.url, idOrConfig)
             genomeConfig = hub.getGenomeConfig("genes")
         } else {
             genomeConfig = idOrConfig //await GenomeUtils.expandReference(this.alert, idOrConfig)
@@ -793,7 +795,7 @@ class Browser {
      */
     async loadTrackHub(options) {
 
-        const hub = await Hub.loadHub(options)
+        const hub = await Hub.loadHub(options.url, options)
         const genomeConfig = hub.getGenomeConfig()
         const initialLocus = hub.getDefaultPosition()
         if (initialLocus) {

js/index.js

@@ -11,6 +11,7 @@ import {registerFileFormats} from "./util/trackUtils.js"
 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"
 
 const setApiKey = igvxhr.setApiKey
 
@@ -45,6 +46,7 @@ export default {
     TrackBase,
     registerTrackClass,
     registerTrackCreatorFunction,
-    registerFileFormats
+    registerFileFormats,
+    Hub
 }
 

js/jbrowse/circularViewUtils.js

@@ -149,15 +149,17 @@ const makeVCFChords = (features) => {
 function makeCircViewChromosomes(genome) {
     const regions = []
     const colors = []
-    for (let chrName of genome.wgChromosomeNames) {
-        const chr = genome.getChromosome(chrName)
-        colors.push(getChrColor(chr.name))
-        regions.push(
-            {
-                name: chr.name,
-                bpLength: chr.bpLength
-            }
-        )
+    if(genome.wgChromosomeNames) {
+        for (let chrName of genome.wgChromosomeNames) {
+            const chr = genome.getChromosome(chrName)
+            colors.push(getChrColor(chr.name))
+            regions.push(
+                {
+                    name: chr.name,
+                    bpLength: chr.bpLength
+                }
+            )
+        }
     }
     return regions
 }

js/ucsc/ucscHub.js

@@ -9,32 +9,27 @@ import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
 
 class Hub {
 
-    static async loadHub(options) {
-
-        if (!options.url) {
-            throw Error("Expected url")
-        }
+    static supportedTypes = new Set(["bigBed", "bigWig", "bigGenePred"])
+    static filterTracks = new Set(["cytoBandIdeo", "assembly", "gap", "gapOverlap", "allGaps",
+        "cpgIslandExtUnmasked", "windowMasker"])
 
-        const stanzas = await loadStanzas(options)
+    static async loadHub(url, options) {
 
+        const stanzas = await loadStanzas(url, options)
         let groups
         if ("genome" === stanzas[1].type) {
             const genome = stanzas[1]
             if (genome.hasProperty("groups")) {
-                const idx = options.url.lastIndexOf("/")
-                const baseURL = options.url.substring(0, idx + 1)
+                const idx = url.lastIndexOf("/")
+                const baseURL = url.substring(0, idx + 1)
                 const groupsTxtURL = baseURL + genome.getProperty("groups")
-                groups = await loadStanzas({url: groupsTxtURL})
+                groups = await loadStanzas(groupsTxtURL)
             }
         }
-        return new Hub(options.url, stanzas, groups)
+        return new Hub(url, stanzas, groups)
     }
 
-    static supportedTypes = new Set(["bigBed", "bigWig", "bigGenePred"])
-    static filterTracks = new Set(["cytoBandIdeo", "assembly", "gap", "gapOverlap", "allGaps",
-        "cpgIslandExtUnmasked", "windowMasker"])
-
-    constructor(url, stanzas, groups) {
+    constructor(url, stanzas, groupStanzas) {
 
         const idx = url.lastIndexOf("/")
         this.baseURL = url.substring(0, idx + 1)
@@ -69,21 +64,60 @@ class Hub {
             }
         }
 
-        if (groups) {
+        if (groupStanzas) {
+            this.groupStanzas = groupStanzas
             this.groupPriorityMap = new Map()
-            for (let g of groups) {
+            for (let g of groupStanzas) {
                 if (g.hasProperty("priority")) {
                     this.groupPriorityMap.set(g.getProperty("name"), Number.parseInt(g.getProperty("priority")) * 10)
                 }
             }
-            this.groupPriorities = new Map()
         }
     }
 
     getDefaultPosition() {
         return this.genomeStanza.getProperty("defaultPos")
     }
 
+    getTrackConfigurations() {
+
+        // Organize track configs by group
+        const trackConfigMap = new Map()
+        for (let c of this.#getTracksConfigs()) {
+            const name = c.group || "other"
+            if (trackConfigMap.has(name)) {
+                trackConfigMap.get(name).push(c)
+            } else {
+                trackConfigMap.set(name, [c])
+            }
+        }
+
+        // Build group structure
+        const t = []
+        if (this.groupStanzas) {
+            for (let g of this.groupStanzas) {
+                const groupName = g.getProperty("name")
+                if(trackConfigMap.has(groupName)) {
+                    t.push(
+                        {
+                            label: g.getProperty("label"),
+                            tracks: trackConfigMap.get(g.getProperty("name"))
+                        }
+                    )
+                }
+            }
+        }
+
+        if(trackConfigMap.has("other")) {
+            t.push({
+                label: "other",
+                tracks: trackConfigMap.get("other")
+            })
+        }
+
+        return t
+    }
+
     /*  Example genome stanza
 genome GCF_000186305.1
 taxId 176946
@@ -123,6 +157,7 @@ isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
         if (this.genomeStanza.hasProperty("twoBitBptURL")) {
             config.twoBitBptURL = this.baseURL + this.genomeStanza.getProperty("twoBitBptURL")
         }
+
         if (this.genomeStanza.hasProperty("twoBitBptUrl")) {
             config.twoBitBptURL = this.baseURL + this.genomeStanza.getProperty("twoBitBptUrl")
         }
@@ -161,7 +196,7 @@ isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
 
         // Tracks.  To prevent loading tracks set `includeTracks`to false
         if (includeTracks) {
-            config.tracks = this.#getTracksConfigs(includeTracks)
+            config.tracks = this.#getTracksConfigs(Hub.filterTracks)
         }
 
         return config
@@ -170,14 +205,12 @@ isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/186/305/GCF_000186305.1
     /**
      * Return collection of igv track config object, organized by "group*
      */
-    #getTracksConfigs(group) {
+    #getTracksConfigs(filter) {
         return this.trackStanzas.filter(t => {
             return t.getProperty("visibility") !== "hide" &&
                 Hub.supportedTypes.has(t.format) &&
-                !Hub.filterTracks.has(t.name) &&
-                t.hasProperty("bigDataUrl") &&
-                ("all" === group || group === t.getProperty("group"))
-
+                (!filter || !Hub.filterTracks.has(t.name) &&
+                    t.hasProperty("bigDataUrl"))
         })
             .map(t => this.#getTrackConfig(t))
     }
@@ -353,9 +386,9 @@ class Stanza {
  * @param url
  * @returns {Promise<*[]>}
  */
-async function loadStanzas(options) {
+async function loadStanzas(url, options) {
 
-    const data = await igvxhr.loadString(options.url)
+    const data = await igvxhr.loadString(url)
     const lines = data.split(/\n|\r\n|\r/g)
 
     const nodes = []

test/testHubs.js

@@ -0,0 +1,47 @@
+import "./utils/mockObjects.js"
+import {assert} from 'chai'
+import Hub from "../js/ucsc/ucscHub.js"
+import Trix from "../js/bigwig/trix.js"
+import BWReader from "../js/bigwig/bwReader.js"
+import BPTree from "../js/bigwig/bpTree.js"
+import {isString} from "../node_modules/igv-utils/src/stringUtils.js"
+
+
+suite("hub.txt", function () {
+
+
+    test("genome", 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 genomeConfig = hub.getGenomeConfig()
+        //const genome = await Genome.loadGenome(genomeConfig)
+
+        assert.ok(genomeConfig)
+        assert.equal("GCF_000186305.1", genomeConfig.id)
+        assert.equal("Python bivittatus", genomeConfig.name)
+        assert.ok(genomeConfig.twoBitBptURL)
+        assert.ok(genomeConfig.twoBitURL)
+        assert.ok(genomeConfig.chromAliasBbURL)
+        assert.ok(genomeConfig.cytobandBbURL)
+    })
+
+    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)
+
+    })
+
+
+})
+

test/testUCSC.js

@@ -3,34 +3,9 @@ import {assert} from 'chai'
 import Hub from "../js/ucsc/ucscHub.js"
 import Trix from "../js/bigwig/trix.js"
 import BWReader from "../js/bigwig/bwReader.js"
-import BPTree from "../js/bigwig/bpTree.js"
-import {isString} from "../node_modules/igv-utils/src/stringUtils.js"
-
 
 suite("ucsc utilities", function () {
 
-
-    test("hub.txt", async function () {
-
-        this.timeout(200000)
-
-        const hub = await Hub.loadHub({url: "test/data/hubs/hub.txt"})
-        assert.ok(hub.hub)
-        assert.ok(hub.genomeStanza)
-        assert.equal(22, hub.trackStanzas.length)
-
-        const genomeConfig = hub.getGenomeConfig()
-        //const genome = await Genome.loadGenome(genomeConfig)
-
-        assert.ok(genomeConfig)
-        assert.equal("GCF_000186305.1", genomeConfig.id)
-        assert.equal("Python bivittatus", genomeConfig.name)
-        assert.ok(genomeConfig.twoBitBptURL)
-        assert.ok(genomeConfig.twoBitURL)
-        assert.ok(genomeConfig.chromAliasBbURL)
-        assert.ok(genomeConfig.cytobandBbURL)
-    })
-
     test("trix", async function () {
 
         this.timeout(200000)