Fixed check for parent tracks

GMOD · Jan 16, 2025 · 518a933 · 518a933
1 parent 86cefcd
commit 518a933
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Showing 4 changed files with 54 additions and 50 deletions.
diff --git a/plugins/data-management/package.json b/plugins/data-management/package.json
@@ -36,7 +36,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/ucsc-hub": "^0.3.0",
+    "@gmod/ucsc-hub": "^1.0.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/x-data-grid": "^7.0.0",
     "react-virtualized-auto-sizer": "^1.0.2",

diff --git a/plugins/data-management/src/UCSCTrackHub/doConnect.ts b/plugins/data-management/src/UCSCTrackHub/doConnect.ts
@@ -95,7 +95,6 @@ export async function doConnect(self: {
           continue
         }
 
-        // @ts-expect-error
         const db = genome.data.trackDb
         if (!db) {
           throw new Error('genomesFile not found on hub')

diff --git a/plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts b/plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts
@@ -53,42 +53,43 @@ export function generateTracks({
   assemblyName: string
   sequenceAdapter: any
 }) {
+  const parentTrackKeys = new Set([
+    'superTrack',
+    'compositeTrack',
+    'container',
+    'view',
+  ])
   return Object.entries(trackDb.data)
     .map(([trackName, track]) => {
-      const trackKeys = Object.keys(track!)
-      const parentTrackKeys = new Set([
-        'superTrack',
-        'compositeTrack',
-        'container',
-        'view',
-      ])
-      if (trackKeys.some(key => parentTrackKeys.has(key))) {
+      const { data } = track
+      if (Object.keys(data).some(key => parentTrackKeys.has(key))) {
         return undefined
-      }
-      const parentTracks = []
-      let currentTrackName = trackName
-      do {
-        currentTrackName = trackDb.data[currentTrackName]?.data.parent || ''
-        if (currentTrackName) {
-          currentTrackName = currentTrackName.split(' ')[0]!
-          parentTracks.push(trackDb.data[currentTrackName])
+      } else {
+        const parentTracks = []
+        let currentTrackName = trackName
+        do {
+          currentTrackName = trackDb.data[currentTrackName]?.data.parent || ''
+          if (currentTrackName) {
+            currentTrackName = currentTrackName.split(' ')[0]!
+            parentTracks.push(trackDb.data[currentTrackName])
+          }
+        } while (currentTrackName)
+        parentTracks.reverse()
+        const categories = parentTracks
+          .map(p => p?.data.shortLabel)
+          .filter((f): f is string => !!f)
+        const res = makeTrackConfig({
+          track,
+          categories,
+          trackDbLoc,
+          trackDb,
+          sequenceAdapter,
+        })
+        return {
+          ...res,
+          trackId: `ucsc-trackhub-${objectHash(res)}`,
+          assemblyNames: [assemblyName],
         }
-      } while (currentTrackName)
-      parentTracks.reverse()
-      const categories = parentTracks
-        .map(p => p?.data.shortLabel)
-        .filter((f): f is string => !!f)
-      const res = makeTrackConfig({
-        track: track!,
-        categories,
-        trackDbLoc,
-        trackDb,
-        sequenceAdapter,
-      })
-      return {
-        ...res,
-        trackId: `ucsc-trackhub-${objectHash(res)}`,
-        assemblyNames: [assemblyName],
       }
     })
     .filter(notEmpty)
@@ -107,11 +108,15 @@ function makeTrackConfig({
   trackDb: TrackDbFile
   sequenceAdapter: any
 }) {
-  const trackType =
-    track.data.type || trackDb.data[track.data.parent || '']?.data.type || ''
-  const name = track.data.shortLabel || ''
-  const bigDataUrl = track.data.bigDataUrl || ''
-  const bigDataIdx = track.data.bigDataIndex || ''
+  const { data } = track
+
+  const parent = data.parent || ''
+  const bigDataUrl = data.bigDataUrl || ''
+  const bigDataIdx = data.bigDataIndex || ''
+  const trackType = data.type || trackDb.data[parent]?.data.type || ''
+  const name =
+    (data.shortLabel || '') + (bigDataUrl?.includes('xeno') ? ' (xeno)' : '')
+
   const isUri = isUriLocation(trackDbLoc)
   let baseTrackType = trackType.split(' ')[0] || ''
   if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
@@ -125,8 +130,8 @@ function makeTrackConfig({
     case 'bam':
       return {
         type: 'AlignmentsTrack',
-        name: track.data.longLabel,
-        description: track.data.longLabel,
+        name,
+        description: data.longLabel,
         category: categories,
         adapter: {
           type: 'BamAdapter',
@@ -143,7 +148,7 @@ function makeTrackConfig({
       return {
         type: 'AlignmentsTrack',
         name,
-        description: track.data.longLabel,
+        description: data.longLabel,
         category: categories,
         adapter: {
           type: 'CramAdapter',
@@ -165,7 +170,7 @@ function makeTrackConfig({
       return {
         type: 'FeatureTrack',
         name,
-        description: track.data.longLabel,
+        description: data.longLabel,
         category: categories,
         adapter: {
           type: 'BigBedAdapter',
@@ -176,7 +181,7 @@ function makeTrackConfig({
       return {
         type: 'QuantitativeTrack',
         name,
-        description: track.data.longLabel,
+        description: data.longLabel,
         category: categories,
         adapter: {
           type: 'BigWigAdapter',
@@ -188,7 +193,7 @@ function makeTrackConfig({
       return {
         type: 'VariantTrack',
         name,
-        description: track.data.longLabel,
+        description: data.longLabel,
         category: categories,
         adapter: {
           type: 'VcfTabixAdapter',
@@ -205,7 +210,7 @@ function makeTrackConfig({
       return {
         type: 'HicTrack',
         name,
-        description: track.data.longLabel,
+        description: data.longLabel,
         category: categories,
         adapter: {
           type: 'HicAdapter',

diff --git a/yarn.lock b/yarn.lock
@@ -2367,10 +2367,10 @@
   dependencies:
     generic-filehandle2 "^1.0.0"
 
-"@gmod/ucsc-hub@^0.3.0":
-  version "0.3.0"
-  resolved "https://registry.yarnpkg.com/@gmod/ucsc-hub/-/ucsc-hub-0.3.0.tgz#375eeab1c515605510c706f6e2d76d6b42454f8c"
-  integrity sha512-M8r1rpmNOVH6UHwUTSOR5Z86upWEhvI3BKbyYVq8imTS+nZAq8Gr9RJTBsGlL0sgX7fmLSXms8/pTyp7e3YAQA==
+"@gmod/ucsc-hub@^1.0.0":
+  version "1.0.0"
+  resolved "https://registry.yarnpkg.com/@gmod/ucsc-hub/-/ucsc-hub-1.0.0.tgz#2fd6251d5ad040b8658e3d4c17987f89bc741322"
+  integrity sha512-BTMPPUS667K2eGQ6ASc69908l3hDWF2sV/ZoTuMqIz1AfiHuaDMpcdELNf61bVeTWvUUFG5qkOQApcWMvlIvjw==
 
 "@gmod/vcf@^6.0.0":
   version "6.0.2"