Generate categoris using group

GMOD · Jan 28, 2025 · 2b2e35b · 2b2e35b
1 parent 7f9afa3
commit 2b2e35b
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Showing 5 changed files with 61 additions and 29 deletions.
diff --git a/packages/core/util/tracks.ts b/packages/core/util/tracks.ts
@@ -247,7 +247,7 @@ export function generateUnsupportedTrackConf(
 export function generateUnknownTrackConf(
   trackName: string,
   trackUrl: string,
-  categories: string[] | undefined,
+  categories?: string[],
 ) {
   const conf = {
     type: 'FeatureTrack',

diff --git a/packages/product-core/src/ui/AboutDialogContents.tsx b/packages/product-core/src/ui/AboutDialogContents.tsx
@@ -61,7 +61,9 @@ const AboutDialogContents = observer(function ({
       },
     },
     { session, config },
-  ) as Record<string, unknown>
+  ) as {
+    config: { metadata?: Record<string, unknown>; [key: string]: unknown }
+  }
 
   const ExtraPanel = pluginManager.evaluateExtensionPoint(
     'Core-extraAboutPanel',
@@ -99,11 +101,20 @@ const AboutDialogContents = observer(function ({
           </span>
         ) : null}
         <Attributes
-          attributes={confPostExt}
-          omit={['displays', 'baseUri', 'refNames', 'formatAbout']}
+          attributes={confPostExt.config}
+          omit={['displays', 'baseUri', 'refNames', 'formatAbout', 'metadata']}
           hideUris={hideUris}
         />
       </BaseCard>
+      {confPostExt.config.metadata ? (
+        <BaseCard title="Metadata">
+          <Attributes
+            attributes={confPostExt.config.metadata}
+            omit={['displays', 'baseUri', 'refNames', 'formatAbout']}
+            hideUris={hideUris}
+          />
+        </BaseCard>
+      ) : null}
       {ExtraPanel ? (
         <BaseCard title={ExtraPanel.name}>
           <ExtraPanel.Component config={config} />

diff --git a/plugins/data-management/src/UCSCTrackHub/doConnect.ts b/plugins/data-management/src/UCSCTrackHub/doConnect.ts
@@ -5,15 +5,11 @@ import { openLocation } from '@jbrowse/core/util/io'
 import { nanoid } from '@jbrowse/core/util/nanoid'
 
 import { generateTracks } from './ucscTrackHub'
-import { fetchGenomesFile, fetchTrackDbFile } from './util'
+import { fetchGenomesFile, fetchTrackDbFile, resolve } from './util'
 
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import type { FileLocation } from '@jbrowse/core/util'
 
-function resolve(uri: string, baseUri: string) {
-  return new URL(uri, baseUri).href
-}
-
 export async function doConnect(self: {
   configuration: AnyConfigurationModel
   addTrackConfs: (arg: Record<string, unknown>[]) => void
@@ -38,6 +34,15 @@ export async function doConnect(self: {
           name: genomeName,
           sequence: {
             type: 'ReferenceSequenceTrack',
+            metadata: {
+              // eslint-disable-next-line @typescript-eslint/no-misused-spread
+              ...genome,
+              ...(genome.data.htmlPath
+                ? {
+                    htmlPath: `<a href="${resolve(genome.data.htmlPath, hubUri)}">${genome.data.htmlPath}</a>`,
+                  }
+                : {}),
+            },
             trackId: `${genomeName}-${nanoid()}`,
             adapter: {
               type: 'TwoBitAdapter',
@@ -58,6 +63,7 @@ export async function doConnect(self: {
         trackDbLoc: hubFileLocation,
         assemblyName: genomeName,
         sequenceAdapter,
+        baseUrl: hubUri,
       })
       self.addTrackConfs(tracksNew)
     } else {
@@ -113,6 +119,7 @@ export async function doConnect(self: {
           trackDbLoc: loc,
           assemblyName: genomeName,
           sequenceAdapter,
+          baseUrl: hubUri,
         })
         self.addTrackConfs(tracks)
         map[genomeName] = tracks.length

diff --git a/plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts b/plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts
@@ -1,7 +1,7 @@
 import { isUriLocation, notEmpty, objectHash } from '@jbrowse/core/util'
 import { generateUnknownTrackConf } from '@jbrowse/core/util/tracks'
 
-import { makeLoc2, makeLoc, makeLocAlt } from './util'
+import { makeLoc2, makeLoc, makeLocAlt, resolve } from './util'
 
 import type { RaStanza, TrackDbFile } from '@gmod/ucsc-hub'
 import type { FileLocation } from '@jbrowse/core/util'
@@ -11,11 +11,13 @@ export function generateTracks({
   trackDbLoc,
   assemblyName,
   sequenceAdapter,
+  baseUrl,
 }: {
   trackDb: TrackDbFile
   trackDbLoc: FileLocation
   assemblyName: string
   sequenceAdapter: any
+  baseUrl: string
 }) {
   const parentTrackKeys = new Set([
     'superTrack',
@@ -38,16 +40,32 @@ export function generateTracks({
             parentTracks.push(trackDb.data[currentTrackName])
           }
         } while (currentTrackName)
-        return makeTrackConfig({
-          track,
-          trackDbLoc,
-          trackDb,
-          sequenceAdapter,
-          categories: parentTracks
-            .reverse()
-            .map(p => p?.data.shortLabel)
-            .filter((f): f is string => !!f),
-        })
+        parentTracks.reverse()
+
+        return {
+          metadata: {
+            ucscConfig: {
+              ...track.data,
+              ...(track.data.html
+                ? {
+                    html: `<a href="${resolve(track.data.html, baseUrl)}">${track.data.html}</a>`,
+                  }
+                : {}),
+            },
+          },
+          category: [
+            track.data.group,
+            ...parentTracks
+              .map(p => p?.data.group)
+              .filter((f): f is string => !!f),
+          ].filter(f => !!f),
+          ...makeTrackConfig({
+            track,
+            trackDbLoc,
+            trackDb,
+            sequenceAdapter,
+          }),
+        }
       }
     })
     .filter(notEmpty)
@@ -60,13 +78,11 @@ export function generateTracks({
 
 function makeTrackConfig({
   track,
-  categories,
   trackDbLoc,
   trackDb,
   sequenceAdapter,
 }: {
   track: RaStanza
-  categories: string[]
   trackDbLoc: FileLocation
   trackDb: TrackDbFile
   sequenceAdapter: any
@@ -94,7 +110,6 @@ function makeTrackConfig({
       type: 'AlignmentsTrack',
       name,
       description: data.longLabel,
-      category: categories,
       adapter: {
         type: 'BamAdapter',
         bamLocation: bigDataLocation,
@@ -110,7 +125,6 @@ function makeTrackConfig({
       type: 'AlignmentsTrack',
       name,
       description: data.longLabel,
-      category: categories,
       adapter: {
         type: 'CramAdapter',
         cramLocation: bigDataLocation,
@@ -125,7 +139,6 @@ function makeTrackConfig({
       type: 'QuantitativeTrack',
       name,
       description: data.longLabel,
-      category: categories,
       adapter: {
         type: 'BigWigAdapter',
         bigWigLocation: bigDataLocation,
@@ -136,7 +149,6 @@ function makeTrackConfig({
       type: 'FeatureTrack',
       name,
       description: data.longLabel,
-      category: categories,
       adapter: {
         type: 'BigBedAdapter',
         bigBedLocation: bigDataLocation,
@@ -147,7 +159,6 @@ function makeTrackConfig({
       type: 'VariantTrack',
       name,
       description: data.longLabel,
-      category: categories,
       adapter: {
         type: 'VcfTabixAdapter',
         vcfGzLocation: bigDataLocation,
@@ -163,7 +174,6 @@ function makeTrackConfig({
       type: 'HicTrack',
       name,
       description: data.longLabel,
-      category: categories,
       adapter: {
         type: 'HicAdapter',
         hicLocation: bigDataLocation,
@@ -184,7 +194,7 @@ function makeTrackConfig({
     //     case 'bedRnaElements':
     //     case 'broadPeak':
     //     case 'coloredExon':
-    return generateUnknownTrackConf(name, baseTrackType, categories)
+    return generateUnknownTrackConf(name, baseTrackType)
   }
 }
 

diff --git a/plugins/data-management/src/UCSCTrackHub/util.ts b/plugins/data-management/src/UCSCTrackHub/util.ts
@@ -38,3 +38,7 @@ export function makeLoc2(first: string, alt?: string) {
         locationType: 'UriLocation',
       }
 }
+
+export function resolve(uri: string, baseUri: string) {
+  return new URL(uri, baseUri).href
+}