Make any non-bigWig bigType track open as BigBedAdapter in UCSC conne…

…ctions (#4796)
GMOD · Jan 28, 2025 · 767f4cc · 767f4cc
1 parent c77d33e
commit 767f4cc
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Showing 19 changed files with 276 additions and 145 deletions.
diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml
@@ -12,7 +12,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install website deps (with cache)
         uses: bahmutov/npm-install@v1
         with:
@@ -37,7 +37,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Build codebase
@@ -69,7 +69,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Build project
@@ -153,7 +153,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install deps and build (with cache)
         uses: bahmutov/npm-install@v1
       - name: Check codebase format

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -23,10 +23,10 @@ jobs:
       - uses: actions/checkout@v4
         with:
           persist-credentials: false
-      - name: Use Node.js 20
+      - name: Use Node.js 22
         uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       - name: Install deps
@@ -53,7 +53,7 @@ jobs:
     name: Build Windows desktop app
     runs-on: ubuntu-latest
     container:
-      image: docker://node:20-bullseye
+      image: docker://node:22-bullseye
     steps:
       - uses: actions/checkout@v4
         with:
@@ -107,10 +107,10 @@ jobs:
         with:
           persist-credentials: false
 
-      - name: Use Node.js 20
+      - name: Use Node.js 22
         uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install build deps
         run: |
           brew install pkg-config cairo pango libpng jpeg giflib librsvg
@@ -135,10 +135,10 @@ jobs:
         with:
           persist-credentials: false
 
-      - name: Use Node.js 20
+      - name: Use Node.js 22
         uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Install deps (with cache)
         uses: bahmutov/npm-install@v1
       - name: Install build deps

diff --git a/.github/workflows/update-docs.yml b/.github/workflows/update-docs.yml
@@ -14,7 +14,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-node@v4
         with:
-          node-version: '20'
+          node-version: '22'
       - name: Configure AWS Credentials
         uses: aws-actions/configure-aws-credentials@v4
         with:

diff --git a/docs/generateConfigDocs.ts b/docs/generateConfigDocs.ts
@@ -8,7 +8,7 @@ import {
   getAllFiles,
   removeComments,
   rm,
-} from './util'
+} from './util.ts'
 
 interface Derives {
   name: string

diff --git a/docs/generateStateModelDocs.ts b/docs/generateStateModelDocs.ts
@@ -8,7 +8,7 @@ import {
   getAllFiles,
   removeComments,
   rm,
-} from './util'
+} from './util.ts'
 
 interface Action {
   name: string

diff --git a/docs/tsconfig.json b/docs/tsconfig.json
@@ -10,6 +10,8 @@
     "strict": true,
     "declaration": true,
     "module": "commonjs",
+    "noEmit": true,
+    "allowImportingTsExtensions": true,
     "moduleResolution": "node"
   },
   "include": ["generateConfigDocs.ts", "generateStateModelDocs.ts", "util.ts"]

diff --git a/plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts b/plugins/data-management/src/UCSCTrackHub/ucscTrackHub.ts
@@ -38,25 +38,24 @@ export function generateTracks({
             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({
+        return makeTrackConfig({
           track,
-          categories,
           trackDbLoc,
           trackDb,
           sequenceAdapter,
+          categories: parentTracks
+            .reverse()
+            .map(p => p?.data.shortLabel)
+            .filter((f): f is string => !!f),
         })
-        return {
-          ...res,
-          trackId: `ucsc-trackhub-${objectHash(res)}`,
-          assemblyNames: [assemblyName],
-        }
       }
     })
     .filter(notEmpty)
+    .map(r => ({
+      ...r,
+      trackId: `ucsc-trackhub-${objectHash(r)}`,
+      assemblyNames: [assemblyName],
+    }))
 }
 
 function makeTrackConfig({
@@ -90,98 +89,87 @@ function makeTrackConfig({
     ? makeLoc(bigDataUrl, trackDbLoc)
     : makeLoc2(bigDataUrl)
 
-  switch (baseTrackType) {
-    case 'bam':
-      return {
-        type: 'AlignmentsTrack',
-        name,
-        description: data.longLabel,
-        category: categories,
-        adapter: {
-          type: 'BamAdapter',
-          bamLocation: bigDataLocation,
-          index: {
-            location: isUri
-              ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
-              : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),
-          },
+  if (baseTrackType === 'bam') {
+    return {
+      type: 'AlignmentsTrack',
+      name,
+      description: data.longLabel,
+      category: categories,
+      adapter: {
+        type: 'BamAdapter',
+        bamLocation: bigDataLocation,
+        index: {
+          location: isUri
+            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
+            : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),
         },
-      }
-
-    case 'cram':
-      return {
-        type: 'AlignmentsTrack',
-        name,
-        description: data.longLabel,
-        category: categories,
-        adapter: {
-          type: 'CramAdapter',
-          cramLocation: bigDataLocation,
-          craiLocation: isUri
-            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
-            : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),
-          sequenceAdapter,
-        },
-      }
-    case 'bigBarChart':
-    case 'bigBed':
-    case 'bigGenePred':
-    case 'bigChain':
-    case 'bigInteract':
-    case 'bigMaf':
-    case 'bigNarrowPeak':
-    case 'bigPsl':
-      return {
-        type: 'FeatureTrack',
-        name,
-        description: data.longLabel,
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-      }
-    case 'bigWig':
-      return {
-        type: 'QuantitativeTrack',
-        name,
-        description: data.longLabel,
-        category: categories,
-        adapter: {
-          type: 'BigWigAdapter',
-          bigWigLocation: bigDataLocation,
+      },
+    }
+  } else if (baseTrackType === 'cram') {
+    return {
+      type: 'AlignmentsTrack',
+      name,
+      description: data.longLabel,
+      category: categories,
+      adapter: {
+        type: 'CramAdapter',
+        cramLocation: bigDataLocation,
+        craiLocation: isUri
+          ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
+          : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),
+        sequenceAdapter,
+      },
+    }
+  } else if (baseTrackType === 'bigWig') {
+    return {
+      type: 'QuantitativeTrack',
+      name,
+      description: data.longLabel,
+      category: categories,
+      adapter: {
+        type: 'BigWigAdapter',
+        bigWigLocation: bigDataLocation,
+      },
+    }
+  } else if (baseTrackType.startsWith('big')) {
+    return {
+      type: 'FeatureTrack',
+      name,
+      description: data.longLabel,
+      category: categories,
+      adapter: {
+        type: 'BigBedAdapter',
+        bigBedLocation: bigDataLocation,
+      },
+    }
+  } else if (baseTrackType === 'vcfTabix') {
+    return {
+      type: 'VariantTrack',
+      name,
+      description: data.longLabel,
+      category: categories,
+      adapter: {
+        type: 'VcfTabixAdapter',
+        vcfGzLocation: bigDataLocation,
+        index: {
+          location: isUri
+            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
+            : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),
         },
-      }
-
-    case 'vcfTabix':
-      return {
-        type: 'VariantTrack',
-        name,
-        description: data.longLabel,
-        category: categories,
-        adapter: {
-          type: 'VcfTabixAdapter',
-          vcfGzLocation: bigDataLocation,
-          index: {
-            location: isUri
-              ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
-              : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),
-          },
-        },
-      }
-
-    case 'hic':
-      return {
-        type: 'HicTrack',
-        name,
-        description: data.longLabel,
-        category: categories,
-        adapter: {
-          type: 'HicAdapter',
-          hicLocation: bigDataLocation,
-        },
-      }
-
+      },
+    }
+  } else if (baseTrackType === 'hic') {
+    return {
+      type: 'HicTrack',
+      name,
+      description: data.longLabel,
+      category: categories,
+      adapter: {
+        type: 'HicAdapter',
+        hicLocation: bigDataLocation,
+      },
+    }
+  } else {
     // unsupported types
     //     case 'peptideMapping':
     //     case 'gvf':
@@ -196,8 +184,7 @@ function makeTrackConfig({
     //     case 'bedRnaElements':
     //     case 'broadPeak':
     //     case 'coloredExon':
-    default:
-      return generateUnknownTrackConf(name, baseTrackType, categories)
+    return generateUnknownTrackConf(name, baseTrackType, categories)
   }
 }
 

diff --git a/tsconfig.json b/tsconfig.json
@@ -22,6 +22,7 @@
   },
   "exclude": [
     "**/build/",
+    "**/docs/",
     "**/dist/",
     "**/esm/",
     "**/lib/",

diff --git a/website/docs/config/BigBedAdapter.md b/website/docs/config/BigBedAdapter.md
@@ -45,6 +45,6 @@ scoreColumn: {
 aggregateField: {
       type: 'string',
       description: 'An attribute to aggregate features with',
-      defaultValue: 'geneName',
+      defaultValue: 'geneName2',
     }
 ```
diff --git a/website/docs/config/VcfAdapter.md b/website/docs/config/VcfAdapter.md
@@ -25,6 +25,23 @@ reference the markdown files in our repo of the checked out git tag
 ```js
 vcfLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
+      defaultValue: {
+        uri: '/path/to/my.vcf',
+        locationType: 'UriLocation',
+      },
+    }
+```
+
+#### slot: samplesTsvLocation
+
+```js
+samplesTsvLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/samples.tsv',
+        description:
+          'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names',
+        locationType: 'UriLocation',
+      },
     }
 ```