Auto-generate evidence definitions from ClinVar expert panel and GWAS tier-1 data

.github/workflows/debug-clingen-sync.yml

@@ -0,0 +1,33 @@
+name: Debug ClinGen sync
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - claude/add-clingen-evidence-w5sm6
+    paths:
+      - scripts/syncClinGen.ts
+      - .github/workflows/debug-clingen-sync.yml
+
+jobs:
+  debug-clingen-sync:
+    name: Debug ClinGen sync
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Bun
+        uses: oven-sh/setup-bun@v2
+        with:
+          bun-version: latest
+
+      - name: Install dependencies
+        run: bun install --frozen-lockfile
+
+      - name: Run ClinGen sync
+        run: bun run scripts/syncClinGen.ts --force
+
+      - name: Print cached JSON (first 50 lines)
+        run: head -50 .evidence-cache/clingen/gene_validity.json || echo "File not found"

.github/workflows/update-evidence-pack.yml

@@ -4,6 +4,11 @@ on:
   schedule:
     - cron: "15 6 1 * *"
   workflow_dispatch:
+    inputs:
+      force_refresh:
+        description: 'Force re-download of all cached evidence sources'
+        type: boolean
+        default: false
 
 permissions:
   contents: write
@@ -25,6 +30,29 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v4
 
+      - name: Set cache month
+        run: echo "CACHE_MONTH=$(date +'%Y-%m')" >> "$GITHUB_ENV"
+
+      - name: Cache Bun packages
+        uses: actions/cache@v4
+        with:
+          path: ~/.bun/install/cache
+          key: bun-install-${{ runner.os }}-${{ hashFiles('bun.lock') }}
+          restore-keys: |
+            bun-install-${{ runner.os }}-
+
+      - name: Cache evidence sources
+        uses: actions/cache@v4
+        with:
+          path: |
+            .evidence-cache/clinvar
+            .evidence-cache/gwas
+            .evidence-cache/snpedia
+            .evidence-cache/pharmgkb
+          key: evidence-sources-${{ runner.os }}-${{ env.CACHE_MONTH }}
+          restore-keys: |
+            evidence-sources-${{ runner.os }}-
+
       - name: Set up Bun
         uses: oven-sh/setup-bun@v2
         with:
@@ -39,16 +67,28 @@ jobs:
         run: bun install --frozen-lockfile
 
       - name: Update evidence pack
-        run: bun run evidence:update:monthly
+        run: |
+          FORCE="${{ inputs.force_refresh && '--force' || '' }}"
+          bun run scripts/syncEvidenceSources.ts $FORCE
+          bun run scripts/syncCpic.ts $FORCE
+          bun run scripts/syncSnpedia.ts $FORCE
+          bun run scripts/syncDbsnp.ts $FORCE
+          bun run scripts/syncPharmgkb.ts $FORCE
+          bun run scripts/syncClinGen.ts $FORCE
+          bun run scripts/buildEvidencePack.ts
 
       - name: Check evidence pack
         run: bun run evidence:check
 
       - name: Run tests
         run: bun run test
+        env:
+          NODE_OPTIONS: --max-old-space-size=6144
 
       - name: Build
         run: bun run build
+        env:
+          NODE_OPTIONS: --max-old-space-size=6144
 
       - name: Open pull request
         uses: peter-evans/create-pull-request@v6

package.json

@@ -12,12 +12,16 @@
     "vercel:login": "vercel login",
     "vercel:link": "vercel link",
     "vercel:env": "vercel env pull .env.local",
-    "evidence:update": "bun run evidence:sources:sync && bun run evidence:snpedia:sync && bun run evidence:pack:build",
-    "evidence:update:monthly": "bun run evidence:sources:sync && bun run evidence:snpedia:sync && bun run evidence:dbsnp:sync && bun run evidence:pack:build",
+    "evidence:update": "bun run evidence:sources:sync && bun run evidence:cpic:sync && bun run evidence:snpedia:sync && bun run evidence:pharmgkb:sync && bun run evidence:clingen:sync && bun run evidence:pack:build",
+    "evidence:update:monthly": "bun run evidence:sources:sync && bun run evidence:cpic:sync && bun run evidence:snpedia:sync && bun run evidence:dbsnp:sync && bun run evidence:pharmgkb:sync && bun run evidence:clingen:sync && bun run evidence:pack:build",
     "evidence:check": "bun run scripts/buildEvidencePack.ts --check",
     "evidence:sources:sync": "bun run scripts/syncEvidenceSources.ts",
+    "evidence:definitions:build": "bun run scripts/buildDefinitions.ts",
     "evidence:dbsnp:sync": "bun run scripts/syncDbsnp.ts",
     "evidence:snpedia:sync": "bun run scripts/syncSnpedia.ts",
+    "evidence:cpic:sync": "bun run scripts/syncCpic.ts",
+    "evidence:pharmgkb:sync": "bun run scripts/syncPharmgkb.ts",
+    "evidence:clingen:sync": "bun run scripts/syncClinGen.ts",
     "evidence:pack:build": "bun run scripts/buildEvidencePack.ts",
     "evidence:seed:bulk": "bun run scripts/seedEvidenceBulk.ts"
   },