Merge oncokb-curation feature branch into master

.dockerignore

@@ -0,0 +1 @@
+node_modules

.eslintrc.json

@@ -16,7 +16,7 @@
     "ecmaFeatures": {
       "jsx": true
     },
-    "project": "./tsconfig.json"
+    "project": ["./tsconfig.json", "./src/test/javascript/tsconfig.json"]
   },
   "settings": {
     "react": {
@@ -30,7 +30,6 @@
         "default": ["static-field", "instance-field", "constructor", "static-method", "instance-method"]
       }
     ],
-    "@typescript-eslint/no-parameter-properties": ["warn", { "allows": ["public", "private", "protected"] }],
     "@typescript-eslint/no-unused-vars": "off",
     "@typescript-eslint/explicit-member-accessibility": "off",
     "@typescript-eslint/explicit-function-return-type": "off",
@@ -43,6 +42,17 @@
     "@typescript-eslint/restrict-template-expressions": "off",
     "@typescript-eslint/restrict-plus-operands": "off",
     "@typescript-eslint/no-floating-promises": "off",
+    "@typescript-eslint/prefer-regexp-exec": "off",
+
+    // Added by Ben while upgrading node
+    "@typescript-eslint/no-unsafe-argument": "off",
+    "@typescript-eslint/no-misused-promises": [
+      "error",
+      {
+        "checksVoidReturn": false
+      }
+    ],
+
     "@typescript-eslint/ban-types": [
       "error",
       {

.github/release-drafter.yml

@@ -42,5 +42,5 @@ template: |
 
   ## 🕵️‍♀️ Full commit logs
 
-  - https://github.com/oncokb/oncokb-transcript/compare/$PREVIOUS_TAG...v$NEXT_PATCH_VERSION
+  - https://github.com/oncokb/oncokb-curation/compare/$PREVIOUS_TAG...v$NEXT_PATCH_VERSION
 

.github/workflows/after-branch-commit.yml

@@ -0,0 +1,122 @@
+name: After branch commit
+
+on:
+  push:
+    branches:
+      - master
+      - rc
+
+jobs:
+  check-version-level-and-update:
+    if: github.repository == 'oncokb/oncokb-transcript'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: 'Update Version Level'
+        run: |
+          git pull
+          VERSION_LEVEL=$(cat .version-level | tr "[:upper:]" "[:lower:]")
+
+          RELEASE_DRAFTER_MINOR='NEXT_MINOR_VERSION'
+          RELEASE_DRAFTER_PATCH='NEXT_PATCH_VERSION'
+
+          if [[ $VERSION_LEVEL == 'minor' ]]; then
+          sed -i "s/$RELEASE_DRAFTER_PATCH/$RELEASE_DRAFTER_MINOR/gi" .github/release-drafter.yml
+          fi
+
+          if [[ $VERSION_LEVEL == 'patch' ]]; then
+          sed -i "s/$RELEASE_DRAFTER_MINOR/$RELEASE_DRAFTER_PATCH/gi" .github/release-drafter.yml
+          fi
+
+          CHANGED=$(git diff --name-only HEAD --)
+          if [ -n "$CHANGED" ]
+          then
+            git config user.name oncokb-bot
+            git config user.email [email protected]
+            git add .
+            git commit -m "Update action files to align the version level to $VERSION_LEVEL"
+            git push
+          fi
+
+  update-draft-release:
+    needs: [check-version-level-and-update]
+    if: github.repository == 'oncokb/oncokb-transcript'
+    runs-on: ubuntu-latest
+    steps:
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - uses: release-drafter/release-drafter@v5
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  update-pom:
+    needs: [check-version-level-and-update]
+    if: github.repository == 'oncokb/oncokb-transcript'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Extract branch name
+        id: extract_branch
+        shell: bash
+        run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
+
+      - name: Find previous release
+        id: find_release
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const branch = '${{ steps.extract_branch.outputs.branch }}';
+            console.log('Looking for a latest release that is based on branch: ${{ steps.extract_branch.outputs.branch }}');
+
+            const releases = await github.rest.repos.listReleases({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+            });
+
+            const release = releases.data.find(r => (r.target_commitish === branch || r.target_commitish === `refs/heads/${branch}`) && !r.draft);
+
+            if (release) {
+              core.setOutput('tag', release.tag_name);
+            } else {
+              core.setFailed("No tag available, fail the action.");
+            }
+
+      - name: 'Get next semantic versions'
+        id: semvers
+        uses: "WyriHaximus/github-action-next-semvers@v1"
+        with:
+          version: ${{ steps.find_release.outputs.tag }}
+
+      - name: 'Setup Java'
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: 17
+
+      - name: 'Get Current Version Level'
+        id: version_level
+        run: |
+          VERSION_LEVEL=$(cat .version-level | tr "[:upper:]" "[:lower:]")
+          echo "::set-output name=VERSION_LEVEL::$VERSION_LEVEL"
+
+      - name: 'Update Pom'
+        if: ${{ success() }}
+        env:
+          NEW_VERSION: ${{ steps.version_level.outputs.VERSION_LEVEL == 'minor' && steps.semvers.outputs.minor || steps.semvers.outputs.patch}}
+        run: |
+          echo "${NEW_VERSION}"
+          git pull
+          mvn --batch-mode versions:set -DnewVersion=${NEW_VERSION} -DgenerateBackupPoms=false
+
+          CHANGED=$(git diff --name-only HEAD --)
+          if [ -n "$CHANGED" ]
+          then
+            git config user.name oncokb-bot
+            git config user.email [email protected]
+            git add .
+            git commit -m 'Update pom version'
+            git push
+          fi

.github/workflows/docker-release.yml

@@ -1,32 +1,63 @@
 name: Build/Push docker image
 on:
+  workflow_dispatch:
+      inputs:
+        tag-name:
+          description: "Tag name to use for the image must start with a v"
+          required: true
+          type: string
   release:
     types: [ published ]
 jobs:
   main:
     if: github.repository == 'oncokb/oncokb-transcript'
     name: Build and Push
     runs-on: ubuntu-latest
+    env:
+      VERSION: ${{ inputs.tag-name || github.ref }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
-          node-version: '12'
-      - uses: actions/setup-java@v2
+          node-version: '20.12.2'
+      - uses: actions/setup-java@v4
         with:
           distribution: 'adopt'
-          java-version: '11'
+          java-version: '17'
       - name: Install node.js packages
-        run: npm install
+        run: yarn install
       - name: Package application with Jib
         env:
           DOCKER_USERNAME: ${{secrets.DOCKER_USERNAME}}
           DOCKER_PASSWORD: ${{secrets.DOCKER_PASSWORD}}
-          TAG_NAME: ${{ github.event.release.tag_name }}
+          TAG_NAME: ${{ inputs.tag-name || github.event.release.tag_name }}
           REPOSITORY: ${{ github.repository }}
         run: |
           ./mvnw -ntp package -Pprod verify jib:build \
           -DskipTests \
-          -Djib.to.image="${REPOSITORY}:${TAG_NAME:1}" \
+          -Djib.to.image="mskcc/oncokb-curation:${TAG_NAME:1}" \
           -Djib.to.auth.username=$DOCKER_USERNAME \
           -Djib.to.auth.password=$DOCKER_PASSWORD
+
+      - name: Create a Sentry.io release in oncokb-curation-website
+        uses: getsentry/[email protected]
+        env:
+          SENTRY_AUTH_TOKEN: ${{ secrets.SENTRY_AUTH_TOKEN }}
+          SENTRY_ORG: memorial-sloan-kettering
+          SENTRY_PROJECT: oncokb-curation-website
+        with:
+          version: ${{ env.VERSION }}
+          environment: production
+          version_prefix: oncokb-curation-website-
+          sourceMapOptions: '{"include": ["target/classes/static/app"]}'
+
+      - name: Create a Sentry.io release in oncokb-curation-backend
+        uses: getsentry/[email protected]
+        env:
+          SENTRY_AUTH_TOKEN: ${{ secrets.SENTRY_AUTH_TOKEN }}
+          SENTRY_ORG: memorial-sloan-kettering
+          SENTRY_PROJECT: oncokb-curation-backend
+        with:
+          version: ${{ env.VERSION }}
+          environment: production
+          version_prefix: oncokb-curation-backend-

.github/workflows/github-ci.yml

@@ -5,15 +5,15 @@ jobs:
     name: OncoKB Build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
-          node-version: "12.16"
-      - uses: actions/setup-java@v2
+          node-version: "20.12.2"
+      - uses: actions/setup-java@v4
         with:
           distribution: 'adopt'
-          java-version: '11'
+          java-version: '17'
       - name: Install node.js packages
-        run: npm install
+        run: yarn install
       - name: Package application
         run: ./mvnw -ntp package -Pprod