merge upstream

.dockerignore

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

.env.development

@@ -1,6 +1,5 @@
-GEN3_COMMONS_NAME=gen3
-NEXT_PUBLIC_GEN3_API=https://localhost:3010
-NEXT_PUBLIC_GEN3_DOMAIN=https://localhost:3010
-
-# set these if you want to use different endpoints
-#NEXT_PUBLIC_GEN3_GUPPY_API=
+NEXT_PUBLIC_GEN3_COMMONS_NAME=gen3
+NEXT_PUBLIC_GEN3_API=http://localhost:3000
+# uncomment and set the follow to connect the development frontend to a Gen3 commons backend. Note that the
+# configuration in config needs to match the backend.
+NEXT_PUBLIC_GEN3_API_TARGET=https://gen3.datacommons.io

.env.production

@@ -1,3 +1,6 @@
-GEN3_COMMONS_NAME=gen3
-NEXT_PUBLIC_GEN3_API=https://localhost/
-NEXT_PUBLIC_GEN3_DOMAIN=https://localhost/
+NEXT_PUBLIC_GEN3_COMMONS_NAME=gen3
+# if you are using a config based deployment set these in your helm values.yaml file
+# Set this for DATADOG tracking
+# DATACOMMONS="commons_frontend_app"
+# DATADOG_APPLICATION_ID=""
+# DATADOG_CLIENT_TOKEN=""

.env.test

@@ -0,0 +1,2 @@
+NEXT_PUBLIC_GEN3_COMMONS_NAME=ci
+DATACOMMONS="ci_commons_frontend_app"

.github/dependabot.yaml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "npm"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    ignore:
+      - dependency-name: "*"
+    allow:
+      - dependency-name: "@gen3/frontend"

.github/workflows/ci.yaml

@@ -4,13 +4,14 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-node@v3
-      with:
-        node-version: 20
-    - name: Setup npm
-      run: npm install -g npm@10.2.4
-    - name: Install modules
-      run: npm ci
-    - name: Run ESLint
-      run: npm run lint
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v4.1.0
+        with:
+          node-version: 24.15.0
+      - name: Get Version
+        run: npm -v
+      - name: Install modules
+
+        run: npm ci
+      - name: Run ESLint
+        run: npm run lint

.github/workflows/ci_image_build_push.yaml

@@ -0,0 +1,36 @@
+name: Build Image and Push to Quay for CI
+
+on: push
+
+jobs:
+  compute_tag:
+    if: ${{ !github.event.repository.fork }}
+    name: Compute tag name
+    runs-on: ubuntu-latest
+    outputs:
+      OVERRIDE_TAG_NAME: ${{ steps.set_tag.outputs.OVERRIDE_TAG_NAME }}
+
+    steps:
+      - name: Compute OVERRIDE_TAG_NAME
+        id: set_tag
+        run: |
+          CLEAN_BRANCH=$(echo "$GITHUB_REF_NAME" | tr '/' '_')
+          OVERRIDE_TAG_NAME="${CLEAN_BRANCH}_test"
+
+          # Set output so the job can pass it to another workflow
+          echo "OVERRIDE_TAG_NAME=$OVERRIDE_TAG_NAME" >> "$GITHUB_OUTPUT"
+          echo "Computed OVERRIDE_TAG_NAME: $OVERRIDE_TAG_NAME"
+  ci:
+    if: ${{ !github.event.repository.fork }}
+    name: Build Image and Push to Quay for CI
+    needs: compute_tag
+    uses: uc-cdis/.github/.github/workflows/image_build_push_native.yaml@master
+    with:
+      USE_QUAY_ONLY: true
+      DOCKERFILE_LOCATION: "Dockerfile.test"
+      OVERRIDE_TAG_NAME: ${{ needs.compute_tag.outputs.OVERRIDE_TAG_NAME }}
+    secrets:
+      ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
+      ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
+      QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
+      QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }}

.github/workflows/image_build_push.yaml

@@ -3,18 +3,52 @@ name: Build Image and Push to Quay
 on: push
 
 jobs:
+  compute_tag:
+    name: Compute tag name
+    runs-on: ubuntu-latest
+    outputs:
+      OVERRIDE_TAG_NAME: ${{ steps.set_tag.outputs.OVERRIDE_TAG_NAME }}
+    steps:
+      - name: Compute OVERRIDE_TAG_NAME
+        id: set_tag
+        shell: bash
+        run: |
+          CLEAN_BRANCH=$(echo "$GITHUB_REF_NAME" | tr '/' '_')
+          echo "OVERRIDE_TAG_NAME=${CLEAN_BRANCH}" >> "$GITHUB_OUTPUT"
+
+  select_build:
+    name: Select build settings
+    runs-on: ubuntu-latest
+    outputs:
+      DOCKERFILE_LOCATION: ${{ steps.pick.outputs.DOCKERFILE_LOCATION }}
+    steps:
+      - name: Pick Dockerfile
+        id: pick
+        shell: bash
+        run: |
+          if [ "${{ github.event.repository.fork }}" = "true" ]; then
+            echo "DOCKERFILE_LOCATION=Dockerfile.production" >> "$GITHUB_OUTPUT"
+          else
+            echo "DOCKERFILE_LOCATION=Dockerfile.config" >> "$GITHUB_OUTPUT"
+          fi
+
   Security:
     name: Security Pipeline
     uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master
     with:
       python-poetry: 'false'
-    secrets: inherit
+    secrets: inherit # pragma: allowlist-secret
+
   ci:
     name: Build Image and Push to Quay
-    uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    needs:
+      - compute_tag
+      - select_build
+    uses: uc-cdis/.github/.github/workflows/image_build_push_native.yaml@master
     with:
-      OVERRIDE_REPO_NAME: "commons-frontend-app"
       USE_QUAY_ONLY: true
+      DOCKERFILE_LOCATION: ${{ needs.select_build.outputs.DOCKERFILE_LOCATION }}
+      OVERRIDE_TAG_NAME: ${{ needs.compute_tag.outputs.OVERRIDE_TAG_NAME }}
     secrets:
       ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
       ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}

.github/workflows/integration_tests.yaml

@@ -0,0 +1,21 @@
+name: Integration Tests
+
+on: pull_request
+
+jobs:
+  integration_tests:
+    if: ${{ !github.event.repository.fork }}
+    name: Integration tests
+    uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@master
+    with:
+      CI_ENV: gen3ff
+    secrets:
+      CI_TEST_ORCID_USERID: ${{ secrets.CI_TEST_ORCID_USERID }}
+      CI_TEST_ORCID_PASSWORD: ${{ secrets.CI_TEST_ORCID_PASSWORD }}
+      CI_TEST_RAS_EMAIL: ${{ secrets.CI_TEST_RAS_EMAIL }}
+      CI_TEST_RAS_PASSWORD: ${{ secrets.CI_TEST_RAS_PASSWORD }}
+      CI_TEST_RAS_2_EMAIL: ${{ secrets.CI_TEST_RAS_2_EMAIL }}
+      CI_TEST_RAS_2_PASSWORD: ${{ secrets.CI_TEST_RAS_2_PASSWORD }}
+      CI_SLACK_BOT_TOKEN: ${{ secrets.CI_SLACK_BOT_TOKEN }}
+      CI_SLACK_CHANNEL_ID: ${{ secrets.CI_SLACK_CHANNEL_ID }}
+      EKS_CLUSTER_NAME: ${{ secrets.EKS_CLUSTER_NAME }}

.github/workflows/sync_fef.yaml

@@ -0,0 +1,16 @@
+name: Sync from FEF Template Repo
+
+on:
+  # 1. Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+  # 2. Runs on a schedule (the 1st of the month and the 23rd to pick up any changes)
+  schedule:
+  - cron: '0 3 1,23 * *'
+
+jobs:
+  sync:
+    if: ${{ github.event.repository.fork }}
+    uses: uc-cdis/.github/.github/workflows/gen3_Sync_FeF.yaml@master
+    secrets:
+      GH_TOKEN: ${{ secrets.PLANXCYBORG_PAT }}

.github/workflows/update_dependencies.yaml

@@ -0,0 +1,28 @@
+name: Update package dependencies
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+    paths:
+      - 'package.json'
+      - 'package-lock.json'
+
+jobs:
+  update-package-dependencies:
+    runs-on: ubuntu-latest
+    if: contains(github.event.pull_request.title, 'bump @gen3/frontend')
+    steps:
+      - uses: actions/checkout@v6
+      - name: Set up Node
+        uses: actions/setup-node@v6
+        with:
+          node-version: '24.15.0'
+      - name: Install Dependencies
+        run: npm install
+      - name: Update @gen3/core and @gen3/toolsff
+        run: |
+          npm install @gen3/core@latest @gen3/toolsff@latest
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git commit -am "Update @gen3/core and @gen3/toolsff"
+          git push

.gitignore

@@ -18,6 +18,7 @@
 # misc
 .DS_Store
 *.pem
+.idea
 
 # debug
 npm-debug.log*

.npmignore

@@ -0,0 +1,3 @@
+.DS_Store
+node_modules
+.next/cache/*

.npmrc

@@ -0,0 +1 @@
+engine-strict=true

.nvmrc

@@ -0,0 +1 @@
+v24.15.0

.prettierignore

@@ -0,0 +1,4 @@
+node_modules
+.next
+public
+dist

.prettierrc

@@ -0,0 +1,6 @@
+{
+  "tabWidth": 2,
+  "useTabs": false,
+  "trailingComma": "all",
+  "singleQuote": true
+}

Dockerfile.config

@@ -0,0 +1,64 @@
+# docker build -t ff .
+# docker run -p 3000:3000 -it ff
+# Build stage
+FROM --platform=$BUILDPLATFORM node:24.15.0-trixie-slim AS builder
+
+ARG TARGETPLATFORM
+ARG BUILDPLATFORM
+WORKDIR /gen3
+
+# Copy dependency files first for better caching
+COPY package.json package-lock.json ./
+
+# Install ALL dependencies once (including dev deps for build)
+RUN npm config set fetch-retries 5 && \
+    npm config set fetch-retry-mintimeout 20000 && \
+    npm config set fetch-retry-maxtimeout 120000 && \
+    npm ci && \
+    npm cache clean --force
+
+# Copy necessary config files
+COPY next.config.js tsconfig.json tailwind.config.js postcss.config.js ./
+COPY .env.production ./
+
+# Copy source files
+COPY ./src ./src
+COPY ./public ./public
+COPY ./config ./config
+COPY ./start_with_config.sh ./start.sh
+
+# Build and prune
+RUN  npm run build:volume && \
+    npm prune --omit=dev;
+
+FROM node:24.15.0-trixie-slim AS runner
+
+WORKDIR /gen3
+
+RUN addgroup --system --gid 1001 nextjs && \
+    adduser --system --uid 1001 nextjs
+
+COPY --from=builder --chown=nextjs:nextjs /gen3/.next/standalone ./.next/standalone
+COPY --from=builder --chown=nextjs:nextjs /gen3/.next/static ./.next/standalone/.next/static
+COPY --from=builder --chown=nextjs:nextjs /gen3/start.sh ./start.sh
+COPY --from=builder --chown=nextjs:nextjs /gen3/config ./config
+COPY --from=builder --chown=nextjs:nextjs /gen3/public ./public
+
+#VOLUME /gen3/config
+#VOLUME /gen3/public
+
+RUN mkdir -p /gen3/.next/cache/images && \
+   chmod -R 777 /gen3/.next/cache && \
+   chown -R nextjs:nextjs /gen3/.next/cache
+
+RUN chmod +x start.sh && \
+    chown -R nextjs:nextjs start.sh
+
+RUN rm -rf .next/standalone/config
+
+RUN cd .next/standalone && \
+    ln -s ../../config ./config && \
+    ln -s ../../public ./public
+
+USER nextjs:nextjs
+CMD ["sh", "./start.sh"]