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ocshawncmlsnsnyk-botShawn O'Connorcraigrbarnes
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Chore/sync upstream (#64)
* fix: package.json & package-lock.json to reduce vulnerabilities (#82) The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-JS-NEXT-9508709 Co-authored-by: snyk-bot <snyk-bot@snyk.io> * update next dependencies to 15.2.4 * Update README.md (#84) * update to @gen3/ff 0.10.85 (#85) * Update README.md (#86) add unrelated-histories information * Fix docker start (#88) * fix Docker not starting * fix Docker not starting * update env files (#89) * Release 0.10.89 (#91) * update to 0.10.89 * update to 0.10.89 * remove old config files/images * update ContentDatabase * update ContentDatabase paths (#93) * update apps config path (uc-cdis#94) * add theme colors into safelist (uc-cdis#95) * update to 0.10.91 (uc-cdis#96) * fix version to 0.10.91 (uc-cdis#97) * update to 0.10.92 (uc-cdis#104) * update to node 22.11, gen3FF 0.10.94 (uc-cdis#107) * update git node version * update gen3 to 0.11.11 * add favicon (uc-cdis#109) * add favicon * add favicon --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Add Datadog/remove faro (uc-cdis#105) * add Datadog/remove faro * remove Grafana * update gen3 to 0.11.18 * update gen3 to 0.11.19 and add footer links * update to Gen3 FEF 0.11.43 (uc-cdis#127) * add GradioApp support (uc-cdis#128) * add GradioApp support * fix default * update dependencies * update more dependencies * update more dependencies * add the hugging face apps (uc-cdis#129) * update tailwind paths for Gen3/frontend (uc-cdis#136) * fix default * update package-lock * fix build error * remove gradio * remove older tailwind path * update gen3 version and package lock * update gen3 to 0.11.47 * update gen3 to 0.11.48 remove unneeded cookies-next * Feat/footer (uc-cdis#139) * add the hugging face apps * Update README for clarity on Gen3 Data Commons * update development configuration * darken footer * partially revert footer changed (uc-cdis#140) * update docker image for faster builds (uc-cdis#141) * Changes to landingPage (uc-cdis#142) * Revert landingPage change (uc-cdis#143) * Update from old Gen3 Docs to new Gen3 Docs link (uc-cdis#146) * Update Gen3 docs link Update the default Documentation link from the old Gen3 docs site (https://gen3.org/resources/user/) to the new Gen3 docs site (https://docs.gen3.org/) * Update to new docs link Change the workspace docs reference from the old docs (https://gen3.org/resources/user/analyze-data/) to the new docs (https://docs.gen3.org/gen3-resources/user-guide/analyze-data/) * Update to v0.11.58 (uc-cdis#147) * add height to tailwind config * add package * add height to tailwind config * update to 0.11.55 * update deps * update to v0.11.58 * update to 0.11.59 (uc-cdis#148) * package lock update * revert unentended changes * revert unentended changes * update package lock * update ci file --------- Co-authored-by: cmlsn <100160785+cmlsn@users.noreply.github.com> Co-authored-by: snyk-bot <snyk-bot@snyk.io> Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> Co-authored-by: Craig Barnes <craig.barnes@intelligentlight.com> Co-authored-by: Krishna Agarwal <159047652+krishnaa05@users.noreply.github.com> Co-authored-by: smvgarcia <111767892+smvgarcia@users.noreply.github.com>
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‎.github/workflows/ci.yaml‎

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fetch-depth: 0
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- uses: actions/setup-node@v4.1.0
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with:
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node-version: 22.11.0
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node-version: 22.16.0
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- name: Install dependencies
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run: npm install
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- name: Install Playwright
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- uses: actions/checkout@v2
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- uses: actions/setup-node@v4.1.0
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with:
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node-version: 22.11.0
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node-version: 22.16.0
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- name: Get Version
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run: npm -v
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- name: Install modules

‎.github/workflows/image_build_push.yaml‎

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secrets: inherit # pragma: allowlist-secret
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ci:
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name: Build Image and Push to Quay
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uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
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uses: uc-cdis/.github/.github/workflows/image_build_push_native.yaml@master
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with:
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USE_QUAY_ONLY: true
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secrets:

‎.nvmrc‎

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v22.11.0
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v22.16.0

‎Dockerfile‎

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# docker build -t ff .
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# docker run -p 3000:3000 -it ff
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# Build stage
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FROM node:22-slim AS builder
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FROM --platform=$BUILDPLATFORM node:22-alpine AS builder
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ARG TARGETPLATFORM
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ARG BUILDPLATFORM
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WORKDIR /gen3
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COPY ./package.json ./package-lock.json ./next.config.js ./tsconfig.json ./.env.development ./tailwind.config.js ./postcss.config.js ./start.sh ./.env.production ./
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RUN npm ci
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# Copy dependency files first for better caching
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COPY package.json package-lock.json ./
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# Install ALL dependencies once (including dev deps for build)
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RUN npm config set fetch-retries 5 && \
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npm config set fetch-retry-mintimeout 20000 && \
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npm config set fetch-retry-maxtimeout 120000 && \
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npm ci && \
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npm cache clean --force
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# Copy necessary config files
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COPY next.config.js tsconfig.json tailwind.config.js postcss.config.js ./
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COPY .env.production ./
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# Copy source files
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COPY ./src ./src
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COPY ./public ./public
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COPY ./config ./config
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COPY ./start.sh ./
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COPY ./next-custom-image-loader.js ./
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RUN npm install @swc/core @napi-rs/magic-string && \
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npm run build
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# Build and prune
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RUN npm run build && \
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npm prune --production
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# Production stage
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FROM node:22-slim AS runner
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FROM node:22-alpine AS runner
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WORKDIR /gen3
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RUN addgroup --system --gid 1001 nextjs && \
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adduser --system --uid 1001 nextjs
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COPY --from=builder /gen3/package.json ./
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COPY --from=builder /gen3/node_modules ./node_modules
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COPY --from=builder /gen3/config ./config
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COPY --from=builder /gen3/.next ./.next
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COPY --from=builder /gen3/public ./public
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COPY --from=builder /gen3/start.sh ./start.sh
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RUN mkdir -p /gen3/.next/cache/images
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RUN chmod -R 777 /gen3/.next/cache
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RUN chown nextjs:nextjs /gen3/.next
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# Copy only production dependencies
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COPY --from=builder --chown=nextjs:nextjs /gen3/package.json ./
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COPY --from=builder --chown=nextjs:nextjs /gen3/node_modules ./node_modules
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COPY --from=builder --chown=nextjs:nextjs /gen3/config ./config
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COPY --from=builder --chown=nextjs:nextjs /gen3/.next ./.next
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COPY --from=builder --chown=nextjs:nextjs /gen3/public ./public
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COPY --from=builder --chown=nextjs:nextjs /gen3/start.sh ./start.sh
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RUN mkdir -p .next/cache/images && \
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chmod +x start.sh && \
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chown -R nextjs:nextjs .next/cache
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USER nextjs:nextjs
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ENV PORT=3000
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CMD bash ./start.sh
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ENV NODE_ENV=production \
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PORT=3000 \
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NEXT_TELEMETRY_DISABLED=1
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CMD ["sh", "./start.sh"]

‎README.md‎

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Get the changes from the parent fork:
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```bash
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git remote add upstream git@github.com:uc-cdis/commons-frontend-app.git
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git remote add upstream git@github.com:uc-cdis/commons-frontend-app.git
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git fetch upstream
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```
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Create a branch and merge changes from upstream:
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You will see merge conflicts. In general: **take the remote's version for everything except the config files**, as those are customized to the commons config. Resolve any remaining config issues and open a PR.
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Test the new common by running it locally or in a staging environment.
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‎config/vpodcqa/discovery.json‎

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"downloadManifestButtonText": "Download Manifest",
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"documentationLinks": {
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"gen3Client": "https://gen3.org/resources/user/gen3-client/",
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"gen3Workspaces": "https://gen3.org/resources/user/analyze-data/"
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"gen3Workspaces": "https://docs.gen3.org/gen3-resources/user-guide/analyze-data/"
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},
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"verifyExternalLogins": true
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},

‎config/vpodcqa/session.json‎

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"sessionConfig" : {
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"updateSessionTime": 5,
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"inactiveTimeLimit": 20,
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"logoutInactiveUsers": true
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"logoutInactiveUsers": false,
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"monitorWorkspace": true
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}
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}

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