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ocshawncmlsnsnyk-botShawn O'Connorcraigrbarnes
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Chore sync upstream 2026-03-11 (#88)
* 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) * update node version in ci * update to nextjs 15.5.7 (uc-cdis#153) * Add Authz Middleware (uc-cdis#156) * update to new auth model * update to 0.12.0 * Setup for data dog * Add missing icons and update tailwind config (uc-cdis#158) * add missing icons * update app with dataDog * update tailwind config * update tailwind config * refactor data dog * update to NextJS 15.5.9 (uc-cdis#162) * Add linkWithIconAndTooltip custom cell renderer (uc-cdis#166) * fix a bug when app page is not found react expecting null * Update middleware to use code generation (uc-cdis#167) * update to NextJS 15.5.9 * fix fetchArboristResources to use the correct endpoint * get working scanPaths and update middleware * set NODE_ENV for dev and prod builds * update to 0.12.5 * update to 0.12.5 * new package-lock.json * add package lock * new package-lock.json part 2 * update dependencies * update dependencies (uc-cdis#169) * update dependencies (uc-cdis#171) * update gen3 to 12.10 * update to node24 (uc-cdis#173) * Remove authz_default.json (uc-cdis#176) * remove support for authz_default.json and update tools to fail if @gen3/toolsff not built or fails * update to @gen3 0.12.12, remove authz record from workspace entry * dont load datadog if values are not set, add comment for adding values * Update copyright year and owner in LICENSE file (uc-cdis#181) * Change license to Apache Software License 2.0 (uc-cdis#182) Updated the license to Apache Software License 2.0 and modified copyright year. * Bump Node.js version to 24.13.0 and update Dockerfile and CI workflow accordingly. (uc-cdis#185) * GFF-281: pull config and mount on volume (uc-cdis#98) * update Dockerfile * update hostname * update hostname * update hostname * update hostname * update hostname * update labnding page * update landing page * update middleware config and Dockerfile * add Dockerfile.main and update workflow to specify Dockerfile location * bump dependencies to version 0.12.16 and update Dockerfile with volume configuration changes * add header metadata configuration file for Gen3 Data Commons * update start script, middleware config, and Dockerfile for standalone server setup and permissions adjustments * update start script and Dockerfile for standalone Next.js server, add config and public directories, and adjust permissions * update start script and Dockerfile for standalone Next.js server, add config and public directories, and adjust permissions * update workflow to use Dockerfile.config and add new icons to gen3.json config * update icons * update workflow to include override tag name and add deployment instructions to documentation * bump dependencies to version 0.12.17 * add debug log to print Datadog application ID environment variable * integrate Datadog initialization with public runtime configuration inputs * remove unnecessary debug logs and update middleware matcher configuration * Associate Tailwind theme names to mantine CSS variables and load theme dynamically. (uc-cdis#187) * Add initial configuration for Canine Data Commons Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> * Refactor Mantine theme handling to dynamically support CSS variables and theme merging * remove canine config * Remove CSS variables support and related environment configuration * Remove debugging console logs from Tailwind config * Update LICENSE to include full Apache License v2.0 text --------- Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> * update gen3 to 0.12.22 * update version number * Update discovery.json (uc-cdis#189) Update docs links to use new Gen3 docs sites * Add Test Config for CI (uc-cdis#186) * Add Test Config for CI * Add fix * revery ci * Fix * Set `NODE_ENV` to `test` in Dockerfile.test * Update image name for test * Add compute_tag job * Add integration tests * File issue * Reduce workflows * Revert the change * Merge into single workflow * Revert change * Update integration_tests.yaml * Switch to `start_with_config.sh` for Dockerfile.config, update shell to Bash in start.sh, standardize `npm prune` flags in Dockerfiles. --------- Co-authored-by: craigrbarnes <craig.barnes@intelligentlight.com> * Skip CI image build and integration tests for forked repository (uc-cdis#191) * Skip CI image build and integration tests for forked repository * Update integration_tests.yaml * Update ci_image_build_push.yaml * Add API rewrites for development environment and bump Gen3 dependencies to v0.12.24 (uc-cdis#192) * Add API rewrites for development environment and bump Gen3 dependencies to v0.12.24 * Remove unused `CustomRowRenderers` and associated registration logic * Add configuration for clinical data analysis and update Gen3 explorer settings - Introduced `clinicalDataAnalysis.json` and `analysisTools.json` for supporting clinical and cohort analysis. - Updated `explorer.json` with new fields, tabs, and chart configurations for subjects and files. - Adjusted development environment API settings. * Bump `lodash` and `@types/lodash` to v4.17.23 * Fix workflow fork check * Update package lock remove victory and validator (uc-cdis#196) * Update package lock remove victory and validator * add back victory --------- Co-authored-by: Shawn O'Connor <shawnoconnor@uchicago.edu> * Update to version 0.12.25 (uc-cdis#197) * Update to version 0.12.25 * Bump version to 0.12.26 and update dependencies to use local . Rename `GdcApp` to `Gen3App` in `[appName].tsx`. * Bump version to 0.12.26 and update dependencies to use local . Rename `GdcApp` to `Gen3App` in `[appName].tsx`. * Bump `@gen3/core` and `@gen3/frontend` to version 0.12.26 and update `package-lock.json`. * Update node to 24.14.0 and npm to 11.9.0 * Add dependabot for frontend packages * Update update_dependencies.yaml * update to Gen3 0.12.27 (uc-cdis#202) * add missing config files * Update integration_tests.yaml * possable build fix * possable build fix * possable build fix * test fix for non gen3 directory builds * fix spacing * fix build ? * Revert "fix build ?" This reverts commit b2e0c7f. * fix build ?2 --------- 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> Co-authored-by: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> Co-authored-by: krishna <krishnaa@uchicago.edu>
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‎.env.development‎

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NEXT_PUBLIC_GEN3_COMMONS_NAME=vpodcqa
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NEXT_PUBLIC_GEN3_API=https://qa-vpodc.planx-pla.net
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NEXT_PUBLIC_GEN3_DOMAIN=https://localhost:3010
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NEXT_PUBLIC_GEN3_API=http://localhost:3000
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NEXT_PUBLIC_DATACOMMONS="vpodc_data_commons"
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# uncomment and set the follow to connect the development frontend to a Gen3 commons backend. Note that the
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# configuration in config needs to match the backend.
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NEXT_PUBLIC_GEN3_API_TARGET=https://qa-vpodc.planx-pla.net

‎.env.production‎

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NEXT_PUBLIC_GEN3_COMMONS_NAME=vpodcprod
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NEXT_PUBLIC_DATACOMMONS="vpodc_data_commons"
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# if you are using a config based deployment set these in your helm values.yaml file
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# Name of the commons
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#NEXT_PUBLIC_DATACOMMONS="commons_frontend_app"
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# Set this for DATADOG tracking
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NEXT_PUBLIC_DATADOG_APPLICATION_ID="25e9ac14-9635-4a8f-a0c1-519f2768c458"
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NEXT_PUBLIC_DATADOG_CLIENT_TOKEN="pub05d4bcea8a70f1212d09ec166af53b62"

‎.env.test‎

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NEXT_PUBLIC_GEN3_COMMONS_NAME=ci
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NEXT_PUBLIC_DATACOMMONS="ci_commons_frontend_app"

‎.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: 24.12.0
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node-version: 24.14.0
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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: 24.12.0
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node-version: 24.14.0
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- name: Get Version
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run: npm -v
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- name: Install modules

‎.github/workflows/ci_image_build_push.yaml‎

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

‎.github/workflows/dependabot.yaml‎

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

‎.github/workflows/image_build_push.yaml‎

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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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DOCKERFILE_LOCATION: "Dockerfile.production"
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OVERRIDE_TAG_NAME: ${{ needs.compute_tag.outputs.OVERRIDE_TAG_NAME }}
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secrets:
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ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
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ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}

‎.github/workflows/integration_tests.yaml‎

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

‎.github/workflows/update_dependencies.yaml‎

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name: Update package dependencies
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on:
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pull_request:
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types: [opened, synchronize]
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paths:
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- 'package.json'
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- 'package-lock.json'
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jobs:
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update-package-dependencies:
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runs-on: ubuntu-latest
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if: github.event.pull_request.title contains 'bump @gen3/frontend'
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steps:
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- uses: actions/checkout@v6
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- name: Set up Node
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uses: actions/setup-node@v6
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with:
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node-version: '24.14.0'
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- name: Install Dependencies
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run: npm install
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- name: Update @gen3/core and @gen3/toolsff
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run: |
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npm install @gen3/core@latest @gen3/toolsff@latest
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git config user.name "github-actions[bot]"
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git config user.email "github-actions[bot]@users.noreply.github.com"
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git commit -am "Update @gen3/core and @gen3/toolsff"
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git push

‎.nvmrc‎

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v24.12.0
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v24.14.0

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