Add Dengue virus DENVx genotypes dataset #454
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| name: build-and-deploy | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - staging | |
| - release | |
| pull_request: | |
| repository_dispatch: | |
| types: build-and-deploy | |
| workflow_dispatch: | |
| workflow_call: | |
| concurrency: | |
| group: cli-${{ github.workflow }}-${{ github.ref_type }}-${{ github.event.pull_request.number || github.ref || github.run_id }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -euxo pipefail {0} | |
| env: | |
| VERBOSE: 1 | |
| jobs: | |
| build-and-deploy-datasets: | |
| # Run only if it's not a fork | |
| if: ${{ !((github.event_name == 'pull_request') && (github.event.pull_request.head.repo.fork || ((github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) != github.repository))) }} | |
| runs-on: ubuntu-20.04 | |
| environment: | |
| name: ${{ github.ref }} | |
| env: | |
| VERBOSE: 0 | |
| PYTHONUNBUFFERED: 1 | |
| GH_TOKEN: ${{ github.token }} | |
| steps: | |
| - name: config | |
| id: config | |
| run: | | |
| echo 'is_fork=${{ (github.event_name == 'pull_request') && (github.event.pull_request.head.repo.fork || ((github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) != github.repository)) }}' >> $GITHUB_OUTPUT | |
| echo 'should_deploy=${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/release' }}' >> $GITHUB_OUTPUT | |
| echo 'is_release=${{ github.ref == 'refs/heads/release' }}' >> $GITHUB_OUTPUT | |
| - name: "DEBUG" | |
| run: | | |
| set +x | |
| echo is_fork=${{ steps.config.outputs.is_fork }} | |
| echo should_deploy=${{ steps.config.outputs.should_deploy }} | |
| echo is_release=${{ steps.config.outputs.is_release }} | |
| echo '\n' | |
| echo 'github.ref =' ${{ github.ref }} | |
| echo 'github.event_name =' ${{ github.event_name }} | |
| echo 'github.repository =' ${{ github.repository }} | |
| echo '\n' | |
| echo 'github.event.pull_request.head.repo.fork =' ${{ github.event.pull_request.head.repo.fork }} | |
| echo 'github.event.pull_request.head.repo.full_name =' ${{ github.event.pull_request.head.repo.full_name }} | |
| echo '\n' | |
| echo 'github.event.pull_request.base.repo.fork =' ${{ github.event.pull_request.base.repo.fork }} | |
| echo 'github.event.pull_request.base.repo.full_name =' ${{ github.event.pull_request.base.repo.full_name }} | |
| echo '\n' | |
| echo 'github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name =' ${{ github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name }} | |
| echo '(github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) == github.repository =' ${{ (github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) == github.repository }} | |
| echo 'github.event_name == 'pull_request' && (github.event.pull_request.head.repo.fork || ((github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) == github.repository)) =' ${{ github.event_name == 'pull_request' && (github.event.pull_request.head.repo.fork || ((github.event.pull_request.head.repo.full_name || github.event.pull_request.base.repo.full_name) == github.repository)) }} | |
| - name: "Checkout code (fork)" | |
| if: ${{ steps.config.outputs.is_fork == 'true' }} | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Number of commits to fetch. 0 indicates all history for all branches and tags. | |
| fetch-tags: true # Whether to fetch tags, even if fetch-depth > 0. | |
| ref: ${{github.event.pull_request.head.ref}} | |
| repository: ${{github.event.pull_request.head.repo.full_name}} | |
| - name: "Checkout code" | |
| if: ${{ steps.config.outputs.is_fork != 'true' }} | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Number of commits to fetch. 0 indicates all history for all branches and tags. | |
| fetch-tags: true # Whether to fetch tags, even if fetch-depth > 0. | |
| ref: ${{ github.head_ref || github.ref }} | |
| - name: "Install system dependencies" | |
| run: | | |
| sudo apt-get install brotli pigz parallel python3 rename --yes -qq >/dev/null | |
| - name: "Install Python dependencies" | |
| run: | | |
| pip3 install -r requirements.txt | |
| - name: "Rebuild datasets (fork)" | |
| if: ${{ steps.config.outputs.is_fork == 'true' }} | |
| run: | | |
| ./scripts/rebuild --input-dir 'data/' --output-dir 'data_output/' --no-pull | |
| - name: "Rebuild, commit and push datasets (non-release branch)" | |
| if: ${{ steps.config.outputs.is_fork != 'true' && steps.config.outputs.is_release != 'true' }} | |
| run: | | |
| git config --global user.email "${{ secrets.BOT_GIT_USER_EMAIL }}" | |
| git config --global user.name "${{ secrets.BOT_GIT_USER_NAME }}" | |
| ./scripts/rebuild --input-dir 'data/' --output-dir 'data_output/' --push --repo="${GITHUB_REPOSITORY}" | |
| - name: "Rebuild, commit, push and make a release (release branch)" | |
| if: ${{ steps.config.outputs.is_fork != 'true' && steps.config.outputs.is_release == 'true' }} | |
| run: | | |
| git config --global user.email "${{ secrets.BOT_GIT_USER_EMAIL }}" | |
| git config --global user.name "${{ secrets.BOT_GIT_USER_NAME }}" | |
| ./scripts/rebuild --input-dir 'data/' --output-dir 'data_output/' --release --repo="${GITHUB_REPOSITORY}" | |
| - name: "Install awscli" | |
| if: ${{ steps.config.outputs.is_fork != 'true' && steps.config.outputs.should_deploy == 'true' }} | |
| run: | | |
| pushd /tmp >/dev/null | |
| curl -fsSL "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" | |
| unzip -oqq awscliv2.zip | |
| sudo ./aws/install --update | |
| popd >/dev/null | |
| aws --version | |
| - name: "Deploy dataset server" | |
| if: ${{ steps.config.outputs.is_fork != 'true' && steps.config.outputs.should_deploy == 'true' }} | |
| env: | |
| DATA_AWS_S3_BUCKET: ${{ secrets.DATA_AWS_S3_BUCKET }} | |
| DATA_AWS_CLOUDFRONT_DISTRIBUTION_ID: ${{ secrets.DATA_AWS_CLOUDFRONT_DISTRIBUTION_ID }} | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| AWS_DEFAULT_REGION: us-east-2 | |
| run: | | |
| ./scripts/upload 'data_output/' | |
| - name: "Upload build artifacts: dataset server" | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: server | |
| path: ./data_output/* | |
| - name: "Upload build artifacts: zip archives" | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: zips | |
| path: ./data_temp/* |