feat: refactor db subset CLI, add subset by VCF and subset by TxId options #1208
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| components: rustfmt | |
| - name: Check format | |
| run: | |
| cargo fmt -- --check | |
| Linting: | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install -y librocksdb-dev libsnappy-dev libsqlite3-dev | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| components: clippy | |
| - name: Setup protoc | |
| uses: arduino/[email protected] | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: Swatinem/rust-cache@v2 | |
| with: | |
| cache-directories: | | |
| ~/.cargo/registry/src/**/librocksdb-sys-* | |
| - name: Lint with clippy | |
| uses: actions-rs/clippy-check@v1 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| Testing: | |
| needs: Formatting | |
| runs-on: ubuntu-24.04 | |
| services: | |
| # The tests need a postgres server; the data will be loaded later | |
| # after checkout. | |
| postgres: | |
| image: postgres | |
| env: | |
| POSTGRES_DB: uta | |
| POSTGRES_USER: uta_admin | |
| POSTGRES_PASSWORD: uta_admin | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install -y librocksdb-dev libsnappy-dev libsqlite3-dev | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| - name: Setup protoc | |
| uses: arduino/[email protected] | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: Swatinem/rust-cache@v2 | |
| with: | |
| cache-directories: | | |
| ~/.cargo/registry/src/**/librocksdb-sys-* | |
| - name: cargo build | |
| run: cargo build --verbose | |
| - name: cargo test | |
| run: cargo test --verbose | |
| - uses: Swatinem/rust-cache@v2 | |
| with: | |
| cache-directories: | | |
| ~/.cargo/registry/src/**/librocksdb-sys-* | |
| - name: Install cargo-llvm-cov | |
| uses: taiki-e/install-action@cargo-llvm-cov | |
| - name: Generate code coverage | |
| run: cargo llvm-cov --all-features --workspace --lcov --output-path lcov.info | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: lcov.info | |
| Schema: | |
| needs: Formatting | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install -y librocksdb-dev libsnappy-dev libsqlite3-dev | |
| - name: Install stable toolchain | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| - name: Setup protoc | |
| uses: arduino/[email protected] | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Write schema | |
| run: cargo run -- server schema --output-file /tmp/openapi.schema.yaml-gen | |
| - name: Copy repo schema and strip versions | |
| run: | | |
| cp openapi.schema.yaml /tmp/openapi.schema.yaml-repo | |
| perl -p -i -e 's/^ version: .*/ version: 0.0.0/' /tmp/*.yaml-* | |
| - name: Compare YAML in git to the one just generated | |
| run: diff /tmp/openapi.schema.yaml-repo /tmp/openapi.schema.yaml-gen |