Remove uniprot_entries.tsv.lz4 again... #13
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Build index binaries | |
| on: | |
| schedule: | |
| # Run on the first day of every month at midnight UTC | |
| - cron: '0 0 1 * *' | |
| push: | |
| branches: | |
| - feature/build_index_action | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Check out the most recent version of the repository with submodules | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| # Set up Rust toolchain | |
| - name: Set up Rust | |
| uses: dtolnay/rust-toolchain@stable | |
| # Compile Rust code | |
| - name: Compile Rust code | |
| run: cargo build --release | |
| # Create a directory "build" | |
| - name: Create build directory | |
| run: mkdir -p build/input | |
| # Download the file "suffix-array.zip" from the most recent release of "unipept-database" | |
| - name: Download suffix-array.zip | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| latest_release_url=$(curl -s https://api.github.com/repos/unipept/unipept-database/releases/latest | grep "browser_download_url.*suffix-array.zip" | cut -d '"' -f 4) | |
| release_date=$(curl -s https://api.github.com/repos/unipept/unipept-database/releases/latest | grep '"published_at":' | cut -d '"' -f 4 | cut -d'T' -f1) | |
| release_date_formatted=$(date -d $release_date "+%Y-%m-%d") | |
| SP_VERSION="SP_$release_date_formatted" | |
| echo "SP_VERSION=$SP_VERSION" >> $GITHUB_ENV | |
| curl -L -o build/suffix-array.zip $latest_release_url | |
| # Extract the contents of the output folder from the zip into a folder "build/input" | |
| - name: Extract zip contents | |
| run: | | |
| unzip build/suffix-array.zip 'output/*' -d build/temp | |
| mv build/temp/output/* build/input/ | |
| rm -r build/temp | |
| # Make a directory with the SP_VERSION and process files | |
| - name: Process files | |
| run: | | |
| mkdir -p build/$SP_VERSION | |
| lz4 -d build/input/uniprot_entries.tsv.lz4 | cut -f2,4,7,8 > build/$SP_VERSION/proteins.tsv | |
| lz4 -d build/input/taxons.tsv.lz4 > build/$SP_VERSION/taxons.tsv | |
| # Step 8: Run the sa-builder command | |
| - name: Run sa-builder | |
| run: | | |
| prefix="build/$SP_VERSION" | |
| ./target/release/sa-builder -d "$prefix/proteins.tsv" -o "$prefix/sa_sparse3_compressed.bin" -s 3 -a lib-div-suf-sort -c | |
| # Zip the contents of the build/$SP_VERSION directory | |
| - name: Zip build contents | |
| run: | | |
| cd "build/$SP_VERSION" && zip "index_$SP_VERSION.zip" "proteins.tsv" "taxons.tsv" "sa_sparse3_compressed.bin" | |
| # Create a GitHub release and upload the zip file | |
| - name: Upload or Update Release | |
| id: upload_or_update_release | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| files: build/${{ env.SP_VERSION }}/index_${{ env.SP_VERSION }}.zip | |
| tag_name: index-${{ env.SP_VERSION }} | |
| name: Index ${{ env.SP_VERSION }} | |
| commitish: ${{ github.sha }} | |
| draft: false | |
| prerelease: false | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |