Static Database #101
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| name: Static Database | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| # * is a special character in YAML so you have to quote this string | |
| - cron: '0 0 1 * *' | |
| jobs: | |
| generate_static_database: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: dtolnay/rust-toolchain@stable | |
| - uses: Swatinem/rust-cache@v2 | |
| id: cache | |
| with: | |
| shared-key: ${{ env.CACHE_KEY }} | |
| - run: cd scripts/helper_scripts/unipept-database-rs && cargo fetch | |
| if: ${{ !steps.cache.outputs.cache-hit }} | |
| - run: ./scripts/build_binaries.sh | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_ENV | |
| - name: Install required utilities | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install git curl unzip gawk sqlite3 libsqlite3-dev pv nodejs wget uuid-runtime pigz lz4 parallel libxml2-utils | |
| - name: Download Taxdmp file | |
| shell: bash | |
| run: wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip | |
| - name: Generate tsv.gz files | |
| shell: bash | |
| run: ./scripts/build_database.sh static-database "swissprot,trembl" "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz,https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.xml.gz" "output" | |
| - name: Build SQLite database from generated files | |
| shell: bash | |
| run: | | |
| # Initialize the database | |
| sqlite3 output.db < workflows/static_database/structure.sql | |
| # Read all generated data into this database | |
| lz4cat output/ec_numbers.tsv.lz4 | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin ec_numbers' | |
| lz4cat output/go_terms.tsv.lz4 | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin go_terms' | |
| lz4cat output/interpro_entries.tsv.lz4 | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin interpro_entries' | |
| lz4cat output/taxons.tsv.lz4 | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin taxons' | |
| lz4cat output/lineages.tsv.lz4 | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin lineages' | |
| # Create virtual tables | |
| sqlite3 output.db < workflows/static_database/init_virtual_tables.sql | |
| # Compress the database before uploading it to a Github release | |
| zip unipept-static-db-${{ env.date }}.zip output.db | |
| - name: Upload or Update Release | |
| id: upload_or_update_release | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| files: | | |
| ./unipept-static-db-${{ env.date }}.zip | |
| ./taxdmp.zip | |
| tag_name: database-${{ env.date }} | |
| name: Static database ${{ env.date }} | |
| commitish: ${{ github.sha }} | |
| draft: false | |
| prerelease: false | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |