Static Database #86
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| name: 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@v2 | |
| - uses: actions/setup-java@v1 | |
| with: | |
| java-version: '11' | |
| java-package: jdk | |
| architecture: x64 | |
| - name: Get current date | |
| id: date | |
| run: echo "::set-output name=date::$(date +'%Y-%m-%d')" | |
| - name: Install required utilities | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install git maven curl unzip gawk sqlite3 libsqlite3-dev pv nodejs wget | |
| - name: Download Taxdmp file | |
| shell: bash | |
| run: wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip | |
| - name: Generate tsv.gz files | |
| shell: bash | |
| run: ./scripts/build_database.sh static-database "swissprot,trembl" "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz,https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.xml.gz" "output" | |
| - name: Build SQLite database from generated files | |
| shell: bash | |
| run: | | |
| # Initialize the database | |
| sqlite3 output.db < workflows/static_database/structure.sql | |
| # Read all generated data into this database | |
| zcat output/ec_numbers.tsv.gz | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin ec_numbers' | |
| zcat output/go_terms.tsv.gz | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin go_terms' | |
| zcat output/interpro_entries.tsv.gz | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin interpro_entries' | |
| zcat output/taxons.tsv.gz | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin taxons' | |
| zcat output/lineages.tsv.gz | sqlite3 -csv -separator ' ' output.db '.import /dev/stdin lineages' | |
| # Create virtual tables | |
| sqlite3 output.db < workflows/static_database/init_virtual_tables.sql | |
| # Compress the database before uploading it to a Github release | |
| zip output.zip output.db | |
| - name: Create new tag | |
| uses: rickstaa/action-create-tag@v1 | |
| id: "tag_create" | |
| with: | |
| tag: database-${{ steps.date.outputs.date }} | |
| message: "Static information database built on ${{ steps.date.outputs.date }}" | |
| - name: Create Release | |
| id: create_release | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tag_name: database-${{ steps.date.outputs.date }} | |
| release_name: Static database ${{ steps.date.outputs.date }} | |
| draft: false | |
| prerelease: false | |
| - name: Upload Static Database Release Asset | |
| id: upload-database-release-asset | |
| uses: actions/upload-release-asset@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ steps.create_release.outputs.upload_url }} | |
| asset_path: ./output.zip | |
| asset_name: unipept-static-db-${{ steps.date.outputs.date }}.zip | |
| asset_content_type: application/zip | |
| - name: Upload NCBI Taxdmp Release Asset | |
| id: upload-taxdmp-release-asset | |
| uses: actions/upload-release-asset@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ steps.create_release.outputs.upload_url }} | |
| asset_path: ./taxdmp.zip | |
| asset_name: ncbi-taxdmp.zip | |
| asset_content_type: application/zip |