download occurrence cube #41
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| name: download occurrence cube | |
| on: | |
| workflow_dispatch: # Manual | |
| push: | |
| branches: # Changes to GRIIS Checklist | |
| - "uat" | |
| paths: | |
| - "data/output/UAT_processing/data_input_checklist_indicators.tsv" | |
| schedule: | |
| - cron: '0 0 1 1-12 *' # 1st of the month 00:00 between january & december | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_TOKEN: ${{ secrets.AUTOMATISATION }} | |
| amiabot: ${{ secrets.AMIABOT }} | |
| jobs: | |
| setup-environment: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.AUTOMATISATION }} | |
| - name: Set R library path | |
| run: echo "R_LIBS_USER=$HOME/.local/share/R" >> $GITHUB_ENV | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| - name: Setup pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install linux libraries | |
| run: | | |
| sudo apt install libsodium-dev libcurl4-openssl-dev libgdal-dev libproj-dev libudunits2-dev libharfbuzz-dev libfribidi-dev | |
| - name: Cache R packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ hashFiles('**/install_packages_cube*.R') }} | |
| restore-keys: | | |
| ${{ runner.os }}-r- | |
| - name: Install R packages | |
| run: | | |
| source("src/get_cubes/install_packages_cube_base.R") | |
| source("src/get_cubes/install_packages_cube_extra.R") | |
| shell: Rscript {0} | |
| build-queries: | |
| needs: setup-environment | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.AUTOMATISATION }} | |
| - name: Set R library path | |
| run: echo "R_LIBS_USER=$HOME/.local/share/R" >> $GITHUB_ENV | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ hashFiles('**/install_packages_cube*.R') }} | |
| - name: create queries | |
| run: source("src/get_cubes/run_build_queries.R") | |
| shell: Rscript {0} | |
| - name: upload queries | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| path: ./data/interim/cube_queries/* | |
| download-cubes: | |
| needs: build-queries | |
| runs-on: ubuntu-latest | |
| env: | |
| gbif_user: ${{ secrets.GBIF_USER }} | |
| email: ${{ secrets.GBIF_EMAIL }} | |
| gbif_pwd: ${{ secrets.GBIF_PWD }} | |
| strategy: | |
| matrix: | |
| param_value: ["FAMILY", "GENUS", "SPECIES", "SUBSPECIES_FORM_VARIETY", "CLASS"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.AUTOMATISATION }} | |
| - name: Set R library path | |
| run: echo "R_LIBS_USER=$HOME/.local/share/R" >> $GITHUB_ENV | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ hashFiles('**/install_packages_cube*.R') }} | |
| - name: download queries | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: ./data/interim/cube_queries/* | |
| - name: download cubes | |
| run: | | |
| Rscript -e "rmarkdown::render('src/get_cubes/download_cubes.Rmd', params = list(rank = '${{ matrix.param_value }}'), knit_root_dir = '../../')" | |
| - name: Upload cube artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.param_value == 'CLASS' && 'be_classes_cube_raw' || format('be_alientaxa_cube_{0}', matrix.param_value) }}.csv | |
| path: ./cube_data/ | |
| compile-cubes: | |
| needs: download-cubes | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.AUTOMATISATION }} | |
| - name: Set R library path | |
| run: echo "R_LIBS_USER=$HOME/.local/share/R" >> $GITHUB_ENV | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ hashFiles('**/install_packages_cube*.R') }} | |
| - name: download rank cubes artifacts | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: be_alientaxa_cube_* | |
| merge-multiple: true | |
| path: ./cube_data/ | |
| - name: compile cubes | |
| run: source("src/get_cubes/run_compile_cubes.R") | |
| shell: Rscript {0} | |
| - name: upload occ cube | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: be_alientaxa_cube.csv | |
| path: ./cube_data/be_alientaxa_cube.csv | |
| compile-class-cube: | |
| needs: download-cubes | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.AUTOMATISATION }} | |
| - name: Set R library path | |
| run: echo "R_LIBS_USER=$HOME/.local/share/R" >> $GITHUB_ENV | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ hashFiles('**/install_packages_cube*.R') }} | |
| - name: download class cube artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: be_classes_cube_raw | |
| merge-multiple: true | |
| path: ./cube_data/ | |
| - name: compile class cube | |
| run: source("src/get_cubes/run_compile_class_cube.R") | |
| shell: Rscript {0} | |
| - name: upload class cube | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: be_classes_cube.csv | |
| path: ./cube_data/be_classes_cube.csv |