get_occ_cube.yaml

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

jobs:
  build-queries:
    runs-on: ${{ matrix.config.os }}
    name: build queries

    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: ubuntu-latest, r: "release" }
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      GITHUB_TOKEN: ${{ secrets.AUTOMATISATION }}
      amiabot: ${{ secrets.AMIABOT }}
      

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          token: ${{ secrets.AUTOMATISATION }}

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}

      - name: Setup pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Install linux libraries
        run: |
          sudo apt install libsodium-dev
          sudo apt-get install libcurl4-openssl-dev
          sudo apt-get install libgdal-dev libproj-dev
          sudo apt install libudunits2-dev
          sudo apt install --yes libharfbuzz-dev libfribidi-dev

      - name: install packages
        run: |
          source("src/get_cubes/install_packages_cube_base.R")
          source("src/get_cubes/install_packages_cube_extra.R")
        shell: Rscript {0}

      - 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:
    runs-on: ${{ matrix.config.os }}
    needs: build-queries
    name: download - cube - ${{ matrix.param_value }}

    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: ubuntu-latest, r: "release" }
        param_value: ["FAMILY", "GENUS", "SPECIES", "SUBSPECIES_FORM_VARIETY", "CLASS"]
        
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      GITHUB_TOKEN: ${{ secrets.AUTOMATISATION }}
      amiabot: ${{ secrets.AMIABOT }}
      gbif_user: ${{ secrets.GBIF_USER }}
      email: ${{ secrets.GBIF_EMAIL }}
      gbif_pwd: ${{ secrets.GBIF_PWD }}
      
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          token: ${{ secrets.AUTOMATISATION }}

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}

      - name: Setup pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Install linux libraries
        run: |
          sudo apt install libsodium-dev
          sudo apt-get install libcurl4-openssl-dev
          sudo apt-get install libgdal-dev libproj-dev
          sudo apt install libudunits2-dev
          sudo apt install --yes libharfbuzz-dev libfribidi-dev
      
      - name: install packages
        run: |
          source("src/get_cubes/install_packages_cube_base.R")
          source("src/get_cubes/install_packages_cube_extra.R")
        shell: Rscript {0}
        
      - name: download queries
        uses: actions/download-artifact@v4
        with: 
          path: ./data/interim/cube_queries/
          merge-multiple: true #to make sure artifacts are downloaded into correct folder and not /artifact-name
          
      - 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: |
          ${{ matrix.param_value == 'CLASS' && 'be_classes_cube_raw' || 
          format('be_alientaxa_cube_{0}', matrix.param_value) }}.csv
          be_cube_metadata_${{ matrix.param_value }}.csv
         path: ./cube_data/
          
          
      - name: Debug info
        run: |
          echo "matrix.param_value: ${{ matrix.param_value }}"
          cat src/get_cubes/download_cubes.Rmd
      
  compile-cubes:
    runs-on: ${{ matrix.config.os }}
    needs: download-cubes
    name: compile cubes

    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: ubuntu-latest, r: "release" }
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      GITHUB_TOKEN: ${{ secrets.AUTOMATISATION }}
      amiabot: ${{ secrets.AMIABOT }}
      

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          token: ${{ secrets.AUTOMATISATION }}

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}

      - name: Setup pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Install linux libraries
        run: |
          sudo apt install libsodium-dev
          sudo apt-get install libcurl4-openssl-dev
          sudo apt-get install libgdal-dev libproj-dev
          sudo apt install libudunits2-dev
          sudo apt install --yes libharfbuzz-dev libfribidi-dev

      - name: install packages
        run: |
          source("src/get_cubes/install_packages_cube_base.R")
        shell: Rscript {0}
        
      - name: download rank cubes artifacts 
        uses: actions/download-artifact@v4 
        with: 
          pattern: be_alientaxa_cube_*
          merge-multiple: true
          path: ./cube_data/
          
      - name: List cube_data directory
        run: ls -R ./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:
    runs-on: ${{ matrix.config.os }}
    needs: download-cubes
    name: compile class cube
    
    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: ubuntu-latest, r: "release" }
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      GITHUB_TOKEN: ${{ secrets.AUTOMATISATION }}
      amiabot: ${{ secrets.AMIABOT }}
      

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          token: ${{ secrets.AUTOMATISATION }}

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}

      - name: Setup pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Install linux libraries
        run: |
          sudo apt install libsodium-dev
          sudo apt-get install libcurl4-openssl-dev
          sudo apt-get install libgdal-dev libproj-dev
          sudo apt install libudunits2-dev
          sudo apt install --yes libharfbuzz-dev libfribidi-dev

      - name: install packages
        run: |
          source("src/get_cubes/install_packages_cube_base.R")
        shell: Rscript {0}
        
      - name: download class cube artifact 
        uses: actions/download-artifact@v4 
        with: 
          pattern: be_classes_cube_raw.csv
          merge-multiple: true
          path: ./cube_data/
          
      - name: List cube_data directory
        run: ls -R ./cube_data/
        
      - name: compile class cube
        run: |
          source("src/get_cubes/run_compile_class_cube.R")
        shell: Rscript {0}
        
      - name: upload occ cube
        uses: actions/upload-artifact@v4
        with:
          name: be_classes_cube.csv
          path: ./cube_data/be_classes_cube.csv

 compile-cube-metadata:
    runs-on: ${{ matrix.config.os }}
    needs: download-cubes
    name: compile cube metadata
    
    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: ubuntu-latest, r: "release" }
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      GITHUB_TOKEN: ${{ secrets.AUTOMATISATION }}
      amiabot: ${{ secrets.AMIABOT }}
      

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          token: ${{ secrets.AUTOMATISATION }}

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}

      - name: Setup pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Install linux libraries
        run: |
          sudo apt install libsodium-dev
          sudo apt-get install libcurl4-openssl-dev
          sudo apt-get install libgdal-dev libproj-dev
          sudo apt install libudunits2-dev
          sudo apt install --yes libharfbuzz-dev libfribidi-dev

      - name: install packages
        run: |
          source("src/get_cubes/install_packages_cube_base.R")
        shell: Rscript {0}
        
      - name: download cube metadata artifact 
        uses: actions/download-artifact@v4 
        with: 
          pattern: be_cube_metadata_*
          merge-multiple: true
          path: ./cube_data/
          
      - name: List cube_data directory
        run: ls -R ./cube_data/
        
      - name: compile cube metadata
        run: |
          source("src/get_cubes/run_compile_metadata.R")
        shell: Rscript {0}
        
      - name: upload cube metadata
        uses: actions/upload-artifact@v4
        with:
          name: be_cube_metadata.csv
          path: ./cube_data/be_cube_metadata.csv