get_vespa_velutina_management.yaml

on:
  workflow_dispatch:
  schedule: 
   - cron: '0 6 * * 1'

  
name: get_vespa_velutina_management

jobs:
  test:
    runs-on: ubuntu-latest
    name: test_secrets

    steps:
      - name: Checkout repository
        uses: actions/checkout@v2

      - name: Check if secrets exist
        run: |
          if [ $(echo "${{secrets.iasset_username}}" | wc -c) -lt 2 ]; then
            echo "The secret 'iasset_user' has not been set."
            echo "Please go to 'Settings > Secrets > Actions' to create it."
            exit 1
          fi
          if [ $(echo "${{secrets.iasset_password}}" | wc -c) -lt 2 ]; then
            echo "The secret 'iasset_password' has not been set."
            echo "Please go to 'Settings > Secrets > Actions' to create it."
            exit 1
          fi
          secret_length=${#{{ secrets.iasset_password }}}
          
          if [ $(echo "${{secrets.GBIF_USER}}" | wc -c) -lt 2 ]; then
            echo "The secret 'iasset_user' has not been set."
            echo "Please go to 'Settings > Secrets > Actions' to create it."
            exit 1
          fi
          if [ $(echo "${{secrets.GBIF_EMAIL}}" | wc -c) -lt 2 ]; then
            echo "The secret 'iasset_user' has not been set."
            echo "Please go to 'Settings > Secrets > Actions' to create it."
            exit 1
          fi
          if [ $(echo "${{secrets.GBIF_PWD}}" | wc -c) -lt 2 ]; then
            echo "The secret 'iasset_user' has not been set."
            echo "Please go to 'Settings > Secrets > Actions' to create it."
            exit 1
          fi

  get_data_from_gbif:
    needs: test
    runs-on: ${{ matrix.config.os }}

    name: get_data_from_gbif

    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 }}
      gbif_user: ${{ secrets.GBIF_USER }}
      email: ${{ secrets.GBIF_EMAIL }}
      gbif_pwd: ${{ secrets.GBIF_PWD }}

    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
        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

      - name: Install R packages
        run: |
          source("src/Vespa velutina management/install_packages_vespa_velutina_gbif.R")
        shell: Rscript {0}
        
      - name: Get data from gbif
        run: |
          source("src/Vespa velutina management/run_get_data_from_gbif.R")
        shell: Rscript {0}

      - name: Commit and push changes
        uses: devops-infra/action-commit-push@master
        with:
          github_token: ${{ secrets.AUTOMATISATION }}
          commit_prefix: "[AUTO]"
          commit_message: "get data from gbif"
          force: true
          target_branch: automatic-vespa-velutina-data
          
  get_data_from_iasset:
    needs: test
    runs-on: ${{ matrix.config.os }}

    name: get_data_from_iasset

    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 }}
      iasset_username: ${{ secrets.iasset_username }}
      iasset_password: ${{ secrets.iasset_password }}
      
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
        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
          R --no-save -e 'install.packages("devtools")'
          R --no-save -e 'devtools::install_github("inbo/iassetR@43-get-keyring-to-work-with-github-actions")'

      - name: Install R packages
        run: |
          source("src/Vespa velutina management/install_packages_vespa_velutina_iasset.R")
        shell: Rscript {0}
        
      - name: Get data from iAsset
        run: |
          source("src/Vespa velutina management/run_get_data_from_iAsset.R")
        shell: Rscript {0}

      - name: Commit and push changes
        uses: devops-infra/action-commit-push@master
        with:
          github_token: ${{ secrets.AUTOMATISATION }}
          commit_prefix: "[AUTO]"
          commit_message: "get data from iasset"
          force: true
          target_branch: automatic-vespa-velutina-data
      
  update_inputs:
    needs: [get_data_from_gbif, get_data_from_iasset]
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    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 }}
      
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
        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

      - name: Install R packages
        run: |
          source("src/Vespa velutina management/install_packages_vespa_velutina_general.R")
        shell: Rscript {0}
        
      - name: Get data from gbif
        run: |
          source("src/Vespa velutina management/run_update_inputs.R")
        shell: Rscript {0}

      - name: Commit and push changes
        uses: devops-infra/action-commit-push@master
        with:
          github_token: ${{ secrets.AUTOMATISATION }}
          commit_prefix: "[AUTO]"
          commit_message: "update inputs"
          force: true
          target_branch: automatic-vespa-velutina-data
      
      - name: Get branch name
        run: |
          git branch --show-current

      - name: Create pull request
        uses: devops-infra/action-pull-request@v0.4.2
        with:
          github_token: ${{ secrets.AUTOMATISATION }}
          target_branch: uat
          title: "[AUTO] get vespa velutina management data"
          template: .github/PR_vespa_velutina_management.md
          reviewer: SanderDevisscher, jrhilae, soriadelva
          label: automated workflow, 
          get_diff: false