get_vespa_velutina_management #20
Workflow file for this run
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| 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 | |
| if [ $(echo "${{secrets.service}}" | wc -c) -lt 2 ]; then | |
| echo "The secret 'service' has not been set." | |
| echo "Please go to 'Settings > Secrets > Actions' to create it." | |
| exit 1 | |
| fi | |
| 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 |