cube preprocessing #62
Workflow file for this run
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| name: cube preprocessing | |
| on: | |
| workflow_dispatch: | |
| workflow_run: | |
| workflows: ["download occurrence cube"] | |
| types: | |
| - completed | |
| jobs: | |
| fetch-data: | |
| runs-on: ${{ matrix.config.os }} | |
| if: ${{ github.event.workflow_run.conclusion == 'success' || github.event_name == 'workflow_dispatch' }} | |
| environment: ${{ github.ref == 'refs/heads/main' && 'PROD' || 'UAT' }} | |
| 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 }} | |
| USERNAME: ${{ secrets.USERNAME }} | |
| S3_BUCKET: ${{ secrets.S3_BUCKET }} | |
| 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 | |
| sudo apt-get install -y libfontconfig1-dev | |
| R --no-save -e 'install.packages("devtools")' | |
| R --no-save -e 'devtools::install_github("inbo/INBOtheme@v0.5.9", force = TRUE)' | |
| R --no-save -e 'devtools::install_github("inbo/alien-species-portal@uat", | |
| subdir = "alienSpecies", force = TRUE)' | |
| - name: install packages | |
| run: | | |
| source("src/install_packages_occ_indic.R") | |
| shell: Rscript {0} | |
| - name: Setup AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v2 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| aws-region: ${{ secrets.AWS_DEFAULT_REGION }} | |
| - name: Assume Role | |
| id: assume_role | |
| run: | | |
| ROLE_ARN="${{ secrets.AWS_ROLE_ARN }}" | |
| TEMP_ROLE=$(aws sts assume-role \ | |
| --role-arn $ROLE_ARN \ | |
| --role-session-name inbo-deployment) | |
| echo "::set-output name=AWS_ACCESS_KEY_ID::$(echo $TEMP_ROLE | jq -r .Credentials.AccessKeyId)" | |
| echo "::set-output name=AWS_SECRET_ACCESS_KEY::$(echo $TEMP_ROLE | jq -r .Credentials.SecretAccessKey)" | |
| echo "::set-output name=AWS_SESSION_TOKEN::$(echo $TEMP_ROLE | jq -r .Credentials.SessionToken)" | |
| - name: Get latest successful run ID | |
| id: get-latest-run | |
| run: | | |
| run_id=$(gh run list -w get_occ_cube.yaml --status success --json databaseId --jq '.[0].databaseId') | |
| echo "run_id=$run_id" >> $GITHUB_OUTPUT | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Download be_alientaxa_cube artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: be_alientaxa_cube.csv | |
| path: ./cube_data/ | |
| run-id: ${{ steps.get-latest-run.outputs.run_id }} | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| merge-multiple: true | |
| - name: Download be_classes_cube artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: be_classes_cube.csv | |
| path: ./cube_data/ | |
| run-id: ${{ steps.get-latest-run.outputs.run_id }} | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| merge-multiple: true | |
| - name: cube_preprocessing | |
| run: | | |
| source("src/run_cube_preprocessing.R") | |
| shell: Rscript {0} | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ steps.assume_role.outputs.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ steps.assume_role.outputs.AWS_SECRET_ACCESS_KEY }} | |
| AWS_SESSION_TOKEN: ${{ steps.assume_role.outputs.AWS_SESSION_TOKEN }} | |
| AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }} | |
| S3_BUCKET: ${{ secrets.S3_BUCKET }} | |
| - name: Commit and push changes | |
| uses: devops-infra/action-commit-push@master | |
| with: | |
| github_token: ${{ secrets.AUTOMATISATION }} | |
| commit_prefix: "[AUTO]" | |
| commit_message: "update cube_preprocessing" | |
| target_branch: automatic-update-occ_indic_preprocessing | |
| add_timestamp: true | |
| - 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] update cube_preprocessing" | |
| template: .github/PR_occ_indic_preprocessing.md | |
| reviewer: SanderDevisscher | |
| label: automated workflow | |
| get_diff: false |