dsBaseClient_test_suite.yaml

################################################################################
# DataSHIELD GHA test suite - dsBaseClient
# Adapted from `armadillo_azure-pipelines.yml` by Roberto Villegas-Diaz
#
# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
# /dsBaseClient                <- Checked out version of datashield/dsBaseClient
# /dsBaseClient/logs           <- Where results of tests and logs are collated
# /testStatus                  <- Checked out version of datashield/testStatus
#
# As of Sept. 2025 this takes ~ 95 mins to run.
################################################################################
name: dsBaseClient tests' suite

on:
  push:
  schedule:
    - cron: '0 0 * * 0'   # Weekly
    - cron: '0 1 * * *'   # Nightly

jobs:
  dsBaseClient_test_suite:
    runs-on: ubuntu-latest
    timeout-minutes: 120
    permissions:
      contents: read

    # This logic automatically selects the image tag
    container:
      image: >-
        ghcr.io/${{ github.repository_owner }}/ds-base-env:${{ env.IMAGE_TAG }}
      options: --user root -v /var/run/docker.sock:/var/run/docker.sock

    env:
      TEST_FILTER: '_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-'
      _r_check_system_clock_: 0
      WORKFLOW_ID: ${{ github.run_id }}-${{ github.run_attempt }}
      PROJECT_NAME: dsBaseClient
      BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
      REPO_OWNER: ${{ github.repository_owner }}
      IMAGE_TAG: ${{ github.event.pull_request.base.ref || github.ref_name }}
      R_KEEP_PKG_SOURCE: yes
      GITHUB_TOKEN: ${{ github.token || 'placeholder-token' }}

    steps:
      - name: Checkout dsBaseClient
        uses: actions/checkout@v4
        with:
          path: dsBaseClient

      - name: Checkout testStatus
        if: ${{ github.actor != 'nektos/act' }} # for local deployment only
        uses: actions/checkout@v4
        with:
          repository: ${{ env.REPO_OWNER }}/testStatus
          ref: master
          path: testStatus
          persist-credentials: false
          token: ${{ env.GITHUB_TOKEN }}

      - name: Install PR version of dsBaseClient
        run: R CMD INSTALL dsBaseClient

      - name: Check manual updated
        run: |
          orig_sum=$(find man -type f | sort -u | xargs cat | md5sum)
          R -q -e "devtools::document()"
          new_sum=$(find man -type f | sort -u | xargs cat | md5sum)
          if [ "$orig_sum" != "$new_sum" ]; then
            echo "Your committed man/*.Rd files are out of sync with the R headers."
            exit 1
          fi
        working-directory: dsBaseClient
        continue-on-error: true

      - name: Devtools checks
        run: |
          R -q -e "devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout
          grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout
        working-directory: dsBaseClient
        continue-on-error: true

      - name: Start Armadillo docker-compose
        run: docker compose -f docker-compose_armadillo.yml up -d --build
        working-directory: dsBaseClient

      - name: Install test datasets
        run: |
          sleep 60
          R -q -f "molgenis_armadillo-upload_testing_datasets.R"
        working-directory: dsBaseClient/tests/testthat/data_files

      - name: Install dsBase to Armadillo
        run: |
          curl -u admin:admin -X GET http://localhost:8080/packages
          curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_7.0.0-permissive.tar.gz" -X POST http://localhost:8080/install-package
          sleep 60
          docker restart dsbaseclient-armadillo-1
          sleep 30
          curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
        working-directory: dsBaseClient

      - name: Run tests with coverage & JUnit report
        run: |
          mkdir -p logs
          R -q -e "devtools::reload();"
          R -q -e '
            write.csv(
              covr::coverage_to_list(
                covr::package_coverage(
                  type = c("none"),
                  code = c('"'"'
                    output_file <- file("test_console_output.txt");
                    sink(output_file);
                    sink(output_file, type = "message");
                    junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results.xml"));
                    progress_rep <- testthat::ProgressReporter$new(max_failures = 999999);
                    multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep));
                    options("datashield.return_errors" = FALSE, "default_driver" = "ArmadilloDriver");
                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.TEST_FILTER }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
                  )
                )
              ),
              "coveragelist.csv"
            )'
          mv coveragelist.csv logs/
          mv test_* logs/
        working-directory: dsBaseClient

      - name: Check for JUnit errors
        run: |
          issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | grep -c errors= || true)
          echo "Number of testsuites with issues: $issue_count"
          sed 's/failures="0" errors="0"//' test_results.xml | grep errors= > issues.log || true
          cat issues.log || true
          exit 0
        working-directory: dsBaseClient/logs

      - name: Write versions to file
        run: |
          echo "branch:${{ env.BRANCH_NAME }}" > ${{ env.WORKFLOW_ID }}.txt
          echo "os:$(lsb_release -ds)" >> ${{ env.WORKFLOW_ID }}.txt
          echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt
        working-directory: dsBaseClient/logs

      - name: Parse results from testthat and covr
        run: |
          Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/ logs/ https://github.com/datashield/${{ env.PROJECT_NAME }}/blob/${{ env.BRANCH_NAME }} '([^:]+)' '(?<=::)[^:]+(?=::)'
        working-directory: dsBaseClient
        env:
          PROJECT_NAME: ${{ env.PROJECT_NAME }}
          BRANCH_NAME: ${{ env.BRANCH_NAME }}

      - name: Render report
        run: |
          cd testStatus
          mkdir -p new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
          mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/