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 * * 6'   # Weekly (on Saturdays @ 0.00)

jobs:
  dsBaseClient_test_suite:
    runs-on: ubuntu-latest
    timeout-minutes: 180
    permissions:
      contents: read

    # These should all be constant, except TEST_FILTER. This can be used to test 
    # subsets of test files in the testthat directory. Options are like:
    # '*'               <- Run all tests.
    # 'asNumericDS*'    <- Run all asNumericDS tests, i.e. all the arg, etc. tests.
    # '*_smk_*'         <- Run all the smoke tests for all functions.
    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 }}
      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: Uninstall default MySQL
        run: |
          curl https://bazel.build/bazel-release.pub.gpg | sudo apt-key add -
          sudo service mysql stop || true
          sudo apt-get update
          sudo apt-get remove --purge mysql-client mysql-server mysql-common -y
          sudo apt-get autoremove -y
          sudo apt-get autoclean -y
          sudo rm -rf /var/lib/mysql/

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

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: release
          http-user-agent: release
          use-public-rspm: true

      - name: Install R and dependencies
        run: |
          sudo apt-get install --no-install-recommends software-properties-common dirmngr -y
          wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
          sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
          sudo apt-get update -qq
          sudo apt-get upgrade -y
          sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
          sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev xml-twig-tools -y
          sudo R -q -e "install.packages(c('devtools','covr','fields','meta','metafor','ggplot2','gridExtra','data.table','DSI','DSOpal','DSLite','MolgenisAuth','MolgenisArmadillo','DSMolgenisArmadillo','DescTools','e1071'), repos='https://cloud.r-project.org')"
          sudo R -q -e "devtools::install_github(repo='datashield/dsDangerClient', ref=Sys.getenv('BRANCH_NAME'))"

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          dependencies: 'c("Imports")'
          extra-packages: |
            any::rcmdcheck
            cran::devtools
            cran::git2r
            cran::RCurl
            cran::readr
            cran::magrittr
            cran::xml2
            cran::purrr
            cran::dplyr
            cran::stringr
            cran::tidyr
            cran::quarto
            cran::knitr
            cran::kableExtra
            cran::rmarkdown
            cran::downlit
          needs: check

      - 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_6.3.5-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
          # continue with workflow even when some tests fail
          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)" >> ${{ env.WORKFLOW_ID }}.txt
          Rscript --vanilla -e 'sessionInfo()' >> session_info_${{ 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 }}/
          mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/

          # Copy logs to new logs directory location
          cp -rv ../dsBaseClient/logs/* new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
          cp -rv ../dsBaseClient/logs/${{ env.WORKFLOW_ID }}.txt new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/

          R -e 'input_dir <- file.path("../new/logs", Sys.getenv("PROJECT_NAME"), Sys.getenv("BRANCH_NAME"), Sys.getenv("WORKFLOW_ID")); quarto::quarto_render("source/test_report.qmd", execute_params = list(input_dir = input_dir))'
          mv source/test_report.html new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/index.html
          cp -r new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/* new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest

        env:
          PROJECT_NAME: ${{ env.PROJECT_NAME }}
          BRANCH_NAME: ${{ env.BRANCH_NAME }}
          WORKFLOW_ID: ${{ env.WORKFLOW_ID }}

      - name: Upload test logs
        uses: actions/upload-artifact@v4
        with:
          name: dsbaseclient-logs
          path: testStatus/new

      - name: Dump environment info
        run: |
          echo -e "\n#############################"
          echo -e "ls /: ######################"
          ls -al .
          echo -e "\n#############################"
          echo -e "lscpu: ######################"
          lscpu
          echo -e "\n#############################"
          echo -e "memory: #####################"
          free -m
          echo -e "\n#############################"
          echo -e "env: ########################"
          env
          echo -e "\n#############################"
          echo -e "R sessionInfo(): ############"
          R -e 'sessionInfo()'
          sudo apt install tree -y
          tree .