From 87a99d75d6a4c2c3b89e5f14e1c5a3d923178670 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 25 Aug 2026 11:03:57 +0200
Subject: [PATCH 01/11] try: ai attempt at updating github actions flow

---
 .../workflows/dsBaseClient_test_suite.yaml    | 1048 +++++++++++++++--
 1 file changed, 943 insertions(+), 105 deletions(-)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index b8a6f3ccf..573d73d1b 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -1,13 +1,35 @@
 ################################################################################
 # DataSHIELD GHA test suite - dsBaseClient
-# Adapted from `armadillo_azure-pipelines.yml` by Roberto Villegas-Diaz
+# Replaces azure-pipelines.yml / opal_azure-pipelines.yml / armadillo_azure-pipelines.yml.
 #
-# 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
+# Structure (all jobs below run in parallel except where "needs" says otherwise):
+#   r-checks        - devtools::document()/check() sync checks. No backend needed.
+#   opal-dsbase      (matrix x4 shards) - dsBase suite against Opal, one shard each.
+#   opal-dsdanger    - dsDanger suite against Opal (small, not sharded).
+#   opal-report      - needs the two Opal jobs above; merges + publishes report.
+#   armadillo-dsbase (matrix x4 shards) - dsBase suite against Armadillo.
+#   armadillo-dsdanger - dsDanger suite against Armadillo.
+#   armadillo-report - needs the two Armadillo jobs above; merges + publishes report.
 #
-# As of Sept. 2025 this takes ~ 95 mins to run.
+# Each dsbase/dsdanger job spins up its OWN backend instance (isolated - no
+# shared server state / concurrency risk between shards). This is what makes
+# splitting the ~260-file dsBase suite into shards safe: shard 4x lets that
+# phase run in roughly a quarter of the wall-clock instead of one long
+# sequential testthat::test_package() call.
+#
+# Opal runs via docker-compose (docker-compose_opal.yml).
+# Armadillo runs as a plain `java -jar` process (not docker-compose): Armadillo
+# self-manages its Rock container over the host Docker socket
+# (docker-management-enabled: true / docker-run-in-container: false), which skips
+# building/pulling the old custom armadillo_citest image. See
+# molgenis-service-armadillo's application.template.yml for that flag pairing.
+#
+# Every job starts its backend as the very first step so it boots in the
+# background while R dependencies install, instead of paying for both serially.
+#
+# As of Sept. 2025 the single-backend, dsBase-only, unsharded version of this
+# took ~ 95 mins; the full (Opal+Armadillo, dsBase+dsDanger) unsharded run is
+# well over an hour.
 ################################################################################
 name: dsBaseClient tests' suite
 
@@ -17,27 +39,94 @@ on:
     - cron: '0 0 * * 0'   # Weekly
     - cron: '0 1 * * *'   # Nightly
 
+permissions:
+  contents: read
+
+env:
+  _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: ${{ github.token || 'placeholder-token' }}
+  # These should all be constant, except the two TEST_FILTER_* values. These can
+  # be used to test subsets of test files in the testthat directory. Options are
+  # like: '*' <- run all tests, '*_smk_*' <- run all the smoke tests.
+  TEST_FILTER_DSBASE: '_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-'
+  TEST_FILTER_DSDANGER: '__dgr-|datachk_dgr-|smk_dgr-|arg_dgr-|disc_dgr-|smk_expt_dgr-|expt_dgr-|math_dgr-'
+
 jobs:
-  dsBaseClient_test_suite:
+
+  ################################################################################
+  # Doc-sync / R CMD check - no backend needed, so this runs once, not per
+  # backend or per shard.
+  ################################################################################
+  r-checks:
+    name: Package checks (doc sync, R CMD check)
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          http-user-agent: release
+          use-public-rspm: true
+
+      - name: Install system libraries
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev -y
+          sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: 'c("Imports")'
+          extra-packages: |
+            any::rcmdcheck
+            cran::devtools
+          needs: check
+
+      - name: Check manual updated
+        run: |
+          orig_sum=$(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
+        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
+        continue-on-error: true
+
+
+  ################################################################################
+  # Opal - dsBase suite, sharded 4 ways. Each shard is a fully isolated job
+  # with its own Opal instance.
+  ################################################################################
+  opal-dsbase:
+    name: Opal dsBase tests (shard ${{ matrix.shard }})
     runs-on: ubuntu-latest
-    timeout-minutes: 120
-    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.
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      # Shard count is hardcoded here and in "Compute shard filter" below (both
+      # must match) - there's no clean way to share a single value between a
+      # matrix definition and a step's env in plain workflow YAML.
+      matrix:
+        shard: [0, 1, 2, 3]
     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' }}
+      DS_DRIVER: OpalDriver
+      DSBASE_REF: v7.0-dev
 
     steps:
       - name: Checkout dsBaseClient
@@ -45,15 +134,148 @@ jobs:
         with:
           path: dsBaseClient
 
-      - name: Checkout testStatus
-        if: ${{ github.actor != 'nektos/act' }} # for local deployment only
+      - name: Start Opal docker-compose
+        run: docker compose -f docker-compose_opal.yml up -d --build
+        working-directory: dsBaseClient
+
+      - 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 system libraries
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev -y
+          sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: 'c("Imports")'
+          extra-packages: |
+            cran::devtools
+            cran::covr
+            cran::fields
+            cran::meta
+            cran::metafor
+            cran::ggplot2
+            cran::gridExtra
+            cran::data.table
+            cran::DSI
+            cran::DSOpal
+            cran::DSLite
+            cran::MolgenisAuth
+            cran::MolgenisArmadillo
+            cran::DSMolgenisArmadillo
+            cran::DescTools
+            cran::e1071
+          needs: check
+
+      - name: Install test datasets to Opal
+        run: |
+          sleep 60
+          R -q -f "obiba_opal-upload_testing_datasets.R"
+        working-directory: dsBaseClient/tests/testthat/data_files
+
+      - name: Install dsBase to Opal, set disclosure test options
+        run: |
+          R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+          R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '${{ env.DSBASE_REF }}'); opal.logout(opal)"
+
+          sleep 60
+
+          expected_version=$(curl -sf "https://raw.githubusercontent.com/datashield/dsBase/${{ env.DSBASE_REF }}/DESCRIPTION" | sed -n 's/^Version: //p' | tr -d '\r')
+          if [ -z "$expected_version" ]; then
+            echo "Could not determine expected dsBase version from GitHub"
+            exit 1
+          fi
+          echo "Expected dsBase version: $expected_version"
+
+          R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); desc <- dsadmin.package_description(opal, 'dsBase'); opal.logout(opal); installed_version <- desc[['Version']]; cat('Installed dsBase version:', installed_version, '\n'); if (is.null(installed_version) || installed_version != '$expected_version') stop('dsBase version mismatch: expected $expected_version, found ', installed_version)"
+          R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
+          R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
+        working-directory: dsBaseClient/tests/testthat/data_files
+
+      - name: Compute shard filter
+        run: |
+          all_files=$(cd tests/testthat && ls test-*.R | grep -E "${{ env.TEST_FILTER_DSBASE }}" | sort)
+          shard_files=$(echo "$all_files" | awk -v n=4 -v s=${{ matrix.shard }} 'NR % n == s')
+          echo "Shard ${{ matrix.shard }}/4 running $(echo "$shard_files" | grep -c .) files:"
+          echo "$shard_files"
+          shard_filter=$(echo "$shard_files" | sed -E 's/^test-//; s/\.R$//' | sed 's/\./\\./g' | paste -sd'|' -)
+          echo "SHARD_FILTER=$shard_filter" >> "$GITHUB_ENV"
+        working-directory: dsBaseClient
+
+      - name: Run dsBase tests with coverage & JUnit report
+        run: |
+          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_dsbase.txt");
+                    sink(output_file);
+                    sink(output_file, type = "message");
+                    junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results_dsbase.xml"));
+                    progress_rep <- testthat::ProgressReporter$new(max_failures = 999999);
+                    multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep));
+                    options("datashield.return_errors" = FALSE, "default_driver" = "${{ env.DS_DRIVER }}");
+                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.SHARD_FILTER }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
+                  )
+                )
+              ),
+              "coveragelist.csv"
+            )'
+          cat test_console_output_dsbase.txt
+        working-directory: dsBaseClient
+
+      - name: Upload shard results
+        uses: actions/upload-artifact@v4
+        with:
+          name: opal-dsbase-shard-${{ matrix.shard }}
+          path: |
+            dsBaseClient/test_results_dsbase.xml
+            dsBaseClient/test_console_output_dsbase.txt
+            dsBaseClient/coveragelist.csv
+
+
+  ################################################################################
+  # Opal - dsDanger suite. Small (~15 files), so it stays a single job rather
+  # than sharding further.
+  ################################################################################
+  opal-dsdanger:
+    name: Opal dsDanger tests
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    env:
+      DS_DRIVER: OpalDriver
+      DSBASE_REF: v7.0-dev
+      DSDANGER_REF: '6.3.4'
+
+    steps:
+      - name: Checkout dsBaseClient
         uses: actions/checkout@v4
         with:
-          repository: ${{ env.REPO_OWNER }}/testStatus
-          ref: master
-          path: testStatus
-          persist-credentials: false
-          token: ${{ env.GITHUB_TOKEN }}
+          path: dsBaseClient
+
+      - name: Start Opal docker-compose
+        run: docker compose -f docker-compose_opal.yml up -d --build
+        working-directory: dsBaseClient
 
       - name: Uninstall default MySQL
         run: |
@@ -73,82 +295,414 @@ jobs:
           http-user-agent: release
           use-public-rspm: true
 
-      - name: Install R and dependencies
+      - name: Install system libraries
         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'))"
+          sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev -y
+          sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
 
       - 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::covr
+            cran::fields
+            cran::meta
+            cran::metafor
+            cran::ggplot2
+            cran::gridExtra
+            cran::data.table
+            cran::DSI
+            cran::DSOpal
+            cran::DSLite
+            cran::MolgenisAuth
+            cran::MolgenisArmadillo
+            cran::DSMolgenisArmadillo
+            cran::DescTools
+            cran::e1071
+          needs: check
+
+      - name: Install dsDangerClient
+        run: R -q -e "devtools::install_github(repo='datashield/dsDangerClient', ref=Sys.getenv('BRANCH_NAME'))"
+
+      - name: Install test datasets to Opal
+        run: |
+          sleep 60
+          R -q -f "obiba_opal-upload_testing_datasets.R"
+        working-directory: dsBaseClient/tests/testthat/data_files
+
+      - name: Install dsBase to Opal, set disclosure test options
+        run: |
+          R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080/'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+          R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '${{ env.DSBASE_REF }}'); opal.logout(opal)"
+
+          sleep 60
+
+          expected_version=$(curl -sf "https://raw.githubusercontent.com/datashield/dsBase/${{ env.DSBASE_REF }}/DESCRIPTION" | sed -n 's/^Version: //p' | tr -d '\r')
+          if [ -z "$expected_version" ]; then
+            echo "Could not determine expected dsBase version from GitHub"
+            exit 1
+          fi
+          echo "Expected dsBase version: $expected_version"
+
+          R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); desc <- dsadmin.package_description(opal, 'dsBase'); opal.logout(opal); installed_version <- desc[['Version']]; cat('Installed dsBase version:', installed_version, '\n'); if (is.null(installed_version) || installed_version != '$expected_version') stop('dsBase version mismatch: expected $expected_version, found ', installed_version)"
+          R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)"
+          R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
+        working-directory: dsBaseClient/tests/testthat/data_files
+
+      - name: Install dsDanger package on Opal server
+        run: |
+          R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'http://localhost:8080'); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
+          R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '${{ env.DSDANGER_REF }}'); opal.logout(opal)"
+        working-directory: dsBaseClient
+
+      - name: Run dsDanger tests with JUnit report
+        run: |
+          R -q -e '
+            library(testthat);
+            output_file <- file("test_console_output_dsdanger.txt");
+            sink(output_file);
+            sink(output_file, type = "message");
+            junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml");
+            progress_rep <- ProgressReporter$new(max_failures = 999999);
+            multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
+            options("datashield.return_errors" = FALSE, "default_driver" = "${{ env.DS_DRIVER }}");
+            testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.TEST_FILTER_DSDANGER }}", reporter = multi_rep, stop_on_failure = FALSE)'
+          cat test_console_output_dsdanger.txt
+        working-directory: dsBaseClient
+
+      - name: Upload dsDanger results
+        uses: actions/upload-artifact@v4
+        with:
+          name: opal-dsdanger
+          path: |
+            dsBaseClient/test_results_dsdanger.xml
+            dsBaseClient/test_console_output_dsdanger.txt
+
+
+  ################################################################################
+  # Opal - merge all shard + dsDanger results and publish the report.
+  ################################################################################
+  opal-report:
+    name: Opal report
+    needs: [opal-dsbase, opal-dsdanger]
+    if: always()
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    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 }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          use-public-rspm: true
+
+      - name: Install xml-twig-tools
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -qq xml-twig-tools -y
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: 'NA'
+          extra-packages: |
             cran::quarto
             cran::knitr
             cran::kableExtra
             cran::rmarkdown
             cran::downlit
-          needs: check
+            cran::xml2
+            cran::purrr
+            cran::dplyr
+            cran::stringr
+            cran::tidyr
+            cran::readr
+            cran::magrittr
 
-      - name: Check manual updated
+      - name: Download shard/dsdanger results
+        uses: actions/download-artifact@v4
+        with:
+          pattern: 'opal-*'
+          path: dsBaseClient/artifacts
+
+      - name: Merge results
         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
+          mkdir -p logs
+          xml_grep --pretty_print indented --wrap "testsuites" --descr "" --cond "testsuite" artifacts/*/test_results_*.xml > logs/test_results.xml
+          cat artifacts/*/test_console_output_*.txt > logs/test_console_output.txt
+
+          first=1
+          for f in artifacts/opal-dsbase-shard-*/coveragelist.csv; do
+            if [ $first -eq 1 ]; then
+              cat "$f" > logs/coveragelist.csv
+              first=0
+            else
+              tail -n +2 "$f" >> logs/coveragelist.csv
+            fi
+          done
         working-directory: dsBaseClient
-        continue-on-error: true
 
-      - name: Devtools checks
+      - name: Check for JUnit errors
         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
+          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
+        working-directory: dsBaseClient/logs
+
+      - name: Parse results from testthat and covr
+        run: Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/
         working-directory: dsBaseClient
-        continue-on-error: true
 
-      - name: Start Armadillo docker-compose
-        run: docker compose -f docker-compose_armadillo.yml up -d --build
+      - 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/
+
+          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-opal
+          path: testStatus/new
+
+
+  ################################################################################
+  # Armadillo - dsBase suite, sharded 4 ways. Each shard downloads and runs its
+  # own Armadillo jar instance.
+  #
+  # Runs as a plain `java -jar` process instead of docker-compose: Armadillo
+  # self-manages its own Rock container over the host Docker socket
+  # (docker-management-enabled: true / docker-run-in-container: false), which
+  # avoids building/pulling the old custom armadillo_citest image and its
+  # dockerised Armadillo layer. The latest GitHub release jar is downloaded at
+  # run time. No process is restarted after installing dsBase - install then
+  # whitelist directly.
+  ################################################################################
+  armadillo-dsbase:
+    name: Armadillo dsBase tests (shard ${{ matrix.shard }})
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        shard: [0, 1, 2, 3]
+    env:
+      DS_DRIVER: ArmadilloDriver
+      DSBASE_TARBALL: dsBase_7.0.0-permissive.tar.gz
+
+    steps:
+      - name: Checkout dsBaseClient
+        uses: actions/checkout@v4
+        with:
+          path: dsBaseClient
+
+      - uses: actions/setup-java@v4
+        with:
+          distribution: temurin
+          java-version: '21'
+
+      - name: Download and start Armadillo (jar)
+        run: |
+          mkdir -p armadillo_home/config armadillo_home/storage armadillo_home/logs
+
+          cat > armadillo_home/config/application.yml <<EOF
+          armadillo:
+            docker-management-enabled: true
+            docker-run-in-container: false
+            profiles:
+              - name: default
+                image: datashield/rock_citest-permissive:latest
+                port: 8085
+                host: default
+                package-whitelist:
+                  - dsBase
+                  - dsTidyverse
+                  - resourcer
+                function-blacklist: [ ]
+                options:
+                  datashield:
+                    seed: 342325352
+          spring:
+            security:
+              user:
+                password: admin
+            servlet:
+              multipart:
+                max-file-size: 1000MB
+                max-request-size: 1000MB
+          storage:
+            root-dir: $(pwd)/armadillo_home/storage
+          audit.log.path: '$(pwd)/armadillo_home/logs/audit.log'
+          stdout.log.path: '$(pwd)/armadillo_home/logs/armadillo.log'
+          logging:
+            level:
+              root: "warn"
+              org.molgenis: "warn"
+          EOF
+
+          release_json=$(curl -sf https://api.github.com/repos/molgenis/molgenis-service-armadillo/releases/latest)
+          jar_url=$(echo "$release_json" | jq -r '.assets[] | select(.name | endswith(".jar")) | .browser_download_url')
+          echo "Installing Armadillo $(echo "$release_json" | jq -r '.tag_name')"
+          curl -fSL -o armadillo_home/armadillo.jar "$jar_url"
+
+          JAVA_TOOL_OPTIONS="-Xms1G -Xmx2G -XX:+UseG1GC" \
+            nohup java -jar armadillo_home/armadillo.jar \
+              --server.port=8080 \
+              --spring.config.additional-location=file:$(pwd)/armadillo_home/config/application.yml \
+              > armadillo_home/logs/stdout.log 2>&1 &
+          echo $! > armadillo_home/armadillo.pid
         working-directory: dsBaseClient
 
-      - name: Install test datasets
+      - name: Uninstall default MySQL
         run: |
-          sleep 60
-          R -q -f "molgenis_armadillo-upload_testing_datasets.R"
+          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 system libraries
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev -y
+          sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: 'c("Imports")'
+          extra-packages: |
+            cran::devtools
+            cran::covr
+            cran::fields
+            cran::meta
+            cran::metafor
+            cran::ggplot2
+            cran::gridExtra
+            cran::data.table
+            cran::DSI
+            cran::DSOpal
+            cran::DSLite
+            cran::MolgenisAuth
+            cran::MolgenisArmadillo
+            cran::DSMolgenisArmadillo
+            cran::DescTools
+            cran::e1071
+          needs: check
+
+      - name: Wait for Armadillo to be ready
+        run: |
+          for i in $(seq 1 60); do
+            if curl -fsS http://localhost:8080/actuator/health 2>/dev/null | grep -q '"status":"UP"'; then
+              echo "Armadillo is ready"
+              exit 0
+            fi
+            sleep 5
+          done
+          echo "Armadillo did not become ready in time"
+          cat armadillo_home/logs/stdout.log || true
+          exit 1
+        working-directory: dsBaseClient
+
+      - name: Install test datasets to Armadillo
+        run: 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
+          install_status=$(curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@${{ env.DSBASE_TARBALL }}" -o /dev/null -w '%{http_code}' -X POST http://localhost:8080/install-package)
+          if [ "$install_status" != "200" ]; then
+            echo "dsBase install request failed with HTTP status $install_status"
+            exit 1
+          fi
+
+          expected_version=$(tar -xOzf ${{ env.DSBASE_TARBALL }} dsBase/DESCRIPTION | sed -n 's/^Version: //p' | tr -d '\r')
+          if [ -z "$expected_version" ]; then
+            echo "Could not determine expected dsBase version from ${{ env.DSBASE_TARBALL }}"
+            exit 1
+          fi
+          echo "Expected dsBase version: $expected_version"
+
+          actual_version=""
+          for i in $(seq 1 30); do
+            packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+            actual_version=$(echo "$packages_json" | jq -r '.[] | select(.name == "dsBase") | .version' 2>/dev/null || true)
+            if [ "$actual_version" == "$expected_version" ]; then
+              break
+            fi
+            sleep 10
+          done
+          echo "Installed dsBase version: $actual_version"
+          if [ "$actual_version" != "$expected_version" ]; then
+            echo "dsBase version mismatch: expected $expected_version, found '$actual_version'"
+            exit 1
+          fi
+
           curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
         working-directory: dsBaseClient
 
-      - name: Run tests with coverage & JUnit report
+      - name: Compute shard filter
+        run: |
+          all_files=$(cd tests/testthat && ls test-*.R | grep -E "${{ env.TEST_FILTER_DSBASE }}" | sort)
+          shard_files=$(echo "$all_files" | awk -v n=4 -v s=${{ matrix.shard }} 'NR % n == s')
+          echo "Shard ${{ matrix.shard }}/4 running $(echo "$shard_files" | grep -c .) files:"
+          echo "$shard_files"
+          shard_filter=$(echo "$shard_files" | sed -E 's/^test-//; s/\.R$//' | sed 's/\./\\./g' | paste -sd'|' -)
+          echo "SHARD_FILTER=$shard_filter" >> "$GITHUB_ENV"
+        working-directory: dsBaseClient
+
+      - name: Run dsBase tests with coverage & JUnit report
         run: |
-          mkdir -p logs
           R -q -e "devtools::reload();"
           R -q -e '
             write.csv(
@@ -156,22 +710,329 @@ jobs:
                 covr::package_coverage(
                   type = c("none"),
                   code = c('"'"'
-                    output_file <- file("test_console_output.txt");
+                    output_file <- file("test_console_output_dsbase.txt");
                     sink(output_file);
                     sink(output_file, type = "message");
-                    junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results.xml"));
+                    junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results_dsbase.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)'"'"'
+                    options("datashield.return_errors" = FALSE, "default_driver" = "${{ env.DS_DRIVER }}");
+                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.SHARD_FILTER }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
                   )
                 )
               ),
               "coveragelist.csv"
             )'
+          cat test_console_output_dsbase.txt
+        working-directory: dsBaseClient
+
+      - name: Upload shard results
+        uses: actions/upload-artifact@v4
+        with:
+          name: armadillo-dsbase-shard-${{ matrix.shard }}
+          path: |
+            dsBaseClient/test_results_dsbase.xml
+            dsBaseClient/test_console_output_dsbase.txt
+            dsBaseClient/coveragelist.csv
+
+
+  ################################################################################
+  # Armadillo - dsDanger suite. Small, so it stays a single job.
+  ################################################################################
+  armadillo-dsdanger:
+    name: Armadillo dsDanger tests
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    env:
+      DS_DRIVER: ArmadilloDriver
+      DSBASE_TARBALL: dsBase_7.0.0-permissive.tar.gz
+      DSDANGER_TARBALL: dsDanger_6.3.4.tar.gz
+
+    steps:
+      - name: Checkout dsBaseClient
+        uses: actions/checkout@v4
+        with:
+          path: dsBaseClient
+
+      - uses: actions/setup-java@v4
+        with:
+          distribution: temurin
+          java-version: '21'
+
+      - name: Download and start Armadillo (jar)
+        run: |
+          mkdir -p armadillo_home/config armadillo_home/storage armadillo_home/logs
+
+          cat > armadillo_home/config/application.yml <<EOF
+          armadillo:
+            docker-management-enabled: true
+            docker-run-in-container: false
+            profiles:
+              - name: default
+                image: datashield/rock_citest-permissive:latest
+                port: 8085
+                host: default
+                package-whitelist:
+                  - dsBase
+                  - dsTidyverse
+                  - resourcer
+                function-blacklist: [ ]
+                options:
+                  datashield:
+                    seed: 342325352
+          spring:
+            security:
+              user:
+                password: admin
+            servlet:
+              multipart:
+                max-file-size: 1000MB
+                max-request-size: 1000MB
+          storage:
+            root-dir: $(pwd)/armadillo_home/storage
+          audit.log.path: '$(pwd)/armadillo_home/logs/audit.log'
+          stdout.log.path: '$(pwd)/armadillo_home/logs/armadillo.log'
+          logging:
+            level:
+              root: "warn"
+              org.molgenis: "warn"
+          EOF
+
+          release_json=$(curl -sf https://api.github.com/repos/molgenis/molgenis-service-armadillo/releases/latest)
+          jar_url=$(echo "$release_json" | jq -r '.assets[] | select(.name | endswith(".jar")) | .browser_download_url')
+          echo "Installing Armadillo $(echo "$release_json" | jq -r '.tag_name')"
+          curl -fSL -o armadillo_home/armadillo.jar "$jar_url"
+
+          JAVA_TOOL_OPTIONS="-Xms1G -Xmx2G -XX:+UseG1GC" \
+            nohup java -jar armadillo_home/armadillo.jar \
+              --server.port=8080 \
+              --spring.config.additional-location=file:$(pwd)/armadillo_home/config/application.yml \
+              > armadillo_home/logs/stdout.log 2>&1 &
+          echo $! > armadillo_home/armadillo.pid
+        working-directory: dsBaseClient
+
+      - 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 system libraries
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev -y
+          sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: 'c("Imports")'
+          extra-packages: |
+            cran::devtools
+            cran::git2r
+            cran::covr
+            cran::fields
+            cran::meta
+            cran::metafor
+            cran::ggplot2
+            cran::gridExtra
+            cran::data.table
+            cran::DSI
+            cran::DSOpal
+            cran::DSLite
+            cran::MolgenisAuth
+            cran::MolgenisArmadillo
+            cran::DSMolgenisArmadillo
+            cran::DescTools
+            cran::e1071
+          needs: check
+
+      - name: Install dsDangerClient
+        run: R -q -e "devtools::install_github(repo='datashield/dsDangerClient', ref=Sys.getenv('BRANCH_NAME'))"
 
-          mv coveragelist.csv logs/
-          mv test_* logs/
+      - name: Wait for Armadillo to be ready
+        run: |
+          for i in $(seq 1 60); do
+            if curl -fsS http://localhost:8080/actuator/health 2>/dev/null | grep -q '"status":"UP"'; then
+              echo "Armadillo is ready"
+              exit 0
+            fi
+            sleep 5
+          done
+          echo "Armadillo did not become ready in time"
+          cat armadillo_home/logs/stdout.log || true
+          exit 1
+        working-directory: dsBaseClient
+
+      - name: Install test datasets to Armadillo
+        run: R -q -f "molgenis_armadillo-upload_testing_datasets.R"
+        working-directory: dsBaseClient/tests/testthat/data_files
+
+      - name: Install dsBase to Armadillo
+        run: |
+          curl -u admin:admin -X GET http://localhost:8080/packages
+          install_status=$(curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@${{ env.DSBASE_TARBALL }}" -o /dev/null -w '%{http_code}' -X POST http://localhost:8080/install-package)
+          if [ "$install_status" != "200" ]; then
+            echo "dsBase install request failed with HTTP status $install_status"
+            exit 1
+          fi
+
+          expected_version=$(tar -xOzf ${{ env.DSBASE_TARBALL }} dsBase/DESCRIPTION | sed -n 's/^Version: //p' | tr -d '\r')
+          if [ -z "$expected_version" ]; then
+            echo "Could not determine expected dsBase version from ${{ env.DSBASE_TARBALL }}"
+            exit 1
+          fi
+          echo "Expected dsBase version: $expected_version"
+
+          actual_version=""
+          for i in $(seq 1 30); do
+            packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+            actual_version=$(echo "$packages_json" | jq -r '.[] | select(.name == "dsBase") | .version' 2>/dev/null || true)
+            if [ "$actual_version" == "$expected_version" ]; then
+              break
+            fi
+            sleep 10
+          done
+          echo "Installed dsBase version: $actual_version"
+          if [ "$actual_version" != "$expected_version" ]; then
+            echo "dsBase version mismatch: expected $expected_version, found '$actual_version'"
+            exit 1
+          fi
+
+          curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
+        working-directory: dsBaseClient
+
+      - name: Install dsDanger package on Armadillo server
+        run: |
+          curl -u admin:admin http://localhost:8080/whitelist
+          install_status=$(curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@${{ env.DSDANGER_TARBALL }}" -o /dev/null -w '%{http_code}' -X POST http://localhost:8080/install-package)
+          if [ "$install_status" != "200" ]; then
+            echo "dsDanger install request failed with HTTP status $install_status"
+            exit 1
+          fi
+
+          for i in $(seq 1 30); do
+            packages_json=$(curl -sf -u admin:admin -X GET http://localhost:8080/packages || true)
+            if echo "$packages_json" | jq -e '.[] | select(.name == "dsDanger")' >/dev/null 2>&1; then
+              break
+            fi
+            sleep 10
+          done
+
+          curl -u admin:admin -X POST http://localhost:8080/whitelist/dsDanger
+          curl -u admin:admin http://localhost:8080/whitelist
+        working-directory: dsBaseClient
+
+      - name: Run dsDanger tests with JUnit report
+        run: |
+          R -q -e '
+            library(testthat);
+            output_file <- file("test_console_output_dsdanger.txt");
+            sink(output_file);
+            sink(output_file, type = "message");
+            junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml");
+            progress_rep <- ProgressReporter$new(max_failures = 999999);
+            multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
+            options("datashield.return_errors" = FALSE, "default_driver" = "${{ env.DS_DRIVER }}");
+            testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.TEST_FILTER_DSDANGER }}", reporter = multi_rep, stop_on_failure = FALSE)'
+          cat test_console_output_dsdanger.txt
+        working-directory: dsBaseClient
+
+      - name: Upload dsDanger results
+        uses: actions/upload-artifact@v4
+        with:
+          name: armadillo-dsdanger
+          path: |
+            dsBaseClient/test_results_dsdanger.xml
+            dsBaseClient/test_console_output_dsdanger.txt
+
+
+  ################################################################################
+  # Armadillo - merge all shard + dsDanger results and publish the report.
+  ################################################################################
+  armadillo-report:
+    name: Armadillo report
+    needs: [armadillo-dsbase, armadillo-dsdanger]
+    if: always()
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    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 }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+          use-public-rspm: true
+
+      - name: Install xml-twig-tools
+        run: |
+          sudo apt-get update -qq
+          sudo apt-get install -qq xml-twig-tools -y
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: 'NA'
+          extra-packages: |
+            cran::quarto
+            cran::knitr
+            cran::kableExtra
+            cran::rmarkdown
+            cran::downlit
+            cran::xml2
+            cran::purrr
+            cran::dplyr
+            cran::stringr
+            cran::tidyr
+            cran::readr
+            cran::magrittr
+
+      - name: Download shard/dsdanger results
+        uses: actions/download-artifact@v4
+        with:
+          pattern: 'armadillo-*'
+          path: dsBaseClient/artifacts
+
+      - name: Merge results
+        run: |
+          mkdir -p logs
+          xml_grep --pretty_print indented --wrap "testsuites" --descr "" --cond "testsuite" artifacts/*/test_results_*.xml > logs/test_results.xml
+          cat artifacts/*/test_console_output_*.txt > logs/test_console_output.txt
+
+          first=1
+          for f in artifacts/armadillo-dsbase-shard-*/coveragelist.csv; do
+            if [ $first -eq 1 ]; then
+              cat "$f" > logs/coveragelist.csv
+              first=0
+            else
+              tail -n +2 "$f" >> logs/coveragelist.csv
+            fi
+          done
         working-directory: dsBaseClient
 
       - name: Check for JUnit errors
@@ -192,8 +1053,7 @@ jobs:
         working-directory: dsBaseClient/logs
 
       - name: Parse results from testthat and covr
-        run: |
-          Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/
+        run: Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/
         working-directory: dsBaseClient
 
       - name: Render report
@@ -204,14 +1064,12 @@ jobs:
           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 }}
@@ -220,25 +1078,5 @@ jobs:
       - name: Upload test logs
         uses: actions/upload-artifact@v4
         with:
-          name: dsbaseclient-logs
+          name: dsbaseclient-logs-armadillo
           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 .

From 3901de8769869f638cfb55c70307a2a45b11045e Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Wed, 26 Aug 2026 10:31:24 +0200
Subject: [PATCH 02/11] update test batch split

---
 .../workflows/dsBaseClient_test_suite.yaml    | 87 ++++++++++---------
 1 file changed, 48 insertions(+), 39 deletions(-)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index 573d73d1b..2e909ce32 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -4,18 +4,24 @@
 #
 # Structure (all jobs below run in parallel except where "needs" says otherwise):
 #   r-checks        - devtools::document()/check() sync checks. No backend needed.
-#   opal-dsbase      (matrix x4 shards) - dsBase suite against Opal, one shard each.
+#   opal-dsbase      (matrix: smk/arg/perf/misc) - dsBase suite against Opal,
+#                    one category per job.
 #   opal-dsdanger    - dsDanger suite against Opal (small, not sharded).
 #   opal-report      - needs the two Opal jobs above; merges + publishes report.
-#   armadillo-dsbase (matrix x4 shards) - dsBase suite against Armadillo.
+#   armadillo-dsbase (matrix: smk/arg/perf/misc) - dsBase suite against Armadillo.
 #   armadillo-dsdanger - dsDanger suite against Armadillo.
 #   armadillo-report - needs the two Armadillo jobs above; merges + publishes report.
 #
+# The dsBase suite (matching TEST_FILTER_DSBASE - same 292 files the Azure
+# pipelines run) is split by matrix into 4 fixed categories - smk (116 files),
+# arg (96), perf (51), and misc (the smaller categories: datachk, disc, expt,
+# smk_expt, math, and the "_-" catch-all - 29 combined) - each with its own
+# testthat filter substring, no file-list partitioning logic. Categories
+# aren't evenly sized, so job durations differ, but a category can be added,
+# removed, or temporarily skipped just by editing the matrix list.
+#
 # Each dsbase/dsdanger job spins up its OWN backend instance (isolated - no
-# shared server state / concurrency risk between shards). This is what makes
-# splitting the ~260-file dsBase suite into shards safe: shard 4x lets that
-# phase run in roughly a quarter of the wall-clock instead of one long
-# sequential testthat::test_package() call.
+# shared server state / concurrency risk between categories running at once).
 #
 # Opal runs via docker-compose (docker-compose_opal.yml).
 # Armadillo runs as a plain `java -jar` process (not docker-compose): Armadillo
@@ -114,16 +120,26 @@ jobs:
   # with its own Opal instance.
   ################################################################################
   opal-dsbase:
-    name: Opal dsBase tests (shard ${{ matrix.shard }})
+    name: Opal dsBase tests (${{ matrix.category }})
     runs-on: ubuntu-latest
     timeout-minutes: 60
     strategy:
       fail-fast: false
-      # Shard count is hardcoded here and in "Compute shard filter" below (both
-      # must match) - there's no clean way to share a single value between a
-      # matrix definition and a step's env in plain workflow YAML.
+      # One matrix entry per test-file category, each with its own testthat
+      # filter substring - not evenly sized (smk/arg are much bigger than
+      # perf/misc), so job durations differ. Traded for the ability to add,
+      # remove, or temporarily skip a whole category by editing this list
+      # alone, with no shell-side partitioning logic to keep in sync.
       matrix:
-        shard: [0, 1, 2, 3]
+        include:
+          - category: smk
+            filter: 'smk-'
+          - category: arg
+            filter: 'arg-'
+          - category: perf
+            filter: 'perf-'
+          - category: misc
+            filter: 'datachk-|disc-|expt-|smk_expt-|math-|_-'
     env:
       DS_DRIVER: OpalDriver
       DSBASE_REF: v7.0-dev
@@ -209,16 +225,6 @@ jobs:
           R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
         working-directory: dsBaseClient/tests/testthat/data_files
 
-      - name: Compute shard filter
-        run: |
-          all_files=$(cd tests/testthat && ls test-*.R | grep -E "${{ env.TEST_FILTER_DSBASE }}" | sort)
-          shard_files=$(echo "$all_files" | awk -v n=4 -v s=${{ matrix.shard }} 'NR % n == s')
-          echo "Shard ${{ matrix.shard }}/4 running $(echo "$shard_files" | grep -c .) files:"
-          echo "$shard_files"
-          shard_filter=$(echo "$shard_files" | sed -E 's/^test-//; s/\.R$//' | sed 's/\./\\./g' | paste -sd'|' -)
-          echo "SHARD_FILTER=$shard_filter" >> "$GITHUB_ENV"
-        working-directory: dsBaseClient
-
       - name: Run dsBase tests with coverage & JUnit report
         run: |
           R -q -e "devtools::reload();"
@@ -235,7 +241,7 @@ jobs:
                     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" = "${{ env.DS_DRIVER }}");
-                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.SHARD_FILTER }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
+                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ matrix.filter }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
                   )
                 )
               ),
@@ -247,7 +253,7 @@ jobs:
       - name: Upload shard results
         uses: actions/upload-artifact@v4
         with:
-          name: opal-dsbase-shard-${{ matrix.shard }}
+          name: opal-dsbase-${{ matrix.category }}
           path: |
             dsBaseClient/test_results_dsbase.xml
             dsBaseClient/test_console_output_dsbase.txt
@@ -449,7 +455,7 @@ jobs:
           cat artifacts/*/test_console_output_*.txt > logs/test_console_output.txt
 
           first=1
-          for f in artifacts/opal-dsbase-shard-*/coveragelist.csv; do
+          for f in artifacts/opal-dsbase-*/coveragelist.csv; do
             if [ $first -eq 1 ]; then
               cat "$f" > logs/coveragelist.csv
               first=0
@@ -519,13 +525,26 @@ jobs:
   # whitelist directly.
   ################################################################################
   armadillo-dsbase:
-    name: Armadillo dsBase tests (shard ${{ matrix.shard }})
+    name: Armadillo dsBase tests (${{ matrix.category }})
     runs-on: ubuntu-latest
     timeout-minutes: 60
     strategy:
       fail-fast: false
+      # One matrix entry per test-file category, each with its own testthat
+      # filter substring - not evenly sized (smk/arg are much bigger than
+      # perf/misc), so job durations differ. Traded for the ability to add,
+      # remove, or temporarily skip a whole category by editing this list
+      # alone, with no shell-side partitioning logic to keep in sync.
       matrix:
-        shard: [0, 1, 2, 3]
+        include:
+          - category: smk
+            filter: 'smk-'
+          - category: arg
+            filter: 'arg-'
+          - category: perf
+            filter: 'perf-'
+          - category: misc
+            filter: 'datachk-|disc-|expt-|smk_expt-|math-|_-'
     env:
       DS_DRIVER: ArmadilloDriver
       DSBASE_TARBALL: dsBase_7.0.0-permissive.tar.gz
@@ -691,16 +710,6 @@ jobs:
           curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
         working-directory: dsBaseClient
 
-      - name: Compute shard filter
-        run: |
-          all_files=$(cd tests/testthat && ls test-*.R | grep -E "${{ env.TEST_FILTER_DSBASE }}" | sort)
-          shard_files=$(echo "$all_files" | awk -v n=4 -v s=${{ matrix.shard }} 'NR % n == s')
-          echo "Shard ${{ matrix.shard }}/4 running $(echo "$shard_files" | grep -c .) files:"
-          echo "$shard_files"
-          shard_filter=$(echo "$shard_files" | sed -E 's/^test-//; s/\.R$//' | sed 's/\./\\./g' | paste -sd'|' -)
-          echo "SHARD_FILTER=$shard_filter" >> "$GITHUB_ENV"
-        working-directory: dsBaseClient
-
       - name: Run dsBase tests with coverage & JUnit report
         run: |
           R -q -e "devtools::reload();"
@@ -717,7 +726,7 @@ jobs:
                     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" = "${{ env.DS_DRIVER }}");
-                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ env.SHARD_FILTER }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
+                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ matrix.filter }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
                   )
                 )
               ),
@@ -729,7 +738,7 @@ jobs:
       - name: Upload shard results
         uses: actions/upload-artifact@v4
         with:
-          name: armadillo-dsbase-shard-${{ matrix.shard }}
+          name: armadillo-dsbase-${{ matrix.category }}
           path: |
             dsBaseClient/test_results_dsbase.xml
             dsBaseClient/test_console_output_dsbase.txt
@@ -1025,7 +1034,7 @@ jobs:
           cat artifacts/*/test_console_output_*.txt > logs/test_console_output.txt
 
           first=1
-          for f in artifacts/armadillo-dsbase-shard-*/coveragelist.csv; do
+          for f in artifacts/armadillo-dsbase-*/coveragelist.csv; do
             if [ $first -eq 1 ]; then
               cat "$f" > logs/coveragelist.csv
               first=0

From c102a50d21e0ae9cb2e467e760b186e70548b5f1 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Wed, 26 Aug 2026 10:36:04 +0200
Subject: [PATCH 03/11] enable workflow dispatch

---
 .github/workflows/dsBaseClient_test_suite.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index 2e909ce32..38be359e4 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -41,6 +41,7 @@ name: dsBaseClient tests' suite
 
 on:
   push:
+  workflow_dispatch:
   schedule:
     - cron: '0 0 * * 0'   # Weekly
     - cron: '0 1 * * *'   # Nightly

From de2d40464e50795bfd772970b9ed4e4903f887b7 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Wed, 26 Aug 2026 10:49:15 +0200
Subject: [PATCH 04/11] try: trigger github actions ci

---
 .github/workflows/dsBaseClient_test_suite.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index 38be359e4..169f50be3 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -1,4 +1,5 @@
 ################################################################################
+# trigger CI
 # DataSHIELD GHA test suite - dsBaseClient
 # Replaces azure-pipelines.yml / opal_azure-pipelines.yml / armadillo_azure-pipelines.yml.
 #

From cd6400579c4ecfdac2b4b97bda0a6c834a32de6e Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Wed, 26 Aug 2026 10:59:23 +0200
Subject: [PATCH 05/11] fix workflow error

---
 .github/workflows/dsBaseClient_test_suite.yaml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index 169f50be3..015e2577c 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -158,7 +158,6 @@ jobs:
 
       - 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
@@ -287,7 +286,6 @@ jobs:
 
       - 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
@@ -616,7 +614,6 @@ jobs:
 
       - 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
@@ -824,7 +821,6 @@ jobs:
 
       - 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

From 06ded578d6a52720e7703f35006969586ac2f203 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Wed, 26 Aug 2026 11:18:53 +0200
Subject: [PATCH 06/11] added opalr dependency

---
 .github/workflows/dsBaseClient_test_suite.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index 015e2577c..83afc697e 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -192,6 +192,7 @@ jobs:
             cran::gridExtra
             cran::data.table
             cran::DSI
+            cran::opalr
             cran::DSOpal
             cran::DSLite
             cran::MolgenisAuth
@@ -321,6 +322,7 @@ jobs:
             cran::gridExtra
             cran::data.table
             cran::DSI
+            cran::opalr
             cran::DSOpal
             cran::DSLite
             cran::MolgenisAuth
@@ -584,6 +586,7 @@ jobs:
           spring:
             security:
               user:
+                name: admin
                 password: admin
             servlet:
               multipart:
@@ -648,6 +651,7 @@ jobs:
             cran::gridExtra
             cran::data.table
             cran::DSI
+            cran::opalr
             cran::DSOpal
             cran::DSLite
             cran::MolgenisAuth
@@ -791,6 +795,7 @@ jobs:
           spring:
             security:
               user:
+                name: admin
                 password: admin
             servlet:
               multipart:
@@ -856,6 +861,7 @@ jobs:
             cran::gridExtra
             cran::data.table
             cran::DSI
+            cran::opalr
             cran::DSOpal
             cran::DSLite
             cran::MolgenisAuth

From e6c9b561a9c416ee720bb615c73dedd7e774e8df Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Thu, 27 Aug 2026 10:10:24 +0200
Subject: [PATCH 07/11] Add missing dependency

---
 .github/workflows/dsBaseClient_test_suite.yaml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index 83afc697e..45e603323 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -97,6 +97,7 @@ jobs:
           extra-packages: |
             any::rcmdcheck
             cran::devtools
+            cran::usethis
           needs: check
 
       - name: Check manual updated
@@ -184,6 +185,7 @@ jobs:
           dependencies: 'c("Imports")'
           extra-packages: |
             cran::devtools
+            cran::usethis
             cran::covr
             cran::fields
             cran::meta
@@ -313,6 +315,7 @@ jobs:
           dependencies: 'c("Imports")'
           extra-packages: |
             cran::devtools
+            cran::usethis
             cran::git2r
             cran::covr
             cran::fields
@@ -643,6 +646,7 @@ jobs:
           dependencies: 'c("Imports")'
           extra-packages: |
             cran::devtools
+            cran::usethis
             cran::covr
             cran::fields
             cran::meta
@@ -852,6 +856,7 @@ jobs:
           dependencies: 'c("Imports")'
           extra-packages: |
             cran::devtools
+            cran::usethis
             cran::git2r
             cran::covr
             cran::fields

From 150c6f5dd210e83019182ab47c9a29205db0204e Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Thu, 27 Aug 2026 11:22:22 +0200
Subject: [PATCH 08/11] docker pull fix

---
 .github/workflows/dsBaseClient_test_suite.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index 45e603323..cd9eee7f2 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -616,6 +616,7 @@ jobs:
               --spring.config.additional-location=file:$(pwd)/armadillo_home/config/application.yml \
               > armadillo_home/logs/stdout.log 2>&1 &
           echo $! > armadillo_home/armadillo.pid
+          docker pull datashield/rock_citest-permissive:latest
         working-directory: dsBaseClient
 
       - name: Uninstall default MySQL
@@ -826,6 +827,7 @@ jobs:
               --spring.config.additional-location=file:$(pwd)/armadillo_home/config/application.yml \
               > armadillo_home/logs/stdout.log 2>&1 &
           echo $! > armadillo_home/armadillo.pid
+          docker pull datashield/rock_citest-permissive:latest
         working-directory: dsBaseClient
 
       - name: Uninstall default MySQL

From bd81862a0664de4d10bc32e99754795db19fc293 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Thu, 27 Aug 2026 11:33:54 +0200
Subject: [PATCH 09/11] debugging install failure

---
 .github/workflows/dsBaseClient_test_suite.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index cd9eee7f2..7eef559c0 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -577,7 +577,6 @@ jobs:
               - name: default
                 image: datashield/rock_citest-permissive:latest
                 port: 8085
-                host: default
                 package-whitelist:
                   - dsBase
                   - dsTidyverse
@@ -788,7 +787,6 @@ jobs:
               - name: default
                 image: datashield/rock_citest-permissive:latest
                 port: 8085
-                host: default
                 package-whitelist:
                   - dsBase
                   - dsTidyverse

From c983a930e923bed04c548f5a1a1c3e31721ce2d0 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Thu, 27 Aug 2026 12:06:26 +0200
Subject: [PATCH 10/11] add logging to debug

---
 .github/workflows/dsBaseClient_test_suite.yaml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index 7eef559c0..391f52063 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -717,6 +717,11 @@ jobs:
           curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
         working-directory: dsBaseClient
 
+      - name: Dump Armadillo server log
+        if: failure()
+        run: tail -c 20000 armadillo_home/logs/stdout.log
+        working-directory: dsBaseClient
+
       - name: Run dsBase tests with coverage & JUnit report
         run: |
           R -q -e "devtools::reload();"
@@ -931,6 +936,11 @@ jobs:
           curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
         working-directory: dsBaseClient
 
+      - name: Dump Armadillo server log
+        if: failure()
+        run: tail -c 20000 armadillo_home/logs/stdout.log
+        working-directory: dsBaseClient
+
       - name: Install dsDanger package on Armadillo server
         run: |
           curl -u admin:admin http://localhost:8080/whitelist

From 4dea902b4f1a9cd898a4cfbcb05d61614f41c771 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Thu, 27 Aug 2026 12:22:32 +0200
Subject: [PATCH 11/11] add more logging to debug

---
 .github/workflows/dsBaseClient_test_suite.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/dsBaseClient_test_suite.yaml b/.github/workflows/dsBaseClient_test_suite.yaml
index 391f52063..3f8345ab8 100644
--- a/.github/workflows/dsBaseClient_test_suite.yaml
+++ b/.github/workflows/dsBaseClient_test_suite.yaml
@@ -719,7 +719,7 @@ jobs:
 
       - name: Dump Armadillo server log
         if: failure()
-        run: tail -c 20000 armadillo_home/logs/stdout.log
+        run: grep "Caused by:" armadillo_home/logs/stdout.log | sort -u
         working-directory: dsBaseClient
 
       - name: Run dsBase tests with coverage & JUnit report
@@ -938,7 +938,7 @@ jobs:
 
       - name: Dump Armadillo server log
         if: failure()
-        run: tail -c 20000 armadillo_home/logs/stdout.log
+        run: grep "Caused by:" armadillo_home/logs/stdout.log | sort -u
         working-directory: dsBaseClient
 
       - name: Install dsDanger package on Armadillo server