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| ################################################################################ | |
| # trigger CI | |
| # DataSHIELD GHA test suite - dsBaseClient | |
| # Replaces azure-pipelines.yml / opal_azure-pipelines.yml / armadillo_azure-pipelines.yml. | |
| # | |
| # 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: 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: 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 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 | |
| # 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 | |
| on: | |
| push: | |
| workflow_dispatch: | |
| schedule: | |
| - 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: ${{ github.token || 'placeholder-token' }} | |
| # These should all be constant, except the two TEST_FILTER_* values. These can | |
| # be used to test subsets of test files in the testthat directory. Options are | |
| # like: '*' <- run all tests, '*_smk_*' <- run all the smoke tests. | |
| TEST_FILTER_DSBASE: '_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-' | |
| TEST_FILTER_DSDANGER: '__dgr-|datachk_dgr-|smk_dgr-|arg_dgr-|disc_dgr-|smk_expt_dgr-|expt_dgr-|math_dgr-' | |
| jobs: | |
| ################################################################################ | |
| # Doc-sync / R CMD check - no backend needed, so this runs once, not per | |
| # backend or per shard. | |
| ################################################################################ | |
| r-checks: | |
| name: Package checks (doc sync, R CMD check) | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 30 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: release | |
| http-user-agent: release | |
| use-public-rspm: true | |
| - name: Install system libraries | |
| run: | | |
| sudo apt-get update -qq | |
| sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev -y | |
| sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: 'c("Depends", "Imports", "LinkingTo")' | |
| extra-packages: | | |
| any::rcmdcheck | |
| cran::devtools | |
| cran::usethis | |
| github::datashield/dsDangerClient | |
| needs: check | |
| - name: Check manual updated | |
| run: | | |
| orig_sum=$(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" != "$new_sum" ]; then | |
| echo "Your committed man/*.Rd files are out of sync with the R headers." | |
| exit 1 | |
| fi | |
| continue-on-error: true | |
| - name: Devtools checks | |
| run: | | |
| R -q -e "devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout | |
| grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout | |
| continue-on-error: true | |
| ################################################################################ | |
| # Opal - dsBase suite, sharded 4 ways. Each shard is a fully isolated job | |
| # with its own Opal instance. | |
| ################################################################################ | |
| opal-dsbase: | |
| name: Opal dsBase tests (${{ 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. smk and perf are split further by the first letter | |
| # of the function name (after any "ds." prefix) rather than an | |
| # enumerated file list, so newly added test files fall into a bucket | |
| # automatically without editing this matrix. perf (50 fixed 30s-loop | |
| # benchmarks) and smk (116 files) dominated wall-clock before this | |
| # split - see armadillo-dsbase timings in job history. | |
| matrix: | |
| include: | |
| - category: smk-1 | |
| filter: 'smk-ds.[a-lA-L]|smk-(checkClass|isDefined)' | |
| - category: smk-2 | |
| filter: 'smk-ds.[m-vM-V]' | |
| - category: arg | |
| filter: 'arg-' | |
| - category: perf-1 | |
| filter: 'perf-ds.[a-cA-C]' | |
| - category: perf-2 | |
| filter: 'perf-ds.[d-mD-M]' | |
| - category: perf-3 | |
| filter: 'perf-ds.[n-vN-V]|perf-(conndisconn|void)' | |
| - category: misc | |
| filter: 'datachk-|disc-|expt-|smk_expt-|math-|_-' | |
| env: | |
| DS_DRIVER: OpalDriver | |
| DSBASE_REF: v7.0-dev | |
| steps: | |
| - name: Checkout dsBaseClient | |
| uses: actions/checkout@v4 | |
| with: | |
| 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: | | |
| 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("Depends", "Imports", "LinkingTo")' | |
| extra-packages: | | |
| cran::devtools | |
| cran::usethis | |
| cran::covr | |
| cran::fields | |
| cran::meta | |
| cran::metafor | |
| cran::ggplot2 | |
| cran::gridExtra | |
| cran::data.table | |
| cran::DSI | |
| cran::opalr | |
| cran::DSOpal | |
| cran::DSLite | |
| cran::MolgenisAuth | |
| cran::MolgenisArmadillo | |
| cran::DSMolgenisArmadillo | |
| cran::DescTools | |
| cran::e1071 | |
| github::datashield/dsDangerClient | |
| 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 $expected_version, found ', installed_version)" | |
| R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); opal.logout(opal)" | |
| R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)" | |
| working-directory: dsBaseClient/tests/testthat/data_files | |
| - name: Run dsBase tests with coverage & JUnit report | |
| run: | | |
| R -q -e "devtools::load_all();" | |
| R -q -e ' | |
| cov <- covr::package_coverage( | |
| type = c("none"), | |
| code = c('"'"' | |
| output_file <- file("test_console_output_dsbase.txt"); | |
| sink(output_file, split = TRUE); | |
| junit_rep <- testthat::JunitReporter$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 = "${{ matrix.filter }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"' | |
| ) | |
| ) | |
| saveRDS(cov, "coverage.rds") | |
| write.csv(covr::coverage_to_list(cov), "coveragelist.csv")' || R_EXIT=$? | |
| cat test_console_output_dsbase.txt | |
| exit "${R_EXIT:-0}" | |
| working-directory: dsBaseClient | |
| - name: Upload shard results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: opal-dsbase-${{ matrix.category }} | |
| path: | | |
| dsBaseClient/test_results_dsbase.xml | |
| dsBaseClient/test_console_output_dsbase.txt | |
| dsBaseClient/coveragelist.csv | |
| dsBaseClient/coverage.rds | |
| ################################################################################ | |
| # 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: | |
| 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: | | |
| 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("Depends", "Imports", "LinkingTo")' | |
| extra-packages: | | |
| cran::devtools | |
| cran::usethis | |
| cran::git2r | |
| cran::covr | |
| cran::fields | |
| cran::meta | |
| cran::metafor | |
| cran::ggplot2 | |
| cran::gridExtra | |
| cran::data.table | |
| cran::DSI | |
| cran::opalr | |
| cran::DSOpal | |
| cran::DSLite | |
| cran::MolgenisAuth | |
| cran::MolgenisArmadillo | |
| cran::DSMolgenisArmadillo | |
| cran::DescTools | |
| cran::e1071 | |
| github::datashield/dsDangerClient | |
| needs: check | |
| - name: Install dsDangerClient | |
| run: | | |
| R -q -e " | |
| ref <- Sys.getenv('BRANCH_NAME') | |
| ok <- tryCatch({ pak::pkg_install(sprintf('github::datashield/dsDangerClient@%s', ref)); TRUE }, error = function(e) FALSE) | |
| if (!ok) pak::pkg_install('github::datashield/dsDangerClient')" | |
| - 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, split = TRUE); | |
| 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)' || R_EXIT=$? | |
| cat test_console_output_dsdanger.txt | |
| exit "${R_EXIT:-0}" | |
| 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 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: release | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: 'c("Depends", "Imports", "LinkingTo")' | |
| extra-packages: | | |
| cran::xml2 | |
| cran::covr | |
| github::datashield/dsDangerClient | |
| - name: Download shard/dsdanger results | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: 'opal-*' | |
| path: dsBaseClient/artifacts | |
| - name: Merge results and write job summary | |
| run: | | |
| mkdir -p logs | |
| cat artifacts/*/test_console_output_*.txt > logs/test_console_output.txt | |
| Rscript -e ' | |
| xml_files <- list.files("artifacts", pattern = "^test_results_.*\\.xml$", recursive = TRUE, full.names = TRUE) | |
| docs <- lapply(xml_files, xml2::read_xml) | |
| root <- xml2::xml_new_root("testsuites") | |
| for (doc in docs) { | |
| for (s in xml2::xml_find_all(doc, ".//testsuite")) xml2::xml_add_child(root, s) | |
| } | |
| xml2::write_xml(root, "logs/test_results.xml") | |
| rds_files <- list.files("artifacts", pattern = "coverage\\.rds$", recursive = TRUE, full.names = TRUE) | |
| if (length(rds_files) > 0) { | |
| tallies <- lapply(rds_files, function(f) covr::tally_coverage(readRDS(f))) | |
| agg <- aggregate(value ~ filename + line, data = do.call(rbind, tallies), FUN = sum) | |
| filecoverage <- tapply(agg$value, agg$filename, function(x) round(sum(x > 0) / length(x) * 100, 2)) | |
| totalcoverage <- round(sum(agg$value > 0) / nrow(agg) * 100, 2) | |
| cl <- list(filecoverage = filecoverage, totalcoverage = totalcoverage) | |
| write.csv(cl, "logs/coveragelist.csv") | |
| low <- head(sort(cl$filecoverage), 5) | |
| cov_lines <- c( | |
| sprintf("**Combined coverage: %.1f%%**", cl$totalcoverage), | |
| "", | |
| "Lowest-covered files:", | |
| paste0("- `", names(low), "`: ", low, "%") | |
| ) | |
| } else { | |
| cov_lines <- "No coverage data found." | |
| } | |
| doc <- xml2::read_xml("logs/test_results.xml") | |
| suites <- xml2::xml_find_all(doc, ".//testsuite") | |
| n_tests <- sum(as.integer(xml2::xml_attr(suites, "tests")), na.rm = TRUE) | |
| n_failures <- sum(as.integer(xml2::xml_attr(suites, "failures")), na.rm = TRUE) | |
| n_errors <- sum(as.integer(xml2::xml_attr(suites, "errors")), na.rm = TRUE) | |
| n_skipped <- sum(as.integer(xml2::xml_attr(suites, "skipped")), na.rm = TRUE) | |
| failed <- xml2::xml_find_all(doc, ".//testcase[failure or error]") | |
| fail_lines <- if (length(failed) > 0) { | |
| msgs <- vapply(failed, function(tc) { | |
| node <- xml2::xml_find_first(tc, "failure|error") | |
| m <- xml2::xml_attr(node, "message") | |
| if (is.na(m) || !nzchar(m)) m <- trimws(xml2::xml_text(node)) | |
| m | |
| }, character(1)) | |
| c("", "### Failed tests", | |
| paste0("- `", xml2::xml_attr(failed, "classname"), "::", xml2::xml_attr(failed, "name"), "` - ", msgs)) | |
| } else { | |
| character(0) | |
| } | |
| summary <- c( | |
| "## Opal dsBase/dsDanger test results", | |
| "", | |
| sprintf("**%d tests** - %d failures, %d errors, %d skipped", n_tests, n_failures, n_errors, n_skipped), | |
| "", | |
| cov_lines, | |
| fail_lines | |
| ) | |
| writeLines(summary, Sys.getenv("GITHUB_STEP_SUMMARY")) | |
| ' | |
| working-directory: dsBaseClient | |
| - name: Upload merged results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: opal-report-results | |
| path: | | |
| dsBaseClient/logs/test_results.xml | |
| dsBaseClient/logs/test_console_output.txt | |
| dsBaseClient/logs/coveragelist.csv | |
| ################################################################################ | |
| # 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 (${{ 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. smk and perf are split further by the first letter | |
| # of the function name (after any "ds." prefix) rather than an | |
| # enumerated file list, so newly added test files fall into a bucket | |
| # automatically without editing this matrix. perf (50 fixed 30s-loop | |
| # benchmarks) and smk (116 files) dominated wall-clock before this | |
| # split - see armadillo-dsbase timings in job history. | |
| matrix: | |
| include: | |
| - category: smk-1 | |
| filter: 'smk-ds.[a-lA-L]|smk-(checkClass|isDefined)' | |
| - category: smk-2 | |
| filter: 'smk-ds.[m-vM-V]' | |
| - category: arg | |
| filter: 'arg-' | |
| - category: perf-1 | |
| filter: 'perf-ds.[a-cA-C]' | |
| - category: perf-2 | |
| filter: 'perf-ds.[d-mD-M]' | |
| - category: perf-3 | |
| filter: 'perf-ds.[n-vN-V]|perf-(conndisconn|void)' | |
| - category: misc | |
| filter: 'datachk-|disc-|expt-|smk_expt-|math-|_-' | |
| 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 | |
| package-whitelist: | |
| - dsBase | |
| - dsTidyverse | |
| - resourcer | |
| function-blacklist: [ ] | |
| options: | |
| datashield: | |
| seed: 342325352 | |
| spring: | |
| security: | |
| user: | |
| name: admin | |
| 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 -H "Authorization: Bearer ${{ env.GITHUB_TOKEN }}" https://api.github.com/repos/molgenis/molgenis-service-armadillo/releases/latest) || { curl -s -H "Authorization: Bearer ${{ env.GITHUB_TOKEN }}" https://api.github.com/repos/molgenis/molgenis-service-armadillo/releases/latest; exit 1; } | |
| jar_url=$(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 | |
| docker pull datashield/rock_citest-permissive:latest | |
| working-directory: dsBaseClient | |
| - name: Uninstall default MySQL | |
| run: | | |
| 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("Depends", "Imports", "LinkingTo")' | |
| extra-packages: | | |
| cran::devtools | |
| cran::usethis | |
| cran::covr | |
| cran::fields | |
| cran::meta | |
| cran::metafor | |
| cran::ggplot2 | |
| cran::gridExtra | |
| cran::data.table | |
| cran::DSI | |
| cran::opalr | |
| cran::DSOpal | |
| cran::DSLite | |
| cran::MolgenisAuth | |
| cran::MolgenisArmadillo | |
| cran::DSMolgenisArmadillo | |
| cran::DescTools | |
| cran::e1071 | |
| github::datashield/dsDangerClient | |
| 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 -sf -u admin:admin -X POST http://localhost:8080/ds-profiles/default/start | |
| profile_status="" | |
| for i in $(seq 1 30); do | |
| profile_status=$(curl -sf -u admin:admin http://localhost:8080/ds-profiles/status | jq -r '.[] | select(.name=="default") | .status') | |
| [ "$profile_status" == "RUNNING" ] && break | |
| sleep 10 | |
| done | |
| if [ "$profile_status" != "RUNNING" ]; then | |
| echo "default profile container did not become RUNNING in time (status: $profile_status)" | |
| exit 1 | |
| fi | |
| install_status=$(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: Dump Armadillo server log | |
| if: failure() | |
| run: grep "Caused by:" armadillo_home/logs/stdout.log | sort -u | |
| working-directory: dsBaseClient | |
| - name: Run dsBase tests with coverage & JUnit report | |
| run: | | |
| R -q -e "devtools::load_all();" | |
| R -q -e ' | |
| cov <- covr::package_coverage( | |
| type = c("none"), | |
| code = c('"'"' | |
| output_file <- file("test_console_output_dsbase.txt"); | |
| sink(output_file, split = TRUE); | |
| 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("${{ env.PROJECT_NAME }}", filter = "${{ matrix.filter }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"' | |
| ) | |
| ) | |
| saveRDS(cov, "coverage.rds") | |
| write.csv(covr::coverage_to_list(cov), "coveragelist.csv")' || R_EXIT=$? | |
| cat test_console_output_dsbase.txt | |
| exit "${R_EXIT:-0}" | |
| working-directory: dsBaseClient | |
| - name: Upload shard results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: armadillo-dsbase-${{ matrix.category }} | |
| path: | | |
| dsBaseClient/test_results_dsbase.xml | |
| dsBaseClient/test_console_output_dsbase.txt | |
| dsBaseClient/coveragelist.csv | |
| dsBaseClient/coverage.rds | |
| ################################################################################ | |
| # 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 | |
| package-whitelist: | |
| - dsBase | |
| - dsTidyverse | |
| - resourcer | |
| function-blacklist: [ ] | |
| options: | |
| datashield: | |
| seed: 342325352 | |
| spring: | |
| security: | |
| user: | |
| name: admin | |
| 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 -H "Authorization: Bearer ${{ env.GITHUB_TOKEN }}" https://api.github.com/repos/molgenis/molgenis-service-armadillo/releases/latest) || { curl -s -H "Authorization: Bearer ${{ env.GITHUB_TOKEN }}" https://api.github.com/repos/molgenis/molgenis-service-armadillo/releases/latest; exit 1; } | |
| jar_url=$(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 | |
| docker pull datashield/rock_citest-permissive:latest | |
| working-directory: dsBaseClient | |
| - name: Uninstall default MySQL | |
| run: | | |
| 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("Depends", "Imports", "LinkingTo")' | |
| extra-packages: | | |
| cran::devtools | |
| cran::usethis | |
| cran::git2r | |
| cran::covr | |
| cran::fields | |
| cran::meta | |
| cran::metafor | |
| cran::ggplot2 | |
| cran::gridExtra | |
| cran::data.table | |
| cran::DSI | |
| cran::opalr | |
| cran::DSOpal | |
| cran::DSLite | |
| cran::MolgenisAuth | |
| cran::MolgenisArmadillo | |
| cran::DSMolgenisArmadillo | |
| cran::DescTools | |
| cran::e1071 | |
| github::datashield/dsDangerClient | |
| needs: check | |
| - name: Install dsDangerClient | |
| run: | | |
| R -q -e " | |
| ref <- Sys.getenv('BRANCH_NAME') | |
| ok <- tryCatch({ pak::pkg_install(sprintf('github::datashield/dsDangerClient@%s', ref)); TRUE }, error = function(e) FALSE) | |
| if (!ok) pak::pkg_install('github::datashield/dsDangerClient')" | |
| - 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 -sf -u admin:admin -X POST http://localhost:8080/ds-profiles/default/start | |
| profile_status="" | |
| for i in $(seq 1 30); do | |
| profile_status=$(curl -sf -u admin:admin http://localhost:8080/ds-profiles/status | jq -r '.[] | select(.name=="default") | .status') | |
| [ "$profile_status" == "RUNNING" ] && break | |
| sleep 10 | |
| done | |
| if [ "$profile_status" != "RUNNING" ]; then | |
| echo "default profile container did not become RUNNING in time (status: $profile_status)" | |
| exit 1 | |
| fi | |
| install_status=$(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: Dump Armadillo server log | |
| if: failure() | |
| run: grep "Caused by:" armadillo_home/logs/stdout.log | sort -u | |
| 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 "$packages_json" | jq -e '.[] | select(.name == "dsDanger")' >/dev/null 2>&1; then | |
| break | |
| fi | |
| sleep 10 | |
| done | |
| curl -u admin:admin -X POST http://localhost:8080/whitelist/dsDanger | |
| curl -u admin:admin http://localhost:8080/whitelist | |
| working-directory: dsBaseClient | |
| - name: Run dsDanger tests with JUnit report | |
| run: | | |
| R -q -e ' | |
| library(testthat); | |
| output_file <- file("test_console_output_dsdanger.txt"); | |
| sink(output_file, split = TRUE); | |
| junit_rep <- JunitReporter$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 = "${{ env.TEST_FILTER_DSDANGER }}", reporter = multi_rep, stop_on_failure = FALSE)' || R_EXIT=$? | |
| cat test_console_output_dsdanger.txt | |
| exit "${R_EXIT:-0}" | |
| working-directory: dsBaseClient | |
| - name: Upload dsDanger results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: armadillo-dsdanger | |
| path: | | |
| dsBaseClient/test_results_dsdanger.xml | |
| dsBaseClient/test_console_output_dsdanger.txt | |
| ################################################################################ | |
| # Armadillo - merge all shard + dsDanger results and publish the report. | |
| ################################################################################ | |
| armadillo-report: | |
| name: Armadillo report | |
| needs: [armadillo-dsbase, armadillo-dsdanger] | |
| if: always() | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 30 | |
| steps: | |
| - name: Checkout dsBaseClient | |
| uses: actions/checkout@v4 | |
| with: | |
| path: dsBaseClient | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: release | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: 'c("Depends", "Imports", "LinkingTo")' | |
| extra-packages: | | |
| cran::xml2 | |
| cran::covr | |
| github::datashield/dsDangerClient | |
| - name: Download shard/dsdanger results | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: 'armadillo-*' | |
| path: dsBaseClient/artifacts | |
| - name: Merge results and write job summary | |
| run: | | |
| mkdir -p logs | |
| cat artifacts/*/test_console_output_*.txt > logs/test_console_output.txt | |
| Rscript -e ' | |
| xml_files <- list.files("artifacts", pattern = "^test_results_.*\\.xml$", recursive = TRUE, full.names = TRUE) | |
| docs <- lapply(xml_files, xml2::read_xml) | |
| root <- xml2::xml_new_root("testsuites") | |
| for (doc in docs) { | |
| for (s in xml2::xml_find_all(doc, ".//testsuite")) xml2::xml_add_child(root, s) | |
| } | |
| xml2::write_xml(root, "logs/test_results.xml") | |
| rds_files <- list.files("artifacts", pattern = "coverage\\.rds$", recursive = TRUE, full.names = TRUE) | |
| if (length(rds_files) > 0) { | |
| tallies <- lapply(rds_files, function(f) covr::tally_coverage(readRDS(f))) | |
| agg <- aggregate(value ~ filename + line, data = do.call(rbind, tallies), FUN = sum) | |
| filecoverage <- tapply(agg$value, agg$filename, function(x) round(sum(x > 0) / length(x) * 100, 2)) | |
| totalcoverage <- round(sum(agg$value > 0) / nrow(agg) * 100, 2) | |
| cl <- list(filecoverage = filecoverage, totalcoverage = totalcoverage) | |
| write.csv(cl, "logs/coveragelist.csv") | |
| low <- head(sort(cl$filecoverage), 5) | |
| cov_lines <- c( | |
| sprintf("**Combined coverage: %.1f%%**", cl$totalcoverage), | |
| "", | |
| "Lowest-covered files:", | |
| paste0("- `", names(low), "`: ", low, "%") | |
| ) | |
| } else { | |
| cov_lines <- "No coverage data found." | |
| } | |
| doc <- xml2::read_xml("logs/test_results.xml") | |
| suites <- xml2::xml_find_all(doc, ".//testsuite") | |
| n_tests <- sum(as.integer(xml2::xml_attr(suites, "tests")), na.rm = TRUE) | |
| n_failures <- sum(as.integer(xml2::xml_attr(suites, "failures")), na.rm = TRUE) | |
| n_errors <- sum(as.integer(xml2::xml_attr(suites, "errors")), na.rm = TRUE) | |
| n_skipped <- sum(as.integer(xml2::xml_attr(suites, "skipped")), na.rm = TRUE) | |
| failed <- xml2::xml_find_all(doc, ".//testcase[failure or error]") | |
| fail_lines <- if (length(failed) > 0) { | |
| msgs <- vapply(failed, function(tc) { | |
| node <- xml2::xml_find_first(tc, "failure|error") | |
| m <- xml2::xml_attr(node, "message") | |
| if (is.na(m) || !nzchar(m)) m <- trimws(xml2::xml_text(node)) | |
| m | |
| }, character(1)) | |
| c("", "### Failed tests", | |
| paste0("- `", xml2::xml_attr(failed, "classname"), "::", xml2::xml_attr(failed, "name"), "` - ", msgs)) | |
| } else { | |
| character(0) | |
| } | |
| summary <- c( | |
| "## Armadillo dsBase/dsDanger test results", | |
| "", | |
| sprintf("**%d tests** - %d failures, %d errors, %d skipped", n_tests, n_failures, n_errors, n_skipped), | |
| "", | |
| cov_lines, | |
| fail_lines | |
| ) | |
| writeLines(summary, Sys.getenv("GITHUB_STEP_SUMMARY")) | |
| ' | |
| working-directory: dsBaseClient | |
| - name: Upload merged results | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: armadillo-report-results | |
| path: | | |
| dsBaseClient/logs/test_results.xml | |
| dsBaseClient/logs/test_console_output.txt | |
| dsBaseClient/logs/coveragelist.csv |