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Merged
StuartWheater merged 4 commits into from
Dec 1, 2025
Merged

Update 'perf' support and fix typo in variable name #637

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10c7f46
Set time limit to 180m
StuartWheater Nov 25, 2025
074660a
Merge branch 'v6.3.5-dev' of github.com:StuartWheater/dsBaseClient in…
StuartWheater Nov 27, 2025
d634965
Fix typo in variable name
StuartWheater Nov 27, 2025
f31f694
Update 'perf' support
StuartWheater Nov 30, 2025
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67 changes: 33 additions & 34 deletions .github/workflows/dsBaseClient_test_suite.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ jobs:
timeout-minutes: 180
permissions:
contents: read

# These should all be constant, except TEST_FILTER. This can be used to test
# subsets of test files in the testthat directory. Options are like:
# '*' <- Run all tests.
Expand All @@ -33,7 +33,7 @@ jobs:
_r_check_system_clock_: 0
WORKFLOW_ID: ${{ github.run_id }}-${{ github.run_attempt }}
PROJECT_NAME: dsBaseClient
BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
REPO_OWNER: ${{ github.repository_owner }}
R_KEEP_PKG_SOURCE: yes
GITHUB_TOKEN: ${{ github.token || 'placeholder-token' }}
Expand All @@ -53,7 +53,7 @@ jobs:
path: testStatus
persist-credentials: false
token: ${{ env.GITHUB_TOKEN }}

- name: Uninstall default MySQL
run: |
curl https://bazel.build/bazel-release.pub.gpg | sudo apt-key add -
Expand All @@ -63,7 +63,7 @@ jobs:
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
Expand All @@ -83,29 +83,29 @@ jobs:
sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev xml-twig-tools -y
sudo R -q -e "install.packages(c('devtools','covr','fields','meta','metafor','ggplot2','gridExtra','data.table','DSI','DSOpal','DSLite','MolgenisAuth','MolgenisArmadillo','DSMolgenisArmadillo','DescTools','e1071'), repos='https://cloud.r-project.org')"
sudo R -q -e "devtools::install_github(repo='datashield/dsDangerClient', ref=Sys.getenv('BRANCH_NAME'))"

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

- name: Check manual updated
run: |
orig_sum=$(find man -type f | sort -u | xargs cat | md5sum)
Expand All @@ -124,7 +124,7 @@ jobs:
grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout
working-directory: dsBaseClient
continue-on-error: true

- name: Start Armadillo docker-compose
run: docker compose -f docker-compose_armadillo.yml up -d --build
working-directory: dsBaseClient
Expand All @@ -144,7 +144,7 @@ jobs:
sleep 30
curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
working-directory: dsBaseClient

- name: Run tests with coverage & JUnit report
run: |
mkdir -p logs
Expand All @@ -168,11 +168,11 @@ jobs:
),
"coveragelist.csv"
)'

mv coveragelist.csv logs/
mv test_* logs/
working-directory: dsBaseClient

- name: Check for JUnit errors
run: |
issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | grep -c errors= || true)
Expand All @@ -190,7 +190,7 @@ jobs:
echo "R:$(R --version | head -n1)" >> ${{ env.WORKFLOW_ID }}.txt
Rscript --vanilla -e 'sessionInfo()' >> session_info_${{ env.WORKFLOW_ID }}.txt
working-directory: dsBaseClient/logs

- name: Parse results from testthat and covr
run: |
Rscript --verbose --vanilla ../testStatus/source/parse_test_report.R logs/ logs/ https://github.com/datashield/${{ env.PROJECT_NAME }}/blob/${{ env.BRANCH_NAME }} '([^:]+)' '(?<=::)[^:]+(?=::)'
Expand All @@ -202,24 +202,24 @@ jobs:
- name: Render report
run: |
cd testStatus

mkdir -p new/logs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/${{ env.WORKFLOW_ID }}/
mkdir -p new/docs/${{ env.PROJECT_NAME }}/${{ env.BRANCH_NAME }}/latest/

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

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

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

- name: Upload test logs
uses: actions/upload-artifact@v4
with:
Expand All @@ -245,4 +245,3 @@ jobs:
R -e 'sessionInfo()'
sudo apt install tree -y
tree .

2 changes: 1 addition & 1 deletion opal_azure-pipelines.yml
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Expand Up @@ -233,7 +233,7 @@ jobs:
# Install dsBase.
# If previous steps have failed then don't run.
- bash: |
R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"
R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)"

Expand Down
11 changes: 9 additions & 2 deletions tests/testthat/perf_tests/perf_rate.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,8 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#-------------------------------------------------------------------------------

.perf.reference.filename <- 'perf_files/default_perf_profile.csv'
.perf.reference.filename <- 'perf_files/default_perf_profile.csv'
.perf.reference.save.filename <- NULL

.perf.reference <- NULL

Expand All @@ -22,7 +23,13 @@ perf.reference.save <- function(perf.ref.name, rate, tolerance.lower, tolerance.

.perf.reference[nrow(.perf.reference)+1,] <- c(perf.ref.name, rate, tolerance.lower, tolerance.upper)

write.csv(.perf.reference, .perf.reference.filename, row.names = FALSE)
if (is.null(.perf.reference.save.filename))
{
.perf.reference.save.filename <<- base::tempfile(pattern = "perf_file_", fileext = ".csv")
message(paste0("Additional perf record added to '", .perf.reference.save.filename, "'"))
}

write.csv(.perf.reference, .perf.reference.save.filename, row.names = FALSE)

.perf.reference <<- .perf.reference
}
Expand Down