Changes to perf-batch-1 updating tests and setup#673

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Merged
StuartWheater merged 10 commits into from
May 21, 2026
Merged

Changes to perf-batch-1 updating tests and setup #673

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8705f86
Updated azure-pipeline specification
StuartWheater May 14, 2026
848c695
Merge branch 'v7.0-dev' of github.com:StuartWheater/dsBaseClient into…
StuartWheater May 14, 2026
b1653ca
Merge branch 'datashield:v7.0-dev' into v7.0-dev
StuartWheater May 14, 2026
19afb23
Merge branch 'datashield:perf-batch-1' into perf-batch-1
StuartWheater May 17, 2026
f47d0b7
Updated perf profile
StuartWheater May 17, 2026
67c9ca7
Updated 'perf_rate.R'
StuartWheater May 17, 2026
2b3151f
Fix result file names
StuartWheater May 18, 2026
566fc17
Reworking to latest Opal
StuartWheater May 18, 2026
3369b38
Updated performance profile
StuartWheater May 19, 2026
5605198
Fixed use of Danger function in testing
StuartWheater May 20, 2026
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6 changes: 3 additions & 3 deletions armadillo_azure-pipelines.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -34,6 +34,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -274,7 +275,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -396,7 +397,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -534,7 +535,6 @@ jobs:
echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
Expand Down
15 changes: 8 additions & 7 deletions azure-pipelines.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -214,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -253,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -342,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -368,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand Down
5 changes: 2 additions & 3 deletions docker-compose_armadillo.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
hostname: armadillo
ports:
- 8080:8080
image: datashield/armadillo_citest:5.11.0
image: datashield/armadillo_citest:latest
environment:
LOGGING_CONFIG: 'classpath:logback-file.xml'
AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

default:
hostname: default
image: datashield/rock-quebrada-lamda:latest
# image: datashield/rserver-panda-lamda:devel
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
5 changes: 3 additions & 2 deletions docker-compose_opal.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@ services:
image: datashield/opal_citest:latest
ports:
- 8443:8443
- 8080:8080
links:
- mongo
- rock
Expand All@@ -15,11 +16,11 @@ services:
- ROCK_HOSTS=rock:8085
- ROCK_ADMINISTRATOR_PASSWORD=foobar
mongo:
image: mongo:4.4.15
image: mongo:8.0
environment:
- MONGO_INITDB_ROOT_USERNAME=root
- MONGO_INITDB_ROOT_PASSWORD=foobar
rock:
image: datashield/rock-quebrada-lamda-permissive:latest
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
103 changes: 8 additions & 95 deletions opal_azure-pipelines.yml
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Expand Up@@ -3,11 +3,9 @@
# Starts with a vanilla Opal docker composition, installs dsBase
# and dsBaseClient (as well as dependencies - including a fully functional
# Opal server).
# Does checks and tests then saves results to testStatus repo.
#
# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
# /dsBaseClient <- Checked out version of datashield/dsBaseClient
# /testStatus <- Checked out version of datashield/testStatus
# /logs <- Where results of tests and lots are collated
#
# As of May 2020 this takes ~ 70 mins to run.
Expand All@@ -34,18 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0


#########################################################################################
# Need to define all the GH repos and their access tokens, see:
# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml
resources:
repositories:
- repository: testStatusRepo
type: github
endpoint: datashield-testing
name: datashield/testStatus
ref: master
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -82,11 +69,6 @@ jobs:
- checkout: self
path: 'dsBaseClient'

- checkout: testStatusRepo
path: 'testStatus'
persistCredentials: true
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# The MySQL install that comes with the VM doesn't seem compatable with our set up
Expand DownExpand Up@@ -233,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -272,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -361,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -387,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -524,75 +506,6 @@ jobs:
displayName: 'Down Opal Docker Composition'
condition: succeeded()

#####################################################################################
# Windup phase
#####################################################################################

#####################################################################################
# Output some important version numbers to file. This gets added to the testStatus
# commit so it can be parsed and used on the status table.
- bash: |

echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
condition: succeededOrFailed()


#####################################################################################
# Checkout the testStatus repo, add the results from here, push back to GH.
# TODO: Automatically pull in better email/name info from somewhere.
# TODO: More debug info in commit message
- bash: |

# Git needs some config set to be able to push to a repo.
git config --global user.email "you@example.com"
git config --global user.name "Azure pipeline"

# This repo is checked out in detatched head state, so reconnect it here.
git checkout master

# It is possible that other commits have been made to the testStatus repo since it
# was checked out. i.e. other pipeline runs might have finished.
git pull

# Make the directories if they dont already exist
mkdir --parents logs/$(projectName)/$(branchName)
mkdir --parents docs/$(projectName)/$(branchName)/latest

cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv

cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml

cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/

# Run the script to parse the results and build the html pages.
# status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch
source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName)

cp status.html docs/$(projectName)/$(branchName)/latest/index.html
git add logs/$(projectName)/$(branchName)/coveragelist.csv
git add logs/$(projectName)/$(branchName)/test_results.xml
git add logs/$(projectName)/$(branchName)/$(datetime).xml
git add logs/$(projectName)/$(branchName)/$(datetime).csv
git add logs/$(projectName)/$(branchName)/$(datetime).txt
git add docs/$(projectName)/$(branchName)/latest/index.html

git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)"
git push
exit 0

workingDirectory: $(Pipeline.Workspace)/testStatus
displayName: 'Parse test results'
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# Output the environment information to the console. This is useful for debugging.
# Always do this, even if some of the above has failed or the job has been cacelled.
Expand Down
16 changes: 8 additions & 8 deletions tests/testthat/connection_to_datasets/login_details.R
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Expand Up@@ -22,12 +22,12 @@ if (! is.null(getOption("default_driver"))) {
}

if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver")) {
ds.test_env$ping_address <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ping_config <- config(timeout=5, ssl_verifyhost=0, ssl_verifypeer=0)
ds.test_env$ping_address <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ping_config <- config(timeout=5)

ds.test_env$ip_address_1 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_2 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_3 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_1 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_2 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_3 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")

ds.test_env$user_1 <- getOption("opal.user", "administrator")
ds.test_env$user_2 <- getOption("opal.user", "administrator")
Expand All@@ -37,9 +37,9 @@ if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver
ds.test_env$password_2 <- getOption("opal.password", "datashield_test&")
ds.test_env$password_3 <- getOption("opal.password", "datashield_test&")

ds.test_env$options_1 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_2 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_3 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_1 <- "list()"
ds.test_env$options_2 <- "list()"
ds.test_env$options_3 <- "list()"

ds.test_env$secure_login_details <- TRUE
} else if (ds.test_env$driver == "ArmadilloDriver") {
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/data_files/obiba_opal-upload_testing_datasets.R
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Expand Up@@ -17,8 +17,8 @@ upload_testing_dataset_table <- function(opal, project_name, table_name, local_f
opal.table_save(opal, data, project_name, table_name, id.name = "_row_id_", force = TRUE)
}

# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/', opts = list())

upload_testing_dataset_table(opal, 'ANTHRO', 'anthro1', 'ANTHRO/anthro1.rda')
upload_testing_dataset_table(opal, 'ANTHRO', 'anthro2', 'ANTHRO/anthro2.rda')
Expand Down
14 changes: 0 additions & 14 deletions tests/testthat/perf_files/armadillo_azure-pipeline.csv
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Merged
StuartWheater merged 10 commits into from
May 21, 2026
Merged

Changes to perf-batch-1 updating tests and setup #673

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8705f86
Updated azure-pipeline specification
StuartWheater May 14, 2026
848c695
Merge branch 'v7.0-dev' of github.com:StuartWheater/dsBaseClient into…
StuartWheater May 14, 2026
b1653ca
Merge branch 'datashield:v7.0-dev' into v7.0-dev
StuartWheater May 14, 2026
19afb23
Merge branch 'datashield:perf-batch-1' into perf-batch-1
StuartWheater May 17, 2026
f47d0b7
Updated perf profile
StuartWheater May 17, 2026
67c9ca7
Updated 'perf_rate.R'
StuartWheater May 17, 2026
2b3151f
Fix result file names
StuartWheater May 18, 2026
566fc17
Reworking to latest Opal
StuartWheater May 18, 2026
3369b38
Updated performance profile
StuartWheater May 19, 2026
5605198
Fixed use of Danger function in testing
StuartWheater May 20, 2026
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6 changes: 3 additions & 3 deletions armadillo_azure-pipelines.yml
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Expand Up@@ -34,6 +34,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -274,7 +275,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -396,7 +397,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -534,7 +535,6 @@ jobs:
echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
Expand Down
15 changes: 8 additions & 7 deletions azure-pipelines.yml
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Expand Up@@ -32,6 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -214,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -253,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -342,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -368,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand Down
5 changes: 2 additions & 3 deletions docker-compose_armadillo.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
hostname: armadillo
ports:
- 8080:8080
image: datashield/armadillo_citest:5.11.0
image: datashield/armadillo_citest:latest
environment:
LOGGING_CONFIG: 'classpath:logback-file.xml'
AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

default:
hostname: default
image: datashield/rock-quebrada-lamda:latest
# image: datashield/rserver-panda-lamda:devel
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
5 changes: 3 additions & 2 deletions docker-compose_opal.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@ services:
image: datashield/opal_citest:latest
ports:
- 8443:8443
- 8080:8080
links:
- mongo
- rock
Expand All@@ -15,11 +16,11 @@ services:
- ROCK_HOSTS=rock:8085
- ROCK_ADMINISTRATOR_PASSWORD=foobar
mongo:
image: mongo:4.4.15
image: mongo:8.0
environment:
- MONGO_INITDB_ROOT_USERNAME=root
- MONGO_INITDB_ROOT_PASSWORD=foobar
rock:
image: datashield/rock-quebrada-lamda-permissive:latest
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
103 changes: 8 additions & 95 deletions opal_azure-pipelines.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,11 +3,9 @@
# Starts with a vanilla Opal docker composition, installs dsBase
# and dsBaseClient (as well as dependencies - including a fully functional
# Opal server).
# Does checks and tests then saves results to testStatus repo.
#
# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
# /dsBaseClient <- Checked out version of datashield/dsBaseClient
# /testStatus <- Checked out version of datashield/testStatus
# /logs <- Where results of tests and lots are collated
#
# As of May 2020 this takes ~ 70 mins to run.
Expand All@@ -34,18 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0


#########################################################################################
# Need to define all the GH repos and their access tokens, see:
# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml
resources:
repositories:
- repository: testStatusRepo
type: github
endpoint: datashield-testing
name: datashield/testStatus
ref: master
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -82,11 +69,6 @@ jobs:
- checkout: self
path: 'dsBaseClient'

- checkout: testStatusRepo
path: 'testStatus'
persistCredentials: true
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# The MySQL install that comes with the VM doesn't seem compatable with our set up
Expand DownExpand Up@@ -233,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -272,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -361,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -387,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -524,75 +506,6 @@ jobs:
displayName: 'Down Opal Docker Composition'
condition: succeeded()

#####################################################################################
# Windup phase
#####################################################################################

#####################################################################################
# Output some important version numbers to file. This gets added to the testStatus
# commit so it can be parsed and used on the status table.
- bash: |

echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
condition: succeededOrFailed()


#####################################################################################
# Checkout the testStatus repo, add the results from here, push back to GH.
# TODO: Automatically pull in better email/name info from somewhere.
# TODO: More debug info in commit message
- bash: |

# Git needs some config set to be able to push to a repo.
git config --global user.email "you@example.com"
git config --global user.name "Azure pipeline"

# This repo is checked out in detatched head state, so reconnect it here.
git checkout master

# It is possible that other commits have been made to the testStatus repo since it
# was checked out. i.e. other pipeline runs might have finished.
git pull

# Make the directories if they dont already exist
mkdir --parents logs/$(projectName)/$(branchName)
mkdir --parents docs/$(projectName)/$(branchName)/latest

cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv

cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml

cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/

# Run the script to parse the results and build the html pages.
# status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch
source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName)

cp status.html docs/$(projectName)/$(branchName)/latest/index.html
git add logs/$(projectName)/$(branchName)/coveragelist.csv
git add logs/$(projectName)/$(branchName)/test_results.xml
git add logs/$(projectName)/$(branchName)/$(datetime).xml
git add logs/$(projectName)/$(branchName)/$(datetime).csv
git add logs/$(projectName)/$(branchName)/$(datetime).txt
git add docs/$(projectName)/$(branchName)/latest/index.html

git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)"
git push
exit 0

workingDirectory: $(Pipeline.Workspace)/testStatus
displayName: 'Parse test results'
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# Output the environment information to the console. This is useful for debugging.
# Always do this, even if some of the above has failed or the job has been cacelled.
Expand Down
16 changes: 8 additions & 8 deletions tests/testthat/connection_to_datasets/login_details.R
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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,12 +22,12 @@ if (! is.null(getOption("default_driver"))) {
}

if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver")) {
ds.test_env$ping_address <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ping_config <- config(timeout=5, ssl_verifyhost=0, ssl_verifypeer=0)
ds.test_env$ping_address <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ping_config <- config(timeout=5)

ds.test_env$ip_address_1 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_2 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_3 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_1 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_2 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_3 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")

ds.test_env$user_1 <- getOption("opal.user", "administrator")
ds.test_env$user_2 <- getOption("opal.user", "administrator")
Expand All@@ -37,9 +37,9 @@ if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver
ds.test_env$password_2 <- getOption("opal.password", "datashield_test&")
ds.test_env$password_3 <- getOption("opal.password", "datashield_test&")

ds.test_env$options_1 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_2 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_3 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_1 <- "list()"
ds.test_env$options_2 <- "list()"
ds.test_env$options_3 <- "list()"

ds.test_env$secure_login_details <- TRUE
} else if (ds.test_env$driver == "ArmadilloDriver") {
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/data_files/obiba_opal-upload_testing_datasets.R
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Expand Up@@ -17,8 +17,8 @@ upload_testing_dataset_table <- function(opal, project_name, table_name, local_f
opal.table_save(opal, data, project_name, table_name, id.name = "_row_id_", force = TRUE)
}

# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/', opts = list())

upload_testing_dataset_table(opal, 'ANTHRO', 'anthro1', 'ANTHRO/anthro1.rda')
upload_testing_dataset_table(opal, 'ANTHRO', 'anthro2', 'ANTHRO/anthro2.rda')
Expand Down
14 changes: 0 additions & 14 deletions tests/testthat/perf_files/armadillo_azure-pipeline.csv
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix"); } } catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Merged
StuartWheater merged 10 commits into from
May 21, 2026
Merged

Changes to perf-batch-1 updating tests and setup #673

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8705f86
Updated azure-pipeline specification
StuartWheater May 14, 2026
848c695
Merge branch 'v7.0-dev' of github.com:StuartWheater/dsBaseClient into…
StuartWheater May 14, 2026
b1653ca
Merge branch 'datashield:v7.0-dev' into v7.0-dev
StuartWheater May 14, 2026
19afb23
Merge branch 'datashield:perf-batch-1' into perf-batch-1
StuartWheater May 17, 2026
f47d0b7
Updated perf profile
StuartWheater May 17, 2026
67c9ca7
Updated 'perf_rate.R'
StuartWheater May 17, 2026
2b3151f
Fix result file names
StuartWheater May 18, 2026
566fc17
Reworking to latest Opal
StuartWheater May 18, 2026
3369b38
Updated performance profile
StuartWheater May 19, 2026
5605198
Fixed use of Danger function in testing
StuartWheater May 20, 2026
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6 changes: 3 additions & 3 deletions armadillo_azure-pipelines.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -34,6 +34,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -274,7 +275,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -396,7 +397,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -534,7 +535,6 @@ jobs:
echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
Expand Down
15 changes: 8 additions & 7 deletions azure-pipelines.yml
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -214,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -253,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -342,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -368,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand Down
5 changes: 2 additions & 3 deletions docker-compose_armadillo.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
hostname: armadillo
ports:
- 8080:8080
image: datashield/armadillo_citest:5.11.0
image: datashield/armadillo_citest:latest
environment:
LOGGING_CONFIG: 'classpath:logback-file.xml'
AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

default:
hostname: default
image: datashield/rock-quebrada-lamda:latest
# image: datashield/rserver-panda-lamda:devel
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
5 changes: 3 additions & 2 deletions docker-compose_opal.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@ services:
image: datashield/opal_citest:latest
ports:
- 8443:8443
- 8080:8080
links:
- mongo
- rock
Expand All@@ -15,11 +16,11 @@ services:
- ROCK_HOSTS=rock:8085
- ROCK_ADMINISTRATOR_PASSWORD=foobar
mongo:
image: mongo:4.4.15
image: mongo:8.0
environment:
- MONGO_INITDB_ROOT_USERNAME=root
- MONGO_INITDB_ROOT_PASSWORD=foobar
rock:
image: datashield/rock-quebrada-lamda-permissive:latest
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
103 changes: 8 additions & 95 deletions opal_azure-pipelines.yml
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,11 +3,9 @@
# Starts with a vanilla Opal docker composition, installs dsBase
# and dsBaseClient (as well as dependencies - including a fully functional
# Opal server).
# Does checks and tests then saves results to testStatus repo.
#
# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
# /dsBaseClient <- Checked out version of datashield/dsBaseClient
# /testStatus <- Checked out version of datashield/testStatus
# /logs <- Where results of tests and lots are collated
#
# As of May 2020 this takes ~ 70 mins to run.
Expand All@@ -34,18 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0


#########################################################################################
# Need to define all the GH repos and their access tokens, see:
# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml
resources:
repositories:
- repository: testStatusRepo
type: github
endpoint: datashield-testing
name: datashield/testStatus
ref: master
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -82,11 +69,6 @@ jobs:
- checkout: self
path: 'dsBaseClient'

- checkout: testStatusRepo
path: 'testStatus'
persistCredentials: true
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# The MySQL install that comes with the VM doesn't seem compatable with our set up
Expand DownExpand Up@@ -233,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -272,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -361,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -387,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -524,75 +506,6 @@ jobs:
displayName: 'Down Opal Docker Composition'
condition: succeeded()

#####################################################################################
# Windup phase
#####################################################################################

#####################################################################################
# Output some important version numbers to file. This gets added to the testStatus
# commit so it can be parsed and used on the status table.
- bash: |

echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
condition: succeededOrFailed()


#####################################################################################
# Checkout the testStatus repo, add the results from here, push back to GH.
# TODO: Automatically pull in better email/name info from somewhere.
# TODO: More debug info in commit message
- bash: |

# Git needs some config set to be able to push to a repo.
git config --global user.email "you@example.com"
git config --global user.name "Azure pipeline"

# This repo is checked out in detatched head state, so reconnect it here.
git checkout master

# It is possible that other commits have been made to the testStatus repo since it
# was checked out. i.e. other pipeline runs might have finished.
git pull

# Make the directories if they dont already exist
mkdir --parents logs/$(projectName)/$(branchName)
mkdir --parents docs/$(projectName)/$(branchName)/latest

cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv

cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml

cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/

# Run the script to parse the results and build the html pages.
# status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch
source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName)

cp status.html docs/$(projectName)/$(branchName)/latest/index.html
git add logs/$(projectName)/$(branchName)/coveragelist.csv
git add logs/$(projectName)/$(branchName)/test_results.xml
git add logs/$(projectName)/$(branchName)/$(datetime).xml
git add logs/$(projectName)/$(branchName)/$(datetime).csv
git add logs/$(projectName)/$(branchName)/$(datetime).txt
git add docs/$(projectName)/$(branchName)/latest/index.html

git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)"
git push
exit 0

workingDirectory: $(Pipeline.Workspace)/testStatus
displayName: 'Parse test results'
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# Output the environment information to the console. This is useful for debugging.
# Always do this, even if some of the above has failed or the job has been cacelled.
Expand Down
16 changes: 8 additions & 8 deletions tests/testthat/connection_to_datasets/login_details.R
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,12 +22,12 @@ if (! is.null(getOption("default_driver"))) {
}

if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver")) {
ds.test_env$ping_address <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ping_config <- config(timeout=5, ssl_verifyhost=0, ssl_verifypeer=0)
ds.test_env$ping_address <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ping_config <- config(timeout=5)

ds.test_env$ip_address_1 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_2 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_3 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_1 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_2 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_3 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")

ds.test_env$user_1 <- getOption("opal.user", "administrator")
ds.test_env$user_2 <- getOption("opal.user", "administrator")
Expand All@@ -37,9 +37,9 @@ if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver
ds.test_env$password_2 <- getOption("opal.password", "datashield_test&")
ds.test_env$password_3 <- getOption("opal.password", "datashield_test&")

ds.test_env$options_1 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_2 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_3 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_1 <- "list()"
ds.test_env$options_2 <- "list()"
ds.test_env$options_3 <- "list()"

ds.test_env$secure_login_details <- TRUE
} else if (ds.test_env$driver == "ArmadilloDriver") {
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/data_files/obiba_opal-upload_testing_datasets.R
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Original file line numberDiff line numberDiff line change
Expand Up@@ -17,8 +17,8 @@ upload_testing_dataset_table <- function(opal, project_name, table_name, local_f
opal.table_save(opal, data, project_name, table_name, id.name = "_row_id_", force = TRUE)
}

# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/', opts = list())

upload_testing_dataset_table(opal, 'ANTHRO', 'anthro1', 'ANTHRO/anthro1.rda')
upload_testing_dataset_table(opal, 'ANTHRO', 'anthro2', 'ANTHRO/anthro2.rda')
Expand Down
14 changes: 0 additions & 14 deletions tests/testthat/perf_files/armadillo_azure-pipeline.csv
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Merged
StuartWheater merged 10 commits into from
May 21, 2026
Merged

Changes to perf-batch-1 updating tests and setup #673

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8705f86
Updated azure-pipeline specification
StuartWheater May 14, 2026
848c695
Merge branch 'v7.0-dev' of github.com:StuartWheater/dsBaseClient into…
StuartWheater May 14, 2026
b1653ca
Merge branch 'datashield:v7.0-dev' into v7.0-dev
StuartWheater May 14, 2026
19afb23
Merge branch 'datashield:perf-batch-1' into perf-batch-1
StuartWheater May 17, 2026
f47d0b7
Updated perf profile
StuartWheater May 17, 2026
67c9ca7
Updated 'perf_rate.R'
StuartWheater May 17, 2026
2b3151f
Fix result file names
StuartWheater May 18, 2026
566fc17
Reworking to latest Opal
StuartWheater May 18, 2026
3369b38
Updated performance profile
StuartWheater May 19, 2026
5605198
Fixed use of Danger function in testing
StuartWheater May 20, 2026
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6 changes: 3 additions & 3 deletions armadillo_azure-pipelines.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -34,6 +34,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -274,7 +275,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -396,7 +397,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -534,7 +535,6 @@ jobs:
echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
Expand Down
15 changes: 8 additions & 7 deletions azure-pipelines.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -214,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -253,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -342,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -368,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand Down
5 changes: 2 additions & 3 deletions docker-compose_armadillo.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
hostname: armadillo
ports:
- 8080:8080
image: datashield/armadillo_citest:5.11.0
image: datashield/armadillo_citest:latest
environment:
LOGGING_CONFIG: 'classpath:logback-file.xml'
AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

default:
hostname: default
image: datashield/rock-quebrada-lamda:latest
# image: datashield/rserver-panda-lamda:devel
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
5 changes: 3 additions & 2 deletions docker-compose_opal.yml
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@ services:
image: datashield/opal_citest:latest
ports:
- 8443:8443
- 8080:8080
links:
- mongo
- rock
Expand All@@ -15,11 +16,11 @@ services:
- ROCK_HOSTS=rock:8085
- ROCK_ADMINISTRATOR_PASSWORD=foobar
mongo:
image: mongo:4.4.15
image: mongo:8.0
environment:
- MONGO_INITDB_ROOT_USERNAME=root
- MONGO_INITDB_ROOT_PASSWORD=foobar
rock:
image: datashield/rock-quebrada-lamda-permissive:latest
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
103 changes: 8 additions & 95 deletions opal_azure-pipelines.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -3,11 +3,9 @@
# Starts with a vanilla Opal docker composition, installs dsBase
# and dsBaseClient (as well as dependencies - including a fully functional
# Opal server).
# Does checks and tests then saves results to testStatus repo.
#
# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
# /dsBaseClient <- Checked out version of datashield/dsBaseClient
# /testStatus <- Checked out version of datashield/testStatus
# /logs <- Where results of tests and lots are collated
#
# As of May 2020 this takes ~ 70 mins to run.
Expand All@@ -34,18 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0


#########################################################################################
# Need to define all the GH repos and their access tokens, see:
# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml
resources:
repositories:
- repository: testStatusRepo
type: github
endpoint: datashield-testing
name: datashield/testStatus
ref: master
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -82,11 +69,6 @@ jobs:
- checkout: self
path: 'dsBaseClient'

- checkout: testStatusRepo
path: 'testStatus'
persistCredentials: true
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# The MySQL install that comes with the VM doesn't seem compatable with our set up
Expand DownExpand Up@@ -233,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -272,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -361,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -387,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -524,75 +506,6 @@ jobs:
displayName: 'Down Opal Docker Composition'
condition: succeeded()

#####################################################################################
# Windup phase
#####################################################################################

#####################################################################################
# Output some important version numbers to file. This gets added to the testStatus
# commit so it can be parsed and used on the status table.
- bash: |

echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
condition: succeededOrFailed()


#####################################################################################
# Checkout the testStatus repo, add the results from here, push back to GH.
# TODO: Automatically pull in better email/name info from somewhere.
# TODO: More debug info in commit message
- bash: |

# Git needs some config set to be able to push to a repo.
git config --global user.email "you@example.com"
git config --global user.name "Azure pipeline"

# This repo is checked out in detatched head state, so reconnect it here.
git checkout master

# It is possible that other commits have been made to the testStatus repo since it
# was checked out. i.e. other pipeline runs might have finished.
git pull

# Make the directories if they dont already exist
mkdir --parents logs/$(projectName)/$(branchName)
mkdir --parents docs/$(projectName)/$(branchName)/latest

cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv

cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml

cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/

# Run the script to parse the results and build the html pages.
# status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch
source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName)

cp status.html docs/$(projectName)/$(branchName)/latest/index.html
git add logs/$(projectName)/$(branchName)/coveragelist.csv
git add logs/$(projectName)/$(branchName)/test_results.xml
git add logs/$(projectName)/$(branchName)/$(datetime).xml
git add logs/$(projectName)/$(branchName)/$(datetime).csv
git add logs/$(projectName)/$(branchName)/$(datetime).txt
git add docs/$(projectName)/$(branchName)/latest/index.html

git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)"
git push
exit 0

workingDirectory: $(Pipeline.Workspace)/testStatus
displayName: 'Parse test results'
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# Output the environment information to the console. This is useful for debugging.
# Always do this, even if some of the above has failed or the job has been cacelled.
Expand Down
16 changes: 8 additions & 8 deletions tests/testthat/connection_to_datasets/login_details.R
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,12 +22,12 @@ if (! is.null(getOption("default_driver"))) {
}

if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver")) {
ds.test_env$ping_address <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ping_config <- config(timeout=5, ssl_verifyhost=0, ssl_verifypeer=0)
ds.test_env$ping_address <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ping_config <- config(timeout=5)

ds.test_env$ip_address_1 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_2 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_3 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_1 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_2 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_3 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")

ds.test_env$user_1 <- getOption("opal.user", "administrator")
ds.test_env$user_2 <- getOption("opal.user", "administrator")
Expand All@@ -37,9 +37,9 @@ if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver
ds.test_env$password_2 <- getOption("opal.password", "datashield_test&")
ds.test_env$password_3 <- getOption("opal.password", "datashield_test&")

ds.test_env$options_1 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_2 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_3 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_1 <- "list()"
ds.test_env$options_2 <- "list()"
ds.test_env$options_3 <- "list()"

ds.test_env$secure_login_details <- TRUE
} else if (ds.test_env$driver == "ArmadilloDriver") {
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/data_files/obiba_opal-upload_testing_datasets.R
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Original file line numberDiff line numberDiff line change
Expand Up@@ -17,8 +17,8 @@ upload_testing_dataset_table <- function(opal, project_name, table_name, local_f
opal.table_save(opal, data, project_name, table_name, id.name = "_row_id_", force = TRUE)
}

# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/', opts = list())

upload_testing_dataset_table(opal, 'ANTHRO', 'anthro1', 'ANTHRO/anthro1.rda')
upload_testing_dataset_table(opal, 'ANTHRO', 'anthro2', 'ANTHRO/anthro2.rda')
Expand Down
14 changes: 0 additions & 14 deletions tests/testthat/perf_files/armadillo_azure-pipeline.csv
View file
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This file was deleted.

Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links"); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + '
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Merged
StuartWheater merged 10 commits into from
May 21, 2026
Merged

Changes to perf-batch-1 updating tests and setup #673

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8705f86
Updated azure-pipeline specification
StuartWheater May 14, 2026
848c695
Merge branch 'v7.0-dev' of github.com:StuartWheater/dsBaseClient into…
StuartWheater May 14, 2026
b1653ca
Merge branch 'datashield:v7.0-dev' into v7.0-dev
StuartWheater May 14, 2026
19afb23
Merge branch 'datashield:perf-batch-1' into perf-batch-1
StuartWheater May 17, 2026
f47d0b7
Updated perf profile
StuartWheater May 17, 2026
67c9ca7
Updated 'perf_rate.R'
StuartWheater May 17, 2026
2b3151f
Fix result file names
StuartWheater May 18, 2026
566fc17
Reworking to latest Opal
StuartWheater May 18, 2026
3369b38
Updated performance profile
StuartWheater May 19, 2026
5605198
Fixed use of Danger function in testing
StuartWheater May 20, 2026
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6 changes: 3 additions & 3 deletions armadillo_azure-pipelines.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -34,6 +34,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -274,7 +275,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -396,7 +397,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -534,7 +535,6 @@ jobs:
echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
Expand Down
15 changes: 8 additions & 7 deletions azure-pipelines.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -214,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -253,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -342,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -368,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand Down
5 changes: 2 additions & 3 deletions docker-compose_armadillo.yml
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
hostname: armadillo
ports:
- 8080:8080
image: datashield/armadillo_citest:5.11.0
image: datashield/armadillo_citest:latest
environment:
LOGGING_CONFIG: 'classpath:logback-file.xml'
AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

default:
hostname: default
image: datashield/rock-quebrada-lamda:latest
# image: datashield/rserver-panda-lamda:devel
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
5 changes: 3 additions & 2 deletions docker-compose_opal.yml
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@ services:
image: datashield/opal_citest:latest
ports:
- 8443:8443
- 8080:8080
links:
- mongo
- rock
Expand All@@ -15,11 +16,11 @@ services:
- ROCK_HOSTS=rock:8085
- ROCK_ADMINISTRATOR_PASSWORD=foobar
mongo:
image: mongo:4.4.15
image: mongo:8.0
environment:
- MONGO_INITDB_ROOT_USERNAME=root
- MONGO_INITDB_ROOT_PASSWORD=foobar
rock:
image: datashield/rock-quebrada-lamda-permissive:latest
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
103 changes: 8 additions & 95 deletions opal_azure-pipelines.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,11 +3,9 @@
# Starts with a vanilla Opal docker composition, installs dsBase
# and dsBaseClient (as well as dependencies - including a fully functional
# Opal server).
# Does checks and tests then saves results to testStatus repo.
#
# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
# /dsBaseClient <- Checked out version of datashield/dsBaseClient
# /testStatus <- Checked out version of datashield/testStatus
# /logs <- Where results of tests and lots are collated
#
# As of May 2020 this takes ~ 70 mins to run.
Expand All@@ -34,18 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0


#########################################################################################
# Need to define all the GH repos and their access tokens, see:
# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml
resources:
repositories:
- repository: testStatusRepo
type: github
endpoint: datashield-testing
name: datashield/testStatus
ref: master
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -82,11 +69,6 @@ jobs:
- checkout: self
path: 'dsBaseClient'

- checkout: testStatusRepo
path: 'testStatus'
persistCredentials: true
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# The MySQL install that comes with the VM doesn't seem compatable with our set up
Expand DownExpand Up@@ -233,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -272,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -361,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -387,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -524,75 +506,6 @@ jobs:
displayName: 'Down Opal Docker Composition'
condition: succeeded()

#####################################################################################
# Windup phase
#####################################################################################

#####################################################################################
# Output some important version numbers to file. This gets added to the testStatus
# commit so it can be parsed and used on the status table.
- bash: |

echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
condition: succeededOrFailed()


#####################################################################################
# Checkout the testStatus repo, add the results from here, push back to GH.
# TODO: Automatically pull in better email/name info from somewhere.
# TODO: More debug info in commit message
- bash: |

# Git needs some config set to be able to push to a repo.
git config --global user.email "you@example.com"
git config --global user.name "Azure pipeline"

# This repo is checked out in detatched head state, so reconnect it here.
git checkout master

# It is possible that other commits have been made to the testStatus repo since it
# was checked out. i.e. other pipeline runs might have finished.
git pull

# Make the directories if they dont already exist
mkdir --parents logs/$(projectName)/$(branchName)
mkdir --parents docs/$(projectName)/$(branchName)/latest

cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv

cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml

cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/

# Run the script to parse the results and build the html pages.
# status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch
source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName)

cp status.html docs/$(projectName)/$(branchName)/latest/index.html
git add logs/$(projectName)/$(branchName)/coveragelist.csv
git add logs/$(projectName)/$(branchName)/test_results.xml
git add logs/$(projectName)/$(branchName)/$(datetime).xml
git add logs/$(projectName)/$(branchName)/$(datetime).csv
git add logs/$(projectName)/$(branchName)/$(datetime).txt
git add docs/$(projectName)/$(branchName)/latest/index.html

git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)"
git push
exit 0

workingDirectory: $(Pipeline.Workspace)/testStatus
displayName: 'Parse test results'
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# Output the environment information to the console. This is useful for debugging.
# Always do this, even if some of the above has failed or the job has been cacelled.
Expand Down
16 changes: 8 additions & 8 deletions tests/testthat/connection_to_datasets/login_details.R
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Original file line numberDiff line numberDiff line change
Expand Up@@ -22,12 +22,12 @@ if (! is.null(getOption("default_driver"))) {
}

if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver")) {
ds.test_env$ping_address <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ping_config <- config(timeout=5, ssl_verifyhost=0, ssl_verifypeer=0)
ds.test_env$ping_address <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ping_config <- config(timeout=5)

ds.test_env$ip_address_1 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_2 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_3 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_1 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_2 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_3 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")

ds.test_env$user_1 <- getOption("opal.user", "administrator")
ds.test_env$user_2 <- getOption("opal.user", "administrator")
Expand All@@ -37,9 +37,9 @@ if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver
ds.test_env$password_2 <- getOption("opal.password", "datashield_test&")
ds.test_env$password_3 <- getOption("opal.password", "datashield_test&")

ds.test_env$options_1 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_2 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_3 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_1 <- "list()"
ds.test_env$options_2 <- "list()"
ds.test_env$options_3 <- "list()"

ds.test_env$secure_login_details <- TRUE
} else if (ds.test_env$driver == "ArmadilloDriver") {
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/data_files/obiba_opal-upload_testing_datasets.R
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Expand Up@@ -17,8 +17,8 @@ upload_testing_dataset_table <- function(opal, project_name, table_name, local_f
opal.table_save(opal, data, project_name, table_name, id.name = "_row_id_", force = TRUE)
}

# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/', opts = list())

upload_testing_dataset_table(opal, 'ANTHRO', 'anthro1', 'ANTHRO/anthro1.rda')
upload_testing_dataset_table(opal, 'ANTHRO', 'anthro2', 'ANTHRO/anthro2.rda')
Expand Down
14 changes: 0 additions & 14 deletions tests/testthat/perf_files/armadillo_azure-pipeline.csv
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default"); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Merged
StuartWheater merged 10 commits into from
May 21, 2026
Merged

Changes to perf-batch-1 updating tests and setup #673

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8705f86
Updated azure-pipeline specification
StuartWheater May 14, 2026
848c695
Merge branch 'v7.0-dev' of github.com:StuartWheater/dsBaseClient into…
StuartWheater May 14, 2026
b1653ca
Merge branch 'datashield:v7.0-dev' into v7.0-dev
StuartWheater May 14, 2026
19afb23
Merge branch 'datashield:perf-batch-1' into perf-batch-1
StuartWheater May 17, 2026
f47d0b7
Updated perf profile
StuartWheater May 17, 2026
67c9ca7
Updated 'perf_rate.R'
StuartWheater May 17, 2026
2b3151f
Fix result file names
StuartWheater May 18, 2026
566fc17
Reworking to latest Opal
StuartWheater May 18, 2026
3369b38
Updated performance profile
StuartWheater May 19, 2026
5605198
Fixed use of Danger function in testing
StuartWheater May 20, 2026
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6 changes: 3 additions & 3 deletions armadillo_azure-pipelines.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -34,6 +34,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -274,7 +275,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -396,7 +397,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -534,7 +535,6 @@ jobs:
echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
Expand Down
15 changes: 8 additions & 7 deletions azure-pipelines.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -214,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -253,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -342,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -368,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand Down
5 changes: 2 additions & 3 deletions docker-compose_armadillo.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
hostname: armadillo
ports:
- 8080:8080
image: datashield/armadillo_citest:5.11.0
image: datashield/armadillo_citest:latest
environment:
LOGGING_CONFIG: 'classpath:logback-file.xml'
AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

default:
hostname: default
image: datashield/rock-quebrada-lamda:latest
# image: datashield/rserver-panda-lamda:devel
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
5 changes: 3 additions & 2 deletions docker-compose_opal.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@ services:
image: datashield/opal_citest:latest
ports:
- 8443:8443
- 8080:8080
links:
- mongo
- rock
Expand All@@ -15,11 +16,11 @@ services:
- ROCK_HOSTS=rock:8085
- ROCK_ADMINISTRATOR_PASSWORD=foobar
mongo:
image: mongo:4.4.15
image: mongo:8.0
environment:
- MONGO_INITDB_ROOT_USERNAME=root
- MONGO_INITDB_ROOT_PASSWORD=foobar
rock:
image: datashield/rock-quebrada-lamda-permissive:latest
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
103 changes: 8 additions & 95 deletions opal_azure-pipelines.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,11 +3,9 @@
# Starts with a vanilla Opal docker composition, installs dsBase
# and dsBaseClient (as well as dependencies - including a fully functional
# Opal server).
# Does checks and tests then saves results to testStatus repo.
#
# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
# /dsBaseClient <- Checked out version of datashield/dsBaseClient
# /testStatus <- Checked out version of datashield/testStatus
# /logs <- Where results of tests and lots are collated
#
# As of May 2020 this takes ~ 70 mins to run.
Expand All@@ -34,18 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0


#########################################################################################
# Need to define all the GH repos and their access tokens, see:
# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml
resources:
repositories:
- repository: testStatusRepo
type: github
endpoint: datashield-testing
name: datashield/testStatus
ref: master
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -82,11 +69,6 @@ jobs:
- checkout: self
path: 'dsBaseClient'

- checkout: testStatusRepo
path: 'testStatus'
persistCredentials: true
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# The MySQL install that comes with the VM doesn't seem compatable with our set up
Expand DownExpand Up@@ -233,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -272,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -361,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -387,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -524,75 +506,6 @@ jobs:
displayName: 'Down Opal Docker Composition'
condition: succeeded()

#####################################################################################
# Windup phase
#####################################################################################

#####################################################################################
# Output some important version numbers to file. This gets added to the testStatus
# commit so it can be parsed and used on the status table.
- bash: |

echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
condition: succeededOrFailed()


#####################################################################################
# Checkout the testStatus repo, add the results from here, push back to GH.
# TODO: Automatically pull in better email/name info from somewhere.
# TODO: More debug info in commit message
- bash: |

# Git needs some config set to be able to push to a repo.
git config --global user.email "you@example.com"
git config --global user.name "Azure pipeline"

# This repo is checked out in detatched head state, so reconnect it here.
git checkout master

# It is possible that other commits have been made to the testStatus repo since it
# was checked out. i.e. other pipeline runs might have finished.
git pull

# Make the directories if they dont already exist
mkdir --parents logs/$(projectName)/$(branchName)
mkdir --parents docs/$(projectName)/$(branchName)/latest

cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv

cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml

cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/

# Run the script to parse the results and build the html pages.
# status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch
source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName)

cp status.html docs/$(projectName)/$(branchName)/latest/index.html
git add logs/$(projectName)/$(branchName)/coveragelist.csv
git add logs/$(projectName)/$(branchName)/test_results.xml
git add logs/$(projectName)/$(branchName)/$(datetime).xml
git add logs/$(projectName)/$(branchName)/$(datetime).csv
git add logs/$(projectName)/$(branchName)/$(datetime).txt
git add docs/$(projectName)/$(branchName)/latest/index.html

git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)"
git push
exit 0

workingDirectory: $(Pipeline.Workspace)/testStatus
displayName: 'Parse test results'
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# Output the environment information to the console. This is useful for debugging.
# Always do this, even if some of the above has failed or the job has been cacelled.
Expand Down
16 changes: 8 additions & 8 deletions tests/testthat/connection_to_datasets/login_details.R
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Expand Up@@ -22,12 +22,12 @@ if (! is.null(getOption("default_driver"))) {
}

if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver")) {
ds.test_env$ping_address <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ping_config <- config(timeout=5, ssl_verifyhost=0, ssl_verifypeer=0)
ds.test_env$ping_address <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ping_config <- config(timeout=5)

ds.test_env$ip_address_1 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_2 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_3 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_1 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_2 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_3 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")

ds.test_env$user_1 <- getOption("opal.user", "administrator")
ds.test_env$user_2 <- getOption("opal.user", "administrator")
Expand All@@ -37,9 +37,9 @@ if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver
ds.test_env$password_2 <- getOption("opal.password", "datashield_test&")
ds.test_env$password_3 <- getOption("opal.password", "datashield_test&")

ds.test_env$options_1 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_2 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_3 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_1 <- "list()"
ds.test_env$options_2 <- "list()"
ds.test_env$options_3 <- "list()"

ds.test_env$secure_login_details <- TRUE
} else if (ds.test_env$driver == "ArmadilloDriver") {
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/data_files/obiba_opal-upload_testing_datasets.R
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Expand Up@@ -17,8 +17,8 @@ upload_testing_dataset_table <- function(opal, project_name, table_name, local_f
opal.table_save(opal, data, project_name, table_name, id.name = "_row_id_", force = TRUE)
}

# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/', opts = list())

upload_testing_dataset_table(opal, 'ANTHRO', 'anthro1', 'ANTHRO/anthro1.rda')
upload_testing_dataset_table(opal, 'ANTHRO', 'anthro2', 'ANTHRO/anthro2.rda')
Expand Down
14 changes: 0 additions & 14 deletions tests/testthat/perf_files/armadillo_azure-pipeline.csv
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Merged
StuartWheater merged 10 commits into from
May 21, 2026
Merged

Changes to perf-batch-1 updating tests and setup #673

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8705f86
Updated azure-pipeline specification
StuartWheater May 14, 2026
848c695
Merge branch 'v7.0-dev' of github.com:StuartWheater/dsBaseClient into…
StuartWheater May 14, 2026
b1653ca
Merge branch 'datashield:v7.0-dev' into v7.0-dev
StuartWheater May 14, 2026
19afb23
Merge branch 'datashield:perf-batch-1' into perf-batch-1
StuartWheater May 17, 2026
f47d0b7
Updated perf profile
StuartWheater May 17, 2026
67c9ca7
Updated 'perf_rate.R'
StuartWheater May 17, 2026
2b3151f
Fix result file names
StuartWheater May 18, 2026
566fc17
Reworking to latest Opal
StuartWheater May 18, 2026
3369b38
Updated performance profile
StuartWheater May 19, 2026
5605198
Fixed use of Danger function in testing
StuartWheater May 20, 2026
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6 changes: 3 additions & 3 deletions armadillo_azure-pipelines.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -34,6 +34,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -274,7 +275,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -396,7 +397,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -534,7 +535,6 @@ jobs:
echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
Expand Down
15 changes: 8 additions & 7 deletions azure-pipelines.yml
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Expand Up@@ -32,6 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -214,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -253,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -342,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -368,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand Down
5 changes: 2 additions & 3 deletions docker-compose_armadillo.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
hostname: armadillo
ports:
- 8080:8080
image: datashield/armadillo_citest:5.11.0
image: datashield/armadillo_citest:latest
environment:
LOGGING_CONFIG: 'classpath:logback-file.xml'
AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

default:
hostname: default
image: datashield/rock-quebrada-lamda:latest
# image: datashield/rserver-panda-lamda:devel
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
5 changes: 3 additions & 2 deletions docker-compose_opal.yml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@ services:
image: datashield/opal_citest:latest
ports:
- 8443:8443
- 8080:8080
links:
- mongo
- rock
Expand All@@ -15,11 +16,11 @@ services:
- ROCK_HOSTS=rock:8085
- ROCK_ADMINISTRATOR_PASSWORD=foobar
mongo:
image: mongo:4.4.15
image: mongo:8.0
environment:
- MONGO_INITDB_ROOT_USERNAME=root
- MONGO_INITDB_ROOT_PASSWORD=foobar
rock:
image: datashield/rock-quebrada-lamda-permissive:latest
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
103 changes: 8 additions & 95 deletions opal_azure-pipelines.yml
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Expand Up@@ -3,11 +3,9 @@
# Starts with a vanilla Opal docker composition, installs dsBase
# and dsBaseClient (as well as dependencies - including a fully functional
# Opal server).
# Does checks and tests then saves results to testStatus repo.
#
# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
# /dsBaseClient <- Checked out version of datashield/dsBaseClient
# /testStatus <- Checked out version of datashield/testStatus
# /logs <- Where results of tests and lots are collated
#
# As of May 2020 this takes ~ 70 mins to run.
Expand All@@ -34,18 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0


#########################################################################################
# Need to define all the GH repos and their access tokens, see:
# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml
resources:
repositories:
- repository: testStatusRepo
type: github
endpoint: datashield-testing
name: datashield/testStatus
ref: master
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -82,11 +69,6 @@ jobs:
- checkout: self
path: 'dsBaseClient'

- checkout: testStatusRepo
path: 'testStatus'
persistCredentials: true
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# The MySQL install that comes with the VM doesn't seem compatable with our set up
Expand DownExpand Up@@ -233,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -272,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -361,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -387,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -524,75 +506,6 @@ jobs:
displayName: 'Down Opal Docker Composition'
condition: succeeded()

#####################################################################################
# Windup phase
#####################################################################################

#####################################################################################
# Output some important version numbers to file. This gets added to the testStatus
# commit so it can be parsed and used on the status table.
- bash: |

echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
condition: succeededOrFailed()


#####################################################################################
# Checkout the testStatus repo, add the results from here, push back to GH.
# TODO: Automatically pull in better email/name info from somewhere.
# TODO: More debug info in commit message
- bash: |

# Git needs some config set to be able to push to a repo.
git config --global user.email "you@example.com"
git config --global user.name "Azure pipeline"

# This repo is checked out in detatched head state, so reconnect it here.
git checkout master

# It is possible that other commits have been made to the testStatus repo since it
# was checked out. i.e. other pipeline runs might have finished.
git pull

# Make the directories if they dont already exist
mkdir --parents logs/$(projectName)/$(branchName)
mkdir --parents docs/$(projectName)/$(branchName)/latest

cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv

cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml

cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/

# Run the script to parse the results and build the html pages.
# status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch
source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName)

cp status.html docs/$(projectName)/$(branchName)/latest/index.html
git add logs/$(projectName)/$(branchName)/coveragelist.csv
git add logs/$(projectName)/$(branchName)/test_results.xml
git add logs/$(projectName)/$(branchName)/$(datetime).xml
git add logs/$(projectName)/$(branchName)/$(datetime).csv
git add logs/$(projectName)/$(branchName)/$(datetime).txt
git add docs/$(projectName)/$(branchName)/latest/index.html

git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)"
git push
exit 0

workingDirectory: $(Pipeline.Workspace)/testStatus
displayName: 'Parse test results'
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# Output the environment information to the console. This is useful for debugging.
# Always do this, even if some of the above has failed or the job has been cacelled.
Expand Down
16 changes: 8 additions & 8 deletions tests/testthat/connection_to_datasets/login_details.R
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -22,12 +22,12 @@ if (! is.null(getOption("default_driver"))) {
}

if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver")) {
ds.test_env$ping_address <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ping_config <- config(timeout=5, ssl_verifyhost=0, ssl_verifypeer=0)
ds.test_env$ping_address <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ping_config <- config(timeout=5)

ds.test_env$ip_address_1 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_2 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_3 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_1 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_2 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_3 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")

ds.test_env$user_1 <- getOption("opal.user", "administrator")
ds.test_env$user_2 <- getOption("opal.user", "administrator")
Expand All@@ -37,9 +37,9 @@ if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver
ds.test_env$password_2 <- getOption("opal.password", "datashield_test&")
ds.test_env$password_3 <- getOption("opal.password", "datashield_test&")

ds.test_env$options_1 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_2 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_3 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_1 <- "list()"
ds.test_env$options_2 <- "list()"
ds.test_env$options_3 <- "list()"

ds.test_env$secure_login_details <- TRUE
} else if (ds.test_env$driver == "ArmadilloDriver") {
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/data_files/obiba_opal-upload_testing_datasets.R
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -17,8 +17,8 @@ upload_testing_dataset_table <- function(opal, project_name, table_name, local_f
opal.table_save(opal, data, project_name, table_name, id.name = "_row_id_", force = TRUE)
}

# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/', opts = list())

upload_testing_dataset_table(opal, 'ANTHRO', 'anthro1', 'ANTHRO/anthro1.rda')
upload_testing_dataset_table(opal, 'ANTHRO', 'anthro2', 'ANTHRO/anthro2.rda')
Expand Down
14 changes: 0 additions & 14 deletions tests/testthat/perf_files/armadillo_azure-pipeline.csv
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode"); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })();
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Merged
StuartWheater merged 10 commits into from
May 21, 2026
Merged

Changes to perf-batch-1 updating tests and setup #673

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8705f86
Updated azure-pipeline specification
StuartWheater May 14, 2026
848c695
Merge branch 'v7.0-dev' of github.com:StuartWheater/dsBaseClient into…
StuartWheater May 14, 2026
b1653ca
Merge branch 'datashield:v7.0-dev' into v7.0-dev
StuartWheater May 14, 2026
19afb23
Merge branch 'datashield:perf-batch-1' into perf-batch-1
StuartWheater May 17, 2026
f47d0b7
Updated perf profile
StuartWheater May 17, 2026
67c9ca7
Updated 'perf_rate.R'
StuartWheater May 17, 2026
2b3151f
Fix result file names
StuartWheater May 18, 2026
566fc17
Reworking to latest Opal
StuartWheater May 18, 2026
3369b38
Updated performance profile
StuartWheater May 19, 2026
5605198
Fixed use of Danger function in testing
StuartWheater May 20, 2026
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6 changes: 3 additions & 3 deletions armadillo_azure-pipelines.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -34,6 +34,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -274,7 +275,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -396,7 +397,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -534,7 +535,6 @@ jobs:
echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
Expand Down
15 changes: 8 additions & 7 deletions azure-pipelines.yml
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -32,6 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -214,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -253,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -342,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -368,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand Down
5 changes: 2 additions & 3 deletions docker-compose_armadillo.yml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -3,7 +3,7 @@ services:
hostname: armadillo
ports:
- 8080:8080
image: datashield/armadillo_citest:5.11.0
image: datashield/armadillo_citest:latest
environment:
LOGGING_CONFIG: 'classpath:logback-file.xml'
AUDIT_LOG_PATH: '/app/logs/audit.log'
Expand All@@ -16,7 +16,6 @@ services:

default:
hostname: default
image: datashield/rock-quebrada-lamda:latest
# image: datashield/rserver-panda-lamda:devel
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
5 changes: 3 additions & 2 deletions docker-compose_opal.yml
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@ services:
image: datashield/opal_citest:latest
ports:
- 8443:8443
- 8080:8080
links:
- mongo
- rock
Expand All@@ -15,11 +16,11 @@ services:
- ROCK_HOSTS=rock:8085
- ROCK_ADMINISTRATOR_PASSWORD=foobar
mongo:
image: mongo:4.4.15
image: mongo:8.0
environment:
- MONGO_INITDB_ROOT_USERNAME=root
- MONGO_INITDB_ROOT_PASSWORD=foobar
rock:
image: datashield/rock-quebrada-lamda-permissive:latest
image: datashield/rock_citest-permissive:latest
environment:
DEBUG: "FALSE"
103 changes: 8 additions & 95 deletions opal_azure-pipelines.yml
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,11 +3,9 @@
# Starts with a vanilla Opal docker composition, installs dsBase
# and dsBaseClient (as well as dependencies - including a fully functional
# Opal server).
# Does checks and tests then saves results to testStatus repo.
#
# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
# /dsBaseClient <- Checked out version of datashield/dsBaseClient
# /testStatus <- Checked out version of datashield/testStatus
# /logs <- Where results of tests and lots are collated
#
# As of May 2020 this takes ~ 70 mins to run.
Expand All@@ -34,18 +32,7 @@ variables:
branchName: $(Build.SourceBranchName)
test_filter: '*'
_r_check_system_clock_: 0


#########################################################################################
# Need to define all the GH repos and their access tokens, see:
# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml
resources:
repositories:
- repository: testStatusRepo
type: github
endpoint: datashield-testing
name: datashield/testStatus
ref: master
perf.profile: 'azure-pipeline'


#########################################################################################
Expand DownExpand Up@@ -82,11 +69,6 @@ jobs:
- checkout: self
path: 'dsBaseClient'

- checkout: testStatusRepo
path: 'testStatus'
persistCredentials: true
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# The MySQL install that comes with the VM doesn't seem compatable with our set up
Expand DownExpand Up@@ -233,13 +215,13 @@ 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v7.0-dev'); 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 = 'v7.0-dev'); opal.logout(opal)"

sleep 60

R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); 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)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install dsBase to Opal, as set disclosure test options'
Expand DownExpand Up@@ -272,7 +254,7 @@ jobs:
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -361,9 +343,9 @@ jobs:
# 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 = '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='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.4'); 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 = '6.3.4'); opal.logout(opal)"

workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
Expand All@@ -387,7 +369,7 @@ jobs:
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
Expand DownExpand Up@@ -524,75 +506,6 @@ jobs:
displayName: 'Down Opal Docker Composition'
condition: succeeded()

#####################################################################################
# Windup phase
#####################################################################################

#####################################################################################
# Output some important version numbers to file. This gets added to the testStatus
# commit so it can be parsed and used on the status table.
- bash: |

echo 'branch:'$(branchName) >> $(datetime).txt
echo 'os:'$(lsb_release -ds) >> $(datetime).txt
echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt

workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Write versions to file'
condition: succeededOrFailed()


#####################################################################################
# Checkout the testStatus repo, add the results from here, push back to GH.
# TODO: Automatically pull in better email/name info from somewhere.
# TODO: More debug info in commit message
- bash: |

# Git needs some config set to be able to push to a repo.
git config --global user.email "you@example.com"
git config --global user.name "Azure pipeline"

# This repo is checked out in detatched head state, so reconnect it here.
git checkout master

# It is possible that other commits have been made to the testStatus repo since it
# was checked out. i.e. other pipeline runs might have finished.
git pull

# Make the directories if they dont already exist
mkdir --parents logs/$(projectName)/$(branchName)
mkdir --parents docs/$(projectName)/$(branchName)/latest

cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv

cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/
cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml

cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/

# Run the script to parse the results and build the html pages.
# status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch
source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName)

cp status.html docs/$(projectName)/$(branchName)/latest/index.html
git add logs/$(projectName)/$(branchName)/coveragelist.csv
git add logs/$(projectName)/$(branchName)/test_results.xml
git add logs/$(projectName)/$(branchName)/$(datetime).xml
git add logs/$(projectName)/$(branchName)/$(datetime).csv
git add logs/$(projectName)/$(branchName)/$(datetime).txt
git add docs/$(projectName)/$(branchName)/latest/index.html

git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)"
git push
exit 0

workingDirectory: $(Pipeline.Workspace)/testStatus
displayName: 'Parse test results'
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))


#####################################################################################
# Output the environment information to the console. This is useful for debugging.
# Always do this, even if some of the above has failed or the job has been cacelled.
Expand Down
16 changes: 8 additions & 8 deletions tests/testthat/connection_to_datasets/login_details.R
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -22,12 +22,12 @@ if (! is.null(getOption("default_driver"))) {
}

if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver")) {
ds.test_env$ping_address <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ping_config <- config(timeout=5, ssl_verifyhost=0, ssl_verifypeer=0)
ds.test_env$ping_address <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ping_config <- config(timeout=5)

ds.test_env$ip_address_1 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_2 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_3 <- paste("https://", ds.test_env$server_ip_address, ":8443", sep="")
ds.test_env$ip_address_1 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_2 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")
ds.test_env$ip_address_3 <- paste("http://", ds.test_env$server_ip_address, ":8080", sep="")

ds.test_env$user_1 <- getOption("opal.user", "administrator")
ds.test_env$user_2 <- getOption("opal.user", "administrator")
Expand All@@ -37,9 +37,9 @@ if ((ds.test_env$driver == "DSLiteDriver") || (ds.test_env$driver == "OpalDriver
ds.test_env$password_2 <- getOption("opal.password", "datashield_test&")
ds.test_env$password_3 <- getOption("opal.password", "datashield_test&")

ds.test_env$options_1 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_2 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_3 <- "list(ssl_verifyhost=0, ssl_verifypeer=0)"
ds.test_env$options_1 <- "list()"
ds.test_env$options_2 <- "list()"
ds.test_env$options_3 <- "list()"

ds.test_env$secure_login_details <- TRUE
} else if (ds.test_env$driver == "ArmadilloDriver") {
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/data_files/obiba_opal-upload_testing_datasets.R
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Original file line numberDiff line numberDiff line change
Expand Up@@ -17,8 +17,8 @@ upload_testing_dataset_table <- function(opal, project_name, table_name, local_f
opal.table_save(opal, data, project_name, table_name, id.name = "_row_id_", force = TRUE)
}

# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
# opal <- opal.login('administrator','datashield_test&', url='https://192.168.56.100:8/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/', opts = list())

upload_testing_dataset_table(opal, 'ANTHRO', 'anthro1', 'ANTHRO/anthro1.rda')
upload_testing_dataset_table(opal, 'ANTHRO', 'anthro2', 'ANTHRO/anthro2.rda')
Expand Down
14 changes: 0 additions & 14 deletions tests/testthat/perf_files/armadillo_azure-pipeline.csv
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