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azure-pipelines.yml
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#########################################################################################
# DataSHIELD Azure test suite.
# Starts with a vanilla Opal and Armadillo docker composition, installs dsBase
# and dsBaseClient (as well as dependencies - including a fully functional
# Opal and Armadillo 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.
# As of Nov 2020 this takes ~ 120 mins to run.
#
# The only things that should ever be changed are the repo branches in the resources.
#
#########################################################################################
#####################################################################################
# These should all be constant, except test_filter. This can be used to test subsets
# of test files in the testthat directory. Options are like:
# '*' <- Run all tests
# 'ds.asNumeric*' <- Run all ds.asNumeric tests, i.e. all the arg, smk etc tests.
# '*_smk_*' <- Run all the smoke tests for all functions.
variables:
datetime: $[format('{0:yyyyMMddHHmmss}', pipeline.startTime)]
repoName: $(Build.Repository.Name)
projectName: 'dsBaseClient'
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
#########################################################################################
# When and under what condition to run the pipeline.
schedules:
- cron: "0 0 * * 0"
displayName: Weekly build - master
branches:
include:
- master
always: true
- cron: "0 2 * * *"
displayName: Nightly build - v6.3.0-dev
branches:
include:
- v6.3.0-dev
always: true
#########################################################################################
# Jobs
jobs:
- job: build_and_run_tests
timeoutInMinutes: 300
pool:
vmImage: ubuntu-20.04
steps:
#####################################################################################
# Checkout the source code to a subfolder.
# This may give an error in the logs like:
# [warning]Unable move and reuse existing repository to required location
# This is an Azure bug - https://github.com/microsoft/azure-pipelines-yaml/issues/403
- 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
# so we delete it.
# If previous steps have failed then don't run.
- bash: |
# Work-around for tempory Bazel's apt repository issue.
curl https://bazel.build/bazel-release.pub.gpg | sudo apt-key add -
# Purge the default mysql installed on the VM as it is incompatible with our stuff.
sudo service mysql stop
sudo apt-get update
sudo apt-get remove --purge mysql-client mysql-server mysql-common -y
sudo apt-get purge mysql-client mysql-server mysql-common -y
sudo apt-get autoremove -y
sudo apt-get autoclean -y
sudo rm -rf /var/lib/mysql/
displayName: 'Uninstall default MySQL'
condition: succeeded()
#####################################################################################
# The Azure VMs have 2 CPUs, so configure R to use both when compile/install packages.
# If previous steps have failed then don't run.
- bash: |
echo "options(Ncpus=4)" >> ~/.Rprofile
displayName: 'Tweak local R env using .Rprofile'
condition: succeeded()
#####################################################################################
# Install R and all the dependencies dsBaseClient requires.
# If previous steps have failed then don't run.
- bash: |
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"
sudo add-apt-repository ppa:cran/libgit2
sudo apt-get update
sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
sudo apt-get install -qq libharfbuzz-dev libfribidi-dev -y
sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table','panelaggregation'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')"
sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='v6.3.0-dev', dependencies = TRUE)"
# XML grep for coverage report merging
sudo apt-get install -qq xml-twig-tools -y
displayName: 'Install all dependencies for dsBaseClient'
condition: succeeded()
#####################################################################################
# Check that the man files in the repo match what is in the function headers. i.e. has
# devtools::document() been run before commiting?
# If previous steps have failed then don't run.
# If this step fails still mark as failed, but don't stop the rest of the steps running.
- bash: |
# Concatenate all the files in the man dir into one long string and md5sum it.
orig_sum=$(find man -type f | sort -u | xargs cat | md5sum)
# Rebuild the documentation.
R -e "devtools::document()"
# Concatenate all the files in the man dir into one long string and md5sum it.
new_sum=$(find man -type f | sort -u | xargs cat | md5sum)
if [ "$orig_sum" != "$new_sum" ]; then
echo "Your committed manual files (man/*.Rd) are out of sync with the documentation in the R files."
echo "Run devtools::document() locally then commit again."
exit 1
else
echo "Documentation up to date."
exit 0
fi
workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Check manual updated before being committed'
condition: succeeded()
continueOnError: true
#####################################################################################
# Run devtools::check on the checked out source code.
# If previous steps have failed then don't run.
# If this step fails still mark as failed, but don't stop the rest of the steps running.
- bash: |
R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout
grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout
workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Devtools checks'
condition: succeeded()
continueOnError: true
#####################################################################################
#
# Opal phase
#
#####################################################################################
#####################################################################################
# Deploy docker for Opal.
# If previous steps have failed then don't run.
- task: DockerCompose@0
inputs:
action: Run Services
dockerComposeFile: ../dsBaseClient/docker-compose_opal.yml
projectName: dsBaseClient
qualifyImageNames: true
buildImages: true
abortOnContainerExit: true
detached: true
displayName: 'Install Opal servers (opal, rserver, mongodb)'
condition: succeeded()
#####################################################################################
# Install test datasets.
# If previous steps have failed then don't run.
- bash: |
sleep 240
R -q -f "obiba_opal-upload_testing_datasets.R"
workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install test datasets to Opal'
condition: succeeded()
#####################################################################################
# Install dsBase.
# If previous steps have failed then don't run.
- bash: |
R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.0-dev'); 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.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'
condition: succeeded()
#####################################################################################
# Essentially run devtools::test() on the checked out code. This is wrapped up with
# code coverage. The actual command is vary convoluted as it had to do some things
# which are not default behaviour: output the results to a JUnit xml file, not stop
# when a small number of errors have happened, run through the code coverage tool.
# TODO: Tidy up variable names - use timestamps here.
# TODO: Why is DSLite needed for this to run?!
- bash: |
# There is an issue with the way we are using packages. The wrapped up test command
# below fails in a way that implies that it is not installed. I cannot figure out
# why this is case. As a work around we can run some of the functions below. My
# best guess is that there is an implicit build or similar that happens. Although
# I cannot replicate that directly with build etc directly.
sudo R --verbose -e 'devtools::check()'
mkdir $(Pipeline.Workspace)/logs
# run the coverage tool and output to coveragelist.csv
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
code = c(
'"'"'
library(testthat);
output_file <- file("test_console_output_dsbase.txt");
sink(output_file);
sink(output_file, type = "message");
library(testthat);
junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml");
progress_rep <- ProgressReporter$new(max_failures = 999999);
multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
options("default_driver" = "OpalDriver");
testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
'"'"'
)
);
base::saveRDS(dsbase.res, "test_results_dsbase.rds")'
# display the test console output
cat test_console_output_dsbase.txt
grep --quiet " FAIL 0 " test_console_output_dsbase.txt
workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Code coverage and JUnit report output, with dsBase'
condition: succeeded()
#####################################################################################
# Parse the JUnit file to see if there are any errors/warnings. If there are then
# echo them so finding bugs should be easier.
# This should run even if previous steps have failed.
- bash: |
# Strip out when error and failure = 0 and count the number of times it does not.
issue_count=$(sed 's/failures="0" errors="0"//' test_results_dsbase.xml | sed 's/errors="0" failures="0"//' | grep --count errors=)
echo "Number of testsuites with issues: "$issue_count
echo "Testsuites with issues:"
sed 's/failures="0" errors="0"//' test_results_dsbase.xml | sed 's/errors="0" failures="0"//' | grep errors= > issues.log
cat issues.log
exit $issue_count
workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Check for errors & Failures in JUnit file'
condition: succeededOrFailed()
#####################################################################################
# Essentially run devtools::test() on the checked out code for discctrl reporting.
# The actual command is vary convoluted as it had to do some things
# which are not default behaviour: output the results to a JUnit xml file, not stop
# when a small number of errors have happened, run through the code coverage tool.
# TODO: Tidy up variable names - use timestamps here.
#- bash: |
# junit reporter output is to test_results_discctrl.xml
# sudo R -q -e '
# library(testthat);
# output_file <- file("test_console_output_discctrl.txt");
# sink(output_file);
# sink(output_file, type = "message");
# junit_rep <- JunitReporter$new(file = "test_results_discctrl.xml");
# progress_rep <- ProgressReporter$new(max_failures = 999999);
# multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
# default_driver <- "OpalDriver";
# testthat::test_package("$(projectName)", filter = "_-|discctrl-", reporter = multi_rep, stop_on_failure = FALSE)'
# cat test_console_output_discctrl.txt
# if [ -e test_results_discctrl.xml ]; then
# mv test_results_discctrl.xml $(Pipeline.Workspace)/logs
# else
# touch $(Pipeline.Workspace)/logs/test_results_discctrl.xml
# fi
# workingDirectory: $(Pipeline.Workspace)/dsBaseClient
# displayName: 'discctrl report output'
# condition: succeededOrFailed()
#####################################################################################
# Install dsDanger on Opal server
# If previous steps have failed then don't run
- bash: |
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 = 'v6.3.0-dev'); opal.logout(opal)"
workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Opal server'
condition: succeeded()
#####################################################################################
# Essentially run devtools::test() on the checked out code. This is wrapped up with
# code coverage. The actual command is vary convoluted as it had to do some things
# which are not default behaviour: output the results to a JUnit xml file, not stop
# when a small number of errors have happened, run through the code coverage tool.
# TODO: Tidy up variable names - use timestamps here.
- bash: |
# See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed.
sudo R --verbose -e 'devtools::check()'
pwd
mkdir $(Pipeline.Workspace)/logs
# run the coverage tool and output to coveragelist.csv
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
code = c(
'"'"'
library(testthat);
output_file <- file("test_console_output_dsdanger.txt");
sink(output_file);
sink(output_file, type = "message");
library(testthat);
junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml");
progress_rep <- ProgressReporter$new(max_failures = 999999);
multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
options("default_driver" = "OpalDriver");
testthat::test_package("$(projectName)", filter = "__dgr-|datachk_dgr-|smk_dgr-|arg_dgr-|disc_dgr-|smk_expt_dgr-|expt_dgr-|math_dgr-", reporter = multi_rep, stop_on_failure = FALSE)
'"'"'
)
);
base::saveRDS(dsdanger.res, "test_results_dsdanger.rds")'
# Merge coverage results
cat test_results_dsbase.txt test_results_dsdanger.txt > $(Pipeline.Workspace)/logs/test_console_output.txt
xml_grep --pretty_print indented --wrap "testsuites" --descr "" --cond "testsuite" test_results_dsbase.xml test_results_dsdanger.xml > test_results.xml
# Create 'coveragelist.csv'
sudo R -q -e '
library(covr);
dsbase.res <- base::readRDS("test_results_dsbase.rds")
write.csv(
coverage_to_list(
dsbase.res
),
"coveragelist.csv"
)'
# display the test console output
cat test_console_output_dsdanger.txt
mv coveragelist.csv $(Pipeline.Workspace)/logs
mv test_results.xml $(Pipeline.Workspace)/logs
grep --quiet " FAIL 0 " test_console_output_dsdanger.txt
workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Code coverage and JUnit report output, with dsBase and dsDanger'
condition: succeeded()
#####################################################################################
# Parse the JUnit file to see if there are any errors/warnings. If there are then
# echo them so finding bugs should be easier.
# This should run even if previous steps have failed.
- bash: |
# Strip out when error and failure = 0 and count the number of times it does not.
issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | sed 's/errors="0" failures="0"//' | grep --count errors=)
echo "Number of testsuites with issues: "$issue_count
echo "Testsuites with issues:"
sed 's/failures="0" errors="0"//' test_results.xml | sed 's/errors="0" failures="0"//' | grep errors= > issues.log
cat issues.log
exit $issue_count
workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Check for errors & Failures in JUnit file'
condition: succeededOrFailed()
#####################################################################################
# Essentially run devtools::test() on the checked out code for bug reporting.
# The actual command is vary convoluted as it had to do some things
# which are not default behaviour: output the results to a JUnit xml file, not stop
# when a small number of errors have happened, run through the code coverage tool.
# TODO: Tidy up variable names - use timestamps here.
# - bash: |
# junit reporter output is to test_results_bug.xml
# sudo R -q -e '
# library(testthat);
# output_file <- file("test_console_output_bug.txt");
# sink(output_file);
# sink(output_file, type = "message");
# junit_rep <- JunitReporter$new(file = "test_results_bug.xml");
# progress_rep <- ProgressReporter$new(max_failures = 999999);
# multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
# options("default_driver" = "OpalDriver");
# testthat::test_package("$(projectName)", filter = "__bug-|datachk_bug-|smk_bug-|arg_bug-|disc_bug-|smk_expt_bug-|expt_bug-|math_bug-", reporter = multi_rep, stop_on_failure = FALSE)'
# cat test_console_output_bug.txt
# if [ -e test_results_bug.xml ]; then
# mv test_results_bug.xml $(Pipeline.Workspace)/logs
# else
# touch $(Pipeline.Workspace)/logs/test_results_bug.xml
# fi
# workingDirectory: $(Pipeline.Workspace)/dsBaseClient
# displayName: 'Bug report output'
# condition: succeededOrFailed()
#####################################################################################
# Parse the JUnit file to see if there are any errors/warnings. If there are then
# echo them so finding bugs should be easier.
# This should run even if previous steps have failed.
- bash: |
# Strip out when error and failure = 0 and count the number of times it does not.
issue_count=$(sed 's/failures="0" errors="0"//' test_results_bug.xml | sed 's/errors="0" failures="0"//' | grep --count errors=)
echo "Number of testsuites with issues: "$issue_count
echo "Testsuites with issues:"
sed 's/failures="0" errors="0"//' test_results_bug.xml | sed 's/errors="0" failures="0"//' | grep errors= > issues.log
cat issues.log
no_issue_count=$(sed 's/failures="0" errors="0"//' test_results_bug.xml | sed 's/errors="0" failures="0"//' | grep -v --count errors=)
echo
echo "Number of testsuites with no issues: "$no_issue_count
echo "Testsuites with issues:"
sed 's/failures="0" errors="0"//' test_results_bug.xml | sed 's/errors="0" failures="0"//' | grep "<testsuite " | grep -v errors= > no_issues.log
cat no_issues.log
exit 0
workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Bug summary report output'
condition: succeededOrFailed()
#####################################################################################
# 'Down' Opal Docker Composition
- bash: |
docker compose -f docker-compose_opal.yml down -v
workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Down Opal Docker Composition'
condition: succeeded()
#####################################################################################
#
# Armadillo phase
#
#####################################################################################
#####################################################################################
# Deploy docker for Opal.
# If previous steps have failed then don't run.
- task: DockerCompose@0
inputs:
action: Run Services
dockerComposeFile: ../dsBaseClient/docker-compose_armadillo.yml
projectName: dsBaseClient
qualifyImageNames: true
buildImages: true
abortOnContainerExit: true
detached: true
displayName: 'Install Armadillo servers (armadillo, rserver, minio)'
condition: succeeded()
#####################################################################################
# Install test datasets.
# If previous steps have failed then don't run.
- bash: |
sleep 240
R -q -f "molgenis_armadillo-upload_testing_datasets.R"
workingDirectory: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
displayName: 'Install test datasets to Armadillo'
condition: succeeded()
#####################################################################################
# Install dsBase.
# If previous steps have failed then don't run.
- bash: |
curl -u admin:admin http://localhost:8080/whitelist
curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.0-permissive.tar.gz" -X POST http://localhost:8080/install-package
docker container restart dsbaseclient_armadillo_1
sleep 120
curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
curl -u admin:admin http://localhost:8080/whitelist
workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsBase to Armadillo'
condition: succeeded()
#####################################################################################
# Essentially run devtools::test() on the checked out code. This is wrapped up with
# code coverage. The actual command is vary convoluted as it had to do some things
# which are not default behaviour: output the results to a JUnit xml file, not stop
# when a small number of errors have happened, run through the code coverage tool.
# TODO: Tidy up variable names - use timestamps here.
# TODO: Why is DSLite needed for this to run?!
- bash: |
# There is an issue with the way we are using packages. The wrapped up test command
# below fails in a way that implies that it is not installed. I cannot figure out
# why this is case. As a work around we can run some of the functions below. My
# best guess is that there is an implicit build or similar that happens. Although
# I cannot replicate that directly with build etc directly.
sudo R --verbose -e 'devtools::check()'
mkdir $(Pipeline.Workspace)/logs
# run the coverage tool and output to coveragelist.csv
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
#
# "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
# testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
sudo R -q -e '
library(covr);
dsbase.res <- covr::package_coverage(
type = c("none"),
code = c(
'"'"'
library(testthat);
output_file <- file("test_console_output_dsbase.txt");
sink(output_file);
sink(output_file, type = "message");
library(testthat);
junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml");
progress_rep <- ProgressReporter$new(max_failures = 999999);
multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
options("default_driver" = "ArmadilloDriver");
testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE)
'"'"'
)
);
base::saveRDS(dsbase.res, "test_results_dsbase.rds")'
# display the test console output
cat test_console_output_dsbase.txt
grep --quiet " FAIL 0 " test_console_output_dsbase.txt
workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Code coverage and JUnit report output, with dsBase'
condition: succeeded()
#####################################################################################
# Parse the JUnit file to see if there are any errors/warnings. If there are then
# echo them so finding bugs should be easier.
# This should run even if previous steps have failed.
- bash: |
# Strip out when error and failure = 0 and count the number of times it does not.
issue_count=$(sed 's/failures="0" errors="0"//' test_results_dsbase.xml | sed 's/errors="0" failures="0"//' | grep --count errors=)
echo "Number of testsuites with issues: "$issue_count
echo "Testsuites with issues:"
sed 's/failures="0" errors="0"//' test_results_dsbase.xml | sed 's/errors="0" failures="0"//' | grep errors= > issues.log
cat issues.log
exit $issue_count
workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Check for errors & Failures in JUnit file'
condition: succeededOrFailed()
#####################################################################################
# Essentially run devtools::test() on the checked out code for discctrl reporting.
# The actual command is vary convoluted as it had to do some things
# which are not default behaviour: output the results to a JUnit xml file, not stop
# when a small number of errors have happened, run through the code coverage tool.
# TODO: Tidy up variable names - use timestamps here.
#- bash: |
# junit reporter output is to test_results_discctrl.xml
# sudo R -q -e '
# library(testthat);
# output_file <- file("test_console_output_discctrl.txt");
# sink(output_file);
# sink(output_file, type = "message");
# junit_rep <- JunitReporter$new(file = "test_results_discctrl.xml");
# progress_rep <- ProgressReporter$new(max_failures = 999999);
# multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
# options("default_driver" = "ArmadilloDriver");
# testthat::test_package("$(projectName)", filter = "_-|discctrl-", reporter = multi_rep, stop_on_failure = FALSE)'
# cat test_console_output_discctrl.txt
# if [ -e test_results_discctrl.xml ]; then
# mv test_results_discctrl.xml $(Pipeline.Workspace)/logs
# else
# touch $(Pipeline.Workspace)/logs/test_results_discctrl.xml
# fi
# workingDirectory: $(Pipeline.Workspace)/dsBaseClient
# displayName: 'discctrl report output'
# condition: succeededOrFailed()
#####################################################################################
# Install dsDanger on Opal server
# If previous steps have failed then don't run
- bash: |
curl -u admin:admin http://localhost:8080/whitelist
curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.0.tar.gz" -X POST http://localhost:8080/install-package
docker container restart dsbaseclient_armadillo_1
sleep 120
curl -u admin:admin -X POST http://localhost:8080/whitelist/dsDanger
curl -u admin:admin http://localhost:8080/whitelist
workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Install dsDanger package on Armadillo server'
condition: succeeded()
#####################################################################################
# Essentially run devtools::test() on the checked out code. This is wrapped up with
# code coverage. The actual command is vary convoluted as it had to do some things
# which are not default behaviour: output the results to a JUnit xml file, not stop
# when a small number of errors have happened, run through the code coverage tool.
# TODO: Tidy up variable names - use timestamps here.
- bash: |
# See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed.
sudo R --verbose -e 'devtools::check()'
pwd
mkdir $(Pipeline.Workspace)/logs
# run the coverage tool and output to coveragelist.csv
# testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
# R output and messages are redirected by sink() to test_console_output.txt
# junit reporter output is to test_results.xml
sudo R -q -e '
library(covr);
dsdanger.res <- covr::package_coverage(
type = c("none"),
code = c(
'"'"'
library(testthat);
output_file <- file("test_console_output_dsdanger.txt");
sink(output_file);
sink(output_file, type = "message");
library(testthat);
junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml");
progress_rep <- ProgressReporter$new(max_failures = 999999);
multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
options("default_driver" = "ArmadilloDriver");
testthat::test_package("$(projectName)", filter = "__dgr-|datachk_dgr-|smk_dgr-|arg_dgr-|disc_dgr-|smk_expt_dgr-|expt_dgr-|math_dgr-", reporter = multi_rep, stop_on_failure = FALSE)
'"'"'
)
);
base::saveRDS(dsdanger.res, "test_results_dsdanger.rds")'
# Merge coverage results
cat test_results_dsbase.txt test_results_dsdanger.txt > $(Pipeline.Workspace)/logs/test_console_output.txt
xml_grep --pretty_print indented --wrap "testsuites" --descr "" --cond "testsuite" test_results_dsbase.xml test_results_dsdanger.xml > test_results.xml
# Create 'coveragelist.csv'
sudo R -q -e '
library(covr);
dsbase.res <- base::readRDS("test_results_dsbase.rds")
write.csv(
coverage_to_list(
dsbase.res
),
"coveragelist.csv"
)'
# display the test console output
cat test_console_output_dsdanger.txt
mv coveragelist.csv $(Pipeline.Workspace)/logs
mv test_results.xml $(Pipeline.Workspace)/logs
grep --quiet " FAIL 0 " test_console_output_dsdanger.txt
workingDirectory: $(Pipeline.Workspace)/dsBaseClient
displayName: 'Code coverage and JUnit report output, with dsBase and dsDanger'
condition: succeeded()
#####################################################################################
# Parse the JUnit file to see if there are any errors/warnings. If there are then
# echo them so finding bugs should be easier.
# This should run even if previous steps have failed.
- bash: |
# Strip out when error and failure = 0 and count the number of times it does not.
issue_count=$(sed 's/failures="0" errors="0"//' test_results.xml | sed 's/errors="0" failures="0"//' | grep --count errors=)
echo "Number of testsuites with issues: "$issue_count
echo "Testsuites with issues:"
sed 's/failures="0" errors="0"//' test_results.xml | sed 's/errors="0" failures="0"//' | grep errors= > issues.log
cat issues.log
exit $issue_count
workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Check for errors & Failures in JUnit file'
condition: succeededOrFailed()
#####################################################################################
# Essentially run devtools::test() on the checked out code for bug reporting.
# The actual command is vary convoluted as it had to do some things
# which are not default behaviour: output the results to a JUnit xml file, not stop
# when a small number of errors have happened, run through the code coverage tool.
# TODO: Tidy up variable names - use timestamps here.
# - bash: |
# junit reporter output is to test_results_bug.xml
# sudo R -q -e '
# library(testthat);
# output_file <- file("test_console_output_bug.txt");
# sink(output_file);
# sink(output_file, type = "message");
# junit_rep <- JunitReporter$new(file = "test_results_bug.xml");
# progress_rep <- ProgressReporter$new(max_failures = 999999);
# multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep));
# options("default_driver" = "ArmadilloDriver");
# testthat::test_package("$(projectName)", filter = "__bug-|datachk_bug-|smk_bug-|arg_bug-|disc_bug-|smk_expt_bug-|expt_bug-|math_bug-", reporter = multi_rep, stop_on_failure = FALSE)'
# cat test_console_output_bug.txt
# if [ -e test_results_bug.xml ]; then
# mv test_results_bug.xml $(Pipeline.Workspace)/logs
# else
# touch $(Pipeline.Workspace)/logs/test_results_bug.xml
# fi
# workingDirectory: $(Pipeline.Workspace)/dsBaseClient
# displayName: 'Bug report output'
# condition: succeededOrFailed()
#####################################################################################
# Parse the JUnit file to see if there are any errors/warnings. If there are then
# echo them so finding bugs should be easier.
# This should run even if previous steps have failed.
- bash: |
# Strip out when error and failure = 0 and count the number of times it does not.
issue_count=$(sed 's/failures="0" errors="0"//' test_results_bug.xml | sed 's/errors="0" failures="0"//' | grep --count errors=)
echo "Number of testsuites with issues: "$issue_count
echo "Testsuites with issues:"
sed 's/failures="0" errors="0"//' test_results_bug.xml | sed 's/errors="0" failures="0"//' | grep errors= > issues.log
cat issues.log
no_issue_count=$(sed 's/failures="0" errors="0"//' test_results_bug.xml | sed 's/errors="0" failures="0"//' | grep -v --count errors=)
echo
echo "Number of testsuites with no issues: "$no_issue_count
echo "Testsuites with issues:"
sed 's/failures="0" errors="0"//' test_results_bug.xml | sed 's/errors="0" failures="0"//' | grep "<testsuite " | grep -v errors= > no_issues.log
cat no_issues.log
exit 0
workingDirectory: $(Pipeline.Workspace)/logs
displayName: 'Bug summary report output'
condition: succeededOrFailed()
#####################################################################################
# Windup phase
#####################################################################################
#####################################################################################
# Output some important version numbers to file. This gets added to the testStatus
# commit so it can be parsed and used on the status table.
- bash: |
echo 'branch:'$(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: $(Pipeline.Workspace)/testStatus
displayName: 'Parse test results'
condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))
#####################################################################################
# Output the environment information to the console. This is useful for debugging.
# Always do this, even if some of the above has failed or the job has been cacelled.
- bash: |
echo 'BranchName: '$(branchName)
echo 'ProjectName: '$(projectName)
echo 'RepoName: '$(repoName)
echo -e "\n#############################"
echo -e "ls /: ######################"
ls $(Pipeline.Workspace)
echo -e "\n#############################"
echo -e "lscpu: ######################"
lscpu
echo -e "\n#############################"
echo -e "memory: #####################"
free -m
echo -e "\n#############################"
echo -e "env: ########################"
env
echo -e "\n#############################"
echo -e "Puppet version: #############"
/opt/puppetlabs/bin/puppet --version
/opt/puppetlabs/puppet/bin/r10k version
echo -e "\n#############################"
echo -e "Rprofile: ###################"
cat $(Pipeline.Workspace)/dsBaseClient/.Rprofile
echo -e "\n#############################"
echo -e "R installed.packages(): #####"
R -e 'installed.packages()'
echo -e "\n#############################"
echo -e "R sessionInfo(): ############"
R -e 'sessionInfo()'
sudo apt install tree -y
pwd
echo -e "\n#############################"
echo -e "File tree: ##################"
tree $(Pipeline.Workspace)
displayName: 'Environment info'
condition: always()