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StuartWheaterStuartWheater
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Added libuv for devtools
1 parent e73f177 commit 1780750

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Lines changed: 4 additions & 92 deletions

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‎armadillo_azure-pipelines.yml‎

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@@ -133,7 +133,7 @@ jobs:
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sudo apt-get upgrade -y
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sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
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sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
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sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
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sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')"

‎azure-pipelines.yml‎

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@@ -114,7 +114,7 @@ jobs:
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sudo apt-get upgrade -y
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sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
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sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
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sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
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sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"

‎opal_azure-pipelines.yml‎

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@@ -3,11 +3,9 @@
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# Starts with a vanilla Opal docker composition, installs dsBase
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# and dsBaseClient (as well as dependencies - including a fully functional
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# Opal server).
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# Does checks and tests then saves results to testStatus repo.
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#
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# Inside the root directory $(Pipeline.Workspace) will be a file tree like:
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# /dsBaseClient <- Checked out version of datashield/dsBaseClient
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# /testStatus <- Checked out version of datashield/testStatus
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# /logs <- Where results of tests and lots are collated
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#
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# As of May 2020 this takes ~ 70 mins to run.
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perf.profile: 'azure-pipeline'
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#########################################################################################
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# Need to define all the GH repos and their access tokens, see:
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# https://docs.microsoft.com/en-us/azure/devops/pipelines/library/service-endpoints?view=azure-devops&tabs=yaml
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resources:
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repositories:
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- repository: testStatusRepo
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type: github
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endpoint: datashield-testing
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name: datashield/testStatus
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ref: master
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#########################################################################################
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# When and under what condition to run the pipeline.
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schedules:
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- checkout: self
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path: 'dsBaseClient'
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- checkout: testStatusRepo
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path: 'testStatus'
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persistCredentials: true
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condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))
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#####################################################################################
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# The MySQL install that comes with the VM doesn't seem compatable with our set up
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sudo apt-get upgrade -y
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sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
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sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
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sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
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sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
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sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
@@ -236,7 +217,7 @@ jobs:
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- bash: |
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R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(opal)"
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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 = 'v6.4.0-dev'); opal.logout(opal)"
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R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)"
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sleep 60
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displayName: 'Down Opal Docker Composition'
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condition: succeeded()
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#####################################################################################
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# Windup phase
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#####################################################################################
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#####################################################################################
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# Output some important version numbers to file. This gets added to the testStatus
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# commit so it can be parsed and used on the status table.
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- bash: |
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echo 'branch:'$(branchName) >> $(datetime).txt
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echo 'os:'$(lsb_release -ds) >> $(datetime).txt
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echo 'R:'$(R --version | head -n 1) >> $(datetime).txt
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echo 'opal:'$(opal system --opal localhost:8443 --user administrator --password "datashield_test&" --version) >> $(datetime).txt
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workingDirectory: $(Pipeline.Workspace)/logs
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displayName: 'Write versions to file'
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condition: succeededOrFailed()
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#####################################################################################
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# Checkout the testStatus repo, add the results from here, push back to GH.
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# TODO: Automatically pull in better email/name info from somewhere.
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# TODO: More debug info in commit message
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- bash: |
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# Git needs some config set to be able to push to a repo.
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git config --global user.email "you@example.com"
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git config --global user.name "Azure pipeline"
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# This repo is checked out in detatched head state, so reconnect it here.
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git checkout master
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# It is possible that other commits have been made to the testStatus repo since it
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# was checked out. i.e. other pipeline runs might have finished.
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git pull
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# Make the directories if they dont already exist
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mkdir --parents logs/$(projectName)/$(branchName)
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mkdir --parents docs/$(projectName)/$(branchName)/latest
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cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/
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cp $(Pipeline.Workspace)/logs/coveragelist.csv logs/$(projectName)/$(branchName)/$(datetime).csv
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cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/
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cp $(Pipeline.Workspace)/logs/test_results.xml logs/$(projectName)/$(branchName)/$(datetime).xml
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cp $(Pipeline.Workspace)/logs/$(datetime).txt logs/$(projectName)/$(branchName)/
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# Run the script to parse the results and build the html pages.
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# status.py JUnit_file.xml coverage_file.csv output_file.html local_repo_path remote_repo_name branch
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source/status.py logs/$(projectName)/$(branchName)/$(datetime).xml logs/$(projectName)/$(branchName)/$(datetime).csv logs/$(projectName)/$(branchName)/$(datetime).txt status.html $(Pipeline.Workspace)/$(projectName) $(projectName) $(branchName)
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cp status.html docs/$(projectName)/$(branchName)/latest/index.html
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git add logs/$(projectName)/$(branchName)/coveragelist.csv
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git add logs/$(projectName)/$(branchName)/test_results.xml
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git add logs/$(projectName)/$(branchName)/$(datetime).xml
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git add logs/$(projectName)/$(branchName)/$(datetime).csv
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git add logs/$(projectName)/$(branchName)/$(datetime).txt
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git add docs/$(projectName)/$(branchName)/latest/index.html
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git commit -m "Azure auto test for $(projectName)/$(branchName) @ $(datetime)" -m "Debug info:\nProjectName:$(projectName)\nBranchName:$(branchName)\nDataTime:$(datetime)"
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git push
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exit 0
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workingDirectory: $(Pipeline.Workspace)/testStatus
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displayName: 'Parse test results'
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condition: and(eq(variables['Build.Repository.Name'], 'datashield/dsBaseClient'), ne(variables['Build.Reason'], 'PullRequest'))
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#####################################################################################
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# Output the environment information to the console. This is useful for debugging.
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# Always do this, even if some of the above has failed or the job has been cacelled.

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