Merge pull request #244 from LeireAbarrategui/v6.1-dev

V6.1 dev

Author: StuartWheater

.Rbuildignore

@@ -4,6 +4,7 @@
 ^LICENSE.md$
 ^azure-pipelines\.yml$
 ^azure-pipelines_site\.pp$
+^azure-pipelines_site-dsdanger\.pp$
 ^azure-pipelines_check\.Rout$
 ^azure-pipelines_test\.Rout$
 ^checkDocumentationUpdated\.sh$

.Rd2pdf14688/Rd2.tex

@@ -0,0 +1,12 @@
+\documentclass[a4paper]{book}
+\usepackage[times,inconsolata,hyper]{Rd}
+\usepackage{makeidx}
+\usepackage[latin1]{inputenc} % @SET ENCODING@
+% \usepackage{graphicx} % @USE GRAPHICX@
+\makeindex{}
+\begin{document}
+\chapter*{}
+\begin{center}
+{\textbf{\huge \R{} documentation}} \par\bigskip{{\Large of \file{ds.skewness.Rd}}}
+\par\bigskip{\large \today}
+\end{center}

.Rd2pdf7124/Rd2.tex

@@ -0,0 +1,12 @@
+\documentclass[a4paper]{book}
+\usepackage[times,inconsolata,hyper]{Rd}
+\usepackage{makeidx}
+\usepackage[latin1]{inputenc} % @SET ENCODING@
+% \usepackage{graphicx} % @USE GRAPHICX@
+\makeindex{}
+\begin{document}
+\chapter*{}
+\begin{center}
+{\textbf{\huge \R{} documentation}} \par\bigskip{{\Large of \file{skewness.Rd}}}
+\par\bigskip{\large \today}
+\end{center}

azure-pipelines.yml

@@ -42,12 +42,12 @@ resources:
     endpoint: datashield-testing
     name: datashield/testStatus
     ref: master
-    
+
   - repository: datashield-infrastructureRepo
     type: github
     endpoint: datashield-testing
-    name: datashield/datashield-infrastructure
-    ref: v6.1-dev
+    name: StuartWheater/datashield-infrastructure
+    ref: v6.1-dev_dsdanger
 
 
 #########################################################################################
@@ -123,15 +123,19 @@ jobs:
     # 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 xenial-cran40/"
       sudo apt-get update
-      
+
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev r-base -y
       sudo R -q -e "install.packages(c('devtools','metafor','fields','covr'), 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('e1071'), 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')"
+
+      # XML grep for coverage report merging
+      sudo apt-get install -qq xml-twig-tools -y
 
     displayName: 'Install all dependencies for dsBaseClient'
     condition: succeeded()
@@ -158,10 +162,10 @@ jobs:
         echo "Run devtools::document() locally then commit again."
         exit 1
       else
-       echo "Documentation up to date."
-       exit 0
+        echo "Documentation up to date."
+        exit 0
       fi
-      
+
     workingDirectory: $(Pipeline.Workspace)/dsBaseClient
     displayName: 'Check manual updated before being committed'
     condition: succeeded()
@@ -173,7 +177,7 @@ jobs:
     # 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
 
@@ -187,7 +191,7 @@ jobs:
     # Install dsBase. This uses the datashield-infrastructure repo (and its dependencies) to do the install with puppet.
     # If previous steps have failed then don't run.
   - bash: |
-  
+
       # Set up puppet and r10k
       wget -nv https://apt.puppetlabs.com/puppet5-release-xenial.deb
       sudo dpkg -i puppet5-release-xenial.deb
@@ -197,11 +201,11 @@ jobs:
 
       sudo apt-get install puppet-agent -y
       sudo /opt/puppetlabs/puppet/bin/gem install r10k
-      
+
       pushd puppet/environments/datashield_azurepipelines
       sudo /opt/puppetlabs/puppet/bin/r10k puppetfile install
       popd
-      
+
       sudo /opt/puppetlabs/bin/puppet apply $(Pipeline.Workspace)/dsBaseClient/azure-pipelines_site.pp --environment datashield_azurepipelines --environmentpath puppet/environments
 
     workingDirectory: $(Pipeline.Workspace)/datashield-infrastructure
@@ -217,62 +221,152 @@ jobs:
     # 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.
-      
+
       # None of the below make the tests run
       #sudo R -e 'devtools::reload(".")'
       #sudo R -e 'library(dsBaseClient)'
       #sudo R -e 'devtools::check_built()'
       #sudo R --verbose -e 'devtools::build()'      
-      
+
       # Any of the below makes the tests work.
       #sudo R --verbose -e 'devtools::test()'
       #sudo R --verbose -e 'devtools::install()'
       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
+      #
+      # "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
       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$new(reporters = list(progress_rep, junit_rep));
+                testthat::test_package("$(projectName)", filter = "_-", 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 "Failed:   0" test_console_output_dsbase.txt
+
+    workingDirectory: $(Pipeline.Workspace)/dsBaseClient
+    displayName: 'Code coverage and JUnit report output, with dsBase'
+    condition: succeeded()
+
+
+    #####################################################################################
+    # Install dsDanger on server
+    # If previous steps have failed then don't run
+  - bash: |
+
+      sudo /opt/puppetlabs/bin/puppet apply $(Pipeline.Workspace)/dsBaseClient/azure-pipelines_site-dsdanger.pp --environment datashield_azurepipelines --environmentpath puppet/environments
+
+    workingDirectory: $(Pipeline.Workspace)/datashield-infrastructure
+    displayName: 'Install dsDanger DataSHIELD package on server'
+    condition: succeeded()
+
+
+    #####################################################################################
+    # Install dsDangerClient.
+    # If previous steps have failed then don't run
+  - bash: |
+
+      sudo R -q -e 'devtools::install()'
+      sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='v6.1-dev', dependencies = TRUE)"
+
+    workingDirectory: $(Pipeline.Workspace)/dsBaseClient
+    displayName: 'Install dsDangerClient DataSHIELD package'
+    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));
+                testthat::test_package("$(projectName)", filter = "smk_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 > $(Pipeline.Workspace)/logs/test_console_output.txt
+      xml_grep --pretty_print indented --wrap "testsuites" --descr "" --cond "testsuite" test_results_dsbase.xml test_results_dsdanger.xml > test_results.xml
+
+      # Create 'coveragelist.csv'
+      sudo R -q -e '
+        library(covr);
+        dsbase.res   <- base::readRDS("test_results_dsbase.rds")
+        dsdanger.res <- base::readRDS("test_results_dsdanger.rds")
         write.csv(
-                  coverage_to_list(
-                                   covr::package_coverage(
-                                                          type = c("none"),
-                                                          code = c(
-                                                                   '"'"'library(testthat); 
-                                                                   output_file <- file("test_console_output.txt"); 
-                                                                   sink(output_file); 
-                                                                   sink(output_file, type = "message"); 
-                                                                   library(testthat); 
-                                                                   junit_rep <- JunitReporter$new(file = "test_results.xml"); 
-                                                                   progress_rep <- ProgressReporter$new(max_failures = 999999); 
-                                                                   multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep)); 
-                                                                   testthat::test_package("$(projectName)", filter = "$(test_filter)",reporter = multi_rep, stop_on_failure = FALSE)'"'"')
-                                                         )
-                                  ),
-                                  "coveragelist.csv"
-                 )'
-      
+            coverage_to_list(
+                c(dsbase.res, dsdanger.res)
+                "coveragelist.csv"
+            )
+        )'
+
       # display the test console output
-      cat test_console_output.txt
+      cat test_console_output_dsdanger.txt
+
       mv coveragelist.csv $(Pipeline.Workspace)/logs
       mv test_results.xml $(Pipeline.Workspace)/logs
-      mv test_console_output.txt $(Pipeline.Workspace)/logs
-      
-      grep --quiet "Failed:   0" $(Pipeline.Workspace)/logs/test_console_output.txt
+
+      grep --quiet "Failed:   0" test_console_output_dsdanger.txt
 
     workingDirectory: $(Pipeline.Workspace)/dsBaseClient
-    displayName: 'Code coverage and JUnit report output'
+    displayName: 'Code coverage and JUnit report output, with dsBase and dsDanger'
     condition: succeeded()
 
 
@@ -281,7 +375,7 @@ jobs:
     # 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=$(sed 's/failures="0" errors="0"//' test_results.xml | grep --count errors=)
       echo "Number of testsuites with issues: "$issue_count

azure-pipelines_site-dsdanger.pp

@@ -0,0 +1,22 @@
+# Datashield for Azure Pipelines testing.
+#
+# Install mysql and mongodb, include test data but don't install the firewall.
+# This is an example please change to meet the needs of your install. Consider changing any passwords in this file!
+#
+
+class { ::datashield:
+  opal_password      => 'datashield_test&',
+  opal_password_hash => '$shiro1$SHA-256$500000$gcnVxdEmOjaN+NfsK/1NsA==$UOobbhJsBBojnbsfzIBX9GTWjWQFi8aJZxFvFKmOiSE=',
+
+  test_data      => true,         # Install the test data
+  firewall       => false,        # Do not install the firewall
+  mysql          => true,         # Install mysql server
+  mongodb        => true,         # Install mongodb server
+  remote_mongodb => false,        # There is not a remote mongodb server
+  remote_mysql   => false,        # There is not a remote mysql server
+
+  dsbase_githubusername      => 'datashield',
+  dsbase_ref                 => 'v6.1-dev',
+  dsdanger_githubusername    => 'datashield',
+  dsdanger_ref               => 'v6.1-dev'
+}

azure-pipelines_site.pp

@@ -17,10 +17,6 @@
 
   dsbase_githubusername      => 'datashield',
   dsbase_ref                 => 'v6.1-dev',
-  dsstats_githubusername     => 'datashield',
-  dsstats_ref                => '',
-  dsgraphics_githubusername  => 'datashield',
-  dsgraphics_ref             => '',
-  dsmodelling_githubusername => 'datashield',
-  dsmodelling_ref            => ''
+  dsdanger_githubusername    => 'datashield',
+  dsdanger_ref               => ''
 }

man/.Rd2pdf7520/Rd2.tex

@@ -0,0 +1,12 @@
+\documentclass[a4paper]{book}
+\usepackage[times,inconsolata,hyper]{Rd}
+\usepackage{makeidx}
+\usepackage[latin1]{inputenc} % @SET ENCODING@
+% \usepackage{graphicx} % @USE GRAPHICX@
+\makeindex{}
+\begin{document}
+\chapter*{}
+\begin{center}
+{\textbf{\huge \R{} documentation}} \par\bigskip{{\Large of \file{skewness.Rd}}}
+\par\bigskip{\large \today}
+\end{center}