Merge pull request #1 from StuartWheater/v6.1-dev_dsdanger

LeireAbarrategui · web-flow · commit 014bd293f374 · 2020-08-24T14:38:56.000+01:00
V6.1 dev dsdanger
diff --git a/.Rbuildignore b/.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$
diff --git a/azure-pipelines.yml b/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 +123,18 @@ 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')"
 
+      # XML grep for coverage report merging
+      sudo apt-get install -qq xml-twig-tools -y
+
     displayName: 'Install all dependencies for dsBaseClient'
     condition: succeeded()
 
@@ -157,10 +160,10 @@ 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()
@@ -172,7 +175,7 @@ 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
 
@@ -186,7 +189,7 @@ 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
@@ -196,11 +199,11 @@ 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
@@ -216,24 +219,99 @@ 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
 
@@ -243,35 +321,50 @@ jobs:
       # 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()
 
 
@@ -280,7 +373,7 @@ 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
diff --git a/azure-pipelines_site-dsdanger.pp b/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'
+}
diff --git a/azure-pipelines_site.pp b/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               => ''
 }
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -11,7 +11,7 @@
 # Datashield test suite set up
 #
 
-context("setup")
+context("setup - start")
 
 library(lme4)
 library(e1071)
diff --git a/tests/testthat/test-smk_dgr-ds.asCharacter.R b/tests/testthat/test-smk_dgr-ds.asCharacter.R
@@ -0,0 +1,50 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2018-2020 University of Newcastle upon Tyne. All rights reserved.
+#
+# This program and the accompanying materials
+# are made available under the terms of the GNU Public License v3.0.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+#
+# Set up
+#
+
+context("ds.asCharacter::smk_dgr::setup")
+
+require(dsDangerClient)
+
+connect.studies.dataset.cnsim(list("LAB_TSC"))
+
+test_that("setup", {
+    ds_expect_variables(c("D"))
+})
+
+#
+# Tests
+#
+
+context("ds.asCharacter::smk_dgr::simple test")
+test_that("simple test", {
+    res <- ds.asCharacter("D$LAB_TSC")
+
+    expect_equal(length(res), 2)
+    expect_equal(res$is.object.created, "A data object <ascharacter.newobj> has been created in all specified data sources")
+    expect_equal(res$validity.check, "<ascharacter.newobj> appears valid in all sources")
+})
+
+#
+# Done
+#
+
+context("ds.asCharacter::smk_dgr::stutdown")
+
+test_that("setup", {
+    ds_expect_variables(c("D", "ascharacter.newobj"))
+})
+
+disconnect.studies.dataset.cnsim()
+
+context("ds.asCharacter::smk_dgr::done")

Original file line number	Diff line number	Diff line change
`@@ -11,7 +11,7 @@`
`11`	`11`	`# Datashield test suite set up`
`12`	`12`	`#`
`13`	`13`
`14`		`-context("setup")`
	`14`	`+context("setup - start")`
`15`	`15`
`16`	`16`	`library(lme4)`
`17`	`17`	`library(e1071)`