Merge pull request datashield#673 from StuartWheater/perf-batch-1

Changes to perf-batch-1 updating tests and setup

Author: StuartWheater

armadillo_azure-pipelines.yml

@@ -34,6 +34,7 @@ variables:
   branchName:  $(Build.SourceBranchName)
   test_filter: '*'
   _r_check_system_clock_: 0
+  perf.profile: 'azure-pipeline'
 
 
 #########################################################################################
@@ -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"),
@@ -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=$PERF_PROFILE R -q -e '
         library(covr);
         dsdanger.res <- covr::package_coverage(
             type = c("none"),
@@ -534,7 +535,6 @@ jobs:
       echo 'branch:'$(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'

azure-pipelines.yml

@@ -32,6 +32,7 @@ variables:
   branchName:  $(Build.SourceBranchName)
   test_filter: '*'
   _r_check_system_clock_: 0
+  perf.profile: 'azure-pipeline'
 
 
 #########################################################################################
@@ -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: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
     displayName: 'Install dsBase to Opal, as set disclosure test options'
@@ -253,7 +254,7 @@ jobs:
       #
       # "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
       # testthat::test_package("$(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"),
@@ -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: $(Pipeline.Workspace)/dsBaseClient
     displayName: 'Install dsDanger package on Opal server'
@@ -368,7 +369,7 @@ jobs:
       # testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
       # R output and messages are redirected by sink() to test_console_output.txt
       # junit reporter output is to test_results.xml
-      sudo R -q -e '
+      sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
         library(covr);
         dsdanger.res <- covr::package_coverage(
             type = c("none"),

docker-compose_armadillo.yml

@@ -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'
@@ -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"

docker-compose_opal.yml

@@ -3,6 +3,7 @@ services:
         image: datashield/opal_citest:latest
         ports:
             - 8443:8443
+            - 8080:8080
         links:
             - mongo
             - rock
@@ -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"

opal_azure-pipelines.yml

@@ -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.
@@ -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'
 
 
 #########################################################################################
@@ -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
@@ -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: $(Pipeline.Workspace)/dsBaseClient/tests/testthat/data_files
     displayName: 'Install dsBase to Opal, as set disclosure test options'
@@ -272,7 +254,7 @@ jobs:
       #
       # "_-|arg-|smk-|datachk-|disc-|math-|expt-|expt_smk-"
       # testthat::test_package("$(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"),
@@ -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: $(Pipeline.Workspace)/dsBaseClient
     displayName: 'Install dsDanger package on Opal server'
@@ -387,7 +369,7 @@ jobs:
       # testthat::testpackage uses a MultiReporter, comprised of a ProgressReporter and JunitReporter
       # R output and messages are redirected by sink() to test_console_output.txt
       # junit reporter output is to test_results.xml
-      sudo R -q -e '
+      sudo env PERF_PROFILE=$PERF_PROFILE R -q -e '
         library(covr);
         dsdanger.res <- covr::package_coverage(
             type = c("none"),
@@ -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.

tests/testthat/connection_to_datasets/login_details.R

@@ -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")
@@ -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") {

tests/testthat/data_files/obiba_opal-upload_testing_datasets.R

@@ -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')