Switch to Opal via http and 8080

Author: StuartWheater

docker-compose_opal.yml

@@ -2,6 +2,7 @@ services:
     opal:
         image: datashield/opal_citest:latest
         ports:
+            - 8443:8443
             - 8080:8080
         links:
             - mongo
@@ -15,7 +16,7 @@ services:
             - ROCK_HOSTS=rock:8085
             - ROCK_ADMINISTRATOR_PASSWORD=foobar
     mongo:
-        image: mongo:6.0.27
+        image: mongo:8.0
         environment:
             - MONGO_INITDB_ROOT_USERNAME=root
             - MONGO_INITDB_ROOT_PASSWORD=foobar

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.
@@ -37,18 +35,6 @@ variables:
   perf.profile: 'azure-pipeline'
 
 
-#########################################################################################
-# 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:
@@ -83,11 +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
@@ -234,13 +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(opal)"
+      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 = 'v6.3.5-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 = 'v6.3.5-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'
@@ -363,9 +344,9 @@ 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(opal)"
+      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'
@@ -526,75 +507,6 @@ 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/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://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0))
+opal <- opal.login('administrator','datashield_test&', url='http://localhost:8080/')
 
 upload_testing_dataset_table(opal, 'ANTHRO', 'anthro1', 'ANTHRO/anthro1.rda')
 upload_testing_dataset_table(opal, 'ANTHRO', 'anthro2', 'ANTHRO/anthro2.rda')