Updates to v6.4.0 from v6.3.6 in 04/06/2026

.github/workflows/dsBaseClient_test_suite.yaml

@@ -138,7 +138,7 @@ jobs:
       - name: Install dsBase to Armadillo
         run: |
           curl -u admin:admin -X GET http://localhost:8080/packages
-          curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.5-permissive.tar.gz" -X POST http://localhost:8080/install-package
+          curl -u admin:admin -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.6-permissive.tar.gz" -X POST http://localhost:8080/install-package
           sleep 60
           docker restart dsbaseclient-armadillo-1
           sleep 30

DESCRIPTION

@@ -81,6 +81,6 @@ Suggests:
     DSOpal,
     DSMolgenisArmadillo,
     DSLite
-RoxygenNote: 7.3.3
 Encoding: UTF-8
 Language: en-GB
+Config/roxygen2/version: 8.0.0

R/ds.glm.R

@@ -565,7 +565,8 @@ ds.glm <- function(formula=NULL, data=NULL, family=NULL, offset=NULL, weights=NU
       # Sum participants only during first iteration.
       nsubs.total<-Reduce(f="+", .select(study.summary, 'numsubs'))
       # Save family
-      f <- study.summary[[1]]$family
+      family.value <- study.summary[[1]]$family
+      f <- if (is.list(family.value) && "family" %in% names(family.value)) family.value$family else family.value
     }
 
     #Create variance covariance matrix as inverse of information matrix
@@ -640,7 +641,7 @@ ds.glm <- function(formula=NULL, data=NULL, family=NULL, offset=NULL, weights=NU
     beta.vect.final<-beta.vect.next
 
     scale.par <- 1
-    if(f$family== 'gaussian') {
+    if(f == 'gaussian') {
       scale.par <- dev.total / (nsubs.total-length(beta.vect.next))
     }
 

armadillo_azure-pipelines.yml

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

azure-pipelines.yml

@@ -114,7 +114,7 @@ jobs:
       sudo apt-get upgrade -y
 
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
-      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
+      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
       sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
@@ -215,13 +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 = 'v6.4.0-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'
@@ -344,9 +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'

docker-compose_opal.yml

@@ -3,6 +3,7 @@ services:
         image: datashield/opal_citest:latest
         ports:
             - 8443:8443
+            - 8080:8080
         links:
             - mongo
             - rock
@@ -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
@@ -133,7 +114,7 @@ jobs:
       sudo apt-get upgrade -y
 
       sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y
-      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y
+      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev libuv1-dev -y
       sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')"
       sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')"
@@ -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 = 'v6.4.0-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 = 'v6.4.0-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'
@@ -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/docker/armadillo/standard/config/application.yml

@@ -67,8 +67,13 @@ stdout.log.path: '/logs/armadillo.log'
 
 logging:
   level:
-    root: INFO
+    root: "warn"
     ## change to DEBUG to have more details, typically when developing
-    org.molgenis: INFO
+    org.molgenis: "warn"
     ## Don't log upload data
-    org.apache.coyote.http11.Http11InputBuffer: INFO
+    org.apache.coyote.http11.Http11InputBuffer: "warn"
+    ## SpringFramework
+    org.springframework.boot: "warn"
+    org.springframework.web: "warn"
+    org.springframework.core: "warn"
+    org.springframework.codex: "warn"