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))
     }
 

azure-pipelines.yml

@@ -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

@@ -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'

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"

tests/testthat/connection_to_datasets/init_discordant_datasets.R

@@ -5,17 +5,17 @@ init.discordant.dataset.simple <- function(variables)
       if (ds.test_env$driver == "OpalDriver")
       {
         builder <- DSI::newDSLoginBuilder(.silent = TRUE)
-        builder$append(server = "discordant1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "DISCORDANT.DISCORDANT_STUDY1", options=ds.test_env$options_1)
-        builder$append(server = "discordant2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "DISCORDANT.DISCORDANT_STUDY2", options=ds.test_env$options_2)
-        builder$append(server = "discordant3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "DISCORDANT.DISCORDANT_STUDY3", options=ds.test_env$options_3)
+        builder$append(server = "discordant1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "DISCORDANT.DISCORDANT_STUDY1", options=ds.test_env$options_1)
+        builder$append(server = "discordant2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "DISCORDANT.DISCORDANT_STUDY2", options=ds.test_env$options_2)
+        builder$append(server = "discordant3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "DISCORDANT.DISCORDANT_STUDY3", options=ds.test_env$options_3)
         ds.test_env$login.data <- builder$build()
       }
       else if (ds.test_env$driver == "ArmadilloDriver")
       {
         builder <- DSI::newDSLoginBuilder(.silent = TRUE)
-        builder$append(server = "discordant1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/discordant/DISCORDANT_STUDY1", driver = "ArmadilloDriver")
-        builder$append(server = "discordant2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/discordant/DISCORDANT_STUDY2", driver = "ArmadilloDriver")
-        builder$append(server = "discordant3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/discordant/DISCORDANT_STUDY3", driver = "ArmadilloDriver")
+        builder$append(server = "discordant1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "datashield/discordant/DISCORDANT_STUDY1", driver = "ArmadilloDriver")
+        builder$append(server = "discordant2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "datashield/discordant/DISCORDANT_STUDY2", driver = "ArmadilloDriver")
+        builder$append(server = "discordant3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "datashield/discordant/DISCORDANT_STUDY3", driver = "ArmadilloDriver")
         ds.test_env$login.data <- builder$build()
       }
       else 

tests/testthat/connection_to_datasets/init_local_settings.R

@@ -1,28 +1,33 @@
-#this file stores some settings for the continuous integration and local testing.
+#
+# The file "connection_to_datasets/local_settings.csv" (within the directory "tests/testthat") contains, if present,
+# values which can be used to affect the behavious of the continuous integration.
+#
+# The server URL is in a CVS file, being the value of the first column, first row.
+#
 
-init.ip.address <- function()
+init.server.url <- function()
 {
    file.name <- init.local.settings()
    if (file.exists(file.name))
    {
-      content <- read.csv(file.name, header = FALSE)
-      ip.address <- as.character(content[[1]][1])
+      content    <- read.csv(file.name, header = FALSE)
+      server.url <- as.character(content[[1]][1])
    }
    else
    {
-      # ip.address <- "127.0.0.1"
-      ip.address <- "localhost"
+      # server.url <- "http://127.0.0.1:8080/"
+      server.url <- "http://localhost:8080/"
    }
-   return (ip.address)
+   return (server.url)
 }
 
 
 
 init.local.settings <- function()
 {
-  path <- getwd()
+  path            <- getwd()
   sub.folder.name <- "/connection_to_datasets/"
-  file.name <- "local_settings.csv"
-  return(paste(path, sub.folder.name,file.name, sep=""))
-
+  file.name       <- "local_settings.csv"
+
+  return(paste(path, sub.folder.name, file.name, sep=""))
 }

tests/testthat/connection_to_datasets/init_mediation_datasets.R

@@ -5,9 +5,9 @@ init.mediation.dataset.upb <- function(variables)
         if (ds.test_env$driver == "OpalDriver")
         {
             builder <- DSI::newDSLoginBuilder(.silent = TRUE)
-            builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.UPBdata1", options=ds.test_env$options_1)
-            builder$append(server = "study2", url = ds.test_env$ip_address_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "MEDIATION.UPBdata2", options=ds.test_env$options_2)
-            builder$append(server = "study3", url = ds.test_env$ip_address_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "MEDIATION.UPBdata3", options=ds.test_env$options_3)
+            builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.UPBdata1", options=ds.test_env$options_1)
+            builder$append(server = "study2", url = ds.test_env$server_url_2, user = ds.test_env$user_2, password = ds.test_env$password_2, table = "MEDIATION.UPBdata2", options=ds.test_env$options_2)
+            builder$append(server = "study3", url = ds.test_env$server_url_3, user = ds.test_env$user_3, password = ds.test_env$password_3, table = "MEDIATION.UPBdata3", options=ds.test_env$options_3)
             ds.test_env$login.data <- builder$build()
         }
         else 
@@ -25,7 +25,7 @@ init.mediation.dataset.student <- function(variables)
         if (ds.test_env$driver == "OpalDriver")
         {
             builder <- DSI::newDSLoginBuilder(.silent = TRUE)
-            builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.student", options=ds.test_env$options_1)
+            builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.student", options=ds.test_env$options_1)
             ds.test_env$login.data <- builder$build()
         }
         else 
@@ -43,7 +43,7 @@ init.mediation.dataset.framing <- function(variables)
         if (ds.test_env$driver == "OpalDriver")
         {
             builder <- DSI::newDSLoginBuilder(.silent = TRUE)
-            builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.framing", options=ds.test_env$options_1)
+            builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.framing", options=ds.test_env$options_1)
             ds.test_env$login.data <- builder$build()
         }
         else 
@@ -61,7 +61,7 @@ init.mediation.dataset.vv2015 <- function(variables)
         if (ds.test_env$driver == "OpalDriver")
         {
             builder <- DSI::newDSLoginBuilder(.silent = TRUE)
-            builder$append(server = "study1", url = ds.test_env$ip_address_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.vv2015", options=ds.test_env$options_1)
+            builder$append(server = "study1", url = ds.test_env$server_url_1, user = ds.test_env$user_1, password = ds.test_env$password_1, table = "MEDIATION.vv2015", options=ds.test_env$options_1)
             ds.test_env$login.data <- builder$build()
         }
         else