Update v6.3.6 dev-feat/standardise-df with latest v6.3.6-dev

azure-pipelines.yml

@@ -221,6 +221,8 @@ jobs:
 
       sleep 60
 
+      R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); 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

opal_azure-pipelines.yml

@@ -221,6 +221,8 @@ jobs:
 
       sleep 60
 
+      R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.profile_init(opal, name = 'default', packages = c('dsBase', 'dsTidyverse', 'resourcer')); 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

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 +1,32 @@
-#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 <- NULL
    }
-   return (ip.address)
+   return (server.url)
 }
 
 
 
 init.local.settings <- function()
 {
-  path <- getwd()
-  sub.folder.name <- "/connection_to_datasets/"
-  file.name <- "local_settings.csv"
-  return(paste(path, sub.folder.name,file.name, sep=""))
-
+   path            <- getwd()
+   sub.folder.name <- "/connection_to_datasets/"
+   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