datashield · StuartWheater · Oct 31, 2023 · Aug 18, 2023 · Aug 21, 2023 · Aug 23, 2023
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,6 +14,6 @@
 ^R/secure.global.ranking.md$
 ^_pkgdown\.yml$
 ^docs$
-^dsBase_6.3.0.tar.gz$
-^dsBase_6.3.0-permissive.tar.gz$
+^dsBase_6.3.1.tar.gz$
+^dsBase_6.3.1-permissive.tar.gz$
 ^dsDanger_6.3.0.tar.gz$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dsBaseClient
 Title: DataSHIELD Client Functions
-Version: 6.3.0
+Version: 6.3.1.9000
 Author: DataSHIELD Developers <datashield@liverpool.ac.uk>
 Maintainer: DataSHIELD Developers <datashield@liverpool.ac.uk>
 Description: DataSHIELD client functions for the client side.

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -55,10 +55,10 @@ schedules:
       - master
     always: true
   - cron: "0 2 * * *"
-    displayName: Nightly build - v6.3.0-dev
+    displayName: Nightly build - v6.3.1-dev
     branches:
       include:
-      - v6.3.0-dev
+      - v6.3.1-dev
     always: true
 
 #########################################################################################
@@ -229,7 +229,7 @@ jobs:
     # Install dsBase.
     # If previous steps have failed then don't run.
   - bash: |
-      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 = 'v6.3.0-dev'); 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 = 'v6.3.1-dev'); 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.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
 
@@ -554,7 +554,7 @@ jobs:
   - bash: |
       curl -u admin:admin http://localhost:8080/whitelist
 
-      curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.0-permissive.tar.gz" -X POST http://localhost:8080/install-package
+      curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.1-permissive.tar.gz" -X POST http://localhost:8080/install-package
 
       docker container restart dsbaseclient_armadillo_1
       sleep 120
@@ -683,7 +683,7 @@ jobs:
   - bash: |
       curl -u admin:admin http://localhost:8080/whitelist
 
-      curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.0.tar.gz" -X POST http://localhost:8080/install-package
+      curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.1.tar.gz" -X POST http://localhost:8080/install-package
 
       docker container restart dsbaseclient_armadillo_1
       sleep 120

diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml
@@ -3,15 +3,15 @@ version: "3.4"
 services:
     armadillo:
         hostname: armadillo
-        image: datashield/armadillo3:test
+        image: datashield/armadillo_citest:1.0.0
         environment:
-            RSERVE_HOST: rserver
             DEBUG: "FALSE"
         ports:
             - 8080:8080
-    rserver:
-        hostname: rserver
-        image: datashield/armadillo-rserver_caravan-yak:1.0.0
+
+    citest_rserver:
+        hostname: citest_rserver
+        image: datashield/armadillo-rserver_ionic-aqueduct:1.0.0
         environment:
             DEBUG: "FALSE"
         ports:

diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml
@@ -2,7 +2,7 @@ version: '3'
 
 services:
     opal:
-        image: obiba/opal:4.5
+        image: obiba/opal:4.6
         ports:
             - "8443:8443"
         links:
@@ -22,4 +22,4 @@ services:
             - MONGO_INITDB_ROOT_USERNAME=root
             - MONGO_INITDB_ROOT_PASSWORD=foobar
     rock:
-        image: obiba/rock:1.0-R4.2
+        image: datashield/rock-base:6.3-R4.3
diff --git a/dsBase_6.3.0-permissive.tar.gz → dsBase_6.3.1-permissive.tar.gz b/dsBase_6.3.0-permissive.tar.gz → dsBase_6.3.1-permissive.tar.gz
diff --git a/dsBase_6.3.0.tar.gz → dsBase_6.3.1.tar.gz b/dsBase_6.3.0.tar.gz → dsBase_6.3.1.tar.gz
diff --git a/tests/testthat/test-arg-ds.dataFrameSubset.R b/tests/testthat/test-arg-ds.dataFrameSubset.R
@@ -1,3 +1,4 @@
+
 #-------------------------------------------------------------------------------
 # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved.
 #
@@ -51,9 +52,9 @@ test_that("dataFrameSubset_erros", {
     res.errors <- DSI::datashield.errors()
 
     expect_length(res.errors, 3)
-    expect_match(res.errors$sim1, "* Error in data\\.frame\\(M\\) : object 'M' not found")
-    expect_match(res.errors$sim2, "* Error in data\\.frame\\(M\\) : object 'M' not found")
-    expect_match(res.errors$sim3, "* Error in data\\.frame\\(M\\) : object 'M' not found")
+    expect_match(res.errors$sim1, "* object 'M' not found\\n")
+    expect_match(res.errors$sim2, "* object 'M' not found\\n")
+    expect_match(res.errors$sim3, "* object 'M' not found\\n")
 })
 
 context("ds.dataFrameSubset::arg::missing 'V1' value server-side")

diff --git a/tests/testthat/test-arg-ds.foobar.R b/tests/testthat/test-arg-ds.foobar.R
@@ -55,13 +55,14 @@ test_that("non existent aggregate foobarDS", {
     expect_error(datashield.aggregate(conns=ds.test_env$connections, expr=calltext))
 
     errs <- datashield.errors()
+
     expect_length(errs, 3)
     expect_length(errs$sim1, 1)
-    expect_true(errs$sim1 %in% c("Command 'fooBarDS()' failed on 'sim1': No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "Bad request: "))
+    expect_true(errs$sim1 %in% c("Command 'fooBarDS()' failed on 'sim1': No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "[Client error: (400) Bad Request] No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "Bad request: No such DataSHIELD 'AGGREGATE' method with name: fooBarDS"))
     expect_length(errs$sim2, 1)
-    expect_true(errs$sim2 %in% c("Command 'fooBarDS()' failed on 'sim2': No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "Bad request: "))
+    expect_true(errs$sim2 %in% c("Command 'fooBarDS()' failed on 'sim2': No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "[Client error: (400) Bad Request] No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "Bad request: No such DataSHIELD 'AGGREGATE' method with name: fooBarDS"))
     expect_length(errs$sim3, 1)
-    expect_true(errs$sim3 %in% c("Command 'fooBarDS()' failed on 'sim3': No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "Bad request: "))
+    expect_true(errs$sim3 %in% c("Command 'fooBarDS()' failed on 'sim3': No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "[Client error: (400) Bad Request] No such DataSHIELD 'AGGREGATE' method with name: fooBarDS", "Bad request: No such DataSHIELD 'AGGREGATE' method with name: fooBarDS"))
 })
 
 context("ds.foobar::arg::assign")
@@ -105,11 +106,11 @@ test_that("non existent assign foobarDS", {
     errs <- datashield.errors()
     expect_length(errs, 3)
     expect_length(errs$sim1, 1)
-    expect_true(errs$sim1 %in% c("Command 'fooBarDS()' failed on 'sim1': No such DataSHIELD 'ASSIGN' method with name: fooBarDS", "Bad request: "))
+    expect_true(errs$sim1 %in% c("Command 'fooBarDS()' failed on 'sim1': No such DataSHIELD 'ASSIGN' method with name: fooBarDS", "[Client error: (400) Bad Request] No such DataSHIELD 'ASSIGN' method with name: fooBarDS", "Bad request: No such DataSHIELD 'ASSIGN' method with name: fooBarDS"))
     expect_length(errs$sim2, 1)
-    expect_true(errs$sim2 %in% c("Command 'fooBarDS()' failed on 'sim2': No such DataSHIELD 'ASSIGN' method with name: fooBarDS", "Bad request: "))
+    expect_true(errs$sim2 %in% c("Command 'fooBarDS()' failed on 'sim2': No such DataSHIELD 'ASSIGN' method with name: fooBarDS", "[Client error: (400) Bad Request] No such DataSHIELD 'ASSIGN' method with name: fooBarDS", "Bad request: No such DataSHIELD 'ASSIGN' method with name: fooBarDS"))
     expect_length(errs$sim3, 1)
-    expect_true(errs$sim3 %in% c("Command 'fooBarDS()' failed on 'sim3': No such DataSHIELD 'ASSIGN' method with name: fooBarDS", "Bad request: "))
+    expect_true(errs$sim3 %in% c("Command 'fooBarDS()' failed on 'sim3': No such DataSHIELD 'ASSIGN' method with name: fooBarDS", "[Client error: (400) Bad Request] No such DataSHIELD 'ASSIGN' method with name: fooBarDS", "Bad request: No such DataSHIELD 'ASSIGN' method with name: fooBarDS"))
 })
 
 #

diff --git a/tests/testthat/test-arg-ds.ranksSecure.R b/tests/testthat/test-arg-ds.ranksSecure.R
@@ -31,9 +31,9 @@ test_that("missing variable", {
     res.errors <- DSI::datashield.errors()
 
     expect_length(res.errors, 3)
-    expect_match(res.errors$study1, "* Error in c\\(\"character\", \"integer\", \"logical\", \"numeric\"\\) %in% class\\(obj\\) : \n  object 'LAB_MISSING' not found")
-    expect_match(res.errors$study2, "* Error in c\\(\"character\", \"integer\", \"logical\", \"numeric\"\\) %in% class\\(obj\\) : \n  object 'LAB_MISSING' not found")
-    expect_match(res.errors$study3, "* Error in c\\(\"character\", \"integer\", \"logical\", \"numeric\"\\) %in% class\\(obj\\) : \n  object 'LAB_MISSING' not found")
+    expect_match(res.errors$study1, "* Error : object 'LAB_MISSING' not found")
+    expect_match(res.errors$study2, "* Error : object 'LAB_MISSING' not found")
+    expect_match(res.errors$study3, "* Error : object 'LAB_MISSING' not found")
 })
 
 context("ds.ranksSecure::arg::NULL variable")

diff --git a/tests/testthat/test-smk-isDefined.R b/tests/testthat/test-smk-isDefined.R
@@ -52,9 +52,9 @@ test_that("default test, dataframe column E$A", {
     expect_length(class(err), 1)
     expect_true(all("list" %in% class(err)))
     expect_length(err, 3)
-    expect_match(err$discordant1, "* Error in base::exists\\(\"A\", E\\) : object 'E' not found")
-    expect_match(err$discordant2, "* Error in base::exists\\(\"A\", E\\) : object 'E' not found")
-    expect_match(err$discordant3, "* Error in base::exists\\(\"A\", E\\) : object 'E' not found")
+    expect_match(err$discordant1, "* Error : object 'E' not found")
+    expect_match(err$discordant2, "* Error : object 'E' not found")
+    expect_match(err$discordant3, "* Error : object 'E' not found")
 })
 
 test_that("default test, dataframe column D$A", {
@@ -123,9 +123,9 @@ test_that("error.message=FALSE test, dataframe column E$A", {
     expect_length(class(err), 1)
     expect_true(all("list" %in% class(err)))
     expect_length(err, 3)
-    expect_match(err$discordant1, "* Error in base::exists\\(\"A\", E\\) : object 'E' not found")
-    expect_match(err$discordant2, "* Error in base::exists\\(\"A\", E\\) : object 'E' not found")
-    expect_match(err$discordant3, "* Error in base::exists\\(\"A\", E\\) : object 'E' not found")
+    expect_match(err$discordant1, "* Error : object 'E' not found")
+    expect_match(err$discordant2, "* Error : object 'E' not found")
+    expect_match(err$discordant3, "* Error : object 'E' not found")
 })
 
 test_that("error.message=FALSE test, dataframe column D$A", {
@@ -222,9 +222,9 @@ test_that("error.message=TRUE test, dataframe column E$A", {
     expect_length(class(err), 1)
     expect_true(all("list" %in% class(err)))
     expect_length(err, 3)
-    expect_match(err$discordant1, "* Error in base::exists\\(\"A\", E\\) : object 'E' not found")
-    expect_match(err$discordant2, "* Error in base::exists\\(\"A\", E\\) : object 'E' not found")
-    expect_match(err$discordant3, "* Error in base::exists\\(\"A\", E\\) : object 'E' not found")
+    expect_match(err$discordant1, "* Error : object 'E' not found")
+    expect_match(err$discordant2, "* Error : object 'E' not found")
+    expect_match(err$discordant3, "* Error : object 'E' not found")
 })
 
 test_that("error.message=TRUE test, dataframe column D$A", {