Merge branch 'v6.3.1-dev' of github.com:StuartWheater/dsBaseClient into v6.3.1-dev

Author: StuartWheater

.Rbuildignore

@@ -7,6 +7,7 @@
 ^azure-pipelines_site-dsdanger\.pp$
 ^azure-pipelines_check\.Rout$
 ^azure-pipelines_test\.Rout$
+^tests/docker/armadillo/standard/log/.gitkeep$
 ^checkDocumentationUpdated\.sh$
 ^docker-compose_armadillo\.yml$
 ^docker-compose_opal\.yml$

.gitignore

@@ -10,3 +10,6 @@
 inst/tests/test-template.R
 azure-pipelines.Rout
 tests/testthat/connection_to_datasets/local_settings.csv
+tests/docker/armadillo/standard/config/
+tests/docker/armadillo/standard/logs/
+tests/docker/armadillo/standard/data/

DESCRIPTION

@@ -18,5 +18,7 @@ Imports:
     panelaggregation,
     methods,
     dplyr
+Suggests:
+    testthat
 RoxygenNote: 7.3.1
 Encoding: UTF-8

azure-pipelines.yml

@@ -12,6 +12,7 @@
 #
 # As of May 2020 this takes ~ 70 mins to run.
 # As of Nov 2020 this takes ~ 120 mins to run.
+# As of Mar 2024 this takes ~ 300+ mins to run!
 #
 # The only things that should ever be changed are the repo branches in the resources.
 #
@@ -66,7 +67,7 @@ schedules:
 
 jobs:
 - job: build_and_run_tests
-  timeoutInMinutes: 300
+  timeoutInMinutes: 360
   pool:
     vmImage: ubuntu-20.04
 
@@ -129,7 +130,7 @@ jobs:
       sudo apt-get update
 
       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 -y
+      sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-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','panelaggregation'), 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')"
@@ -556,9 +557,10 @@ jobs:
       curl -u admin:admin -X GET http://localhost:8080/packages
 
       curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.1-permissive.tar.gz" -X POST http://localhost:8080/install-package
+      sleep 600
 
       docker container restart dsbaseclient_armadillo_1
-      sleep 120
+      sleep 30
 
       curl -u admin:admin -X POST http://localhost:8080/whitelist/dsBase
 

docker-compose_armadillo.yml

@@ -1,18 +1,21 @@
-version: "3.4"
-
 services:
     armadillo:
         hostname: armadillo
-        image: datashield/armadillo_citest:1.1.0
-        environment:
-            DEBUG: "FALSE"
         ports:
             - 8080:8080
+        image: datashield/armadillo_citest:4.7.1
+        environment:
+            LOGGING_CONFIG: 'classpath:logback-file.xml'
+            AUDIT_LOG_PATH: '/app/logs/audit.log'
+            SPRING_SECURITY_USER_PASSWORD: 'admin'
+        volumes:
+            - ./tests/docker/armadillo/standard/logs:/logs
+            - ./tests/docker/armadillo/standard/data:/data
+            - ./tests/docker/armadillo/standard/config:/config
+            - /var/run/docker.sock:/var/run/docker.sock
 
-    citest_rserver:
-        hostname: citest_rserver
-        image: datashield/armadillo-rserver_ionic-babel:1.0.0
+    default:
+        hostname: default
+        image: datashield/rock-junction-xenon-permissive:latest
         environment:
             DEBUG: "FALSE"
-        ports:
-            - 6311:6311

docker-compose_opal.yml

@@ -1,8 +1,6 @@
-version: '3'
-
 services:
     opal:
-        image: obiba/opal:4.6
+        image: obiba/opal:4.7.2
         ports:
             - "8443:8443"
         links:
@@ -22,4 +20,4 @@ services:
             - MONGO_INITDB_ROOT_USERNAME=root
             - MONGO_INITDB_ROOT_PASSWORD=foobar
     rock:
-        image: datashield/rock-base:6.3-R4.3
+        image: datashield/rock-junction-xenon-permissive:latest