26.3 fb updating java

docker/build.gradle

@@ -98,7 +98,7 @@ tasks.register("buildEhrCronPlug", DockerBuildImage){
     group 'DockerPlugin'
 }
 
-tasks.register("buildTomcat") { Task t ->
+tasks.register("buildCranr") { Task t ->
     doLast {
         if (!project.hasProperty("nocache")){
             ext.nocache = "false"
@@ -125,32 +125,32 @@ tasks.register("buildTomcat") { Task t ->
             if (nocache.equals("true")){
                 println "building image without cache"
                 t.project.exec{
-                    workingDir "$projectDir/tomcat"
+                    workingDir "$projectDir/cranrnutils"
                     executable "docker"
-                    args "build", ".", "--no-cache", "-t", "wnprcehr/tomcat:tomcat9_"+branch
+                    args "build", "--platform","linux/arm64,linux/amd64" ,"--no-cache", "-t", "wnprcehr/cranrnutils:cranrnutils_"+branch, "."
                 }
             }else{
                 t.project.exec{
-                    workingDir "$projectDir/tomcat"
+                    workingDir "$projectDir/cranrnutils"
                     executable "docker"
-                    args "build", ".", "-t", "wnprcehr/tomcat:tomcat9_"+branch
+                    args "build", "--platform","linux/arm64,linux/amd64" ,"-t", "wnprcehr/cranrnutils:cranrnutils_"+branch, "."
                 }
             }
 
         }else {
-            logger.warn 'Must provide docker string via command line. (ex. ./gradlew buildTomcat -PbranchName=22.11_fb)'
+            logger.warn 'Must provide docker string via command line. (ex. ./gradlew buildCranr -PbranchName=22.11_fb)'
         }
     }
 
 }
-configure(buildTomcat){
+configure(buildCranr){
     group 'Docker'
     description 'Generates the Tomcat docker image (with R)'
     dependsOn  "checkDocker", "dockerLogin", "processbranchName"
     onlyIf {buildType != ''}
 } 
 
-tasks.register("buildTomcatPlug", DockerBuildImage){
+tasks.register("buildCranrPlug", DockerBuildImage){
     def dockerStr = providers.gradleProperty("branchName")
     if (dockerStr.present){
       //  String branch = ""
@@ -169,13 +169,13 @@ tasks.register("buildTomcatPlug", DockerBuildImage){
                 break;
         }
         inputDir.set(file("tomcat/"))
-        images.add("wnprcehr/tomcat:tomcat9_${branch}")
+        images.add("wnprcehr/cranrnutils:cranrnutils_${branch}")
 
     }else {
-        logger.warn 'Must provide docker string via command line. (ex. ./gradlew buildTomcatPlug -PbranchName=22.11_fb)'
+        logger.warn 'Must provide docker string via command line. (ex. ./gradlew buildCranrPlug -PbranchName=22.11_fb)'
     }    
 }
-configure(buildTomcatPlug){
+configure(buildCranrPlug){
     group 'DockerPlugin'
     description 'Generates the Tomcat docker image (with R)'
     dependsOn  "checkDocker", "dockerLogin", "processbranchName"
@@ -184,7 +184,7 @@ configure(buildTomcatPlug){
 //Building LabKey with hooks/build for consistancy with Docker Hub and used of environment variables duirng the build process
 //Source: https://stackoverflow.com/questions/36322536/how-to-set-an-environment-variable-from-a-gradle-build / https://stackoverflow.com/a/63140816
 tasks.register("buildLabkey") { Task t ->
-//task("buildLabkey", group: "Docker", description: "Generates the LabKey docker image", dependsOn: ["buildTomcat", "buildEhrCron", "buildPostfix"]) { Task t ->
+//task("buildLabkey", group: "Docker", description: "Generates the LabKey docker image", dependsOn: ["buildCranr", "buildEhrCron", "buildPostfix"]) { Task t ->
     doLast {
         def dockerStr = providers.gradleProperty("branchName")
 
@@ -317,7 +317,7 @@ configure(tagPostfixPlug){
 tasks.register("buildAll"){
     group 'Docker'
     description 'Generates all the docker images in the subfolders'
-    dependsOn "buildTomcat", "buildEhrcron", "buildLabkey", "buildPostfix" 
+    dependsOn "buildCranr", "buildEhrcron", "buildLabkey", "buildPostfix" 
 
 }
 
@@ -445,7 +445,7 @@ tasks.register("downloadPostfixPlug",DockerPullImage){
     dependsOn 'checkDocker'
 }
 
-tasks.register("downloadTomcat"){
+tasks.register("downloadCranr"){
     doLast {
         def dockerStr = providers.gradleProperty("branchName")
         if (dockerStr.present)
@@ -454,11 +454,11 @@ tasks.register("downloadTomcat"){
             String branchName = dockerStr.get()
             t.project.exec {
                 executable "docker"
-                args "pull", "wnprcehr/tomcat:tomcat9_${branchName}"
+                args "pull", "wnprcehr/cranrnutils:cranrnutils_${branch}"
             }
         }
         else{
-            logger.warn 'Must provide docker string via command line. (ex. ./gradlew downloadTomcat -PbranchName=22.11_fb)'
+            logger.warn 'Must provide docker string via command line. (ex. ./gradlew downloadCranr -PbranchName=22.11_fb)'
         }
     }
     group 'Docker'
@@ -467,8 +467,8 @@ tasks.register("downloadTomcat"){
 
 }
 
-tasks.register("downloadTomcatPlug",DockerPullImage){
-    image = "wnprcehr/tomcat:tomcat9_${branchName}"
+tasks.register("downloadCranrPlug",DockerPullImage){
+    image = "wnprcehr/cranrnutils:cranrnutils_${branch}"
 
     onComplete{
         def dockerStr = providers.gradleProperty("branchName")
@@ -478,7 +478,7 @@ tasks.register("downloadTomcatPlug",DockerPullImage){
         }
         else{
 
-            logger.warn 'Must provide docker string via command line. (ex. ./gradlew downloadTomcatPlug -PbranchName=22.11_fb)'
+            logger.warn 'Must provide docker string via command line. (ex. ./gradlew downloadCranrPlug -PbranchName=22.11_fb)'
         }
     }
     doLast{

docker/cranrnutils/Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:17-jre-jammy
+FROM eclipse-temurin:25-jre-noble
 
 # Set noninteractive mode for apt-get
 ENV DEBIAN_FRONTEND=noninteractive
@@ -7,37 +7,35 @@ ENV LANG=en_US.utf8
 
 RUN apt-get update \
     && apt-get -qq install -y   lsb-release             \
-                                software-properties-common \
+    software-properties-common \
+    curl                        \
     && apt-get clean
 
 
-# Download and add siging key for Postgres 15
-# https://www.linuxtechi.com/how-to-install-postgresql-on-ubuntu/
-# https://askubuntu.com/a/1456015    
-RUN echo "deb http://apt.postgresql.org/pub/repos/apt $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list 
-RUN wget -qO- https://www.postgresql.org/media/keys/ACCC4CF8.asc | tee /etc/apt/trusted.gpg.d/pgdg.asc > /dev/null 2>&1
+# Download and add signing key for Postgres 15 
+RUN mkdir -p /etc/apt/keyrings \
+    && curl -fsSL https://www.postgresql.org/media/keys/ACCC4CF8.asc -o /etc/apt/keyrings/pgdg.asc \
+    && echo "deb [signed-by=/etc/apt/keyrings/pgdg.asc] http://apt.postgresql.org/pub/repos/apt/ $(lsb_release -cs)-pgdg main" > /etc/apt/sources.list.d/pgdg.list
 
 # Download and add signing key for CRAN repository
-# https://www.r-bloggers.com/2022/08/installation-of-r-4-2-on-ubuntu-22-04-1-lts-and-tips-for-spatial-packages/
-# https://phoenixnap.com/kb/install-r-ubuntu
-RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc > /dev/null 2>&1
-RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+RUN curl -fsSL https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc -o /etc/apt/keyrings/cran_ubuntu_key.asc \
+    && echo "deb [signed-by=/etc/apt/keyrings/cran_ubuntu_key.asc] https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" > /etc/apt/sources.list.d/cran.list
 
 # Adding various application to download packages to install Postgres 15 and CRAN-R
 RUN apt-get update \
     && apt-get -qq install -y   texinfo                 \
-                                tzdata                  \
-                                gettext                 \
-                                make                    \
-                                openssl                 \
-                                #Linux packages needed for installing CRAN-R
-                                dirmngr                 \
-                                #Linux packages needed for RlabKey
-                                libcurl4-openssl-dev    \
-                                libssl-dev              \
-                                postgresql-client-15    \
-                                r-base                  \
-                                r-base-dev              \
+    tzdata                  \
+    gettext                 \
+    make                    \
+    openssl                 \
+    #Linux packages needed for installing CRAN-R
+    dirmngr                 \
+    #Linux packages needed for RlabKey
+    libcurl4-openssl-dev    \
+    libssl-dev              \
+    postgresql-client-15    \
+    r-base                  \
+    r-base-dev              \
     && apt-get clean
 
 # install the necessary R packages

docker/gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.5.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.3.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

docker/labkey/Dockerfile

@@ -22,7 +22,7 @@ RUN echo -e "Downloading LabKey build from \033[1;33m${Z}\033[0m" \
 
 # -----------------------------------------------------------------------------
 # MAIN IMAGE BUILD DEFINITION
-FROM --platform=$BUILDPLATFORM wnprcehr/cranrnutils:cranrnutils_${LK_VERSION}${FB_NAME}
+FROM wnprcehr/cranrnutils:cranrnutils_${LK_VERSION}${FB_NAME}
 
 # creating folders for LabKey installation
 RUN mkdir -p /labkey/labkey