From f7a60f31fc3d0443f9446d9fe6208e43a39437ca Mon Sep 17 00:00:00 2001 From: Clemens Tolboom Date: Thu, 14 Mar 2024 11:08:33 +0100 Subject: [PATCH 1/5] Add use-latest-versions plugin --- build.gradle | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/build.gradle b/build.gradle index 734390598..bd1063d97 100644 --- a/build.gradle +++ b/build.gradle @@ -12,15 +12,16 @@ * - ui/build.gradle */ plugins { - id 'org.springframework.boot' version '3.1.5' + id 'org.springframework.boot' version '3.2.3' id "io.spring.dependency-management" version "1.1.4" id "java" - id "org.sonarqube" version "3.5.0.2730" + id "org.sonarqube" version "4.4.1.3373" id 'maven-publish' id 'application' id "jacoco" - id 'com.palantir.docker' version '0.35.0' - id 'com.github.ben-manes.versions' version '0.50.0' + id 'com.palantir.docker' version '0.36.0' + id 'se.patrikerdes.use-latest-versions' version '0.2.18' + id 'com.github.ben-manes.versions' version '0.51.0' } targetCompatibility = '17' From 49b1ed9b4d6135706f2ec6f12113e8981e649451 Mon Sep 17 00:00:00 2001 From: Clemens Tolboom Date: Thu, 14 Mar 2024 11:09:35 +0100 Subject: [PATCH 2/5] Upgrade by tool and manual --- armadillo/build.gradle | 10 +++++----- r/build.gradle | 8 ++++---- ui/build.gradle | 2 +- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/armadillo/build.gradle b/armadillo/build.gradle index 2efff801b..eb75f8633 100644 --- a/armadillo/build.gradle +++ b/armadillo/build.gradle @@ -3,7 +3,7 @@ plugins { id 'io.spring.dependency-management' id "jacoco" id "java" - id "com.diffplug.spotless" version "6.15.0" + id "com.diffplug.spotless" version "6.25.0" } repositories { @@ -48,8 +48,8 @@ dependencies { implementation 'com.google.auto.value:auto-value-annotations:1.10.4' implementation 'org.obiba.datashield:ds4j-core:2.0.0' implementation 'org.obiba.datashield:ds4j-r:2.0.0' - implementation 'com.github.docker-java:docker-java:3.3.4' - implementation 'com.github.docker-java:docker-java-transport-zerodep:3.3.4' + implementation 'com.github.docker-java:docker-java:3.3.6' + implementation 'com.github.docker-java:docker-java-transport-zerodep:3.3.6' implementation 'net.logstash.logback:logstash-logback-encoder:7.2' implementation 'org.apache.parquet:parquet-hadoop:1.12.3' implementation 'org.apache.hadoop:hadoop-client:3.3.6' @@ -57,8 +57,8 @@ dependencies { //Overrides docker-java's sub-dependency to fix compatibility issues with apple ARM chips //https://github.com/docker-java/docker-java/issues/1876 --> - implementation 'com.kohlschutter.junixsocket:junixsocket-common:2.3.3' - implementation 'com.kohlschutter.junixsocket:junixsocket-native-common:2.3.3' + implementation 'com.kohlschutter.junixsocket:junixsocket-common:2.9.0' + implementation 'com.kohlschutter.junixsocket:junixsocket-native-common:2.9.0' //test outside spring testImplementation 'com.c4-soft.springaddons:spring-security-oauth2-test-webmvc-addons:4.5.1' diff --git a/r/build.gradle b/r/build.gradle index 28728a53f..55598ce7f 100644 --- a/r/build.gradle +++ b/r/build.gradle @@ -1,7 +1,7 @@ plugins { id "jacoco" id "java" - id "com.diffplug.spotless" version "6.15.0" + id "com.diffplug.spotless" version "6.25.0" id 'org.springframework.boot' id 'io.spring.dependency-management' } @@ -18,7 +18,7 @@ bootJar.enabled = false dependencies { //spring implementation 'org.springframework.boot:spring-boot-starter' - implementation 'jakarta.validation:jakarta.validation-api' + implementation 'jakarta.validation:jakarta.validation-api:3.1.0-M1' implementation 'org.springframework.boot:spring-boot-starter-json' implementation 'org.springframework.retry:spring-retry' annotationProcessor 'org.springframework.boot:spring-boot-configuration-processor' @@ -28,10 +28,10 @@ dependencies { implementation 'org.springframework.security:spring-security-oauth2-jose' //other - implementation 'commons-io:commons-io:2.11.0' + implementation 'commons-io:commons-io:2.15.1' implementation 'org.rosuda.REngine:REngine:2.1.0' implementation 'org.rosuda.REngine:Rserve:1.8.1' - implementation 'com.google.guava:guava:31.1-jre' + implementation 'com.google.guava:guava:33.1.0-jre' implementation 'com.google.auto.value:auto-value-annotations:1.10.4' implementation 'org.apache.commons:commons-text:1.10.0' implementation 'org.json:json:20230227' diff --git a/ui/build.gradle b/ui/build.gradle index c51c5e99c..4c2e86c96 100644 --- a/ui/build.gradle +++ b/ui/build.gradle @@ -1,6 +1,6 @@ plugins { id "base" - id "com.github.node-gradle.node" version "3.5.1" + id "com.github.node-gradle.node" version "7.0.2" } def nodeSpec = { From e3c49e2feb3db21c46485afc1b7e4b4c85b1ad89 Mon Sep 17 00:00:00 2001 From: Clemens Tolboom Date: Thu, 14 Mar 2024 11:35:01 +0100 Subject: [PATCH 3/5] Add more updates --- armadillo/build.gradle | 10 +++++----- r/build.gradle | 4 ++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/armadillo/build.gradle b/armadillo/build.gradle index eb75f8633..846a1bec2 100644 --- a/armadillo/build.gradle +++ b/armadillo/build.gradle @@ -29,7 +29,7 @@ dependencies { implementation 'org.springframework.security:spring-security-oauth2-jose' implementation 'org.springframework.security:spring-security-oauth2-resource-server' implementation 'org.springframework.boot:spring-boot-starter-actuator' - implementation 'io.micrometer:micrometer-registry-prometheus' + implementation 'io.micrometer:micrometer-registry-prometheus:1.12.4' implementation 'org.springframework.boot:spring-boot-starter-web' implementation 'org.springframework.boot:spring-boot-starter-validation' implementation 'org.springframework:spring-aspects' @@ -46,14 +46,14 @@ dependencies { implementation 'org.rosuda.REngine:Rserve:1.8.1' implementation 'io.swagger.core.v3:swagger-annotations:2.2.20' implementation 'com.google.auto.value:auto-value-annotations:1.10.4' - implementation 'org.obiba.datashield:ds4j-core:2.0.0' - implementation 'org.obiba.datashield:ds4j-r:2.0.0' + implementation 'org.obiba.datashield:ds4j-core:2.1.0' + implementation 'org.obiba.datashield:ds4j-r:2.1.0' implementation 'com.github.docker-java:docker-java:3.3.6' implementation 'com.github.docker-java:docker-java-transport-zerodep:3.3.6' - implementation 'net.logstash.logback:logstash-logback-encoder:7.2' + implementation 'net.logstash.logback:logstash-logback-encoder:7.4' implementation 'org.apache.parquet:parquet-hadoop:1.12.3' implementation 'org.apache.hadoop:hadoop-client:3.3.6' - implementation 'org.springdoc:springdoc-openapi-starter-webmvc-ui:2.1.0' + implementation 'org.springdoc:springdoc-openapi-starter-webmvc-ui:2.4.0' //Overrides docker-java's sub-dependency to fix compatibility issues with apple ARM chips //https://github.com/docker-java/docker-java/issues/1876 --> diff --git a/r/build.gradle b/r/build.gradle index 55598ce7f..9ced8369f 100644 --- a/r/build.gradle +++ b/r/build.gradle @@ -33,8 +33,8 @@ dependencies { implementation 'org.rosuda.REngine:Rserve:1.8.1' implementation 'com.google.guava:guava:33.1.0-jre' implementation 'com.google.auto.value:auto-value-annotations:1.10.4' - implementation 'org.apache.commons:commons-text:1.10.0' - implementation 'org.json:json:20230227' + implementation 'org.apache.commons:commons-text:1.11.0' + implementation 'org.json:json:20240303' //test testImplementation('org.springframework.boot:spring-boot-starter-test') { From 2b6b99324d51fd61853804820478928e8a94a2cd Mon Sep 17 00:00:00 2001 From: Clemens Tolboom Date: Thu, 14 Mar 2024 11:43:28 +0100 Subject: [PATCH 4/5] Add parquet update --- armadillo/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/armadillo/build.gradle b/armadillo/build.gradle index 846a1bec2..e75f2608d 100644 --- a/armadillo/build.gradle +++ b/armadillo/build.gradle @@ -51,7 +51,7 @@ dependencies { implementation 'com.github.docker-java:docker-java:3.3.6' implementation 'com.github.docker-java:docker-java-transport-zerodep:3.3.6' implementation 'net.logstash.logback:logstash-logback-encoder:7.4' - implementation 'org.apache.parquet:parquet-hadoop:1.12.3' + implementation 'org.apache.parquet:parquet-hadoop:1.13.1' implementation 'org.apache.hadoop:hadoop-client:3.3.6' implementation 'org.springdoc:springdoc-openapi-starter-webmvc-ui:2.4.0' From 08cad8a92b995495e6d501987cfecacca5a1d756 Mon Sep 17 00:00:00 2001 From: Clemens Tolboom Date: Thu, 14 Mar 2024 12:19:14 +0100 Subject: [PATCH 5/5] Add steps to the documentation --- CONTRIBUTING.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7dbd1d6ab..13ea503be 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -34,6 +34,23 @@ As we now have the option to download the logfile from the application we need t ./gradlew test ``` +## Upgrade plugins + +Use the commands listed below. + +```bash +./gradlew useLatestVersions +./gradlew useLatestVersionsCheck +``` + +Some plugins need manually editing the build files. + +To help find the right `build.gradle` use the command below with your keyword. + +```bash +find . -type f -name "build.gradle" -exec echo {} \; -exec grep YOUR_KEY_WORD {} \; +``` + ## Upgrading gradle ```bash