Upgrade gradle to v7.2

.github/workflows/build.yml

@@ -15,16 +15,18 @@ on:
 
 jobs:
   build:
-    name: Build and Test
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        java: ['11', '16', '17' ]
 
+    name: Java ${{ matrix.java }} Build and Test
     steps:
       - name: Set up java
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
-          java-version: 11.0.2
-          java-package: jdk
-          architecture: x64
+          distribution: 'temurin'
+          java-version: ${{ matrix.java }}
       - name: Set up python
         uses: actions/setup-python@v2
         with:

.github/workflows/cwl_compliance.yml

@@ -19,11 +19,10 @@ jobs:
 
     steps:
       - name: Set up java
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
-          java-version: 11.0.2
-          java-package: jdk
-          architecture: x64
+          distribution: 'temurin'
+          java-version: '17'
       - name: Set up python
         uses: actions/setup-python@v2
         with:

.gitignore

@@ -6,7 +6,12 @@ build/
 .settings
 *.iws
 .DS_Store
+.vscode
 
+# Ignore yarn
+src/main/frontend/yarn-v1.22.0/
+
+# Xenonflow logs
 log/
 db/
 xenon-flow.log

build.gradle

@@ -4,7 +4,7 @@ plugins {
     id 'idea'
     id 'eclipse'
     id 'application'
-    id 'org.springframework.boot' version '2.2.4.RELEASE'
+    id 'org.springframework.boot' version '2.3.12.RELEASE'
     id 'io.spring.dependency-management' version '1.0.7.RELEASE'
     id 'jacoco'
     id "com.github.node-gradle.node" version "2.2.2"
@@ -15,7 +15,7 @@ sourceCompatibility = JavaVersion.VERSION_11
 targetCompatibility = JavaVersion.VERSION_11
 
 application {
-	mainClassName = 'nl.esciencecenter.computeservice.rest.Application'
+	mainClass = 'nl.esciencecenter.computeservice.rest.Application'
 }
 
 
@@ -43,26 +43,27 @@ dependencies {
     implementation group: 'nl.esciencecenter.xenon.adaptors', name: 'xenon-adaptors-cloud', version: '3.0.2'
 
     //Spring(boot)
-    implementation group: 'org.springframework.boot', name: 'spring-boot-starter-web', version: '2.2.4.RELEASE'
-    implementation group: 'org.springframework.boot', name: 'spring-boot-starter', version: '2.2.4.RELEASE'
-    implementation group: 'org.springframework.boot', name: 'spring-boot-starter-tomcat', version: '2.2.4.RELEASE'
-    implementation group: 'org.springframework.boot', name: 'spring-boot-devtools', version: '2.2.4.RELEASE'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-starter-web', version: '2.3.12.RELEASE'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-starter', version: '2.3.12.RELEASE'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-starter-tomcat', version: '2.3.12.RELEASE'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-devtools', version: '2.3.12.RELEASE'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-starter-validation', version: '2.3.12.RELEASE'
     implementation group: 'io.springfox', name: 'springfox-boot-starter', version: '3.0.0'
 
     //Jackson, match version used in Spring
-    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.9.8'
-    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.9.8'
-    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.9.8'
+    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.11.4'
+    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.11.4'
+    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.11.4'
 
     //compile group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310'
     implementation group: 'javax.validation', name: 'validation-api', version: '2.0.1.Final'
 
 	//JPA, hibernate and h2 database persistance libraries
-	implementation group: 'org.springframework.boot', name: 'spring-boot-starter-data-jpa', version: '2.2.4.RELEASE'
+	implementation group: 'org.springframework.boot', name: 'spring-boot-starter-data-jpa', version: '2.3.12.RELEASE'
 	runtimeOnly group: 'com.h2database', name: 'h2', version: '1.4.199'
 
 	// Security
-	implementation group: 'org.springframework.boot', name: 'spring-boot-starter-security', version: '2.2.4.RELEASE'
+	implementation group: 'org.springframework.boot', name: 'spring-boot-starter-security', version: '2.3.12.RELEASE'
 
 	// Admin Interface
 
@@ -75,18 +76,20 @@ dependencies {
 	testImplementation group: 'org.hamcrest', name:'hamcrest', version:'2.2'
     testImplementation group: 'org.hamcrest', name:'hamcrest-library', version:'2.2'
     testImplementation group: 'junit', name:'junit', version:'4.13'
-    testImplementation group: 'org.springframework.boot', name: 'spring-boot-starter-test', version: '2.2.4.RELEASE'
+    testImplementation group: 'org.springframework.boot', name: 'spring-boot-starter-test', version: '2.3.12.RELEASE'
+
+    runtimeOnly group: 'org.springframework.boot', name: 'spring-boot-properties-migrator', version: '2.3.12.RELEASE'
 }
 
 bootJar {
-	baseName = 'xenonflow'
+    baseName = 'xenonflow'
 }
 
 // Include some more files in the distribution zip
 // Don't use include an extra directory in the dist zip.
 distributions {
     boot {
-    	baseName = 'xenonflow'
+    	distributionBaseName = 'xenonflow'
         contents {
 			from(['config/config.yml', 'config/application.properties']) {
 				into '/config'

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.8.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.3-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

src/test/java/nl/esciencecenter/computeservice/rest/CwlResultTest.java

@@ -54,6 +54,10 @@ public class CwlResultTest {
 
 	@After
 	public void deleteJob() throws Exception {
+		if (xenonService.getConfig().getSourceFilesystemConfig().shouldClearOnJobDone()) {
+			// Make sure we do not throw away the input if the testDeleteInput test fails
+			xenonService.getConfig().getSourceFilesystemConfig().setClearOnJobDone(false);
+		}
 		for (Job job : CwlTestUtils.getCreated()) {
 			mockMvc.perform(
 					delete(job.getUri())