chore(deps): Upgrade java from 11 to 17

.github/workflows/ci-test.yml

@@ -65,10 +65,10 @@ jobs:
           mysql database: ${{ env.MYSQL_DATABASE }}
           mysql user: ${{ env.MYSQL_USER }}
           mysql password: ${{ env.MYSQL_PASSWORD }}
-      - name: Set up JDK 11 # Installs java 11
+      - name: Set up JDK 17 # Installs java 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
       - name: Validate Gradle wrapper
         uses: gradle/wrapper-validation-action@v1
       - name: Setup Gradle
@@ -123,10 +123,10 @@ jobs:
           mysql password: ${{ env.MYSQL_PASSWORD }}
       - name: Setup Ruby
         uses: actions/setup-ruby@v1
-      - name: Set up JDK 11 # Installs java 11
+      - name: Set up JDK 17 # Installs java 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
       - name: Validate Gradle wrapper
         uses: gradle/wrapper-validation-action@v1
       - name: Setup Gradle

.github/workflows/grype-scan.yml

@@ -33,10 +33,10 @@ jobs:
           key: ${{ runner.os }}-pnpm-store-${{ hashFiles('**/pnpm-lock.yaml') }}
           restore-keys: |
             ${{ runner.os }}-pnpm-store-
-      - name: Set up JDK 11 # Installs java 11
+      - name: Set up JDK 17 # Installs java 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
       - name: Validate Gradle wrapper
         uses: gradle/wrapper-validation-action@v1
       - name: Setup Gradle

.github/workflows/linting.yml

@@ -23,10 +23,10 @@ jobs:
           key: ${{ runner.os }}-pnpm-store-${{ hashFiles('**/pnpm-lock.yaml') }}
           restore-keys: |
             ${{ runner.os }}-pnpm-store-
-      - name: Set up JDK 11 # Installs java 11
+      - name: Set up JDK 17 # Installs java 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
       - name: Validate Gradle wrapper
         uses: gradle/wrapper-validation-action@v1
       - name: Setup Gradle
@@ -48,10 +48,10 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v3 #Checkout the project from git
-      - name: Set up JDK 11 # Installs java 11
+      - name: Set up JDK 17 # Installs java 17
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: 17
       - name: Validate Gradle wrapper
         uses: gradle/wrapper-validation-action@v1
       - name: Setup Gradle

build.gradle.kts

@@ -18,8 +18,8 @@ version = "23.10.1"
 description = "irida"
 
 java {
-    sourceCompatibility = JavaVersion.VERSION_11
-    targetCompatibility = JavaVersion.VERSION_11
+    sourceCompatibility = JavaVersion.VERSION_17
+    targetCompatibility = JavaVersion.VERSION_17
     withJavadocJar()
     withSourcesJar()
 }
@@ -196,7 +196,9 @@ dependencies {
 
     // Customized blend4j
     implementation("com.sun.jersey:jersey-client:1.19.4")
-    implementation("com.sun.jersey:jersey-json:1.19.4")
+    implementation("com.sun.jersey:jersey-json:1.19.4") {
+        exclude(group = "com.sun.xml.bind", module = "jaxb-impl")
+    }
     implementation("com.sun.jersey:jersey-core:1.19.4")
     implementation("com.sun.jersey.contribs:jersey-multipart:1.19.4")
     implementation("org.codehaus.jackson:jackson-core-asl:1.9.12")

settings.gradle.kts

@@ -5,9 +5,9 @@ pluginManagement {
     }
     plugins {
         id("com.github.node-gradle.node") version "7.1.0"
-        id("io.spring.dependency-management") version "1.0.11.RELEASE"
+        id("io.spring.dependency-management") version "1.1.6"
         id("org.gradle.test-retry") version "1.6.0"
-        id("org.springframework.boot") version "2.7.6"
+        id("org.springframework.boot") version "2.7.18"
         id("org.springdoc.openapi-gradle-plugin") version "1.9.0"
     }
 }

src/test/java/ca/corefacility/bioinformatics/irida/service/impl/integration/SequencingObjectServiceImplIT.java

@@ -78,7 +78,7 @@ public class SequencingObjectServiceImplIT {
 
 	private static final String CHECKSUM = "85e440ab2f17636ab24b12e8e4b4d445b6131e7df785cbd02d56c2688eef55fb";
 
-	private static final String ZIPPED_CHECKSUM = "a2ff0d0790029822b4a2457a2912414ffc532136729ad2fd06efc70fe428ab32";
+	private static final String ZIPPED_CHECKSUM = "123f53507f29a3375f6c1ddd054dadaf4e90cacda536452019b7a37a678f8d7d";
 
 	@Autowired
 	private PasswordEncoder passwordEncoder;