feat: Create version TOML file, upgrade gradle and all dependencies [COMP-1266]

HEADER.txt

@@ -1,4 +1,4 @@
-Copyright ${year}, ${name}.
+Copyright 2021-2026, Seqera.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -10,5 +10,4 @@ Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
-limitations under the License.
-
+limitations under the License.

VERSION

@@ -1,3 +1,3 @@
-0.21.0
+0.22.0
 
 

VERSION-API

@@ -1,4 +1,4 @@
-1.98.0
+1.109.0
 // Only first line of this file is read
 // This version should be bumped to the minimum version where dependent API changes were introduced
 // But never higher then the current Platform API Version deployed in Cloud Production: https://cloud.seqera.io/api/service-info

build.gradle

@@ -2,9 +2,9 @@ plugins {
     id 'java'
     id 'application'
     id 'jacoco'
-    id 'org.cadixdev.licenser' version '0.6.1'
-    id 'org.graalvm.buildtools.native' version '0.10.6'
-    id 'com.gradleup.shadow' version '8.3.9'
+    alias(libs.plugins.yumiLicenser)
+    alias(libs.plugins.graalvmNative)
+    alias(libs.plugins.shadow)
 }
 
 // define these in the `gradle.properties` file
@@ -23,53 +23,95 @@ repositories {
 }
 
 dependencies {
-    implementation 'javax.annotation:javax.annotation-api:1.3.2'
-    implementation 'jakarta.annotation:jakarta.annotation-api:3.0.0'
-    implementation 'org.slf4j:slf4j-api:1.7.36'
-    implementation 'ch.qos.logback:logback-core:1.5.25'
-    implementation 'ch.qos.logback:logback-classic:1.5.25'
+    implementation(libs.javaxAnnotation)
+    implementation(libs.jakartaAnnotation)
+    implementation(libs.slf4jApi)
+    implementation(libs.logbackCore)
+    implementation(libs.logbackClassic)
 
-    implementation 'io.seqera.tower:tower-java-sdk:1.107.0'
+    implementation(libs.towerJavaSdk)
     // Upgrade transitive Jersey client dependencies to non-vulnerable 2.x version
-    implementation "org.glassfish.jersey.core:jersey-client:2.47"
-    implementation "org.glassfish.jersey.media:jersey-media-multipart:2.47"
-    implementation "org.glassfish.jersey.media:jersey-media-json-jackson:2.47"
-    implementation "org.glassfish.jersey.inject:jersey-hk2:2.47"
-
-    implementation 'info.picocli:picocli:4.6.3'
-    implementation 'org.apache.commons:commons-compress:1.28.0'
-    implementation 'org.tukaani:xz:1.9'
-    implementation 'io.github.classgraph:classgraph:4.8.165'
-    annotationProcessor 'info.picocli:picocli-codegen:4.6.3'
-
-    testImplementation 'org.mock-server:mockserver-client-java:5.15.0'
-    testImplementation 'org.mock-server:mockserver-netty:5.15.0'
-    testImplementation 'org.mock-server:mockserver-junit-jupiter:5.15.0'
+    implementation(libs.jerseyClient)
+    implementation(libs.jerseyMediaMultipart)
+    implementation(libs.jerseyMediaJsonJackson)
+    implementation(libs.jerseyHk2)
+
+    implementation(libs.picocli)
+    implementation(libs.commonsCompress)
+    implementation(libs.xz)
+    implementation(libs.classgraph)
+    annotationProcessor(libs.picocliCodegen)
+
+    testImplementation(libs.mockserverClientJava)
+    testImplementation(libs.mockserverNetty)
+    testImplementation(libs.mockserverJunitJupiter)
     // Upgrade transitive mock-server dependencies to non-vulnerable 2.x version
-    testImplementation 'commons-io:commons-io:2.20.0'
+    testImplementation(libs.commonsIo)
 
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:5.8.2'
-    testImplementation 'org.junit.jupiter:junit-jupiter-params:5.8.2'
-    testRuntimeOnly 'org.junit.jupiter:junit-jupiter-engine:5.8.2'
+    testImplementation(libs.junitJupiterApi)
+    testImplementation(libs.junitJupiterParams)
+    testRuntimeOnly(libs.junitJupiterEngine)
+    testRuntimeOnly(libs.junitPlatformLauncher)
 
 }
 
 license {
-    header = project.file('HEADER.txt')
-    properties {
-        name = 'Seqera'
-        year = '2021-2023'
+    rule(file('HEADER.txt'))
+    exclude('**/*.properties')
+    exclude('**/*.xml')
+    exclude('gradlew')
+    exclude('conf/**')
+}
+
+application {
+    mainClass.set('io.seqera.tower.cli.Tower')
+}
+
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(21)
     }
-    exclude '**/*.properties'
-    exclude 'gradlew'
-    exclude 'conf/**'
 }
 
-task buildInfo {
+graalvmNative {
+    toolchainDetection = true
+    binaries {
+        main {
+            imageName = 'tw'
+            mainClass = 'io.seqera.tower.cli.Tower'
+            configurationFileDirectories.from(file('conf'))
+
+            if (System.env.getOrDefault("PLATFORM", "") == "linux-x86_64") {
+                buildArgs(['--static', '--libc=musl', '--gc=G1', '-march=compatibility'])
+            }
+            buildArgs.add('--allow-incomplete-classpath')
+            buildArgs.add('--report-unsupported-elements-at-runtime')
+            buildArgs.add('-H:+AddAllCharsets')
+            buildArgs.add('-H:EnableURLProtocols=https,http')
+            buildArgs.add('-H:+ReportExceptionStackTraces')
+
+            javaLauncher = javaToolchains.launcherFor {
+                languageVersion = JavaLanguageVersion.of(21)
+                vendor = JvmVendorSpec.matching("Oracle Corporation")
+            }
+
+        }
+
+        test {
+            verbose = true
+        }
+    }
+}
+
+configurations.configureEach {
+    resolutionStrategy.cacheChangingModulesFor 0, 'seconds'
+}
+
+tasks.register('buildInfo') {
     doLast {
         def version = rootProject.file('VERSION').text.trim()
         def versionApi = rootProject.file('VERSION-API').readLines().get(0).trim()
-        def commitId = System.env.getOrDefault("GITHUB_SHA", "unknown").substring(0,7)
+        def commitId = System.env.getOrDefault("GITHUB_SHA", "unknown").substring(0, 7)
         def platform = System.env.getOrDefault("PLATFORM", "java")
         def info = """\
                     version=${version}
@@ -83,24 +125,13 @@ task buildInfo {
     }
 }
 
-java {
-    toolchain {
-        languageVersion = JavaLanguageVersion.of(21)
-    }
-}
-
-compileJava {
-    sourceCompatibility = JavaVersion.toVersion("11")
-    targetCompatibility = JavaVersion.toVersion("11")
+tasks.named('compileJava') {
+    options.release = 21
     options.compilerArgs += ["-Aproject=${project.name}"]
-    dependsOn buildInfo
+    dependsOn tasks.named('buildInfo')
 }
 
-application {
-    mainClass.set('io.seqera.tower.cli.Tower')
-}
-
-run {
+tasks.named('run') {
     // Pass CLI arguments via: `./gradlew run --args='arg1 arg2'`, or via: `./gradlew run -Pargs='arg1 arg2'`
     if (project.hasProperty('args')) {
         args project.args.split('\\s+')
@@ -120,56 +151,22 @@ tasks.register('runReflectionConfigGenerator', JavaExec) {
     jvmArgs = ["-agentlib:native-image-agent=access-filter-file=conf/access-filter-file.json,config-merge-dir=conf/"]
 }
 
-shadowJar {
+tasks.named('shadowJar') {
     archiveBaseName.set('tw')
     archiveClassifier.set('')
     archiveVersion.set('')
 }
 
-test {
+tasks.named('test') {
     // Use junit platform for unit tests
     useJUnitPlatform()
-    dependsOn checkLicenses
+    dependsOn tasks.named('checkLicenses')
     // Run tests with GraalVM Tracing Agent enabled
     if (System.getProperty('tracing-agent')?.toBoolean()) {
         jvmArgs = ["-agentlib:native-image-agent=access-filter-file=conf/access-filter-file.json,config-merge-dir=conf/"]
     }
 }
 
-graalvmNative {
-    toolchainDetection = true
-    binaries {
-        main {
-            imageName = 'tw'
-            mainClass = 'io.seqera.tower.cli.Tower'
-            configurationFileDirectories.from(file('conf'))
-
-            if (System.env.getOrDefault("PLATFORM", "") == "linux-x86_64") {
-                buildArgs(['--static', '--libc=musl', '--gc=G1', '-march=compatibility'])
-            }
-            buildArgs.add('--allow-incomplete-classpath')
-            buildArgs.add('--report-unsupported-elements-at-runtime')
-            buildArgs.add('-H:+AddAllCharsets')
-            buildArgs.add('-H:EnableURLProtocols=https,http')
-            buildArgs.add('-H:+ReportExceptionStackTraces')
-
-            javaLauncher = javaToolchains.launcherFor {
-                languageVersion = JavaLanguageVersion.of(21)
-                vendor = JvmVendorSpec.matching("Oracle Corporation")
-            }
-
-        }
-
-        test {
-            verbose = true
-        }
-    }
-}
-
-configurations.all {
-    resolutionStrategy.cacheChangingModulesFor 0, 'seconds'
-}
-
-jacocoTestReport {
-    dependsOn test // tests are required to run before generating the report
+tasks.named('jacocoTestReport') {
+    dependsOn tasks.named('test') // tests are required to run before generating the report
 }

gradle/libs.versions.toml

@@ -0,0 +1,47 @@
+[versions]
+classgraphVersion = "4.8.180"
+commonsCompressVersion = "1.28.0"
+commonsIoVersion = "2.21.0"
+graalvmNativeVersion = "0.10.6"
+jakartaAnnotationVersion = "3.0.0"
+javaxAnnotationVersion = "1.3.2"
+jerseyVersion = "2.47"
+junitVersion = "5.12.2"
+licenserVersion = "2.2.2"
+logbackVersion = "1.5.32"
+mockserverVersion = "5.15.0"
+picocliVersion = "4.6.3"
+shadowVersion = "9.3.1"
+slf4jVersion = "2.0.17"
+towerJavaSdkVersion = "1.107.0"
+xzVersion = "1.10"
+
+[libraries]
+classgraph = { group = "io.github.classgraph", name = "classgraph", version.ref = "classgraphVersion" }
+commonsCompress = { group = "org.apache.commons", name = "commons-compress", version.ref = "commonsCompressVersion" }
+commonsIo = { group = "commons-io", name = "commons-io", version.ref = "commonsIoVersion" }
+jakartaAnnotation = { group = "jakarta.annotation", name = "jakarta.annotation-api", version.ref = "jakartaAnnotationVersion" }
+javaxAnnotation = { group = "javax.annotation", name = "javax.annotation-api", version.ref = "javaxAnnotationVersion" }
+jerseyClient = { group = "org.glassfish.jersey.core", name = "jersey-client", version.ref = "jerseyVersion" }
+jerseyHk2 = { group = "org.glassfish.jersey.inject", name = "jersey-hk2", version.ref = "jerseyVersion" }
+jerseyMediaJsonJackson = { group = "org.glassfish.jersey.media", name = "jersey-media-json-jackson", version.ref = "jerseyVersion" }
+jerseyMediaMultipart = { group = "org.glassfish.jersey.media", name = "jersey-media-multipart", version.ref = "jerseyVersion" }
+junitJupiterApi = { group = "org.junit.jupiter", name = "junit-jupiter-api", version.ref = "junitVersion" }
+junitJupiterEngine = { group = "org.junit.jupiter", name = "junit-jupiter-engine", version.ref = "junitVersion" }
+junitJupiterParams = { group = "org.junit.jupiter", name = "junit-jupiter-params", version.ref = "junitVersion" }
+junitPlatformLauncher = { group = "org.junit.platform", name = "junit-platform-launcher" }
+logbackClassic = { group = "ch.qos.logback", name = "logback-classic", version.ref = "logbackVersion" }
+logbackCore = { group = "ch.qos.logback", name = "logback-core", version.ref = "logbackVersion" }
+mockserverClientJava = { group = "org.mock-server", name = "mockserver-client-java", version.ref = "mockserverVersion" }
+mockserverJunitJupiter = { group = "org.mock-server", name = "mockserver-junit-jupiter", version.ref = "mockserverVersion" }
+mockserverNetty = { group = "org.mock-server", name = "mockserver-netty", version.ref = "mockserverVersion" }
+picocli = { group = "info.picocli", name = "picocli", version.ref = "picocliVersion" }
+picocliCodegen = { group = "info.picocli", name = "picocli-codegen", version.ref = "picocliVersion" }
+slf4jApi = { group = "org.slf4j", name = "slf4j-api", version.ref = "slf4jVersion" }
+towerJavaSdk = { group = "io.seqera.tower", name = "tower-java-sdk", version.ref = "towerJavaSdkVersion" }
+xz = { group = "org.tukaani", name = "xz", version.ref = "xzVersion" }
+
+[plugins]
+yumiLicenser = { id = "dev.yumi.gradle.licenser", version.ref = "licenserVersion" }
+graalvmNative = { id = "org.graalvm.buildtools.native", version.ref = "graalvmNativeVersion" }
+shadow = { id = "com.gradleup.shadow", version.ref = "shadowVersion" }

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.3.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

settings.gradle

@@ -11,7 +11,7 @@ plugins {
     // required to download the toolchain (jdk) from a remote repository
     // https://github.com/gradle/foojay-toolchains
     // https://docs.gradle.org/current/userguide/toolchains.html#sub:download_repositories
-    id("org.gradle.toolchains.foojay-resolver-convention") version "0.7.0"
+    id("org.gradle.toolchains.foojay-resolver-convention") version "1.0.0"
 }
 
 rootProject.name = 'tower-cli'

src/main/java/io/seqera/tower/cli/Tower.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021-2023, Seqera.
+ * Copyright 2021-2026, Seqera.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,7 +12,6 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- *
  */
 
 /*

src/main/java/io/seqera/tower/cli/commands/AbstractApiCmd.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021-2023, Seqera.
+ * Copyright 2021-2026, Seqera.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,7 +12,6 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- *
  */
 
 package io.seqera.tower.cli.commands;

src/main/java/io/seqera/tower/cli/commands/AbstractCmd.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021-2023, Seqera.
+ * Copyright 2021-2026, Seqera.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,7 +12,6 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- *
  */
 
 package io.seqera.tower.cli.commands;

src/main/java/io/seqera/tower/cli/commands/AbstractRootCmd.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021-2023, Seqera.
+ * Copyright 2021-2026, Seqera.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,7 +12,6 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- *
  */
 
 package io.seqera.tower.cli.commands;

src/main/java/io/seqera/tower/cli/commands/ActionsCmd.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021-2023, Seqera.
+ * Copyright 2021-2026, Seqera.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -12,7 +12,6 @@
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- *
  */
 
 package io.seqera.tower.cli.commands;