chore: upgrade to Java 21 and Gradle 8.5 #405

.github/workflows/lapis2.yml

@@ -12,10 +12,10 @@ jobs:
       -
         uses: actions/checkout@v4
       -
-        name: Set up JDK 19
+        name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: '19'
+          java-version: '21'
           distribution: 'adopt'
       -
         name: Execute Tests
@@ -39,10 +39,10 @@ jobs:
       -
         uses: actions/checkout@v4
       -
-        name: Set up JDK 19
+        name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: '19'
+          java-version: '21'
           distribution: 'adopt'
       -
         name: Login to GitHub Container Registry
@@ -90,10 +90,10 @@ jobs:
       -
         uses: actions/checkout@v4
       -
-        name: Set up JDK 19
+        name: Set up JDK
         uses: actions/setup-java@v4
         with:
-          java-version: '19'
+          java-version: '21'
           distribution: 'adopt'
       -
         name: Setup Node.js

lapis2/build.gradle

@@ -1,20 +1,27 @@
 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
 import org.gradle.api.tasks.testing.logging.TestLogEvent
-import org.jetbrains.kotlin.gradle.dsl.JvmTarget
 
 plugins {
-    id 'org.springframework.boot' version '3.1.5'
+    id 'org.springframework.boot' version '3.2.0'
     id 'io.spring.dependency-management' version '1.1.4'
-    id 'org.jetbrains.kotlin.jvm' version '1.9.20'
-    id 'org.jetbrains.kotlin.plugin.spring' version '1.9.20'
+    id 'org.jetbrains.kotlin.jvm' version '1.9.21'
+    id 'org.jetbrains.kotlin.plugin.spring' version '1.9.21'
     id 'org.jlleitschuh.gradle.ktlint' version "11.6.1"
     id 'org.springdoc.openapi-gradle-plugin' version "1.8.0"
     id 'antlr'
 }
 
 group = 'org.genspectrum'
 version = '0.0.1-SNAPSHOT'
-sourceCompatibility = '19'
+
+java {
+    sourceCompatibility = '21'
+    targetCompatibility = '21'
+}
+
+kotlin {
+    jvmToolchain(21)
+}
 
 repositories {
     mavenCentral()
@@ -43,10 +50,6 @@ dependencies {
 
 compileKotlin {
     dependsOn generateGrammarSource
-    compilerOptions {
-        freeCompilerArgs.add("-Xexport-kdoc")
-        jvmTarget.set(JvmTarget.JVM_19)
-    }
 }
 
 tasks.named('runKtlintCheckOverMainSourceSet') {
@@ -69,7 +72,7 @@ tasks.named('test') {
 }
 
 tasks.named('bootBuildImage') {
-    environment["BP_JVM_VERSION"] = "20"
+    environment["BP_JVM_VERSION"] = "21"
     environment["BPE_SPRING_PROFILES_ACTIVE"] = "docker"
     environment["BPE_LAPIS_REFERENCE_GENOME_FILENAME"] = "./reference_genomes.json"
     imageName = "ghcr.io/genspectrum/${project.name}"

lapis2/gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
-networkTimeout=10000
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

lapis2/gradlew

@@ -55,7 +55,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -80,11 +80,11 @@ do
     esac
 done
 
-# This is normally unused
-# shellcheck disable=SC2034
-APP_BASE_NAME=${0##*/}
 APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
+APP_NAME="Gradle"
+APP_BASE_NAME=${0##*/}
+
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
 DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
@@ -143,16 +143,12 @@ fi
 if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
-        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
-        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac

lapis2/gradlew.bat

@@ -26,7 +26,6 @@ if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
 if "%DIRNAME%"=="" set DIRNAME=.
-@rem This is normally unused
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 

lapis2/src/main/kotlin/org/genspectrum/lapis/controller/ExceptionHandler.kt

@@ -3,6 +3,7 @@ package org.genspectrum.lapis.controller
 import mu.KotlinLogging
 import org.genspectrum.lapis.model.SiloNotImplementedError
 import org.genspectrum.lapis.silo.SiloException
+import org.springframework.core.annotation.Order
 import org.springframework.http.HttpStatus
 import org.springframework.http.HttpStatusCode
 import org.springframework.http.MediaType
@@ -12,11 +13,32 @@ import org.springframework.web.bind.annotation.ControllerAdvice
 import org.springframework.web.bind.annotation.ExceptionHandler
 import org.springframework.web.bind.annotation.ResponseStatus
 import org.springframework.web.servlet.mvc.method.annotation.ResponseEntityExceptionHandler
+import org.springframework.web.servlet.resource.NoResourceFoundException
 
 private val log = KotlinLogging.logger {}
 
 private typealias ErrorResponse = ResponseEntity<LapisErrorResponse>
 
+/**
+ * Taken from https://github.com/spring-projects/spring-framework/issues/31569#issuecomment-1825444419
+ * Due to https://github.com/spring-projects/spring-framework/commit/c00508d6cf2408d06a0447ed193ad96466d0d7b4
+ *
+ * This forwards "404" errors to the ErrorController to allow it to return a view.
+ * Thus, browsers get their own error page.
+ *
+ * Spring reworked handling of "404 not found" errors. This was introduced with the upgrade to Spring boot 3.2.0.
+ * This can be removed/reworked once Spring decides on how to return a view from an ExceptionHandler
+ * or allows them to respect the Accept header.
+ */
+@ControllerAdvice
+@Order(-1)
+internal class ExceptionToErrorControllerBypass {
+    @ExceptionHandler(NoResourceFoundException::class)
+    fun handleResourceNotFound(e: Exception): Nothing {
+        throw e
+    }
+}
+
 @ControllerAdvice
 class ExceptionHandler : ResponseEntityExceptionHandler() {
     @ExceptionHandler(Throwable::class)

lapis2/src/main/kotlin/org/genspectrum/lapis/logging/StatisticsLogObjectMapper.kt

@@ -10,15 +10,12 @@ import org.springframework.stereotype.Component
 
 @Component
 class StatisticsLogObjectMapper(objectMapperBuilder: Jackson2ObjectMapperBuilder) {
-    private val mapper: ObjectMapper
-
-    init {
-        mapper = objectMapperBuilder.build()
-        mapper.registerModule(JavaTimeModule())
-        mapper.registerModule(kotlinModule())
-        mapper.configure(SerializationFeature.FAIL_ON_EMPTY_BEANS, false)
-        mapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false)
-        mapper.setSerializationInclusion(JsonInclude.Include.NON_NULL)
+    private val mapper = objectMapperBuilder.build<ObjectMapper>().apply {
+        registerModule(JavaTimeModule())
+        registerModule(kotlinModule())
+        configure(SerializationFeature.FAIL_ON_EMPTY_BEANS, false)
+        configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false)
+        setSerializationInclusion(JsonInclude.Include.NON_NULL)
     }
 
     fun writeValueAsString(requestContext: RequestContext): String {