chore(backend): bump some dependencies, bump gradle to 9.3.1, fix some deprecation warnings

backend/build.gradle.kts

@@ -1,10 +1,10 @@
 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
 
 plugins {
-    kotlin("jvm") version "2.0.21"
-    kotlin("plugin.spring") version "2.0.21"
+    kotlin("jvm") version "2.3.10"
+    kotlin("plugin.spring") version "2.3.10"
     id("org.springframework.boot") version "3.4.0"
-    id("io.spring.dependency-management") version "1.1.6"
+    id("io.spring.dependency-management") version "1.1.7"
     id("org.jlleitschuh.gradle.ktlint") version "12.1.2"
     id("org.springdoc.openapi-gradle-plugin") version "1.9.0"
 }
@@ -29,10 +29,10 @@ dependencies {
     implementation("org.jetbrains.kotlin:kotlin-stdlib")
     implementation("org.springdoc:springdoc-openapi-starter-webmvc-ui:2.7.0")
     implementation("org.flywaydb:flyway-database-postgresql:11.0.0")
-    implementation("org.postgresql:postgresql:42.7.7")
+    implementation("org.postgresql:postgresql:42.7.9")
     implementation("org.jetbrains.exposed:exposed-spring-boot-starter:0.56.0")
     implementation("org.jetbrains.exposed:exposed-json:0.56.0")
-    implementation("org.jetbrains.kotlinx:kotlinx-datetime:0.6.1")
+    implementation("org.jetbrains.kotlinx:kotlinx-datetime:0.7.1-0.6.x-compat")
     implementation("com.fasterxml.jackson.module:jackson-module-kotlin")
 
     testImplementation("org.springframework.boot:spring-boot-starter-test") {
@@ -43,6 +43,13 @@ dependencies {
     testImplementation("org.testcontainers:testcontainers-postgresql:2.0.3")
     testImplementation("org.mock-server:mockserver-netty:5.15.0")
     testImplementation("org.mock-server:mockserver-spring-test-listener:5.15.0")
+
+    testRuntimeOnly("org.junit.platform:junit-platform-launcher")
+}
+
+// taken from https://github.com/JLLeitschuh/ktlint-gradle/issues/809#issuecomment-2515514826
+ktlint {
+    version.set("1.4.1")
 }
 
 kotlin {

backend/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

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/api/Subscription.kt

@@ -48,10 +48,7 @@ sealed interface Trigger {
     }
 
     @Schema(description = "A trigger that is triggered when a certain count is reached")
-    data class CountTrigger @JsonCreator constructor(
-        val count: Int,
-        val filter: LapisFilter,
-    ) : Trigger {
+    data class CountTrigger @JsonCreator constructor(val count: Int, val filter: LapisFilter) : Trigger {
         val type: CountTriggerType = CountTriggerType.COUNT
     }
 

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/api/TriggerEvaluation.kt

@@ -1,38 +1,27 @@
 package org.genspectrum.dashboardsbackend.api
 
-data class TriggerEvaluationResponse(
-    val result: TriggerEvaluationResult,
-)
+data class TriggerEvaluationResponse(val result: TriggerEvaluationResult)
 
 sealed interface TriggerEvaluationResult {
-    data class EvaluationError(
-        val message: String,
-        val statusCode: Int,
-    ) : TriggerEvaluationResult {
+    data class EvaluationError(val message: String, val statusCode: Int) : TriggerEvaluationResult {
         val type = EvaluationErrorType.EvaluationError
 
         enum class EvaluationErrorType {
             EvaluationError,
         }
     }
 
-    data class ConditionMet(
-        val evaluatedValue: Number,
-        val threshold: Number,
-        val lapisDataVersion: String?,
-    ) : TriggerEvaluationResult {
+    data class ConditionMet(val evaluatedValue: Number, val threshold: Number, val lapisDataVersion: String?) :
+        TriggerEvaluationResult {
         val type = ConditionMetType.ConditionMet
 
         enum class ConditionMetType {
             ConditionMet,
         }
     }
 
-    data class ConditionNotMet(
-        val evaluatedValue: Number?,
-        val threshold: Number,
-        val lapisDataVersion: String?,
-    ) : TriggerEvaluationResult {
+    data class ConditionNotMet(val evaluatedValue: Number?, val threshold: Number, val lapisDataVersion: String?) :
+        TriggerEvaluationResult {
         val type = ConditionNotMetType.ConditionNotMet
 
         enum class ConditionNotMetType {

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/config/DashboardsConfig.kt

@@ -3,27 +3,13 @@ package org.genspectrum.dashboardsbackend.config
 import org.springframework.boot.context.properties.ConfigurationProperties
 
 @ConfigurationProperties(prefix = "dashboards")
-data class DashboardsConfig(
-    val organisms: Map<String, OrganismConfig>,
-) {
+data class DashboardsConfig(val organisms: Map<String, OrganismConfig>) {
     fun getOrganismConfig(organism: String) = organisms[organism]
         ?: throw IllegalArgumentException("No configuration found for organism $organism")
 }
 
-data class OrganismConfig(
-    val lapis: LapisConfig,
-    val externalNavigationLinks: List<ExternalNavigationLink>?,
-)
+data class OrganismConfig(val lapis: LapisConfig, val externalNavigationLinks: List<ExternalNavigationLink>?)
 
-data class LapisConfig(
-    val url: String,
-    val mainDateField: String,
-    val additionalFilters: Map<String, String>?,
-)
+data class LapisConfig(val url: String, val mainDateField: String, val additionalFilters: Map<String, String>?)
 
-data class ExternalNavigationLink(
-    val url: String,
-    val label: String,
-    val menuIcon: String,
-    val description: String,
-)
+data class ExternalNavigationLink(val url: String, val label: String, val menuIcon: String, val description: String)

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/controller/SubscriptionsController.kt

@@ -34,21 +34,18 @@ class SubscriptionsController(
     fun getSubscription(
         @IdParameter @PathVariable id: String,
         @UserIdParameter @RequestParam userId: String,
-    ): Subscription {
-        return subscriptionModel.getSubscription(
-            subscriptionId = id,
-            userId = userId,
-        )
-    }
+    ): Subscription = subscriptionModel.getSubscription(
+        subscriptionId = id,
+        userId = userId,
+    )
 
     @GetMapping("/subscriptions", produces = [MediaType.APPLICATION_JSON_VALUE])
     @Operation(
         summary = "Get all subscriptions of a user",
         description = "Returns a list of all subscriptions of a user.",
     )
-    fun getSubscriptions(@UserIdParameter @RequestParam userId: String): List<Subscription> {
-        return subscriptionModel.getSubscriptions(userId)
-    }
+    fun getSubscriptions(@UserIdParameter @RequestParam userId: String): List<Subscription> =
+        subscriptionModel.getSubscriptions(userId)
 
     @PostMapping("/subscriptions")
     @ResponseStatus(HttpStatus.CREATED)
@@ -59,12 +56,10 @@ class SubscriptionsController(
     fun postSubscriptions(
         @RequestBody subscription: SubscriptionRequest,
         @UserIdParameter @RequestParam userId: String,
-    ): Subscription {
-        return subscriptionModel.postSubscriptions(
-            request = subscription,
-            userId = userId,
-        )
-    }
+    ): Subscription = subscriptionModel.postSubscriptions(
+        request = subscription,
+        userId = userId,
+    )
 
     @DeleteMapping("/subscriptions/{id}")
     @ResponseStatus(HttpStatus.NO_CONTENT)
@@ -88,13 +83,11 @@ class SubscriptionsController(
         @RequestBody subscription: SubscriptionUpdate,
         @IdParameter @PathVariable id: String,
         @UserIdParameter @RequestParam userId: String,
-    ): Subscription {
-        return subscriptionModel.putSubscription(
-            subscriptionId = id,
-            subscriptionUpdate = subscription,
-            userId = userId,
-        )
-    }
+    ): Subscription = subscriptionModel.putSubscription(
+        subscriptionId = id,
+        subscriptionUpdate = subscription,
+        userId = userId,
+    )
 
     @GetMapping("/subscriptions/evaluateTrigger")
     @Operation(

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/subscription/SubscriptionModel.kt

@@ -14,26 +14,20 @@ import javax.sql.DataSource
 
 @Service
 @Transactional
-class SubscriptionModel(
-    pool: DataSource,
-    private val dashboardsConfig: DashboardsConfig,
-) {
+class SubscriptionModel(pool: DataSource, private val dashboardsConfig: DashboardsConfig) {
     init {
         Database.connect(pool)
     }
 
-    fun getSubscription(subscriptionId: String, userId: String): Subscription {
-        return SubscriptionEntity.findForUser(convertToUuid(subscriptionId), userId)
+    fun getSubscription(subscriptionId: String, userId: String): Subscription =
+        SubscriptionEntity.findForUser(convertToUuid(subscriptionId), userId)
             ?.toSubscription()
             ?: throw NotFoundException("Subscription $subscriptionId not found")
-    }
 
-    fun getSubscriptions(userId: String): List<Subscription> {
-        return SubscriptionEntity.find {
-            SubscriptionTable.userId eq userId
-        }.map {
-            it.toSubscription()
-        }
+    fun getSubscriptions(userId: String): List<Subscription> = SubscriptionEntity.find {
+        SubscriptionTable.userId eq userId
+    }.map {
+        it.toSubscription()
     }
 
     fun postSubscriptions(request: SubscriptionRequest, userId: String): Subscription {

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/triggerevaluation/LapisClient.kt

@@ -99,35 +99,21 @@ class LapisClient(
         }
     }
 
-    private fun String.truncateAfter(maxLength: Int): String {
-        return if (length > maxLength) {
-            substring(0, maxLength) + "..."
-        } else {
-            this
-        }
+    private fun String.truncateAfter(maxLength: Int): String = if (length > maxLength) {
+        substring(0, maxLength) + "..."
+    } else {
+        this
     }
 }
 
 sealed interface LapisResponse
 
-data class LapisAggregatedResponse(
-    val data: List<AggregatedData>,
-    val info: LapisInfo,
-) : LapisResponse
+data class LapisAggregatedResponse(val data: List<AggregatedData>, val info: LapisInfo) : LapisResponse
 
-data class AggregatedData(
-    val count: Int,
-)
+data class AggregatedData(val count: Int)
 
-data class LapisError(
-    val error: ProblemDetail,
-    val info: LapisInfo,
-) : LapisResponse
+data class LapisError(val error: ProblemDetail, val info: LapisInfo) : LapisResponse
 
-data class LapisInfo(
-    val dataVersion: String? = null,
-)
+data class LapisInfo(val dataVersion: String? = null)
 
-data class LapisNotReachableError(
-    val message: String,
-) : LapisResponse
+data class LapisNotReachableError(val message: String) : LapisResponse

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/triggerevaluation/TriggerEvaluator.kt

@@ -59,9 +59,8 @@ class TriggerEvaluator(
         )
     }
 
-    private fun additionalFilters(organism: String): Map<String, String> {
-        return dashboardsConfig.getOrganismConfig(organism).lapis.additionalFilters ?: emptyMap()
-    }
+    private fun additionalFilters(organism: String): Map<String, String> =
+        dashboardsConfig.getOrganismConfig(organism).lapis.additionalFilters ?: emptyMap()
 }
 
 private interface TriggerComputation {

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/util/DateProvider.kt

@@ -1,9 +1,9 @@
 package org.genspectrum.dashboardsbackend.util
 
-import kotlinx.datetime.Clock
 import kotlinx.datetime.TimeZone
 import kotlinx.datetime.toLocalDateTime
 import org.springframework.stereotype.Component
+import kotlin.time.Clock
 
 @Component
 class DateProvider {

backend/src/test/kotlin/org/genspectrum/dashboardsbackend/SwaggerUiTest.kt

@@ -17,7 +17,7 @@ import org.springframework.test.web.servlet.result.MockMvcResultMatchers.status
 
 @SpringBootTest
 @AutoConfigureMockMvc
-class SwaggerUiTest(@Autowired val mockMvc: MockMvc) {
+class SwaggerUiTest(@param:Autowired val mockMvc: MockMvc) {
 
     @Test
     fun `Swagger UI endpoint is reachable`() {

backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/InfoControllerTest.kt

@@ -13,7 +13,7 @@ import org.springframework.test.web.servlet.result.MockMvcResultMatchers.status
 
 @SpringBootTest
 @AutoConfigureMockMvc
-class InfoControllerTest(@Autowired val mockMvc: MockMvc) {
+class InfoControllerTest(@param:Autowired val mockMvc: MockMvc) {
     @Test
     fun `WHEN calling root THEN responds with a hello page`() {
         mockMvc.perform(get("/"))

backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/SubscriptionsClient.kt

@@ -15,10 +15,7 @@ import org.springframework.test.web.servlet.request.MockMvcRequestBuilders.put
 import org.springframework.test.web.servlet.result.MockMvcResultMatchers.content
 import org.springframework.test.web.servlet.result.MockMvcResultMatchers.status
 
-class SubscriptionsClient(
-    private val mockMvc: MockMvc,
-    private val objectMapper: ObjectMapper,
-) {
+class SubscriptionsClient(private val mockMvc: MockMvc, private val objectMapper: ObjectMapper) {
     fun getSubscriptionRaw(id: String, userId: String) = mockMvc.perform(get("/subscriptions/$id?userId=$userId"))
 
     fun getSubscription(id: String, userId: String): Subscription = deserializeJsonResponse(

backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/SubscriptionsControllerTest.kt

@@ -23,16 +23,12 @@ import org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPat
 import org.springframework.test.web.servlet.result.MockMvcResultMatchers.status
 import java.util.*
 
-fun getNewUserId(): String {
-    return UUID.randomUUID().toString()
-}
+fun getNewUserId(): String = UUID.randomUUID().toString()
 
 @SpringBootTest
 @AutoConfigureMockMvc
 @Import(SubscriptionsClient::class)
-class SubscriptionsControllerTest(
-    @Autowired private val subscriptionsClient: SubscriptionsClient,
-) {
+class SubscriptionsControllerTest(@param:Autowired private val subscriptionsClient: SubscriptionsClient) {
     @Test
     fun `GIVEN I created a subscription WHEN getting subscriptions THEN contains created subscription`() {
         val userId = getNewUserId()

backend/src/test/kotlin/org/genspectrum/dashboardsbackend/controller/SubscriptionsControllerTriggerEvaluationTest.kt

@@ -30,7 +30,7 @@ import org.springframework.test.web.servlet.result.MockMvcResultMatchers.status
 @AutoConfigureMockMvc
 @Import(SubscriptionsClient::class)
 class SubscriptionsControllerTriggerEvaluationTest(
-    @Autowired private val subscriptionsClient: SubscriptionsClient,
+    @param:Autowired private val subscriptionsClient: SubscriptionsClient,
 ) {
     @MockkBean
     private lateinit var lapisClientProviderMock: LapisClientProvider

backend/src/test/kotlin/org/genspectrum/dashboardsbackend/model/triggerevaluation/CountTriggerEvaluatorTest.kt

@@ -41,9 +41,7 @@ import org.springframework.boot.test.context.SpringBootTest
     ],
 )
 @MockServerTest
-class CountTriggerEvaluatorTest(
-    @Autowired private val underTest: TriggerEvaluator,
-) {
+class CountTriggerEvaluatorTest(@param:Autowired private val underTest: TriggerEvaluator) {
     private lateinit var mockServerClient: MockServerClient
 
     @MockkBean
@@ -261,13 +259,12 @@ class CountTriggerEvaluatorTest(
         assertThat(exception.message, containsString("Failed to deserialize error response from LAPIS"))
     }
 
-    private fun isEvaluationErrorWith(message: Matcher<String>, statusCode: Int): Matcher<TriggerEvaluationResult> {
-        return allOf(
+    private fun isEvaluationErrorWith(message: Matcher<String>, statusCode: Int): Matcher<TriggerEvaluationResult> =
+        allOf(
             instanceOf(TriggerEvaluationResult.EvaluationError::class.java),
             hasProperty("message", message),
             hasProperty("statusCode", `is`(statusCode)),
         )
-    }
 
     private fun requestingAggregatedDataWith(organism: String, body: String): HttpRequest? = request()
         .withMethod("POST")