Merge pull request #1215 from GenSpectrum/main

chore: update prod from main

Author: fhennig

backend/build.gradle.kts

@@ -31,10 +31,10 @@ dependencies {
     implementation("org.springdoc:springdoc-openapi-starter-webmvc-ui:2.8.6")
     implementation("org.flywaydb:flyway-database-postgresql:11.0.0")
     implementation("org.postgresql:postgresql:42.7.11")
-    implementation("org.jetbrains.exposed:exposed-spring-boot-starter:1.2.0")
-    implementation("org.jetbrains.exposed:exposed-json:1.2.0")
-    implementation("org.jetbrains.exposed:exposed-jdbc:1.2.0")
-    implementation("org.jetbrains.exposed:exposed-kotlin-datetime:1.2.0")
+    implementation("org.jetbrains.exposed:exposed-spring-boot-starter:1.3.0")
+    implementation("org.jetbrains.exposed:exposed-json:1.3.0")
+    implementation("org.jetbrains.exposed:exposed-jdbc:1.3.0")
+    implementation("org.jetbrains.exposed:exposed-kotlin-datetime:1.3.0")
     implementation("org.jetbrains.kotlinx:kotlinx-datetime:0.8.0-0.6.x-compat")
     implementation("com.fasterxml.jackson.module:jackson-module-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-9.5.0-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.5.1-bin.zip
 networkTimeout=10000
 retries=0
 retryBackOffMs=500

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

@@ -0,0 +1,15 @@
+package org.genspectrum.dashboardsbackend.api
+
+import kotlin.time.Instant
+
+/** Public metadata about a user's API key. The raw key is never returned after creation. */
+data class ApiKeyMetadata(val createdAt: Instant, val lastUsedAt: Instant?)
+
+/** Returned once when a key is first generated. The raw key is never stored and cannot be retrieved again. */
+data class GeneratedApiKey(val key: String, val createdAt: Instant)
+
+/** Request body for the internal validate endpoint called by the proxy. */
+data class ValidateApiKeyRequest(val key: String)
+
+/** Response from the internal validate endpoint — contains the internal user ID for the validated key. */
+data class ValidateApiKeyResponse(val userId: Long)

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

@@ -1,5 +1,6 @@
 package org.genspectrum.dashboardsbackend.api
 
+import com.fasterxml.jackson.annotation.JsonInclude
 import io.swagger.v3.oas.annotations.media.Schema
 import kotlin.time.Instant
 
@@ -9,10 +10,10 @@ import kotlin.time.Instant
 {
     "id": 1,
     "name": "My Collection",
-    "ownedBy": "user123",
+    "ownedBy": 123,
     "organism": "covid",
     "description": "A collection of interesting variants",
-    "variants": [],
+    "variantCount": 1,
     "createdAt": "2026-01-01T00:00:00Z",
     "updatedAt": "2026-01-02T00:00:00Z"
 }
@@ -21,10 +22,12 @@ import kotlin.time.Instant
 data class Collection(
     val id: Long,
     val name: String,
-    val ownedBy: String,
+    val ownedBy: Long,
     val organism: String,
     val description: String?,
-    val variants: List<Variant>,
+    val variantCount: Int,
+    @JsonInclude(JsonInclude.Include.NON_NULL)
+    val variants: List<Variant>?,
     val createdAt: Instant,
     val updatedAt: Instant,
 )

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

@@ -0,0 +1,16 @@
+package org.genspectrum.dashboardsbackend.api
+
+import kotlin.time.Instant
+
+data class User(
+    val id: Long,
+    val githubId: String?,
+    val name: String,
+    val email: String?,
+    val createdAt: Instant,
+    val updatedAt: Instant,
+)
+
+data class UserSyncRequest(val githubId: String, val name: String, val email: String?)
+
+data class PublicUser(val id: Long, val name: String)

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

@@ -4,7 +4,7 @@ import org.genspectrum.dashboardsbackend.controller.BadRequestException
 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>, val systemUser: SystemUserConfig? = null) {
     fun getOrganismConfig(organism: String) = organisms[organism]
         ?: throw IllegalArgumentException("No configuration found for organism $organism")
 
@@ -35,3 +35,17 @@ data class LapisConfig(
 )
 
 data class ExternalNavigationLink(val url: String, val label: String, val menuIcon: String, val description: String)
+
+data class SystemUserConfig(
+    val githubId: String,
+    val name: String,
+    val email: String? = null,
+    val apiKey: String? = null,
+) {
+    init {
+        require(apiKey == null || apiKey.length >= 32) { "systemUser.apiKey must be at least 32 characters" }
+    }
+
+    override fun toString() =
+        "SystemUserConfig(githubId=$githubId, name=$name, email=$email, apiKey=${if (apiKey != null) "***" else "null"})"
+}

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

@@ -0,0 +1,30 @@
+package org.genspectrum.dashboardsbackend.config
+
+import mu.KotlinLogging
+import org.genspectrum.dashboardsbackend.api.UserSyncRequest
+import org.genspectrum.dashboardsbackend.model.apikey.ApiKeyModel
+import org.genspectrum.dashboardsbackend.model.user.UserModel
+import org.springframework.boot.ApplicationArguments
+import org.springframework.boot.ApplicationRunner
+import org.springframework.stereotype.Component
+
+private val log = KotlinLogging.logger {}
+
+@Component
+class SystemUserInitializer(
+    private val dashboardsConfig: DashboardsConfig,
+    private val userModel: UserModel,
+    private val apiKeyModel: ApiKeyModel,
+) : ApplicationRunner {
+    override fun run(args: ApplicationArguments) {
+        val config = dashboardsConfig.systemUser ?: return
+        val user = userModel.syncUser(
+            UserSyncRequest(githubId = config.githubId, name = config.name, email = config.email),
+        )
+        log.info { "System user ready: id=${user.id}, $config" }
+        config.apiKey?.let {
+            apiKeyModel.upsertApiKey(userId = user.id, rawKey = it)
+            log.info { "System user API key upserted for userId=${user.id}" }
+        }
+    }
+}

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

@@ -0,0 +1,57 @@
+package org.genspectrum.dashboardsbackend.controller
+
+import io.swagger.v3.oas.annotations.Operation
+import org.genspectrum.dashboardsbackend.api.ApiKeyMetadata
+import org.genspectrum.dashboardsbackend.api.GeneratedApiKey
+import org.genspectrum.dashboardsbackend.api.ValidateApiKeyRequest
+import org.genspectrum.dashboardsbackend.api.ValidateApiKeyResponse
+import org.genspectrum.dashboardsbackend.model.apikey.ApiKeyModel
+import org.springframework.http.HttpStatus
+import org.springframework.http.MediaType
+import org.springframework.web.bind.annotation.DeleteMapping
+import org.springframework.web.bind.annotation.GetMapping
+import org.springframework.web.bind.annotation.PostMapping
+import org.springframework.web.bind.annotation.RequestBody
+import org.springframework.web.bind.annotation.RequestParam
+import org.springframework.web.bind.annotation.ResponseStatus
+import org.springframework.web.bind.annotation.RestController
+
+@RestController
+class ApiKeyController(private val apiKeyModel: ApiKeyModel) {
+    @GetMapping("/api-keys", produces = [MediaType.APPLICATION_JSON_VALUE])
+    @Operation(
+        summary = "Get API key metadata",
+        description = "Returns metadata for the user's current API key. Returns 404 if no key exists.",
+    )
+    fun getApiKey(@RequestParam userId: Long): ApiKeyMetadata = apiKeyModel.getApiKey(userId)
+
+    @PostMapping("/api-keys", produces = [MediaType.APPLICATION_JSON_VALUE])
+    @ResponseStatus(HttpStatus.CREATED)
+    @Operation(
+        summary = "Generate a new API key",
+        description = "Generates a new API key for the user. Returns the raw key once - it is never stored. " +
+            "Returns 409 if a key already exists.",
+    )
+    fun generateApiKey(@RequestParam userId: Long): GeneratedApiKey = apiKeyModel.generateApiKey(userId)
+
+    @DeleteMapping("/api-keys")
+    @ResponseStatus(HttpStatus.NO_CONTENT)
+    @Operation(
+        summary = "Revoke API key",
+        description = "Deletes the user's current API key. Returns 404 if no key exists.",
+    )
+    fun revokeApiKey(@RequestParam userId: Long) = apiKeyModel.revokeApiKey(userId)
+
+    @PostMapping("/internal/api-keys/validate", produces = [MediaType.APPLICATION_JSON_VALUE])
+    @Operation(
+        summary = "Validate an API key",
+        description = """Takes a raw API key and returns the associated userId on success (200).
+Returns 404 if the key does not match any stored hash - the proxy treats this as an invalid
+credential and falls through to the session cookie check. Only reachable within the internal
+Docker network, so no additional access control is applied.""",
+    )
+    fun validateApiKey(@RequestBody request: ValidateApiKeyRequest): ValidateApiKeyResponse {
+        val userId = apiKeyModel.validateApiKey(request.key)
+        return ValidateApiKeyResponse(userId = userId)
+    }
+}

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

@@ -23,14 +23,17 @@ class CollectionsController(private val collectionModel: CollectionModel) {
     @GetMapping("/collections", produces = [MediaType.APPLICATION_JSON_VALUE])
     @Operation(
         summary = "Get collections",
-        description = "Returns collections filtered by optional userId and/or organism parameters.",
+        description = "Returns collections filtered by optional userId and/or organism parameters. " +
+            "Set includeVariants=true to include the full variant list; by default only variantCount is returned.",
     )
     fun getCollections(
-        @RequestParam(required = false) userId: String?,
+        @RequestParam(required = false) userId: Long?,
         @RequestParam(required = false) organism: String?,
+        @RequestParam(required = false, defaultValue = "false") includeVariants: Boolean,
     ): List<Collection> = collectionModel.getCollections(
         userId = userId,
         organism = organism,
+        includeVariants = includeVariants,
     )
 
     @GetMapping("/collections/{id}", produces = [MediaType.APPLICATION_JSON_VALUE])
@@ -50,7 +53,7 @@ class CollectionsController(private val collectionModel: CollectionModel) {
     )
     fun postCollection(
         @RequestBody collection: CollectionRequest,
-        @UserIdParameter @RequestParam userId: String,
+        @UserIdParameter @RequestParam userId: Long,
     ): Collection = collectionModel.createCollection(
         request = collection,
         userId = userId,
@@ -65,7 +68,7 @@ class CollectionsController(private val collectionModel: CollectionModel) {
     fun putCollection(
         @RequestBody collection: CollectionUpdate,
         @Parameter(description = "The ID of the collection", example = "1") @PathVariable id: Long,
-        @UserIdParameter @RequestParam userId: String,
+        @UserIdParameter @RequestParam userId: Long,
     ): Collection = collectionModel.putCollection(id, collection, userId)
 
     @DeleteMapping("/collections/{id}")
@@ -76,6 +79,6 @@ class CollectionsController(private val collectionModel: CollectionModel) {
     )
     fun deleteCollection(
         @Parameter(description = "The ID of the collection", example = "1") @PathVariable id: Long,
-        @UserIdParameter @RequestParam userId: String,
+        @UserIdParameter @RequestParam userId: Long,
     ) = collectionModel.deleteCollection(id, userId)
 }

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

@@ -58,6 +58,17 @@ class ExceptionHandler : ResponseEntityExceptionHandler() {
         )
     }
 
+    @ExceptionHandler(ConflictException::class)
+    @ResponseStatus(HttpStatus.CONFLICT)
+    fun handleConflictException(e: Exception): ResponseEntity<ProblemDetail> {
+        log.info { "Caught ${e.javaClass}: ${e.message}" }
+
+        return responseEntity(
+            HttpStatus.CONFLICT,
+            e.message,
+        )
+    }
+
     private fun responseEntity(httpStatus: HttpStatus, detail: String?): ResponseEntity<ProblemDetail> =
         responseEntity(httpStatus, httpStatus.reasonPhrase, detail)
 
@@ -92,3 +103,4 @@ class ExceptionHandler : ResponseEntityExceptionHandler() {
 class BadRequestException(message: String) : RuntimeException(message)
 class NotFoundException(message: String) : RuntimeException(message)
 class ForbiddenException(message: String) : RuntimeException(message)
+class ConflictException(message: String) : RuntimeException(message)