Merge pull request #1133 from GenSpectrum/main

chore: update prod from main

Author: fhennig

.github/workflows/backend.yml

@@ -27,6 +27,13 @@ jobs:
       - name: Execute Tests
         run: ./gradlew test
 
+      - name: Upload test report
+        uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: backend-test-report
+          path: backend/build/reports/tests/test/
+
       - name: Check Format And Lint
         run: ./gradlew ktlintCheck
 

.github/workflows/e2e.yml

@@ -37,14 +37,14 @@ jobs:
       run: echo "branchTag=${TAG##*:}" >> $GITHUB_OUTPUT
 
     - name: Wait for website Docker image
-      uses: lewagon/wait-on-check-action@v1.6.0
+      uses: lewagon/wait-on-check-action@v1.6.1
       with:
         ref: ${{ github.sha }}
         check-name: Build Website Docker Image
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         wait-interval: 10
     - name: Wait for backend Docker image
-      uses: lewagon/wait-on-check-action@v1.6.0
+      uses: lewagon/wait-on-check-action@v1.6.1
       with:
         ref: ${{ github.sha }}
         check-name: Build Backend Docker Image

AGENTS.md

@@ -0,0 +1,39 @@
+# AGENTS.md — Coding Agent Guidelines
+
+This monorepo contains two packages:
+- **`website/`** — Astro + React frontend (TypeScript), see `website/AGENTS.md`
+- **`backend/`** — Kotlin + Spring Boot backend, see `backend/AGENTS.md`
+
+---
+
+## Repository Structure
+
+```
+/
+├── website/        # Astro/React frontend
+├── backend/        # Kotlin/Spring Boot backend
+├── docs/           # Architecture documentation (arc42)
+└── docker-compose.yml
+```
+
+---
+
+## Commit Messages
+
+Follow [Conventional Commits](https://www.conventionalcommits.org):
+```
+feat: add new organism dashboard
+fix: correct date range calculation
+chore: update dependencies
+```
+- PR titles become the squash-merge commit message — they must also follow conventional commits.
+- Messages should explain **why** a change was made, not just what.
+
+---
+
+## Architecture Notes
+
+- **State in URL**: View state (filters, selected variants) is stored as query parameters so pages are bookmarkable and shareable.
+- **LAPIS**: All genomic data queries go directly from the browser to LAPIS instances — they do not go through the backend.
+- **Backend**: Only handles subscriptions and collections features; authentication is handled in the frontend (Astro middleware) and proxied to the backend.
+- **Organisms**: Adding a new organism requires entries in `website/src/types/Organism.ts`, `website/src/views/`, and corresponding Astro pages.

backend/AGENTS.md

@@ -0,0 +1,73 @@
+# AGENTS.md — Backend
+
+Kotlin + Spring Boot backend. All commands run from `backend/`. Docker must be running (tests use Testcontainers).
+
+---
+
+## Build & Dev Commands
+
+```bash
+./gradlew build                   # Build
+./gradlew test                    # Run all tests
+./gradlew bootRun --args='--spring.profiles.active=local-db,dashboards-prod'  # Run locally
+```
+
+The backend will be available at `http://localhost:8080`. Swagger UI at `http://localhost:8080/swagger-ui/index.html`.
+The database from the top-level Docker Compose file needs to be running.
+
+## Running a Single Test
+
+```bash
+# Run a single test class:
+./gradlew test --tests "org.genspectrum.dashboardsbackend.controller.SubscriptionsControllerTest"
+
+# Run a single test method (use the full backtick-quoted name):
+./gradlew test --tests "org.genspectrum.dashboardsbackend.controller.SubscriptionsControllerTest.GIVEN I created a subscription WHEN getting subscriptions THEN contains created subscription"
+```
+
+## Lint
+
+```bash
+./gradlew ktlintCheck
+./gradlew ktlintFormat
+```
+
+---
+
+## Code Style
+
+### Style
+- Enforced by **ktlint** (version 1.4.1). Run `./gradlew ktlintFormat` to auto-fix.
+- Follow standard Kotlin idioms: data classes, sealed interfaces, extension functions.
+
+### Naming
+- Classes/interfaces: `PascalCase`
+- Functions/variables: `camelCase`
+- Constants: `UPPER_CASE`
+- Test method names use backtick syntax describing behavior:
+  ```kotlin
+  @Test
+  fun `GIVEN some state WHEN action THEN expected result`() { ... }
+  ```
+
+### Logging
+Use `kotlin-logging` (`io.github.microutils:kotlin-logging-jvm`):
+```kotlin
+private val log = KotlinLogging.logger {}
+log.info { "message" }
+```
+
+(There should be one global logger instance that can be reused everywhere)
+
+### Error Handling
+- Throw typed exceptions: `BadRequestException`, `NotFoundException`, `ForbiddenException`.
+- The global `ExceptionHandler` maps these to appropriate HTTP status codes with `ProblemDetail` bodies.
+- Log unexpected exceptions at `error` level; expected/handled exceptions at `info` or `warn`.
+
+### Testing
+- Use `@SpringBootTest` + `@AutoConfigureMockMvc` for integration tests.
+- Since the API is a relatively thin layer around the database, most tests should focus on interacting with the code via the endpoints.
+  Only add dedicated unit tests for isolated logic that is more complex.
+- Use **MockK** (via `springmockk`) instead of Mockito.
+- Use **Testcontainers** for database tests (Docker required).
+- Tests are organized by controller/feature, not by test type.

backend/README.md

@@ -52,6 +52,13 @@ Run tests:
 ./gradlew test
 ```
 
+## Authentication
+While the backend uses user IDs internally, for example to track owners
+of collections or subscriptions, it doesn't handle authentication of users.
+This is done in the frontend. All requests are proxied through the frontend
+server, where authentication is handled, and then the authenticated requests
+are sent to the backend.
+
 ## Logging
 Logs to rotating files are stored in `./logs` and written to stdout.
 In the Docker container, log files are stored in `/workspace/logs`

backend/build.gradle.kts

@@ -1,9 +1,10 @@
 import org.gradle.api.tasks.testing.logging.TestExceptionFormat
+import java.io.ByteArrayOutputStream
 
 plugins {
     kotlin("jvm") version "2.3.20"
     kotlin("plugin.spring") version "2.3.20"
-    id("org.springframework.boot") version "3.4.0"
+    id("org.springframework.boot") version "3.5.13"
     id("io.spring.dependency-management") version "1.1.7"
     id("org.jlleitschuh.gradle.ktlint") version "14.2.0"
     id("org.springdoc.openapi-gradle-plugin") version "1.9.0"
@@ -27,11 +28,13 @@ dependencies {
     implementation("org.jetbrains.kotlin:kotlin-reflect")
     implementation("io.github.microutils:kotlin-logging-jvm:3.0.5")
     implementation("org.jetbrains.kotlin:kotlin-stdlib")
-    implementation("org.springdoc:springdoc-openapi-starter-webmvc-ui:2.7.0")
+    implementation("org.springdoc:springdoc-openapi-starter-webmvc-ui:2.8.6")
     implementation("org.flywaydb:flyway-database-postgresql:11.0.0")
     implementation("org.postgresql:postgresql:42.7.10")
-    implementation("org.jetbrains.exposed:exposed-spring-boot-starter:0.56.0")
-    implementation("org.jetbrains.exposed:exposed-json:0.56.0")
+    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.kotlinx:kotlinx-datetime:0.7.1-0.6.x-compat")
     implementation("com.fasterxml.jackson.module:jackson-module-kotlin")
 
@@ -58,7 +61,20 @@ kotlin {
     }
 }
 
+val checkDockerAvailable by tasks.registering(Exec::class) {
+    commandLine("docker", "info")
+    standardOutput = ByteArrayOutputStream()
+    errorOutput = ByteArrayOutputStream()
+    isIgnoreExitValue = true
+    doLast {
+        if (executionResult.get().exitValue != 0) {
+            throw GradleException("Docker is not available. Please start Docker before running tests.")
+        }
+    }
+}
+
 tasks.withType<Test> {
+    dependsOn(checkDockerAvailable)
     useJUnitPlatform()
     testLogging {
         events("FAILED")

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

@@ -1,6 +1,7 @@
 package org.genspectrum.dashboardsbackend.api
 
 import io.swagger.v3.oas.annotations.media.Schema
+import kotlin.time.Instant
 
 @Schema(
     description = "A collection of variants",
@@ -11,7 +12,9 @@ import io.swagger.v3.oas.annotations.media.Schema
     "ownedBy": "user123",
     "organism": "covid",
     "description": "A collection of interesting variants",
-    "variants": []
+    "variants": [],
+    "createdAt": "2026-01-01T00:00:00Z",
+    "updatedAt": "2026-01-02T00:00:00Z"
 }
 """,
 )
@@ -22,6 +25,8 @@ data class Collection(
     val organism: String,
     val description: String?,
     val variants: List<Variant>,
+    val createdAt: Instant,
+    val updatedAt: Instant,
 )
 
 @Schema(

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

@@ -7,6 +7,7 @@ import com.fasterxml.jackson.annotation.JsonTypeInfo
 import io.swagger.v3.oas.annotations.media.Schema
 import org.genspectrum.dashboardsbackend.api.Variant.FilterObjectVariant
 import org.genspectrum.dashboardsbackend.api.Variant.QueryVariant
+import kotlin.time.Instant
 
 enum class QueryVariantType {
     @JsonProperty("query")
@@ -44,7 +45,9 @@ sealed interface Variant {
     "name": "BA.2 in USA",
     "description": "BA.2 lineage cases in USA",
     "countQuery": "country='USA' & lineage='BA.2'",
-    "coverageQuery": "country='USA'"
+    "coverageQuery": "country='USA'",
+    "createdAt": "2026-01-01T00:00:00Z",
+    "updatedAt": "2026-01-02T00:00:00Z"
 }
 """,
     )
@@ -55,6 +58,8 @@ sealed interface Variant {
         val description: String?,
         val countQuery: String,
         val coverageQuery: String? = null,
+        val createdAt: Instant,
+        val updatedAt: Instant,
     ) : Variant {
         val type: QueryVariantType = QueryVariantType.QUERY
     }
@@ -70,7 +75,9 @@ sealed interface Variant {
     "description": "Key mutations for Omicron",
     "filterObject": {
         "aminoAcidMutations": ["S:N501Y", "S:E484K", "S:K417N"]
-    }
+    },
+    "createdAt": "2026-01-01T00:00:00Z",
+    "updatedAt": "2026-01-02T00:00:00Z"
 }
 """,
     )
@@ -80,6 +87,8 @@ sealed interface Variant {
         val name: String,
         val description: String?,
         val filterObject: FilterObject,
+        val createdAt: Instant,
+        val updatedAt: Instant,
     ) : Variant {
         val type: FilterObjectVariantType = FilterObjectVariantType.FILTER_OBJECT
     }

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

@@ -6,8 +6,8 @@ import io.swagger.v3.oas.models.parameters.HeaderParameter
 import org.flywaydb.core.Flyway
 import org.genspectrum.dashboardsbackend.logging.REQUEST_ID_HEADER
 import org.genspectrum.dashboardsbackend.logging.REQUEST_ID_HEADER_DESCRIPTION
-import org.jetbrains.exposed.spring.autoconfigure.ExposedAutoConfiguration
-import org.jetbrains.exposed.sql.Database
+import org.jetbrains.exposed.v1.jdbc.Database
+import org.jetbrains.exposed.v1.spring.boot.autoconfigure.ExposedAutoConfiguration
 import org.springdoc.core.customizers.OperationCustomizer
 import org.springframework.boot.autoconfigure.ImportAutoConfiguration
 import org.springframework.boot.autoconfigure.jdbc.DataSourceTransactionManagerAutoConfiguration

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

@@ -13,9 +13,19 @@ data class DashboardsConfig(val organisms: Map<String, OrganismConfig>) {
             throw BadRequestException("Organism '$organism' is not supported")
         }
     }
+
+    fun validateCollectionsEnabled(organism: String) {
+        if (!getOrganismConfig(organism).hasCollections) {
+            throw BadRequestException("Collections are not supported for organism '$organism'")
+        }
+    }
 }
 
-data class OrganismConfig(val lapis: LapisConfig, val externalNavigationLinks: List<ExternalNavigationLink>?)
+data class OrganismConfig(
+    val lapis: LapisConfig,
+    val externalNavigationLinks: List<ExternalNavigationLink>?,
+    val hasCollections: Boolean = true,
+)
 
 data class LapisConfig(
     val url: String,