chore: revive and update the backend (#1016)

* 974 update dependencies to fix docker incompatibility

* 974 update dependency to without known CVEs

* 974 decouple actual organisms from the backend code

* 974 add missing field from config

* 974 replace deprecated class

* 974 update docs

Author: fengelniederhammer

README.md

@@ -31,9 +31,15 @@ when there is new data above a configurable threshold for certain variant of an
 
 This monorepo contains the following packages:
 
-- [`backend/`](./backend): The backend for additional features of the dashboard website, currently the notification features.
+- [`backend/`](./backend): 
+  The backend for additional features of the dashboard website, currently the notification features.
+
+- [`website/`](./website): 
+  The dashboard website: delivery of the (basically static, via Astro) HTML pages with the embedded Dashboard Components
+  (which are included via npm), 
+  which retrieve data from LAPIS instances directly,
+  and some additional client side features accessing the backend.
 
-- [`website/`](./website): The dashboard website: delivery of the (basically static, via Astro) HTML pages with the embedded Dashboard Components (which are included via npm), which retrieve data from LAPIS instances directly, and some additional client side features accessing the backend.
 
 ## Local setup
 

backend.inactive.md

@@ -1,19 +1,7 @@
-> [!NOTE]
-> 
-> This backend is *not currently used* as the subscription feature is
-> currently on hold and not fully implemented yet, and can currently
-> be ignored when setting up a dashboards installation.  It is also
-> partially out of date. An exception are these two configuration
-> files which are shared with the frontend (`website` folder) and thus
-> in use and up to date:
-> [application-dashboards-prod.yaml](src/main/resources/application-dashboards-prod.yaml),
-> [application-dashboards-staging.yaml](src/main/resources/application-dashboards-staging.yaml)
-
 # Dashboards backend
 
-This backend exists to serve the subscription feature (unfinished,
-currently on hold, note the banner above). Genomic queries are served
-by LAPIS instances and do not go through this backend.
+This backend exists to serve the subscription feature (which is not fully implemented and currently on hold).
+Genomic queries are served by LAPIS instances and do not go through this backend.
 
 See [docs/arc42/03-context.md](../docs/arc42/03-context.md) for its
 place in the whole context.

backend/README.md

@@ -29,7 +29,7 @@ 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:42.7.4")
+    implementation("org.postgresql:postgresql:42.7.7")
     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")
@@ -39,7 +39,8 @@ dependencies {
         exclude(group = "org.mockito")
     }
     testImplementation("com.ninja-squad:springmockk:4.0.2")
-    testImplementation("org.testcontainers:postgresql:1.20.4")
+    testImplementation("org.testcontainers:testcontainers:2.0.3")
+    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")
 }

backend/build.gradle.kts

@@ -13,26 +13,6 @@ enum class DateWindow {
     LAST_6_MONTHS,
 }
 
-enum class Organism {
-    @JsonProperty("covid")
-    Covid,
-
-    @JsonProperty("h5n1")
-    H5N1,
-
-    @JsonProperty("mpox")
-    Mpox,
-
-    @JsonProperty("westNile")
-    WestNile,
-
-    @JsonProperty("rsvA")
-    RsvA,
-
-    @JsonProperty("rsvB")
-    RsvB,
-}
-
 enum class EvaluationInterval {
     @JsonProperty("daily")
     DAILY,
@@ -87,15 +67,6 @@ sealed interface Trigger {
 
 typealias LapisFilter = Map<String, String>
 
-interface BaseSubscription {
-    val name: String?
-    val interval: EvaluationInterval?
-    val organism: Organism?
-    val dateWindow: DateWindow?
-    val trigger: Trigger?
-    val active: Boolean?
-}
-
 @Schema(
     description = "A subscription",
     example = """
@@ -112,13 +83,13 @@ interface BaseSubscription {
 )
 data class Subscription(
     val id: String,
-    override val name: String,
-    override val interval: EvaluationInterval,
-    override val active: Boolean,
-    override val organism: Organism,
-    override val dateWindow: DateWindow,
-    override val trigger: Trigger,
-) : BaseSubscription
+    val name: String,
+    val interval: EvaluationInterval,
+    val active: Boolean,
+    val organism: String,
+    val dateWindow: DateWindow,
+    val trigger: Trigger,
+)
 
 @Schema(
     description = "A subscription request",
@@ -133,13 +104,13 @@ data class Subscription(
 """,
 )
 data class SubscriptionRequest(
-    override val name: String,
-    override val interval: EvaluationInterval,
-    override val organism: Organism,
-    override val dateWindow: DateWindow,
-    override val trigger: Trigger,
-    override val active: Boolean,
-) : BaseSubscription
+    val name: String,
+    val interval: EvaluationInterval,
+    val organism: String,
+    val dateWindow: DateWindow,
+    val trigger: Trigger,
+    val active: Boolean,
+)
 
 @Schema(
     description = "A subscription update request",
@@ -154,10 +125,10 @@ data class SubscriptionRequest(
 """,
 )
 data class SubscriptionUpdate(
-    override val name: String? = null,
-    override val interval: EvaluationInterval? = null,
-    override val organism: Organism? = null,
-    override val dateWindow: DateWindow? = null,
-    override val trigger: Trigger? = null,
-    override val active: Boolean? = null,
-) : BaseSubscription
+    val name: String? = null,
+    val interval: EvaluationInterval? = null,
+    val organism: String? = null,
+    val dateWindow: DateWindow? = null,
+    val trigger: Trigger? = null,
+    val active: Boolean? = null,
+)

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

@@ -1,13 +1,12 @@
 package org.genspectrum.dashboardsbackend.config
 
-import org.genspectrum.dashboardsbackend.api.Organism
 import org.springframework.boot.context.properties.ConfigurationProperties
 
 @ConfigurationProperties(prefix = "dashboards")
 data class DashboardsConfig(
-    val organisms: Map<Organism, OrganismConfig>,
+    val organisms: Map<String, OrganismConfig>,
 ) {
-    fun getOrganismConfig(organism: Organism) = organisms[organism]
+    fun getOrganismConfig(organism: String) = organisms[organism]
         ?: throw IllegalArgumentException("No configuration found for organism $organism")
 }
 
@@ -26,4 +25,5 @@ data class ExternalNavigationLink(
     val url: String,
     val label: String,
     val menuIcon: String,
+    val description: String,
 )

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

@@ -3,6 +3,7 @@ package org.genspectrum.dashboardsbackend.model.subscription
 import org.genspectrum.dashboardsbackend.api.Subscription
 import org.genspectrum.dashboardsbackend.api.SubscriptionRequest
 import org.genspectrum.dashboardsbackend.api.SubscriptionUpdate
+import org.genspectrum.dashboardsbackend.config.DashboardsConfig
 import org.genspectrum.dashboardsbackend.controller.BadRequestException
 import org.genspectrum.dashboardsbackend.controller.NotFoundException
 import org.jetbrains.exposed.sql.Database
@@ -15,6 +16,7 @@ import javax.sql.DataSource
 @Transactional
 class SubscriptionModel(
     pool: DataSource,
+    private val dashboardsConfig: DashboardsConfig,
 ) {
     init {
         Database.connect(pool)
@@ -34,17 +36,21 @@ class SubscriptionModel(
         }
     }
 
-    fun postSubscriptions(request: SubscriptionRequest, userId: String) = SubscriptionEntity
-        .new {
-            name = request.name
-            interval = request.interval.name
-            dateWindow = request.dateWindow.name
-            trigger = request.trigger
-            organism = request.organism.name
-            active = request.active
-            this.userId = userId
-        }
-        .toSubscription()
+    fun postSubscriptions(request: SubscriptionRequest, userId: String): Subscription {
+        validateIsValidOrganism(request.organism)
+
+        return SubscriptionEntity
+            .new {
+                name = request.name
+                interval = request.interval.name
+                dateWindow = request.dateWindow.name
+                trigger = request.trigger
+                organism = request.organism
+                active = request.active
+                this.userId = userId
+            }
+            .toSubscription()
+    }
 
     fun deleteSubscription(subscriptionId: String, userId: String) {
         val subscription = SubscriptionEntity.findForUser(convertToUuid(subscriptionId), userId)
@@ -54,6 +60,8 @@ class SubscriptionModel(
     }
 
     fun putSubscription(subscriptionId: String, subscriptionUpdate: SubscriptionUpdate, userId: String): Subscription {
+        subscriptionUpdate.organism?.also { validateIsValidOrganism(it) }
+
         val subscription = SubscriptionEntity.findForUser(convertToUuid(subscriptionId), userId)
             ?: throw NotFoundException("Subscription $subscriptionId not found")
 
@@ -70,7 +78,7 @@ class SubscriptionModel(
             subscription.trigger = subscriptionUpdate.trigger
         }
         if (subscriptionUpdate.organism != null) {
-            subscription.organism = subscriptionUpdate.organism.name
+            subscription.organism = subscriptionUpdate.organism
         }
         if (subscriptionUpdate.active != null) {
             subscription.active = subscriptionUpdate.active
@@ -79,6 +87,12 @@ class SubscriptionModel(
         return subscription.toSubscription()
     }
 
+    private fun validateIsValidOrganism(organism: String) {
+        if (!dashboardsConfig.organisms.containsKey(organism)) {
+            throw BadRequestException("Organism '$organism' is not supported")
+        }
+    }
+
     private fun convertToUuid(id: String) = try {
         UUID.fromString(id)
     } catch (_: IllegalArgumentException) {

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

@@ -39,7 +39,7 @@ class SubscriptionEntity(id: EntityID<UUID>) : UUIDEntity(id) {
         name = name,
         interval = enumValueOf(interval),
         active = active,
-        organism = enumValueOf(organism),
+        organism = organism,
         dateWindow = enumValueOf(dateWindow),
         trigger = trigger,
     )

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

@@ -3,7 +3,6 @@ package org.genspectrum.dashboardsbackend.model.triggerevaluation
 import com.fasterxml.jackson.databind.ObjectMapper
 import com.fasterxml.jackson.module.kotlin.readValue
 import org.genspectrum.dashboardsbackend.api.LapisFilter
-import org.genspectrum.dashboardsbackend.api.Organism
 import org.genspectrum.dashboardsbackend.config.DashboardsConfig
 import org.genspectrum.dashboardsbackend.log
 import org.genspectrum.dashboardsbackend.logging.REQUEST_ID_HEADER
@@ -27,15 +26,15 @@ class LapisClientProvider(
     objectMapper: ObjectMapper,
     requestIdContext: RequestIdContext,
 ) {
-    private val clients = Organism.entries.associateWith {
+    private val clients = dashboardsConfig.organisms.mapValues {
         LapisClient(
-            baseUrl = dashboardsConfig.getOrganismConfig(it).lapis.url,
+            baseUrl = it.value.lapis.url,
             objectMapper = objectMapper,
             requestIdContext = requestIdContext,
         )
     }
 
-    fun provide(organism: Organism) = clients[organism]
+    fun provide(organism: String) = clients[organism]
         ?: throw IllegalArgumentException("No LAPIS client for organism $organism registered")
 }
 

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

@@ -3,7 +3,6 @@ package org.genspectrum.dashboardsbackend.model.triggerevaluation
 import kotlinx.datetime.DateTimeUnit
 import kotlinx.datetime.minus
 import org.genspectrum.dashboardsbackend.api.DateWindow
-import org.genspectrum.dashboardsbackend.api.Organism
 import org.genspectrum.dashboardsbackend.api.Subscription
 import org.genspectrum.dashboardsbackend.api.Trigger
 import org.genspectrum.dashboardsbackend.api.TriggerEvaluationResult
@@ -60,7 +59,7 @@ class TriggerEvaluator(
         )
     }
 
-    private fun additionalFilters(organism: Organism): Map<String, String> {
+    private fun additionalFilters(organism: String): Map<String, String> {
         return dashboardsConfig.getOrganismConfig(organism).lapis.additionalFilters ?: emptyMap()
     }
 }
@@ -76,9 +75,7 @@ private class CountComputation(
     private val threshold: Int,
 ) : TriggerComputation {
     override fun evaluate(): TriggerEvaluationResult {
-        val lapisResponse = lapisClient.aggregated(lapisFilter)
-
-        return when (lapisResponse) {
+        return when (val lapisResponse = lapisClient.aggregated(lapisFilter)) {
             is LapisAggregatedResponse -> {
                 if (lapisResponse.data.isEmpty()) {
                     log.error {