feat(website): disable collections for Influenza A and B

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,

backend/src/main/kotlin/org/genspectrum/dashboardsbackend/model/collection/CollectionModel.kt

@@ -22,6 +22,10 @@ import org.springframework.transaction.annotation.Transactional
 @Transactional
 class CollectionModel(private val dashboardsConfig: DashboardsConfig) {
     fun getCollections(userId: String?, organism: String?): List<Collection> {
+        if (organism != null) {
+            dashboardsConfig.validateIsValidOrganism(organism)
+            dashboardsConfig.validateCollectionsEnabled(organism)
+        }
         val query = if (userId == null && organism == null) {
             CollectionEntity.all()
         } else {
@@ -60,12 +64,16 @@ class CollectionModel(private val dashboardsConfig: DashboardsConfig) {
         }
     }
 
-    fun getCollection(id: Long): Collection = CollectionEntity.findById(id)
-        ?.toCollection()
-        ?: throw NotFoundException("Collection $id not found")
+    fun getCollection(id: Long): Collection {
+        val entity = CollectionEntity.findById(id)
+            ?: throw NotFoundException("Collection $id not found")
+        dashboardsConfig.validateCollectionsEnabled(entity.organism)
+        return entity.toCollection()
+    }
 
     fun createCollection(request: CollectionRequest, userId: String): Collection {
         dashboardsConfig.validateIsValidOrganism(request.organism)
+        dashboardsConfig.validateCollectionsEnabled(request.organism)
 
         val collectionEntity = CollectionEntity.new {
             name = request.name
@@ -94,6 +102,7 @@ class CollectionModel(private val dashboardsConfig: DashboardsConfig) {
         // Find with ownership check
         val entity = CollectionEntity.findForUser(id, userId)
             ?: throw ForbiddenException("Collection $id not found or you don't have permission to delete it")
+        dashboardsConfig.validateCollectionsEnabled(entity.organism)
 
         // Delete (variants cascade automatically via DB constraint)
         entity.delete()
@@ -102,6 +111,7 @@ class CollectionModel(private val dashboardsConfig: DashboardsConfig) {
     fun putCollection(id: Long, update: CollectionUpdate, userId: String): Collection {
         val collectionEntity = CollectionEntity.findForUser(id, userId)
             ?: throw ForbiddenException("Collection $id not found or you don't have permission to update it")
+        dashboardsConfig.validateCollectionsEnabled(collectionEntity.organism)
 
         if (update.name != null) {
             collectionEntity.name = update.name

backend/src/main/resources/application-dashboards-prod.yaml

@@ -49,6 +49,7 @@ dashboards:
           menuIcon: "database"
           description: "Browse the underlying data in the Loculus database."
     influenzaA:
+      hasCollections: false
       lapis:
         url: "https://api.loculus.genspectrum.org/influenza-a"
         mainDateField: "sampleCollectionDateRangeLower"
@@ -61,6 +62,7 @@ dashboards:
           menuIcon: "database"
           description: "Browse the underlying data in the Loculus database."
     influenzaB:
+      hasCollections: false
       lapis:
         url: "https://api.loculus.genspectrum.org/influenza-b"
         mainDateField: "sampleCollectionDateRangeLower"

backend/src/main/resources/application-dashboards-staging.yaml

@@ -46,6 +46,7 @@ dashboards:
           menuIcon: "database"
           description: "Browse the underlying data in the Loculus database."
     influenzaA:
+      hasCollections: false
       lapis:
         url: "https://api.loculus.staging.genspectrum.org/influenza-a"
         mainDateField: "sampleCollectionDateRangeLower"
@@ -58,6 +59,7 @@ dashboards:
           menuIcon: "database"
           description: "Browse the underlying data in the Loculus database."
     influenzaB:
+      hasCollections: false
       lapis:
         url: "https://api.loculus.staging.genspectrum.org/influenza-b"
         mainDateField: "sampleCollectionDateRangeLower"

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

@@ -13,6 +13,8 @@ enum class KnownTestOrganisms {
     WestNile,
 }
 
+const val ORGANISM_WITHOUT_COLLECTIONS = "InfluenzaA"
+
 val dummySubscriptionRequest = SubscriptionRequest(
     name = "My search",
     interval = EvaluationInterval.MONTHLY,

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

@@ -1,6 +1,7 @@
 package org.genspectrum.dashboardsbackend.controller
 
 import org.genspectrum.dashboardsbackend.KnownTestOrganisms
+import org.genspectrum.dashboardsbackend.ORGANISM_WITHOUT_COLLECTIONS
 import org.genspectrum.dashboardsbackend.api.Variant
 import org.genspectrum.dashboardsbackend.dummyCollectionRequest
 import org.hamcrest.MatcherAssert.assertThat
@@ -266,4 +267,11 @@ class CollectionsGetTest(
         mockMvc.perform(get("/collections/not-a-number"))
             .andExpect(status().isBadRequest)
     }
+
+    @Test
+    fun `WHEN getting collections for organism with collections disabled THEN returns 400`() {
+        collectionsClient.getCollectionsRaw(organism = ORGANISM_WITHOUT_COLLECTIONS)
+            .andExpect(status().isBadRequest)
+            .andExpect(jsonPath("$.detail").value("Collections are not supported for organism 'InfluenzaA'"))
+    }
 }

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

@@ -1,5 +1,6 @@
 package org.genspectrum.dashboardsbackend.controller
 
+import org.genspectrum.dashboardsbackend.ORGANISM_WITHOUT_COLLECTIONS
 import org.genspectrum.dashboardsbackend.api.FilterObject
 import org.genspectrum.dashboardsbackend.api.Variant
 import org.genspectrum.dashboardsbackend.api.VariantRequest
@@ -92,6 +93,17 @@ class CollectionsPostTest(
             .andExpect(jsonPath("\$.detail").value("Organism 'unknown organism' is not supported"))
     }
 
+    @Test
+    fun `WHEN creating collection for organism with collections disabled THEN returns 400`() {
+        val userId = getNewUserId()
+        collectionsClient.postCollectionRaw(
+            dummyCollectionRequest.copy(organism = ORGANISM_WITHOUT_COLLECTIONS),
+            userId,
+        )
+            .andExpect(status().isBadRequest)
+            .andExpect(jsonPath("\$.detail").value("Collections are not supported for organism 'InfluenzaA'"))
+    }
+
     @Test
     fun `WHEN creating variant with lineage filter THEN succeeds`() {
         val userId = getNewUserId()

backend/src/test/resources/application.yaml

@@ -28,3 +28,8 @@ dashboards:
         mainDateField: "westnile_date"
         additionalFilters:
           someAdditionalFilter: "westnile_additional_filter"
+    InfluenzaA:
+      hasCollections: false
+      lapis:
+        url: "https://influenzaA.lapis.dummy"
+        mainDateField: "influenzaA_date"

website/routeMocker.ts

@@ -272,12 +272,14 @@ function getError(error: unknown) {
 
 export const testOrganismsConfig = {
     covid: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'date',
         },
     },
     influenzaA: {
+        hasCollections: false,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -288,6 +290,7 @@ export const testOrganismsConfig = {
         },
     },
     h3n2: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -298,6 +301,7 @@ export const testOrganismsConfig = {
         },
     },
     h1n1pdm: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -308,6 +312,7 @@ export const testOrganismsConfig = {
         },
     },
     h5n1: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -318,6 +323,7 @@ export const testOrganismsConfig = {
         },
     },
     influenzaB: {
+        hasCollections: false,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -328,6 +334,7 @@ export const testOrganismsConfig = {
         },
     },
     victoria: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -338,6 +345,7 @@ export const testOrganismsConfig = {
         },
     },
     westNile: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -348,6 +356,7 @@ export const testOrganismsConfig = {
         },
     },
     rsvA: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -358,6 +367,7 @@ export const testOrganismsConfig = {
         },
     },
     rsvB: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -368,6 +378,7 @@ export const testOrganismsConfig = {
         },
     },
     mpox: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -378,6 +389,7 @@ export const testOrganismsConfig = {
         },
     },
     ebolaSudan: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -388,6 +400,7 @@ export const testOrganismsConfig = {
         },
     },
     ebolaZaire: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -398,6 +411,7 @@ export const testOrganismsConfig = {
         },
     },
     cchf: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -408,6 +422,7 @@ export const testOrganismsConfig = {
         },
     },
     denv1: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -418,6 +433,7 @@ export const testOrganismsConfig = {
         },
     },
     denv2: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -428,6 +444,7 @@ export const testOrganismsConfig = {
         },
     },
     denv3: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -438,6 +455,7 @@ export const testOrganismsConfig = {
         },
     },
     denv4: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',
@@ -448,6 +466,7 @@ export const testOrganismsConfig = {
         },
     },
     measles: {
+        hasCollections: true,
         lapis: {
             url: DUMMY_LAPIS_URL,
             mainDateField: 'sampleCollectionDateRangeLower',

website/src/config.ts

@@ -25,6 +25,7 @@ const externalNavigationLinksSchema = z.optional(z.array(externalNavigationLinkS
 const organismConfigSchema = z.object({
     lapis: lapisConfigSchema,
     externalNavigationLinks: externalNavigationLinksSchema,
+    hasCollections: z.boolean().default(true),
 });
 export type OrganismConfig = z.infer<typeof organismConfigSchema>;
 
@@ -120,7 +121,7 @@ function processEnvOrMetaEnv<T>(key: string, schema: z.ZodType<T>) {
     );
 }
 
-function readTypedConfigFile<T>(fileName: string, schema: z.ZodType<T>) {
+function readTypedConfigFile<T>(fileName: string, schema: z.ZodType<T, z.ZodTypeDef, unknown>) {
     const configFilePath = path.join(getConfigDir(), fileName);
     const yaml = YAML.parse(fs.readFileSync(configFilePath, 'utf8'));
     try {

website/src/layouts/base/header/getPathogenMegaMenuSections.ts

@@ -1,5 +1,5 @@
 import type { MenuIconType } from '../../../components/iconCss.ts';
-import { isStaging } from '../../../config.ts';
+import { getOrganismConfig, isStaging } from '../../../config.ts';
 import { type Organism, organismConfig, paths } from '../../../types/Organism.ts';
 import { Page } from '../../../types/pages.ts';
 import {
@@ -49,20 +49,21 @@ export function getPathogenMegaMenuSections(): PathogenMegaMenuSections {
                 };
             });
 
+        const supplementaryEntries: MegaMenuSection[] = [];
+
         // only on staging for now, remove when enabling on prod: https://github.com/GenSpectrum/dashboards/issues/1108
-        if (isStaging()) {
-            megaMenuSections.push({
+        if (isStaging() && getOrganismConfig(config.organism).hasCollections) {
+            supplementaryEntries.push({
                 label: 'Collections',
                 href: Page.collectionsForOrganism(config.organism),
                 underlineColor: config.menuListEntryDecoration,
                 iconType: 'table',
                 externalLink: false,
                 description: `Browse ${config.label} variant collections`,
-                hasSeparatorAbove: true,
             });
         }
 
-        megaMenuSections.push(
+        supplementaryEntries.push(
             ...ServerSide.routing.externalPages[config.organism].map((externalPage) => ({
                 label: externalPage.label,
                 href: externalPage.url,
@@ -73,6 +74,12 @@ export function getPathogenMegaMenuSections(): PathogenMegaMenuSections {
             })),
         );
 
+        if (supplementaryEntries.length > 0) {
+            supplementaryEntries[0] = { ...supplementaryEntries[0], hasSeparatorAbove: true };
+        }
+
+        megaMenuSections.push(...supplementaryEntries);
+
         acc[config.organism] = {
             headline: config.label,
             headlineBackgroundColor: config.backgroundColor,