feat(website): introduce DB_ID_SPACE env var for environment-specific collection IDs

docker-compose.yml

@@ -8,6 +8,7 @@ services:
     environment:
       BACKEND_URL: http://backend:8080
       DASHBOARDS_ENVIRONMENT: dashboards-prod
+      DB_ID_SPACE: local
       GITHUB_CLIENT_ID: "dummy"
       GITHUB_CLIENT_SECRET: "dummy"
       AUTH_SECRET: "e2e-test-auth-secret-do-not-use-in-production"

website/.env.e2e

@@ -1,4 +1,5 @@
 CONFIG_DIR=../backend/src/main/resources/
 DASHBOARDS_ENVIRONMENT=dashboards-prod
+DB_ID_SPACE=local
 
 AUTH_SECRET="e2e-test-auth-secret-do-not-use-in-production"

website/.env.example

@@ -1,6 +1,7 @@
 CONFIG_DIR=../backend/src/main/resources/
 BACKEND_URL=http://localhost:8080
 DASHBOARDS_ENVIRONMENT=dashboards-prod
+# DB_ID_SPACE=local  # optional override; defaults to 'prod'/'staging' based on DASHBOARDS_ENVIRONMENT
 LOG_DIR=./logs
 LOG_LEVEL=info
 

website/src/components/views/wasap/Wasap.astro

@@ -2,22 +2,18 @@
 import { WasapPage } from './WasapPage';
 import { fetchResistanceData, type ResistanceData } from './resistanceData';
 import { BackendService } from '../../../backendApi/backendService.ts';
-import { isStaging, getBackendHost } from '../../../config.ts';
+import { getBackendHost } from '../../../config.ts';
 import BaseLayout from '../../../layouts/base/BaseLayout.astro';
 import { getInstanceLogger } from '../../../logger.ts';
-import {
-    wastewaterOrganismConfigs,
-    wastewaterOrganismStagingConfigs,
-    type WastewaterOrganismName,
-} from '../../../types/wastewaterConfig';
+import { type WastewaterOrganismName, wastewaterOrganismConfigs } from '../../../types/wastewaterConfig';
 import { getErrorLogMessage } from '../../../util/getErrorLogMessage';
 
 type Props = {
     wastewaterOrganism: WastewaterOrganismName;
 };
 
 const { wastewaterOrganism } = Astro.props;
-const config = (isStaging() ? wastewaterOrganismStagingConfigs : wastewaterOrganismConfigs)[wastewaterOrganism];
+const config = wastewaterOrganismConfigs()[wastewaterOrganism];
 const backendService = new BackendService(getBackendHost());
 let resistanceData: ResistanceData = { mutationAnnotations: [], displayMutationsBySet: {} };
 

website/src/env.d.ts

@@ -17,6 +17,8 @@ declare namespace App {
 interface ImportMetaEnv {
     // eslint-disable-next-line @typescript-eslint/naming-convention
     readonly DASHBOARDS_ENVIRONMENT: 'dashboards-staging' | 'dashboards-prod';
+    // eslint-disable-next-line @typescript-eslint/naming-convention
+    readonly DB_ID_SPACE?: import('./types/dbIdSpace').DbIdSpace;
 }
 
 interface ImportMeta {

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

@@ -99,24 +99,24 @@ export function getPathogenMegaMenuSections(): PathogenMegaMenuSections {
             {
                 label: 'SARS-CoV-2',
                 iconType: 'table',
-                href: wastewaterOrganismConfigs[wastewaterOrganisms.covid].path,
-                description: wastewaterOrganismConfigs[wastewaterOrganisms.covid].description,
+                href: wastewaterOrganismConfigs()[wastewaterOrganisms.covid].path,
+                description: wastewaterOrganismConfigs()[wastewaterOrganisms.covid].description,
                 underlineColor: wastewaterConfig.menuListEntryDecoration,
                 externalLink: false,
             },
             {
                 label: 'RSV-A',
                 iconType: 'table',
-                href: wastewaterOrganismConfigs[wastewaterOrganisms.rsvA].path,
-                description: wastewaterOrganismConfigs[wastewaterOrganisms.rsvA].description,
+                href: wastewaterOrganismConfigs()[wastewaterOrganisms.rsvA].path,
+                description: wastewaterOrganismConfigs()[wastewaterOrganisms.rsvA].description,
                 underlineColor: wastewaterConfig.menuListEntryDecoration,
                 externalLink: false,
             },
             {
                 label: 'RSV-B',
                 iconType: 'table',
-                href: wastewaterOrganismConfigs[wastewaterOrganisms.rsvB].path,
-                description: wastewaterOrganismConfigs[wastewaterOrganisms.rsvB].description,
+                href: wastewaterOrganismConfigs()[wastewaterOrganisms.rsvB].path,
+                description: wastewaterOrganismConfigs()[wastewaterOrganisms.rsvB].description,
                 underlineColor: wastewaterConfig.menuListEntryDecoration,
                 externalLink: false,
             },
@@ -139,24 +139,24 @@ export function getPathogenMegaMenuSections(): PathogenMegaMenuSections {
             {
                 label: 'Browse SARS-CoV-2 data',
                 iconType: 'database',
-                href: wastewaterOrganismConfigs[wastewaterOrganisms.covid].browseDataUrl,
-                description: wastewaterOrganismConfigs[wastewaterOrganisms.covid].browseDataDescription,
+                href: wastewaterOrganismConfigs()[wastewaterOrganisms.covid].browseDataUrl,
+                description: wastewaterOrganismConfigs()[wastewaterOrganisms.covid].browseDataDescription,
                 underlineColor: wastewaterConfig.menuListEntryDecoration,
                 externalLink: true,
             },
             {
                 label: 'Browse RSV-A data',
                 iconType: 'database',
-                href: wastewaterOrganismConfigs[wastewaterOrganisms.rsvA].browseDataUrl,
-                description: wastewaterOrganismConfigs[wastewaterOrganisms.rsvA].browseDataDescription,
+                href: wastewaterOrganismConfigs()[wastewaterOrganisms.rsvA].browseDataUrl,
+                description: wastewaterOrganismConfigs()[wastewaterOrganisms.rsvA].browseDataDescription,
                 underlineColor: wastewaterConfig.menuListEntryDecoration,
                 externalLink: true,
             },
             {
                 label: 'Browse RSV-B data',
                 iconType: 'database',
-                href: wastewaterOrganismConfigs[wastewaterOrganisms.rsvB].browseDataUrl,
-                description: wastewaterOrganismConfigs[wastewaterOrganisms.rsvB].browseDataDescription,
+                href: wastewaterOrganismConfigs()[wastewaterOrganisms.rsvB].browseDataUrl,
+                description: wastewaterOrganismConfigs()[wastewaterOrganisms.rsvB].browseDataDescription,
                 underlineColor: wastewaterConfig.menuListEntryDecoration,
                 externalLink: true,
             },

website/src/types/dbIdSpace.ts

@@ -0,0 +1,22 @@
+export const dbIdSpaces = {
+    prod: 'prod',
+    staging: 'staging',
+    local: 'local',
+} as const;
+
+export type DbIdSpace = (typeof dbIdSpaces)[keyof typeof dbIdSpaces];
+
+export function getDbIdSpace(): DbIdSpace {
+    const envValue = process.env.DB_ID_SPACE ?? import.meta.env.DB_ID_SPACE;
+    if (envValue) {
+        const validValues: string[] = [dbIdSpaces.prod, dbIdSpaces.staging, dbIdSpaces.local];
+        if (validValues.includes(envValue)) {
+            return envValue as DbIdSpace;
+        }
+        throw new Error(
+            `Environment variable DB_ID_SPACE (value '${envValue}') is not valid. Expected one of: ${validValues.join(', ')}`,
+        );
+    }
+    const dashboardsEnv = process.env.DASHBOARDS_ENVIRONMENT ?? import.meta.env.DASHBOARDS_ENVIRONMENT;
+    return dashboardsEnv === 'dashboards-staging' ? dbIdSpaces.staging : dbIdSpaces.prod;
+}

website/src/types/wastewaterConfig.spec.ts

@@ -3,7 +3,7 @@ import { describe, expect, test } from 'vitest';
 import { wastewaterOrganismConfigs, wastewaterOrganisms } from './wastewaterConfig';
 import { enabledAnalysisModes } from '../components/views/wasap/wasapPageConfig';
 
-describe.each(Object.entries(wastewaterOrganismConfigs))('wastewaterConfig %s', (_configName, config) => {
+describe.each(Object.entries(wastewaterOrganismConfigs()))('wastewaterConfig %s', (_configName, config) => {
     test('default resistance set name is valid', () => {
         if (config.resistanceAnalysisModeEnabled) {
             const resistanceSetNames = config.resistanceMutationCollections.map((s) => s.name);
@@ -24,7 +24,7 @@ describe.each(Object.entries(wastewaterOrganismConfigs))('wastewaterConfig %s',
 });
 
 test('COVID wastewater opens on Spike resistance mutations by default', () => {
-    const covidConfig = wastewaterOrganismConfigs[wastewaterOrganisms.covid];
+    const covidConfig = wastewaterOrganismConfigs()[wastewaterOrganisms.covid];
 
     // This pins the default requested for the COVID wastewater dashboard landing state.
     expect(covidConfig.defaultAnalysisMode).toBe('resistance');

website/src/types/wastewaterConfig.ts

@@ -1,8 +1,20 @@
 import type { MutationAnnotation } from '@genspectrum/dashboard-components/util';
 
+import { getDbIdSpace, dbIdSpaces, type DbIdSpace } from './dbIdSpace';
 import type { ResistanceMutationCollectionConfig } from '../components/views/wasap/wasapPageConfig';
 import { VARIANT_TIME_FRAME, type WasapPageConfig } from '../components/views/wasap/wasapPageConfig';
 
+function byEnv<T>(env: DbIdSpace, vars: { prod: T; staging: T; local: T }): T {
+    switch (env) {
+        case dbIdSpaces.prod:
+            return vars.prod;
+        case dbIdSpaces.staging:
+            return vars.staging;
+        case dbIdSpaces.local:
+            return vars.local;
+    }
+}
+
 export const wastewaterOrganisms = {
     covid: 'covid',
     rsvA: 'rsv-a',
@@ -13,7 +25,7 @@ export type WastewaterOrganismName = (typeof wastewaterOrganisms)[keyof typeof w
 
 export const wastewaterPathFragment = 'swiss-wastewater';
 
-function buildWastewaterOrganismConfigs(isStaging: boolean): Record<WastewaterOrganismName, WasapPageConfig> {
+function buildWastewaterOrganismConfigs(env: DbIdSpace): Record<WastewaterOrganismName, WasapPageConfig> {
     return {
         [wastewaterOrganisms.covid]: {
             internalName: wastewaterOrganisms.covid,
@@ -34,21 +46,21 @@ function buildWastewaterOrganismConfigs(isStaging: boolean): Record<WastewaterOr
             defaultAnalysisMode: 'resistance',
             resistanceMutationCollections: [
                 {
-                    collectionId: isStaging ? 1 : 4,
+                    collectionId: byEnv(env, { prod: 4, staging: 1, local: 1 }),
                     name: '3CLpro',
                     annotationSymbol: 'c',
                     description:
                         'SARS-CoV-2 3C-like protease (3CLpro, or Mpro for Main protease) inhibitor resistance mutation as per <a class="link" href="https://covdb.stanford.edu/drms">Stanford Coronavirus Antiviral & Resistance database</a> (last updated on 21 August 2024).',
                 },
                 {
-                    collectionId: isStaging ? 2 : 5,
+                    collectionId: byEnv(env, { prod: 5, staging: 2, local: 2 }),
                     name: 'RdRp',
                     annotationSymbol: 'r',
                     description:
                         'SARS-CoV-2 RNA-dependent RNA polymerase (RdRP) inhibitor resistance mutation as per <a class="link" href="https://covdb.stanford.edu/drms">Stanford Coronavirus Antiviral & Resistance database</a> (last updated on 21 August 2024).',
                 },
                 {
-                    collectionId: isStaging ? 3 : 6,
+                    collectionId: byEnv(env, { prod: 6, staging: 3, local: 3 }),
                     name: 'Spike',
                     annotationSymbol: 's',
                     description:
@@ -59,7 +71,7 @@ function buildWastewaterOrganismConfigs(isStaging: boolean): Record<WastewaterOr
             samplingDateField: 'samplingDate',
             locationNameField: 'locationName',
             predefinedVariantsSource: {
-                collectionsUserId: isStaging ? 1 : 3,
+                collectionsUserId: byEnv(env, { prod: 3, staging: 1, local: 1 }),
                 collectionsTag: '#pango-lineage',
                 variantSourceLabel: 'Nextclade',
             },
@@ -90,7 +102,7 @@ function buildWastewaterOrganismConfigs(isStaging: boolean): Record<WastewaterOr
                     minCount: 15,
                     minJaccard: 0.75,
                     timeFrame: VARIANT_TIME_FRAME.all,
-                    collectionId: isStaging ? 4944 : 4943, // XFG lineage
+                    collectionId: byEnv(env, { prod: 4943, staging: 4944, local: 5019 }),
                 },
                 resistance: {
                     mode: 'resistance',
@@ -136,14 +148,14 @@ function buildWastewaterOrganismConfigs(isStaging: boolean): Record<WastewaterOr
             clinicalSequenceCountWarningThreshold: 50,
             resistanceMutationCollections: [
                 {
-                    collectionId: isStaging ? 4 : 4983,
+                    collectionId: byEnv(env, { prod: 4983, staging: 4, local: 4 }),
                     name: 'Nirsevimab',
                     annotationSymbol: 'n',
                     description:
                         'RSV-A F protein resistance mutations against Nirsevimab as per <a class="link" href="https://viralzone.expasy.org/11605">ViralZone</a>.',
                 },
                 {
-                    collectionId: isStaging ? 5 : 4984,
+                    collectionId: byEnv(env, { prod: 4984, staging: 5, local: 5 }),
                     name: 'Palivizumab',
                     annotationSymbol: 'p',
                     description:
@@ -201,14 +213,14 @@ function buildWastewaterOrganismConfigs(isStaging: boolean): Record<WastewaterOr
             clinicalSequenceCountWarningThreshold: 50,
             resistanceMutationCollections: [
                 {
-                    collectionId: isStaging ? 6 : 4985,
+                    collectionId: byEnv(env, { prod: 4985, staging: 6, local: 6 }),
                     name: 'Nirsevimab',
                     annotationSymbol: 'n',
                     description:
                         'RSV-B F protein resistance mutations against Nirsevimab as per <a class="link" href="https://viralzone.expasy.org/11605">ViralZone</a>.',
                 },
                 {
-                    collectionId: isStaging ? 7 : 4986,
+                    collectionId: byEnv(env, { prod: 4986, staging: 7, local: 7 }),
                     name: 'Palivizumab',
                     annotationSymbol: 'p',
                     description:
@@ -241,8 +253,16 @@ function buildWastewaterOrganismConfigs(isStaging: boolean): Record<WastewaterOr
     };
 }
 
-export const wastewaterOrganismConfigs = buildWastewaterOrganismConfigs(false);
-export const wastewaterOrganismStagingConfigs = buildWastewaterOrganismConfigs(true);
+export function wastewaterOrganismConfigs() {
+    switch (getDbIdSpace()) {
+        case dbIdSpaces.prod:
+            return buildWastewaterOrganismConfigs(dbIdSpaces.prod);
+        case dbIdSpaces.staging:
+            return buildWastewaterOrganismConfigs(dbIdSpaces.staging);
+        case dbIdSpaces.local:
+            return buildWastewaterOrganismConfigs(dbIdSpaces.local);
+    }
+}
 
 export const wastewaterConfig = {
     menuListEntryDecoration: 'decoration-teal',

website/tests/WasapPage.ts

@@ -7,7 +7,7 @@ export class WasapPage {
     constructor(public readonly page: Page) {}
 
     public async goto(organism: WastewaterOrganismName) {
-        await this.page.goto(wastewaterOrganismConfigs[organism].path);
+        await this.page.goto(wastewaterOrganismConfigs()[organism].path);
     }
 
     public async submitFilters() {

website/tests/wastewater.spec.ts

@@ -23,7 +23,7 @@ test.describe('WASAP Pages', () => {
     test.setTimeout(60_000);
 
     for (const organism of Object.values(wastewaterOrganisms)) {
-        const { name } = wastewaterOrganismConfigs[organism];
+        const { name } = wastewaterOrganismConfigs()[organism];
 
         test.describe(name, () => {
             test('should load with default filters and show mutation data', async ({ wasapPage }) => {