feat(website,kubernetes): make it possible to disable login and submi…

…t flow on website (#3223) * chore(website): delete unused function * fix(website): delete duplicate "to" in sentence It would show "Please select the organism for which you want to to browse data:" * feat(website,kubernetes): make it possible to disable login and submit flow on website resolves #3211 * chore(website): delete unused types * docs: add missing spec for `website.runtimeConfig`
loculus-project · Nov 19, 2024 · a6b3bb7 · a6b3bb7
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diff --git a/docs/src/content/docs/reference/helm-chart-config.mdx b/docs/src/content/docs/reference/helm-chart-config.mdx
@@ -164,6 +164,77 @@ The configuration for the Helm chart is provided as a YAML file. It has the foll
     </table>
 </div>
 
+## Website Settings
+
+<div className='overflow-x-scroll'>
+    <table className='min-w-[700px]'>
+        <thead>
+            <tr>
+                <th className='w-56'>Field</th>
+                <th>Type</th>
+                <th className='w-32'>Default</th>
+                <th>Description</th>
+            </tr>
+        </thead>
+        <tbody>
+            <tr>
+                <td>`website`</td>
+                <td>Object</td>
+                <td></td>
+                <td>Website specific setting</td>
+            </tr>
+            <tr>
+                <td>`website.websiteConfig`</td>
+                <td>Object</td>
+                <td></td>
+                <td>Settings for the `website_config.json`</td>
+            </tr>
+            <tr>
+                <td>`website.websiteConfig.enableLoginNavigationItem`</td>
+                <td>Boolean</td>
+                <td>true</td>
+                <td>Whether the website should show the login button.</td>
+            </tr>
+            <tr>
+                <td>`website.websiteConfig.enableSubmissionNavigationItem`</td>
+                <td>Boolean</td>
+                <td>true</td>
+                <td>Whether the website should show "Submit" link in the top navigation bar.</td>
+            </tr>
+            <tr>
+                <td>`website.websiteConfig.enableSubmissionPages`</td>
+                <td>Boolean</td>
+                <td>true</td>
+                <td>Whether to completely disable submission related pages. Setting this to false is useful when hosting Loculus for analysis-only purposes.</td>
+            </tr>
+            <tr>
+                <td>`website.runtimeConfig.public`</td>
+                <td>Object</td>
+                <td></td>
+                <td>Settings for the `public` section of the `runtime_config.json`</td>
+            </tr>
+            <tr>
+                <td>`website.runtimeConfig.public.backendUrl`</td>
+                <td>String</td>
+                <td>true</td>
+                <td>Overwrite the URL where the client-side website code expects the Loculus backend</td>
+            </tr>
+            <tr>
+                <td>`website.runtimeConfig.public.keycloakUrl`</td>
+                <td>String</td>
+                <td>true</td>
+                <td>Overwrite the URL where the client-side website code expects the Keycloak</td>
+            </tr>
+            <tr>
+                <td>`website.runtimeConfig.public.lapisUrlTemplate`</td>
+                <td>String</td>
+                <td>true</td>
+                <td>Overwrite the URLs where the client-side website code expects the LAPIS instances. Must contain `%organism%` as a placeholder.</td>
+            </tr>
+        </tbody>
+    </table>
+</div>
+
 ## User registration and authentication
 
 <table>
@@ -236,6 +307,12 @@ The configuration for the Helm chart is provided as a YAML file. It has the foll
             <td>true</td>
             <td>If true, allows users to reset their passwords</td>
         </tr>
+        <tr>
+            <td>`auth.registrationAllowed`</td>
+            <td>Boolean</td>
+            <td>true</td>
+            <td>If true, allows users to register new accounts in Keycloak.</td>
+        </tr>
         <tr>
             <td>`insecureCookies`</td>
             <td>Boolean</td>

diff --git a/kubernetes/loculus/templates/_common-metadata.tpl b/kubernetes/loculus/templates/_common-metadata.tpl
@@ -150,6 +150,9 @@ welcomeMessageHTML: {{ quote $.Values.welcomeMessageHTML }}
 additionalHeadHTML: {{ quote $.Values.additionalHeadHTML }}
 {{end}}
 
+enableLoginNavigationItem: {{ $.Values.website.websiteConfig.enableLoginNavigationItem }}
+enableSubmissionNavigationItem: {{ $.Values.website.websiteConfig.enableSubmissionNavigationItem }}
+enableSubmissionPages: {{ $.Values.website.websiteConfig.enableSubmissionPages }}
 enableSeqSets: {{ $.Values.seqSets.enabled }}
 accessionPrefix: {{ quote $.Values.accessionPrefix }}
 {{- $commonMetadata := (include "loculus.commonMetadata" . | fromYaml).fields }}

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -10,6 +10,11 @@ disableBackend: false
 disablePreprocessing: false
 disableIngest: false
 disableEnaSubmission: true
+website:
+  websiteConfig:
+    enableLoginNavigationItem: true
+    enableSubmissionNavigationItem: true
+    enableSubmissionPages: true
 siloImportLimitSeconds: 3600
 ingestLimitSeconds: 1800
 getSubmissionListLimitSeconds: 600

diff --git a/website/src/config.ts b/website/src/config.ts
@@ -25,10 +25,6 @@ export function getWebsiteConfig(): WebsiteConfig {
     return _config;
 }
 
-export function getWebsiteName(): string {
-    return getWebsiteConfig().name;
-}
-
 export function getMetadataDisplayNames(organism: string): Map<string, string> {
     return new Map(
         getWebsiteConfig().organisms[organism].schema.metadata.map(({ name, displayName }) => [

diff --git a/website/src/middleware.ts b/website/src/middleware.ts
@@ -1,8 +1,15 @@
 import { sequence } from 'astro:middleware';
 
+import { getWebsiteConfig } from './config.ts';
 import { authMiddleware } from './middleware/authMiddleware.ts';
 import { catchErrorMiddleware } from './middleware/catchErrorMiddleware.ts';
 import { organismValidatorMiddleware } from './middleware/organismValidatorMiddleware.ts';
+import { submissionPagesDisablingMiddleware } from './middleware/submissionPagesDisablingMiddleware.ts';
+
+const middlewares = [catchErrorMiddleware, organismValidatorMiddleware, authMiddleware];
+if (!getWebsiteConfig().enableSubmissionPages) {
+    middlewares.push(submissionPagesDisablingMiddleware);
+}
 
 // Astro middleware
-export const onRequest = sequence(catchErrorMiddleware, organismValidatorMiddleware, authMiddleware);
+export const onRequest = sequence(...middlewares);
diff --git a/website/src/middleware/submissionPagesDisablingMiddleware.ts b/website/src/middleware/submissionPagesDisablingMiddleware.ts
@@ -0,0 +1,11 @@
+import { defineMiddleware } from 'astro/middleware';
+
+export const submissionPagesDisablingMiddleware = defineMiddleware(async (context, next) => {
+    const organism = context.params.organism;
+
+    if (organism !== undefined && context.url.pathname.includes(`${organism}/submission`)) {
+        return context.rewrite('/404');
+    }
+
+    return next();
+});
diff --git a/website/src/pages/organism-selector/[redirectTo].astro b/website/src/pages/organism-selector/[redirectTo].astro
@@ -1,31 +1,34 @@
 ---
 import { NeedAGroup } from '../../components/common/NeedAGroup.tsx';
 import NeedToLogin from '../../components/common/NeedToLogin.astro';
-import { getConfiguredOrganisms } from '../../config';
+import { getConfiguredOrganisms, getWebsiteConfig } from '../../config';
 import BaseLayout from '../../layouts/BaseLayout.astro';
 import { routes } from '../../routes/routes';
 import { GroupManagementClient } from '../../services/groupManagementClient';
 import { getAccessToken } from '../../utils/getAccessToken';
 
-const redirectTo = Astro.params.redirectTo;
-const accessToken = getAccessToken(Astro.locals.session)!;
-const groupsResult = await GroupManagementClient.create().getGroupsOfUser(accessToken);
+type ValidRedirectTo = 'submission' | 'search';
 
-const purposes: { [key: string]: string } = {
-    submission: 'to access the submission portal',
+const purposes: Partial<Record<ValidRedirectTo, string>> = {
     search: 'to browse data',
 };
+if (getWebsiteConfig().enableSubmissionPages) {
+    purposes.submission = 'to access the submission portal';
+}
 
-interface Routes {
-    [key: string]: (organism: string) => string;
+if (!(Astro.params.redirectTo! in purposes)) {
+    return Astro.rewrite('/404');
 }
+const redirectTo = Astro.params.redirectTo as ValidRedirectTo;
 
-const myRoutes: Routes = {
+const accessToken = getAccessToken(Astro.locals.session)!;
+const groupsResult = await GroupManagementClient.create().getGroupsOfUser(accessToken);
+
+const myRoutes = {
     submission: routes.submissionPageWithoutGroup,
     search: routes.searchPage,
 };
-
-const purpose = purposes[redirectTo!];
+const purpose = purposes[redirectTo];
 
 // Prevent caching to allow back button after user creates group
 Astro.response.headers.append('Cache-Control', 'no-cache, no-store, must-revalidate');
@@ -45,11 +48,11 @@ const requiresGroup = redirectTo === 'submission';
                 <NeedAGroup />
             ) : (
                 <div>
-                    <p class='text-gray-700 my-4'>Please select the organism for which you want to {purpose}:</p>
+                    <p class='text-gray-700 my-4'>Please select the organism for which you want {purpose}:</p>
                     <div class='flex flex-wrap'>
                         {getConfiguredOrganisms().map(({ key, displayName }) => (
                             <a
-                                href={myRoutes[redirectTo!](key)}
+                                href={myRoutes[redirectTo](key)}
                                 class='block rounded border border-gray-300 p-4 m-2 w-64 text-center hover:bg-gray-100'
                             >
                                 <h3 class='font-semibold text-gray-700'>{displayName}</h3>

diff --git a/website/src/routes/navigationItems.ts b/website/src/routes/navigationItems.ts
@@ -11,19 +11,23 @@ export const navigationItems = {
 export type TopNavigationItems = ReturnType<(typeof navigationItems)['top']>;
 
 function getSequenceRelatedItems(organism: string | undefined) {
-    return [
-        {
-            text: 'Browse',
-            path: organism !== undefined ? routes.searchPage(organism) : routes.organismSelectorPage('search'),
-        },
-        {
-            text: 'Submit',
-            path:
-                organism !== undefined
-                    ? routes.submissionPageWithoutGroup(organism)
-                    : routes.organismSelectorPage('submission'),
-        },
-    ];
+    const browseItem = {
+        text: 'Browse',
+        path: organism !== undefined ? routes.searchPage(organism) : routes.organismSelectorPage('search'),
+    };
+
+    if (!getWebsiteConfig().enableSubmissionNavigationItem) {
+        return [browseItem];
+    }
+
+    const submitItem = {
+        text: 'Submit',
+        path:
+            organism !== undefined
+                ? routes.submissionPageWithoutGroup(organism)
+                : routes.organismSelectorPage('submission'),
+    };
+    return [browseItem, submitItem];
 }
 
 function getSeqSetsItems() {
@@ -39,22 +43,27 @@ function getSeqSetsItems() {
     ];
 }
 
-function getAccountItem(isLoggedIn: boolean, loginUrl: string | undefined, organism: string | undefined) {
-    return isLoggedIn
+function getAccountItems(isLoggedIn: boolean, loginUrl: string, organism: string | undefined) {
+    if (!getWebsiteConfig().enableLoginNavigationItem) {
+        return [];
+    }
+
+    const accountItem = isLoggedIn
         ? {
               text: 'My account',
               path: organism !== undefined ? routes.userOverviewPage(organism) : routes.userOverviewPage(),
           }
         : {
               text: 'Login',
-              path: loginUrl!,
+              path: loginUrl,
           };
+    return [accountItem];
 }
 
-function topNavigationItems(organism: string | undefined, isLoggedIn: boolean, loginUrl: string | undefined) {
+function topNavigationItems(organism: string | undefined, isLoggedIn: boolean, loginUrl: string) {
     const sequenceRelatedItems = getSequenceRelatedItems(organism);
     const seqSetsItems = getSeqSetsItems();
-    const accountItem = getAccountItem(isLoggedIn, loginUrl, organism);
+    const accountItems = getAccountItems(isLoggedIn, loginUrl, organism);
 
-    return [...sequenceRelatedItems, ...seqSetsItems, ...extraTopNavigationItems, accountItem];
+    return [...sequenceRelatedItems, ...seqSetsItems, ...extraTopNavigationItems, ...accountItems];
 }
diff --git a/website/src/types/config.ts b/website/src/types/config.ts
@@ -74,17 +74,6 @@ export type GroupedMetadataFilter = {
     initiallyVisible?: boolean;
 };
 
-export type AccessionFilter = {
-    accession?: string[];
-};
-
-export type MutationFilter = {
-    aminoAcidMutationQueries?: string[];
-    nucleotideMutationQueries?: string[];
-    aminoAcidInsertionQueries?: string[];
-    nucleotideInsertionQueries?: string[];
-};
-
 const schema = z.object({
     organismName: z.string(),
     image: z.string().optional(),
@@ -121,6 +110,9 @@ export const websiteConfig = z.object({
     gitHubEditLink: z.string().optional(),
     gitHubMainUrl: z.string().optional(),
     enableSeqSets: z.boolean(),
+    enableLoginNavigationItem: z.boolean(),
+    enableSubmissionNavigationItem: z.boolean(),
+    enableSubmissionPages: z.boolean(),
 });
 export type WebsiteConfig = z.infer<typeof websiteConfig>;