Merge branch 'main' into ena_submission_pod

backend/build.gradle

@@ -52,7 +52,7 @@ dependencies {
     implementation 'org.tukaani:xz:1.9'
 
     implementation("org.redundent:kotlin-xml-builder:1.9.1")
-    implementation("org.jsoup:jsoup:1.17.2")
+    implementation("org.jsoup:jsoup:1.18.1")
 
     testImplementation("org.springframework.boot:spring-boot-starter-test") {
         exclude group: "org.mockito"

docs/package.json

@@ -11,8 +11,8 @@
     "format": "prettier --write ."
   },
   "dependencies": {
-    "@astrojs/check": "^0.8.0",
-    "@astrojs/starlight": "^0.25.0",
+    "@astrojs/check": "^0.8.1",
+    "@astrojs/starlight": "^0.25.1",
     "astro": "^4.11.5",
     "sharp": "^0.33.4",
     "typescript": "^5.5.3"

kubernetes/loculus/templates/keycloak-config-map.yaml

@@ -281,7 +281,9 @@ data:
           "publicClient": true,
           "directAccessGrantsEnabled": true,
           "redirectUris": [
-            "*"
+            "https://{{$.Values.host}}/*",
+            "http://{{$.Values.host}}/*",
+            "http://localhost:3000/*"
           ]
         },
               {

kubernetes/loculus/values.yaml

@@ -616,7 +616,6 @@ defaultOrganismConfig: &defaultOrganismConfig
         autocomplete: true
         header: "Host"
         ingest: ncbi_is_lab_host
-        noInput: true
       - name: cell_line
         generateIndex: true
         autocomplete: true
@@ -660,6 +659,7 @@ defaultOrganismConfig: &defaultOrganismConfig
           url: "https://www.ncbi.nlm.nih.gov/sra/?term=__value__"
         header: "INSDC"
         ingest: ncbi_sra_accessions
+        noInput: true
       - name: total_snps
         type: int
         header: "Alignment states and QC metrics"
@@ -1207,5 +1207,6 @@ runDevelopmentKeycloakDatabase: true
 runDevelopmentMainDatabase: true
 enforceHTTPS: true
 registrationTermsMessage: >
-   You must agree to the <a href="http://main.loculus.org/terms">terms of use</a>.
-subdomainSeparator: "-"
+  You must agree to the <a href="http://main.loculus.org/terms">terms of use</a>.
+
+subdomainSeparator: "-"

website/.nvmrc

@@ -1 +1 @@
-v22
+v22.4.1

website/package.json

@@ -49,21 +49,21 @@
         "react-dom": "^18.3.1",
         "react-toastify": "^10.0.5",
         "react-tooltip": "^5.27.1",
-        "rsuite": "^5.65.1",
+        "rsuite": "^5.66.0",
         "unplugin-icons": "^0.19.0",
-        "winston": "^3.13.0",
+        "winston": "^3.13.1",
         "zod": "^3.23.6"
     },
     "devDependencies": {
-        "@astrojs/check": "^0.8.0",
+        "@astrojs/check": "^0.8.1",
         "@astrojs/react": "^3.6.0",
         "@astrojs/tailwind": "^5.1.0",
         "@emotion/styled": "^11.11.5",
-        "@iconify/json": "^2.2.225",
+        "@iconify/json": "^2.2.228",
         "@playwright/test": "^1.45.1",
         "@tailwindcss/forms": "^0.5.7",
-        "@tanstack/eslint-plugin-query": "^5.50.1",
-        "@testing-library/dom": "^10.3.1",
+        "@tanstack/eslint-plugin-query": "^5.51.1",
+        "@testing-library/dom": "^10.3.2",
         "@testing-library/jest-dom": "^6.4.6",
         "@testing-library/react": "^16.0.0",
         "@testing-library/user-event": "^14.5.2",
@@ -74,27 +74,27 @@
         "@types/react": "^18.3.3",
         "@types/react-dom": "^18.3.0",
         "@types/uuid": "^10.0.0",
-        "@typescript-eslint/eslint-plugin": "^7.16.0",
-        "@typescript-eslint/parser": "^7.16.0",
+        "@typescript-eslint/eslint-plugin": "^7.16.1",
+        "@typescript-eslint/parser": "^7.16.1",
         "@vitejs/plugin-react": "^4.3.1",
         "cross-env": "^7.0.3",
         "daisyui": "^4.12.10",
         "eslint": "^8.57.0",
-        "eslint-plugin-astro": "^1.2.2",
+        "eslint-plugin-astro": "^1.2.3",
         "eslint-plugin-import": "^2.29.1",
         "eslint-plugin-jsx-a11y": "^6.9.0",
         "eslint-plugin-prefer-arrow": "^1.2.3",
-        "eslint-plugin-react": "^7.34.3",
+        "eslint-plugin-react": "^7.34.4",
         "eslint-plugin-react-hooks": "^4.6.2",
         "jsdom": "^24.1.0",
         "msw": "^2.3.1",
-        "prettier": "3.3.2",
+        "prettier": "3.3.3",
         "prettier-plugin-astro": "^0.14.0",
         "resize-observer-polyfill": "^1.5.1",
-        "sass": "^1.77.6",
-        "tailwindcss": "^3.4.4",
+        "sass": "^1.77.8",
+        "tailwindcss": "^3.4.5",
         "typescript": "^5.5.3",
         "uuid": "^10.0.0",
-        "vitest": "2.0.1"
+        "vitest": "2.0.3"
     }
 }

website/src/components/Edit/EditPage.tsx

@@ -209,7 +209,7 @@ const Subtitle: FC<SubtitleProps> = ({ title, bold, customKey }) => (
     <Fragment key={snakeCase(customKey ?? title) + '_fragment'}>
         <tr key={snakeCase(customKey ?? title) + '_spacing'} className='h-4' />
         <tr key={snakeCase(customKey ?? title)} className='subtitle'>
-            <td className={bold ?? false ? 'font-semibold' : 'font-normal'} colSpan={3}>
+            <td className={(bold ?? false) ? 'font-semibold' : 'font-normal'} colSpan={3}>
                 {title}
             </td>
         </tr>

website/src/components/Navigation/DocsMenu.tsx

@@ -10,6 +10,7 @@ type Page = MDXInstance<Record<string, any>>;
 interface DocsMenuProps {
     docsPages: MDXInstance<Record<string, any>>[];
     currentPageUrl: string;
+    title: string;
 }
 
 const groupPagesByDirectory = (pages: Page[]): Record<string, Page[]> => {
@@ -43,15 +44,15 @@ const toTitleCase = (str: string): string => {
     return str.replace(/\b\w/g, (char) => char.toUpperCase());
 };
 
-const DocsMenu: React.FC<DocsMenuProps> = ({ docsPages, currentPageUrl }) => {
+const DocsMenu: React.FC<DocsMenuProps> = ({ docsPages, currentPageUrl, title }) => {
     const groupedPages = groupPagesByDirectory(docsPages);
 
     return (
         <Disclosure as='nav' className='docs-menu bg-white border rounded-lg overflow-hidden mt-5 sticky sm:min-w-64'>
             {({ open }) => (
                 <>
                     <div className='flex items-center justify-between px-4 py-3 bg-gray-100'>
-                        <div className='text-lg font-semibold text-primary-600'>Documentation</div>
+                        <div className='text-lg font-semibold text-primary-600'>{title}</div>
                         <div className='sm:hidden'>
                             <DisclosureButton className='text-primary-600 hover:text-primary-800 focus:outline-none'>
                                 {open ? (

website/src/components/SearchPage/DisplaySearchDocs.tsx

@@ -102,7 +102,7 @@ const DisplaySearchDocs: React.FC = () => {
                                         </p>
                                         <p className='mb-2'>
                                             You can also use wildcards to match any insertion at a given position. For
-                                            example <b>ins_S:214:?:</b> will match any (but at least one) insertion
+                                            example <b>ins_S:214:?</b> will match any (but at least one) insertion
                                             between the positions 214 and 215.
                                         </p>
                                     </div>

website/src/components/SearchPage/SearchForm.tsx

@@ -110,7 +110,6 @@ export const SearchForm = ({
                             value={'mutation' in fieldValues ? (fieldValues.mutation as string) : ''}
                             onChange={(value) => setAFieldValue('mutation', value)}
                         />
-
                         {visibleFields.map((filter) => (
                             <SearchField
                                 field={filter}

website/src/components/SearchPage/SearchFullUI.spec.tsx

@@ -98,6 +98,9 @@ function renderSearchFullUI({
             tableColumns: ['field1', 'field3'],
             primaryKey: 'accession',
         } as Schema,
+        initialData: [],
+        initialCount: 0,
+        initialQueryDict: {},
     };
 
     render(