feat(website): Mirror backend filename validation in website

backend/src/main/kotlin/org/loculus/backend/service/submission/FileMappingPreconditionValidator.kt

@@ -151,6 +151,8 @@ class FileMappingPreconditionValidator(
      * - Trailing periods: Windows silently strips these, and single or double period names break path normalisation
      * - Whitespace characters
      *
+     * The website mirrors this validation in fileNameValidation.ts - any changes here must also be made there.
+     *
      * References:
      * - https://en.wikipedia.org/wiki/Comparison_of_file_systems#Limits
      * - https://learn.microsoft.com/en-us/windows/win32/fileio/naming-a-file
@@ -206,6 +208,8 @@ class FileMappingPreconditionValidator(
      * - Underscores (_)
      * - Hyphens (-)
      * - Periods (.)
+     *
+     * The website mirrors this validation in fileNameValidation.ts - any changes here must also be made there.
      */
     private fun strictValidateFilename(filename: String, category: FileCategory) {
         if (!STRICT_FILENAME_REGEX.matches(filename)) {

kubernetes/loculus/templates/_common-metadata.tpl

@@ -239,6 +239,10 @@ enableDataUseTerms: {{ $.Values.dataUseTerms.enabled }}
 {{ if $.Values.dataUseTerms.agreementHTML }}
 dataUseTermsAgreementHTML: {{ quote $.Values.dataUseTerms.agreementHTML }}
 {{- end }}
+{{- if .Values.fileSharing }}
+fileSharing:
+  {{ .Values.fileSharing | toYaml | nindent 2 }}
+{{- end }}
 accessionPrefix: {{ quote $.Values.accessionPrefix }}
 dateFieldForGroupGraph: {{ if $.Values.dateFieldForGroupGraph }}{{ quote $.Values.dateFieldForGroupGraph }}{{ else }}null{{ end }}
 {{- $commonMetadata := (include "loculus.commonMetadata" . | fromYaml).fields }}

website/src/components/Edit/EditPage.spec.tsx

@@ -79,6 +79,7 @@ function renderEditPage({
                     maxSequencesPerEntry: 1,
                 }}
                 sequenceEntryHistory={sequenceEntryHistory}
+                fileSharingConfig={{ disableStrictFilenameValidation: false }}
             />
         </QueryClientProvider>,
     );

website/src/components/Edit/EditPage.tsx

@@ -10,7 +10,7 @@ import { routes } from '../../routes/routes.ts';
 import { backendApi } from '../../services/backendApi.ts';
 import { backendClientHooks } from '../../services/serviceHooks.ts';
 import { type FilesByCategory, type SequenceEntryToEdit, approvedForReleaseStatus } from '../../types/backend.ts';
-import { type InputField, type SubmissionDataTypes } from '../../types/config.ts';
+import { type FileSharingConfig, type InputField, type SubmissionDataTypes } from '../../types/config.ts';
 import {
     getLatestAccessionVersionForRevision,
     isLatestVersionRevocation,
@@ -41,6 +41,7 @@ type EditPageProps = {
     accessToken: string;
     groupedInputFields: Map<string, InputField[]>;
     submissionDataTypes: SubmissionDataTypes;
+    fileSharingConfig: FileSharingConfig;
     sequenceEntryHistory?: SequenceEntryHistory;
 };
 
@@ -66,6 +67,7 @@ const InnerEditPage: FC<EditPageProps> = ({
     accessToken,
     groupedInputFields,
     submissionDataTypes,
+    fileSharingConfig,
     sequenceEntryHistory,
 }) => {
     const [editableMetadata, setEditableMetadata] = useState(EditableMetadata.fromInitialData(dataToEdit));
@@ -256,6 +258,7 @@ const InnerEditPage: FC<EditPageProps> = ({
                         fileUploadStates={fileUploadStates}
                         setFileUploadStates={setFileUploadStates}
                         onError={(msg) => toast.error(msg, { position: 'top-center', autoClose: false })}
+                        fileSharingConfig={fileSharingConfig}
                     />
                 </div>
             )}

website/src/components/Submission/DataUploadForm.tsx

@@ -19,7 +19,7 @@ import {
     openDataUseTermsOption,
     restrictedDataUseTermsOption,
 } from '../../types/backend.ts';
-import type { FileCategory, InputField } from '../../types/config.ts';
+import type { FileCategory, FileSharingConfig, InputField } from '../../types/config.ts';
 import type { SubmissionDataTypes } from '../../types/config.ts';
 import type { ClientConfig } from '../../types/runtimeConfig.ts';
 import { createAuthorizationHeader } from '../../utils/createAuthorizationHeader.ts';
@@ -57,6 +57,7 @@ type DataUploadFormProps = {
     onError: (message: string) => void;
     submissionDataTypes: SubmissionDataTypes;
     dataUseTermsEnabled: boolean;
+    fileSharingConfig: FileSharingConfig;
 };
 
 const logger = getClientLogger('DataUploadForm');
@@ -74,6 +75,7 @@ const InnerDataUploadForm = ({
     metadataTemplateFields,
     submissionDataTypes,
     dataUseTermsEnabled,
+    fileSharingConfig,
 }: DataUploadFormProps) => {
     const extraFilesEnabled = submissionDataTypes.files?.enabled ?? false;
 
@@ -240,6 +242,7 @@ const InnerDataUploadForm = ({
                     metadataTemplateFields={metadataTemplateFields}
                     submissionDataTypes={submissionDataTypes}
                     onError={onError}
+                    fileSharingConfig={fileSharingConfig}
                 />
                 <hr />
                 {extraFilesEnabled && (
@@ -254,6 +257,7 @@ const InnerDataUploadForm = ({
                             fileUploadStates={fileUploadStates}
                             setFileUploadStates={setFileUploadStates}
                             fileLinkage={fileLinkage}
+                            fileSharingConfig={fileSharingConfig}
                         />
                         <hr />
                     </>
@@ -441,6 +445,7 @@ export const ExtraFilesUpload = ({
     setFileUploadStates,
     fileLinkage,
     onError,
+    fileSharingConfig,
 }: {
     accessToken: string;
     clientConfig: ClientConfig;
@@ -451,6 +456,7 @@ export const ExtraFilesUpload = ({
     setFileUploadStates: Dispatch<SetStateAction<Map<string, FileUploadState>>>;
     fileLinkage?: FileLinkage;
     onError: (message: string) => void;
+    fileSharingConfig: FileSharingConfig;
 }) => {
     const setCategoryFileUploadState =
         (category: string): Dispatch<SetStateAction<FileUploadState | undefined>> =>
@@ -490,6 +496,7 @@ export const ExtraFilesUpload = ({
                             onError={onError}
                             fileUploadState={fileUploadStates.get(fileCategory.name)}
                             setFileUploadState={setCategoryFileUploadState(fileCategory.name)}
+                            fileSharingConfig={fileSharingConfig}
                         />
                         {inputMode === 'bulk' && (
                             <CategoryLinkageStatus categoryLinkage={fileLinkage?.get(fileCategory.name)} />

website/src/components/Submission/FileUpload/FolderUploadComponent.spec.tsx

@@ -65,6 +65,7 @@ const defaultProps = {
     clientConfig: { backendUrl: 'http://test-backend', lapisUrls: {} },
     groupId: 1,
     onError: mockOnError,
+    fileSharingConfig: { disableStrictFilenameValidation: true },
 };
 
 const previousUploadsState = (files: { fileId: string; path: string }[]): FileUploadState => ({
@@ -258,7 +259,8 @@ describe('FolderUploadComponent', () => {
 
             await userEvent.upload(screen.getByTestId('extraFiles'), file);
 
-            expect(mockOnError).toHaveBeenCalledWith('File names cannot contain whitespace.');
+            expect(mockOnError).toHaveBeenCalledWith(expect.stringContaining('File'));
+            expect(mockOnError).toHaveBeenCalledWith(expect.stringContaining('may not contain whitespace'));
             expect(mockRequestMultipartUpload).not.toHaveBeenCalled();
         });
 
@@ -273,7 +275,8 @@ describe('FolderUploadComponent', () => {
 
             await userEvent.upload(screen.getByTestId('extraFiles'), file);
 
-            expect(mockOnError).toHaveBeenCalledWith('Folder names cannot contain whitespace.');
+            expect(mockOnError).toHaveBeenCalledWith(expect.stringContaining('Folder'));
+            expect(mockOnError).toHaveBeenCalledWith(expect.stringContaining('cannot contain whitespace'));
             expect(mockRequestMultipartUpload).not.toHaveBeenCalled();
         });
 
@@ -285,7 +288,8 @@ describe('FolderUploadComponent', () => {
 
             await userEvent.upload(screen.getByTestId('add_extraFiles'), file);
 
-            expect(mockOnError).toHaveBeenCalledWith('File names cannot contain whitespace.');
+            expect(mockOnError).toHaveBeenCalledWith(expect.stringContaining('File'));
+            expect(mockOnError).toHaveBeenCalledWith(expect.stringContaining('may not contain whitespace'));
             expect(mockRequestMultipartUpload).not.toHaveBeenCalled();
         });
     });

website/src/components/Submission/FileUpload/FolderUploadComponent.tsx

@@ -2,18 +2,19 @@ import { produce } from 'immer';
 import React, { useEffect, useState, type Dispatch, type FC, type SetStateAction } from 'react';
 import { toast } from 'react-toastify';
 
-import type {
-    Awaiting,
-    FileUploadState,
-    Pending,
-    PreviousUpload,
-    SingleFileUpload,
-    Uploaded,
-    UploadStatus,
+import { validateFileNames, getFileNameErrorMessage } from './fileNameValidation';
+import {
+    type Awaiting,
+    type FileUploadState,
+    type Pending,
+    type PreviousUpload,
+    type SingleFileUpload,
+    type Uploaded,
+    type UploadStatus,
 } from './fileUpload';
 import useClientFlag from '../../../hooks/isClient';
 import { BackendClient } from '../../../services/backendClient';
-import { type FileCategory } from '../../../types/config';
+import { type FileCategory, type FileSharingConfig } from '../../../types/config';
 import type { ClientConfig } from '../../../types/runtimeConfig';
 import { calculatePartSizeAndCount, splitFileIntoParts, uploadPart } from '../../../utils/multipartUpload';
 import { displayConfirmationDialog } from '../../ConfirmationDialog';
@@ -32,6 +33,7 @@ type FolderUploadComponentProps = {
     fileUploadState: FileUploadState | undefined;
     setFileUploadState: Dispatch<SetStateAction<FileUploadState | undefined>>;
     onError: (message: string) => void;
+    fileSharingConfig: FileSharingConfig;
 };
 
 const FileInput = ({
@@ -89,6 +91,7 @@ export const FolderUploadComponent: FC<FolderUploadComponentProps> = ({
     fileUploadState,
     setFileUploadState,
     onError,
+    fileSharingConfig,
 }) => {
     const [isDragging, setIsDragging] = useState(false);
 
@@ -227,7 +230,7 @@ export const FolderUploadComponent: FC<FolderUploadComponentProps> = ({
             // Reset the input so the same folder can be selected again
             e.target.value = '';
 
-            const error = isFilesArrayValid(filesArray, inputMode);
+            const error = isFilesArrayValid(filesArray, inputMode, fileSharingConfig);
             if (error) {
                 onError(error);
                 return;
@@ -269,7 +272,7 @@ export const FolderUploadComponent: FC<FolderUploadComponentProps> = ({
             // Reset the input so the same file can be selected again
             e.target.value = '';
 
-            const error = isFilesArrayValid(filesArray, inputMode);
+            const error = isFilesArrayValid(filesArray, inputMode, fileSharingConfig);
             if (error) {
                 onError(error);
                 return;
@@ -524,15 +527,23 @@ const filterDotFiles = (files: File[]): File[] => {
 /**
  * Returns `undefined` if the files are fine, or an error otherwise.
  */
-const isFilesArrayValid = (files: File[], inputMode: InputMode): string | undefined => {
+const isFilesArrayValid = (
+    files: File[],
+    inputMode: InputMode,
+    fileSharingConfig: FileSharingConfig,
+): string | undefined => {
     if (inputMode === 'form') {
         if (files.some((f) => f.webkitRelativePath.split('/').length > 2)) {
             return 'Subdirectories are not supported for individual submissions.';
         }
     }
-    const fileNames = files.map((f) => f.name);
     const folderNames = files.flatMap((f) => f.webkitRelativePath.split('/').slice(1, -1));
+    const fileNames = files.map((f) => f.name);
 
-    if (fileNames.some((n) => /\s/.test(n))) return 'File names cannot contain whitespace.';
     if (folderNames.some((p) => /\s/.test(p))) return 'Folder names cannot contain whitespace.';
+
+    const fileNameValidationResult = validateFileNames(fileNames, fileSharingConfig);
+    if (fileNameValidationResult.isErr()) {
+        return 'Encountered errors in uploaded files: ' + getFileNameErrorMessage(fileNameValidationResult.error);
+    }
 };

website/src/components/Submission/FileUpload/fileMapping.spec.ts

@@ -20,6 +20,7 @@ const RAW_READS_COLUMN = `${FILES_HEADER_PREFIX}${RAW_READS}`;
 const OTHER_FILES = 'otherFiles';
 const OTHER_FILES_COLUMN = `${FILES_HEADER_PREFIX}${OTHER_FILES}`;
 const FILE_CATEGORIES = [RAW_READS, OTHER_FILES];
+const FILE_SHARING_CONFIG = { disableStrictFilenameValidation: false };
 
 const tsv = (rows: string[][]) => rows.map((row) => row.join('\t')).join('\n');
 const declaredFile = (name: string, path: string = name) => ({ type: 'declaredFile' as const, name, path });
@@ -44,12 +45,12 @@ const errorMessageOf = <T>(result: Result<T, Error>): string => {
 };
 
 const entriesOf = (text: string, submissionId: string, category: string) => {
-    const mapping = valueOf(parseSubmissionFileMapping(text, FILE_CATEGORIES));
+    const mapping = valueOf(parseSubmissionFileMapping(text, FILE_CATEGORIES, FILE_SHARING_CONFIG));
     return [...(mapping.get(submissionId)?.get(category)?.values() ?? [])];
 };
 
 const errorOf = (text: string, categories: string[] = FILE_CATEGORIES): string => {
-    const result = parseSubmissionFileMapping(text, categories);
+    const result = parseSubmissionFileMapping(text, categories, FILE_SHARING_CONFIG);
     if (result.isOk()) throw new Error('expected the parse to fail');
     return result.error.message;
 };
@@ -138,9 +139,12 @@ describe('parseSubmissionFileMapping', () => {
                 ['e1', 'CH'],
             ]),
             FILE_CATEGORIES,
+            FILE_SHARING_CONFIG,
         );
         expect(valueOf(result)).toEqual(new Map());
-        expect(valueOf(parseSubmissionFileMapping(tsv([['country'], ['CH']]), FILE_CATEGORIES))).toEqual(new Map());
+        expect(
+            valueOf(parseSubmissionFileMapping(tsv([['country'], ['CH']]), FILE_CATEGORIES, FILE_SHARING_CONFIG)),
+        ).toEqual(new Map());
     });
 
     it('rejects a file column without an id column', () => {
@@ -188,6 +192,14 @@ describe('parseSubmissionFileMapping', () => {
         expect(errorOf(text)).toContain(`Found duplicate file names for entry e1 in the ${RAW_READS} category: a.txt`);
     });
 
+    it.each(['CON.txt', 'CON.txt::sub/reads.fastq', 'CON.txt:fileId'])('rejects invalid file name %s', (entry) => {
+        const text = tsv([
+            ['id', RAW_READS_COLUMN],
+            ['e1', entry],
+        ]);
+        expect(errorOf(text)).toContain('may not use Windows reserved device names');
+    });
+
     it('allows two different names to share the same explicit path', () => {
         const text = tsv([
             ['id', RAW_READS_COLUMN],
@@ -201,7 +213,7 @@ describe('parseSubmissionFileMapping', () => {
             ['id', RAW_READS_COLUMN, OTHER_FILES_COLUMN],
             ['e1', 'a.txt', ''],
         ]);
-        const result = valueOf(parseSubmissionFileMapping(text, FILE_CATEGORIES));
+        const result = valueOf(parseSubmissionFileMapping(text, FILE_CATEGORIES, FILE_SHARING_CONFIG));
         expect([...result.get('e1')!.keys()]).toEqual([RAW_READS]);
     });
 
@@ -211,7 +223,7 @@ describe('parseSubmissionFileMapping', () => {
             ['e1', 'CH', 'a.txt', 'a.json'],
             ['e2', 'DE', 'b.txt', 'b.json'],
         ]);
-        const result = valueOf(parseSubmissionFileMapping(text, FILE_CATEGORIES));
+        const result = valueOf(parseSubmissionFileMapping(text, FILE_CATEGORIES, FILE_SHARING_CONFIG));
         expect([...result.keys()]).toEqual(['e1', 'e2']);
         expect(entriesOf(text, 'e1', OTHER_FILES).map((f) => f.name)).toEqual(['a.json']);
         expect(entriesOf(text, 'e2', RAW_READS).map((f) => f.name)).toEqual(['b.txt']);

website/src/components/Submission/FileUpload/fileMapping.ts

@@ -1,7 +1,9 @@
 import { type Result, ok, err } from 'neverthrow';
 import Papa from 'papaparse';
 
+import { validateFileNames, getFileNameErrorMessage } from './fileNameValidation';
 import { FILES_HEADER_PREFIX, SUBMISSION_ID_INPUT_FIELD } from '../../../settings';
+import type { FileSharingConfig } from '../../../types/config';
 
 const ID_COLUMNS = [SUBMISSION_ID_INPUT_FIELD, 'submissionId'];
 
@@ -378,6 +380,7 @@ const parseMetadataText = (text: string): Result<ParsedMetadata, Error> => {
 export function parseSubmissionFileMapping(
     text: string,
     categories: FileCategory[],
+    fileSharingConfig: FileSharingConfig,
 ): Result<SubmissionFileMapping, Error> {
     const parsedMetadataResult = parseMetadataText(text);
     if (parsedMetadataResult.isErr()) return err(parsedMetadataResult.error);
@@ -456,6 +459,23 @@ export function parseSubmissionFileMapping(
         submissionFileMapping.set(submissionId, categoryMapping);
     }
 
+    // Validate file names
+    const fileNames = [
+        ...new Set(
+            [...submissionFileMapping.values()]
+                .flatMap((categoryMapping) => [...categoryMapping.values()])
+                .flatMap((fileEntries) => [...fileEntries.keys()]),
+        ),
+    ];
+    const fileNameValidationResult = validateFileNames(fileNames, fileSharingConfig);
+    if (fileNameValidationResult.isErr())
+        return err(
+            new Error(
+                'Encountered errors in file names within metadata: ' +
+                    getFileNameErrorMessage(fileNameValidationResult.error),
+            ),
+        );
+
     return ok(submissionFileMapping);
 }