feat(website): allow organisms without sequences

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

@@ -6,7 +6,7 @@ import { beforeEach, describe, expect, test } from 'vitest';
 
 import { EditPage } from './EditPage.tsx';
 import { defaultReviewData, editableEntry, metadataKey, testAccessToken, testOrganism } from '../../../vitest.setup.ts';
-import type { SequenceEntryToEdit, UnprocessedMetadataRecord } from '../../types/backend.ts';
+import type { UnprocessedMetadataRecord } from '../../types/backend.ts';
 import type { ClientConfig } from '../../types/runtimeConfig.ts';
 
 const queryClient = new QueryClient();
@@ -19,7 +19,11 @@ const inputFields = [
     },
 ];
 
-function renderEditPage(editedData: SequenceEntryToEdit = defaultReviewData, clientConfig: ClientConfig = dummyConfig) {
+function renderEditPage({
+    editedData = defaultReviewData,
+    clientConfig = dummyConfig,
+    allowSubmissionOfConsensusSequences = true,
+} = {}) {
     render(
         <QueryClientProvider client={queryClient}>
             <EditPage
@@ -28,6 +32,7 @@ function renderEditPage(editedData: SequenceEntryToEdit = defaultReviewData, cli
                 clientConfig={clientConfig}
                 accessToken={testAccessToken}
                 inputFields={inputFields}
+                allowSubmissionOfConsensusSequences={allowSubmissionOfConsensusSequences}
             />
         </QueryClientProvider>,
     );
@@ -51,6 +56,13 @@ describe('EditPage', () => {
         await userEvent.click(submitButton);
     });
 
+    test('should render without allowed submission of consensus sequences', () => {
+        renderEditPage({ allowSubmissionOfConsensusSequences: false });
+
+        expect(screen.getByText(/Original Data/i)).toBeInTheDocument();
+        expectTextInSequenceData.originalMetadata(defaultReviewData.originalData.metadata);
+    });
+
     test('should show original data and processed data', () => {
         renderEditPage();
 

website/src/components/Edit/EditPage.tsx

@@ -28,6 +28,7 @@ type EditPageProps = {
     dataToEdit: SequenceEntryToEdit;
     accessToken: string;
     inputFields: InputField[];
+    allowSubmissionOfConsensusSequences: boolean;
 };
 
 const logger = getClientLogger('EditPage');
@@ -75,7 +76,8 @@ const InnerEditPage: FC<EditPageProps> = ({
     clientConfig,
     accessToken,
     inputFields,
-}: EditPageProps) => {
+    allowSubmissionOfConsensusSequences,
+}) => {
     const [editedMetadata, setEditedMetadata] = useState(mapMetadataToRow(dataToEdit));
     const [editedSequences, setEditedSequences] = useState(mapSequencesToRow(dataToEdit));
     const [processedSequenceTab, setProcessedSequenceTab] = useState(0);
@@ -141,25 +143,31 @@ const InnerEditPage: FC<EditPageProps> = ({
                         setEditedMetadata={setEditedMetadata}
                         inputFields={inputFields}
                     />
-                    <EditableOriginalSequences
-                        editedSequences={editedSequences}
-                        setEditedSequences={setEditedSequences}
-                    />
+                    {allowSubmissionOfConsensusSequences && (
+                        <EditableOriginalSequences
+                            editedSequences={editedSequences}
+                            setEditedSequences={setEditedSequences}
+                        />
+                    )}
 
                     <Subtitle title='Processed Data' bold />
-                    <ProcessedInsertions
-                        processedInsertions={processedInsertions}
-                        insertionType='nucleotideInsertions'
-                    />
-                    <ProcessedInsertions
-                        processedInsertions={processedInsertions}
-                        insertionType='aminoAcidInsertions'
-                    />
-                    <Subtitle title='Sequences' />
+                    {allowSubmissionOfConsensusSequences && (
+                        <>
+                            <ProcessedInsertions
+                                processedInsertions={processedInsertions}
+                                insertionType='nucleotideInsertions'
+                            />
+                            <ProcessedInsertions
+                                processedInsertions={processedInsertions}
+                                insertionType='aminoAcidInsertions'
+                            />
+                            <Subtitle title='Sequences' />
+                        </>
+                    )}
                 </tbody>
             </table>
 
-            {processedSequences.length > 0 && (
+            {allowSubmissionOfConsensusSequences && processedSequences.length > 0 && (
                 <div>
                     <BoxWithTabsTabBar>
                         {processedSequences.map(({ label }, i) => (
@@ -199,16 +207,18 @@ const InnerEditPage: FC<EditPageProps> = ({
                     Submit
                 </button>
 
-                <button
-                    className='btn normal-case'
-                    onClick={() => generateAndDownloadFastaFile(editedSequences, dataToEdit)}
-                    title={`Download the original, unaligned sequence${
-                        editedSequences.length > 1 ? 's' : ''
-                    } as provided by the submitter`}
-                    disabled={isLoading}
-                >
-                    Download Sequence{editedSequences.length > 1 ? 's' : ''}
-                </button>
+                {allowSubmissionOfConsensusSequences && (
+                    <button
+                        className='btn normal-case'
+                        onClick={() => generateAndDownloadFastaFile(editedSequences, dataToEdit)}
+                        title={`Download the original, unaligned sequence${
+                            editedSequences.length > 1 ? 's' : ''
+                        } as provided by the submitter`}
+                        disabled={isLoading}
+                    >
+                        Download Sequence{editedSequences.length > 1 ? 's' : ''}
+                    </button>
+                )}
             </div>
         </>
     );

website/src/components/SequenceDetailsPage/SequenceDataUI.tsx

@@ -96,6 +96,7 @@ export const SequenceDataUI: FC<Props> = ({
                         />
                     )}
 
+                    {/* TODO ! */}
                     <a
                         href={routes.editPage(organism, {
                             accession: accessionVersion.split('.')[0],

website/src/components/Submission/DataUploadForm.tsx

@@ -36,6 +36,7 @@ type DataUploadFormProps = {
     referenceGenomeSequenceNames: ReferenceGenomesSequenceNames;
     onSuccess: () => void;
     onError: (message: string) => void;
+    allowSubmissionOfConsensusSequences: boolean;
 };
 
 const logger = getClientLogger('DataUploadForm');
@@ -84,15 +85,13 @@ const DataUseTerms = ({
 const DevExampleData = ({
     setExampleEntries,
     exampleEntries,
-    metadataFile,
-    sequenceFile,
     handleLoadExampleData,
+    dataIsLoaded,
 }: {
     setExampleEntries: (entries: number) => void;
     exampleEntries: number | undefined;
-    metadataFile: File | null;
-    sequenceFile: File | null;
     handleLoadExampleData: () => void;
+    dataIsLoaded: boolean;
 }) => {
     return (
         <p className='text-gray-800 text-xs mt-5 opacity-50'>
@@ -108,7 +107,7 @@ const DevExampleData = ({
                 Load Example Data
             </button>{' '}
             <br />
-            {metadataFile && sequenceFile && <span className='text-xs text-gray-500'>Example data loaded</span>}
+            {dataIsLoaded && <span className='text-xs text-gray-500'>Example data loaded</span>}
         </p>
     );
 };
@@ -122,9 +121,10 @@ const InnerDataUploadForm = ({
     onError,
     group,
     referenceGenomeSequenceNames,
+    allowSubmissionOfConsensusSequences,
 }: DataUploadFormProps) => {
-    const [metadataFile, setMetadataFile] = useState<File | null>(null);
-    const [sequenceFile, setSequenceFile] = useState<File | null>(null);
+    const [metadataFile, setMetadataFile] = useState<File | undefined>(undefined);
+    const [sequenceFile, setSequenceFile] = useState<File | undefined>(undefined);
     const [exampleEntries, setExampleEntries] = useState<number | undefined>(10);
 
     const { submit, revise, isLoading } = useSubmitFiles(accessToken, organism, clientConfig, onSuccess, onError);
@@ -143,10 +143,12 @@ const InnerDataUploadForm = ({
         const exampleMetadataContent = action === `submit` ? metadataFileContent : revisedMetadataFileContent;
 
         const metadataFile = createTempFile(exampleMetadataContent, 'text/tab-separated-values', 'metadata.tsv');
-        const sequenceFile = createTempFile(sequenceFileContent, 'application/octet-stream', 'sequences.fasta');
-
         setMetadataFile(metadataFile);
-        setSequenceFile(sequenceFile);
+
+        if (allowSubmissionOfConsensusSequences) {
+            const sequenceFile = createTempFile(sequenceFileContent, 'application/octet-stream', 'sequences.fasta');
+            setSequenceFile(sequenceFile);
+        }
     };
 
     const handleSubmit = (event: FormEvent) => {
@@ -168,7 +170,7 @@ const InnerDataUploadForm = ({
             onError('Please select metadata file');
             return;
         }
-        if (!sequenceFile) {
+        if (!sequenceFile && allowSubmissionOfConsensusSequences) {
             onError('Please select a sequences file');
             return;
         }
@@ -201,8 +203,12 @@ const InnerDataUploadForm = ({
             <div className='flex-col flex gap-8 divide-y'>
                 <div className='grid sm:grid-cols-3 gap-x-16'>
                     <div className=''>
-                        <h2 className='font-medium text-lg'>Sequences and metadata</h2>
-                        <p className='text-gray-500 text-sm'>Select your sequence data and metadata files</p>
+                        <h2 className='font-medium text-lg'>
+                            {allowSubmissionOfConsensusSequences ? 'Sequences and metadata' : 'Metadata'}
+                        </h2>
+                        <p className='text-gray-500 text-sm'>
+                            Select your {allowSubmissionOfConsensusSequences && 'sequence data and'}metadata files
+                        </p>
                         <p className='text-gray-400 text-xs mt-5'>
                             {action === 'revise' && (
                                 <span>
@@ -250,28 +256,30 @@ const InnerDataUploadForm = ({
                             .
                         </p>
 
-                        {(organism.startsWith('not-aligned-organism') || organism.startsWith('dummy-organism')) &&
-                            action === 'submit' && (
-                                <DevExampleData
-                                    setExampleEntries={setExampleEntries}
-                                    exampleEntries={exampleEntries}
-                                    metadataFile={metadataFile}
-                                    sequenceFile={sequenceFile}
-                                    handleLoadExampleData={handleLoadExampleData}
-                                />
-                            )}
+                        {organism.startsWith('dummy-organism') && action === 'submit' && (
+                            <DevExampleData
+                                setExampleEntries={setExampleEntries}
+                                exampleEntries={exampleEntries}
+                                handleLoadExampleData={handleLoadExampleData}
+                                dataIsLoaded={
+                                    !!metadataFile && (!allowSubmissionOfConsensusSequences || !!sequenceFile)
+                                }
+                            />
+                        )}
                     </div>
                     <form className='sm:col-span-2'>
                         <div className='flex flex-col lg:flex-row gap-6'>
-                            <div className='w-60 space-y-2'>
-                                <label className='text-gray-900 font-medium text-sm block'>Sequence File</label>
-                                <UploadComponent
-                                    setFile={setSequenceFile}
-                                    name='sequence_file'
-                                    ariaLabel='Sequence File'
-                                    fileKind={FASTA_FILE_KIND}
-                                />
-                            </div>
+                            {allowSubmissionOfConsensusSequences && (
+                                <div className='w-60 space-y-2'>
+                                    <label className='text-gray-900 font-medium text-sm block'>Sequence File</label>
+                                    <UploadComponent
+                                        setFile={setSequenceFile}
+                                        name='sequence_file'
+                                        ariaLabel='Sequence File'
+                                        fileKind={FASTA_FILE_KIND}
+                                    />
+                                </div>
+                            )}
                             <div className='w-60 space-y-2'>
                                 <label className='text-gray-900 font-medium text-sm block'>Metadata File</label>
                                 <UploadComponent

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

@@ -10,7 +10,7 @@ export const UploadComponent = ({
     ariaLabel,
     fileKind,
 }: {
-    setFile: (file: File | null) => void;
+    setFile: (file: File | undefined) => void;
     name: string;
     ariaLabel: string;
     fileKind: FileKind;
@@ -37,7 +37,7 @@ export const UploadComponent = ({
                     },
                 );
             }
-            setFile(processedFile !== null ? processedFile.inner() : null);
+            setFile(processedFile !== null ? processedFile.inner() : undefined);
             rawSetMyFile(processedFile);
         },
         [setFile, rawSetMyFile],

website/src/components/Submission/SubmissionForm.spec.tsx

@@ -1,12 +1,12 @@
 import { render, waitFor } from '@testing-library/react';
 import userEvent from '@testing-library/user-event';
 import { toast } from 'react-toastify';
-import { describe, expect, test, vi } from 'vitest';
+import { afterEach, describe, expect, test, vi } from 'vitest';
 
 import { SubmissionForm } from './SubmissionForm';
 import { mockRequest, testAccessToken, testConfig, testGroups, testOrganism } from '../../../vitest.setup.ts';
 import type { Group, ProblemDetail, SubmissionIdMapping } from '../../types/backend.ts';
-import type { ReferenceGenomesSequenceNames, ReferenceAccession } from '../../types/referencesGenomes.ts';
+import type { ReferenceAccession, ReferenceGenomesSequenceNames } from '../../types/referencesGenomes.ts';
 
 vi.mock('../../api', () => ({
     getClientLogger: () => ({
@@ -48,14 +48,15 @@ const defaultReferenceGenomesSequenceNames: ReferenceGenomesSequenceNames = {
     insdcAccessionFull: [defaultAccession],
 };
 
-function renderSubmissionForm() {
+function renderSubmissionForm({ allowSubmissionOfConsensusSequences = true } = {}) {
     return render(
         <SubmissionForm
             accessToken={testAccessToken}
             referenceGenomeSequenceNames={defaultReferenceGenomesSequenceNames}
             organism={testOrganism}
             clientConfig={testConfig.public}
             group={group}
+            allowSubmissionOfConsensusSequences={allowSubmissionOfConsensusSequences}
         />,
     );
 }
@@ -69,6 +70,10 @@ const testResponse: SubmissionIdMapping[] = [
 ];
 
 describe('SubmitForm', () => {
+    afterEach(() => {
+        vi.clearAllMocks();
+    });
+
     test('should handle file upload and server response', async () => {
         mockRequest.backend.submit(200, testResponse);
         mockRequest.backend.getGroupsOfUser();
@@ -180,4 +185,25 @@ describe('SubmitForm', () => {
             });
         });
     }
+
+    test('should accept submission without sequence file for organism that does not allow consensus sequences', async () => {
+        mockRequest.backend.submit(200, testResponse);
+        mockRequest.backend.getGroupsOfUser();
+
+        const { getByLabelText } = renderSubmissionForm({
+            allowSubmissionOfConsensusSequences: false,
+        });
+
+        await userEvent.upload(getByLabelText(/Metadata File/i), metadataFile);
+        await userEvent.click(
+            getByLabelText(/I confirm I have not and will not submit this data independently to INSDC/i),
+        );
+        await userEvent.click(
+            getByLabelText(/I confirm that the data submitted is not sensitive or human-identifiable/i),
+        );
+
+        await waitFor(() => {
+            expect(toast.error).not.toHaveBeenCalled();
+        });
+    });
 });

website/src/components/Submission/SubmissionForm.tsx

@@ -13,6 +13,7 @@ type SubmissionFormProps = {
     clientConfig: ClientConfig;
     group: Group;
     referenceGenomeSequenceNames: ReferenceGenomesSequenceNames;
+    allowSubmissionOfConsensusSequences: boolean;
 };
 
 export const SubmissionForm: FC<SubmissionFormProps> = ({
@@ -21,6 +22,7 @@ export const SubmissionForm: FC<SubmissionFormProps> = ({
     clientConfig,
     group,
     referenceGenomeSequenceNames,
+    allowSubmissionOfConsensusSequences,
 }) => {
     return (
         <div className='flex flex-col items-center'>
@@ -35,6 +37,7 @@ export const SubmissionForm: FC<SubmissionFormProps> = ({
                 onSuccess={() => {
                     window.location.href = routes.userSequenceReviewPage(organism, group.groupId);
                 }}
+                allowSubmissionOfConsensusSequences={allowSubmissionOfConsensusSequences}
             />
         </div>
     );