Fix metadata types

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

@@ -6,7 +6,7 @@ import { beforeEach, describe, expect, test } from 'vitest';
 
 import { EditPage } from './EditPage.tsx';
 import { testAccessToken, testOrganism } from '../../../vitest.setup.ts';
-import type { MetadataField, SequenceEntryToEdit } from '../../types/backend.ts';
+import type { MetadataField, SequenceEntryToEdit, UnprocessedMetadataRecord } from '../../types/backend.ts';
 import type { ClientConfig } from '../../types/runtimeConfig.ts';
 
 const queryClient = new QueryClient();
@@ -49,6 +49,7 @@ const defaultReviewData: SequenceEntryToEdit = {
     processedData: {
         metadata: {
             processedMetaDataField: 'processedMetaDataValue',
+            nullField: null,
         },
         unalignedNucleotideSequences: {
             unalignedProcessedSequenceName: 'processedUnalignedNucleotideSequencesValue',
@@ -158,24 +159,24 @@ describe('EditPage', () => {
 });
 
 const expectTextInSequenceData = {
-    original: (metadata: Record<string, MetadataField>): void =>
+    original: (metadata: Record<string, string>): void =>
         Object.entries(metadata).forEach(([key, value]) => {
             expect(screen.getByText(key + ':')).toBeInTheDocument();
-            expect(screen.getByDisplayValue(value.toString())).toBeInTheDocument();
+            expect(screen.getByDisplayValue(value)).toBeInTheDocument();
         }),
-    originalMetadata: (metadata: Record<string, MetadataField>): void =>
+    originalMetadata: (metadata: UnprocessedMetadataRecord): void =>
         Object.entries(metadata).forEach(([key, value]) => {
             expect(screen.getByText(sentenceCase(key) + ':')).toBeInTheDocument();
-            expect(screen.getByDisplayValue(value.toString())).toBeInTheDocument();
+            expect(screen.getByDisplayValue(value)).toBeInTheDocument();
         }),
-    processed: (metadata: Record<string, MetadataField>): void =>
+    processed: (metadata: Record<string, string>): void =>
         Object.entries(metadata).forEach(([key, value]) => {
             expect(screen.getByText(key + ':')).toBeInTheDocument();
             expect(screen.getByText(value.toString())).toBeInTheDocument();
         }),
     processedMetadata: (metadata: Record<string, MetadataField>): void =>
         Object.entries(metadata).forEach(([key, value]) => {
             expect(screen.getByText(sentenceCase(key) + ':')).toBeInTheDocument();
-            expect(screen.getByText(value.toString())).toBeInTheDocument();
+            expect(screen.getByText((value ?? 'null').toString())).toBeInTheDocument();
         }),
 };

website/src/components/Edit/EditPage.tsx

@@ -10,6 +10,7 @@ import { ACCESSION_FIELD } from '../../settings.ts';
 import type { MetadataRecord, ProcessingAnnotationSourceType, SequenceEntryToEdit } from '../../types/backend.ts';
 import type { ClientConfig } from '../../types/runtimeConfig.ts';
 import { createAuthorizationHeader } from '../../utils/createAuthorizationHeader.ts';
+import { displayMetadataField } from '../../utils/displayMetadataField.ts';
 import { getAccessionVersionString } from '../../utils/extractAccessionVersion.ts';
 import { ConfirmationDialog } from '../DeprecatedConfirmationDialog.tsx';
 import { ManagedErrorFeedback, useErrorFeedbackState } from '../common/ManagedErrorFeedback.tsx';
@@ -248,7 +249,10 @@ const ProcessedMetadata: FC<ProcessedMetadataProps> = ({ processedMetadata }) =>
     <>
         <Subtitle title='Metadata' customKey='preprocessing_metadata' />
         {Object.entries(processedMetadata).map(([key, value]) => (
-            <ProcessedDataRow key={'processed' + key} row={{ key: sentenceCase(key), value: value.toString() }} />
+            <ProcessedDataRow
+                key={'processed' + key}
+                row={{ key: sentenceCase(key), value: displayMetadataField(value) }}
+            />
         ))}
     </>
 );
@@ -282,8 +286,8 @@ const ProcessedInsertions: FC<ProcessedInsertionsProps> = ({ processedInsertions
 const mapMetadataToRow = (editedData: SequenceEntryToEdit): Row[] =>
     Object.entries(editedData.originalData.metadata).map(([key, value]) => ({
         key,
-        initialValue: value.toString(),
-        value: value.toString(),
+        value,
+        initialValue: value,
         ...mapErrorsAndWarnings(editedData, key, 'Metadata'),
     }));
 

website/src/components/ReviewPage/ReviewCard.tsx

@@ -16,6 +16,7 @@ import {
 } from '../../types/backend.ts';
 import type { ClientConfig } from '../../types/runtimeConfig.ts';
 import { createAuthorizationHeader } from '../../utils/createAuthorizationHeader.ts';
+import { displayMetadataField } from '../../utils/displayMetadataField.ts';
 import Edit from '~icons/bxs/edit';
 import Trash from '~icons/bxs/trash';
 import Send from '~icons/fa/send';
@@ -126,18 +127,15 @@ const isAnnotationPresent = (metadataField: string) => (item: ProcessingAnnotati
 const MetadataList: FC<MetadataListProps> = ({ data, isLoading }) => (
     <div className='flex flex-row flex-wrap'>
         {!isLoading &&
-            Object.entries(data.processedData.metadata).map((entry, index) => {
-                const valueString = entry[1].toString();
-                return (
-                    <KeyValueComponent
-                        key={index}
-                        keyName={entry[0]}
-                        value={valueString}
-                        warnings={data.warnings?.filter(isAnnotationPresent(entry[0]))}
-                        errors={data.errors?.filter(isAnnotationPresent(entry[0]))}
-                    />
-                );
-            })}
+            Object.entries(data.processedData.metadata).map(([metadataName, value], index) => (
+                <KeyValueComponent
+                    key={index}
+                    keyName={metadataName}
+                    value={displayMetadataField(value)}
+                    warnings={data.warnings?.filter(isAnnotationPresent(metadataName))}
+                    errors={data.errors?.filter(isAnnotationPresent(metadataName))}
+                />
+            ))}
     </div>
 );
 

website/src/types/backend.ts

@@ -32,7 +32,10 @@ const processingAnnotation = z.object({
 });
 export type ProcessingAnnotation = z.infer<typeof processingAnnotation>;
 
-export const metadataField = z.union([z.string(), z.number(), z.date()]);
+const unprocessedMetadataRecord = z.record(z.string());
+export type UnprocessedMetadataRecord = z.infer<typeof unprocessedMetadataRecord>;
+
+export const metadataField = z.union([z.string(), z.number(), z.date(), z.null()]);
 export type MetadataField = z.infer<typeof metadataField>;
 
 const metadataRecord = z.record(metadataField);
@@ -104,7 +107,7 @@ export type SubmissionIdMapping = z.infer<typeof submissionIdMapping>;
 export const unprocessedData = accessionVersion.merge(
     z.object({
         data: z.object({
-            metadata: metadataRecord,
+            metadata: unprocessedMetadataRecord,
             unalignedNucleotideSequences: z.record(z.string()),
         }),
     }),
@@ -117,7 +120,7 @@ export const sequenceEntryToEdit = accessionVersion.merge(
         errors: z.array(processingAnnotation).nullable(),
         warnings: z.array(processingAnnotation).nullable(),
         originalData: z.object({
-            metadata: metadataRecord,
+            metadata: unprocessedMetadataRecord,
             unalignedNucleotideSequences: z.record(z.string()),
         }),
         processedData: z.object({

website/src/utils/displayMetadataField.ts

@@ -0,0 +1,3 @@
+import type { MetadataField } from '../types/backend.ts';
+
+export const displayMetadataField = (value: MetadataField) => (value === null ? 'null' : value.toString());