Various fixes

loculus-project · Jan 8, 2025 · 3bbd86a · 3bbd86a
1 parent f93e5c3
commit 3bbd86a
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Showing 5 changed files with 16 additions and 12 deletions.
diff --git a/website/src/components/Submission/DataUploadForm.tsx b/website/src/components/Submission/DataUploadForm.tsx
@@ -25,7 +25,7 @@ import { dateTimeInMonths } from '../../utils/DateTimeInMonths.tsx';
 import { createAuthorizationHeader } from '../../utils/createAuthorizationHeader.ts';
 import { stringifyMaybeAxiosError } from '../../utils/stringifyMaybeAxiosError.ts';
 import { withQueryProvider } from '../common/withQueryProvider.tsx';
-import { FASTA_FILE_KIND, METADATA_FILE_KIND, ProcessedFile, RawFile } from './FileUpload/fileProcessing.ts';
+import { FASTA_FILE_KIND, METADATA_FILE_KIND, type ProcessedFile, RawFile } from './FileUpload/fileProcessing.ts';
 
 export type UploadAction = 'submit' | 'revise';
 
@@ -201,7 +201,7 @@ const InnerDataUploadForm = ({
                 break;
             }
             case 'revise':
-                revise({ metadataFile: finalMetadataFile, sequenceFile });
+                revise({ metadataFile: finalMetadataFile, sequenceFile: sequenceFile.inner() });
                 break;
         }
     };
@@ -267,8 +267,8 @@ const InnerDataUploadForm = ({
                                 <DevExampleData
                                     setExampleEntries={setExampleEntries}
                                     exampleEntries={exampleEntries}
-                                    metadataFile={metadataFile.inner()}
-                                    sequenceFile={sequenceFile.inner()}
+                                    metadataFile={metadataFile ? metadataFile.inner() : null}
+                                    sequenceFile={sequenceFile ? sequenceFile.inner() : null}
                                     handleLoadExampleData={handleLoadExampleData}
                                 />
                             )}

diff --git a/website/src/components/Submission/FileUpload/ColumnMapping.spec.ts b/website/src/components/Submission/FileUpload/ColumnMapping.spec.ts
@@ -1,6 +1,7 @@
 import { describe, it, expect } from 'vitest';
 
 import { ColumnMapping } from './ColumnMapping';
+import { RawFile } from './fileProcessing';
 
 describe('ColumnMapping', () => {
     it('should create a mapping from columns', () => {
@@ -45,7 +46,7 @@ describe('ColumnMapping', () => {
 
         const tsvFile = new File([tsvContent], 'input.tsv');
 
-        const remappedFile = await updatedMapping.applyTo(tsvFile);
+        const remappedFile = await updatedMapping.applyTo(new RawFile(tsvFile));
         const remappedContent = await remappedFile.text();
 
         expect(remappedContent).toBe('location\tdate\n' + 'USA\t2023-01-01\n' + 'Canada\t2023-01-02');

diff --git a/website/src/components/Submission/FileUpload/ColumnMapping.ts b/website/src/components/Submission/FileUpload/ColumnMapping.ts
@@ -1,5 +1,6 @@
 import { stringSimilarity } from 'string-similarity-js';
-import { ProcessedFile } from './fileProcessing';
+
+import { type ProcessedFile } from './fileProcessing';
 
 export class ColumnMapping {
     private readonly map: ReadonlyMap<string, string>;
@@ -36,7 +37,7 @@ export class ColumnMapping {
     /* Create a new mapping with the given columns, doing a best-effort to pre-match columns. */
     public static fromColumns(sourceColumns: string[], targetColumns: Map<string, string | undefined>) {
         const mapping = new Map<string, string>();
-        [...targetColumns.entries()].forEach(([targetColumn, targetColumnDisplayName]) => {
+        Array.from(targetColumns.entries()).forEach(([targetColumn, targetColumnDisplayName]) => {
             const bestMatch = this.getBestMatchingSourceColumn(targetColumn, targetColumnDisplayName, sourceColumns);
             mapping.set(targetColumn, bestMatch);
         });
@@ -47,7 +48,7 @@ export class ColumnMapping {
        mapping intact as possible. */
     public update(newSourceColumns: string[], newTargetColumns: Map<string, string | undefined>): ColumnMapping {
         const newMapping = new Map<string, string>();
-        [...newTargetColumns.entries()].forEach(([targetColumn, _targetColumnDisplayName]) => {
+        Array.from(newTargetColumns.entries()).forEach(([targetColumn, _targetColumnDisplayName]) => {
             const prevSourceCol = this.map.get(targetColumn);
             if (prevSourceCol && newSourceColumns.includes(prevSourceCol)) {
                 newMapping.set(targetColumn, prevSourceCol);

diff --git a/website/src/components/Submission/FileUpload/ColumnMappingModal.tsx b/website/src/components/Submission/FileUpload/ColumnMappingModal.tsx
@@ -3,7 +3,7 @@ import { useEffect, useState, type Dispatch, type FC, type SetStateAction } from
 import { toast } from 'react-toastify';
 
 import { ColumnMapping } from './ColumnMapping';
-import { ProcessedFile } from './fileProcessing';
+import { type ProcessedFile } from './fileProcessing';
 import { BaseDialog } from '../../common/BaseDialog';
 
 interface ColumnMappingModalProps {
@@ -28,6 +28,7 @@ export const ColumnMappingModal: FC<ColumnMappingModalProps> = ({
     const [inputColumns, setInputColumns] = useState<string[] | null>(null);
 
     useEffect(() => {
+        if (!isOpen) return;
         const loadColumns = async () => {
             const columnExtractionResult = await extractColumns(inputFile);
             columnExtractionResult.match(
@@ -36,7 +37,7 @@ export const ColumnMappingModal: FC<ColumnMappingModalProps> = ({
             );
         };
         void loadColumns();
-    }, [inputFile, setInputColumns]);
+    }, [isOpen, inputFile, setInputColumns]);
 
     useEffect(() => {
         if (inputColumns === null) return;

diff --git a/website/src/components/Submission/FileUpload/fileProcessing.ts b/website/src/components/Submission/FileUpload/fileProcessing.ts
@@ -79,6 +79,8 @@ export interface ProcessedFile {
     warnings(): string[];
 }
 
+export const dummy = 0;
+
 export class RawFile implements ProcessedFile {
     private innerFile: File;
 
@@ -104,7 +106,6 @@ export class RawFile implements ProcessedFile {
 }
 
 export class CompressedFile extends RawFile {
-
     async text(): Promise<string> {
         const compressedData = new Uint8Array(await this.inner().arrayBuffer());
         return fflate.strFromU8(fflate.decompressSync(compressedData));
@@ -124,7 +125,7 @@ export class ExcelFile implements ProcessedFile {
         this.processingWarnings = [];
     }
 
-    private async getRawData(): Promise<ArrayBuffer> {
+    private async getRawData(): Promise<ArrayBufferLike> {
         if (!this.compressed) {
             return this.originalFile.arrayBuffer();
         } else {