@opencloning/utils 1.6.0 → 1.7.1

package/CHANGELOG.md

@@ -1,5 +1,25 @@
 # @opencloning/utils
 
+## 1.7.1
+
+### Patch Changes
+
+- [#672](https://github.com/manulera/OpenCloning_frontend/pull/672) [`cfe95f5`](https://github.com/manulera/OpenCloning_frontend/commit/cfe95f5d79a4f147646d46d51b19a155941b2ad8) Thanks [@manulera](https://github.com/manulera)! - Ignore header case when importing primers from tabular file
+
+- Updated dependencies []:
+  - @opencloning/store@1.7.1
+
+## 1.7.0
+
+### Minor Changes
+
+- [#670](https://github.com/manulera/OpenCloning_frontend/pull/670) [`2943c1c`](https://github.com/manulera/OpenCloning_frontend/commit/2943c1c3a8b29a7081841d8ca9e2b36a2ad14a61) Thanks [@manulera](https://github.com/manulera)! - Fix import structure
+
+### Patch Changes
+
+- Updated dependencies [[`2943c1c`](https://github.com/manulera/OpenCloning_frontend/commit/2943c1c3a8b29a7081841d8ca9e2b36a2ad14a61)]:
+  - @opencloning/store@1.7.0
+
 ## 1.6.0
 
 ### Patch Changes

package/package.json

@@ -1,7 +1,7 @@
 {
   "license": "MIT",
   "name": "@opencloning/utils",
-  "version": "1.6.0",
+  "version": "1.7.1",
   "type": "module",
   "main": "./src/utils/index.js",
   "exports": {
@@ -29,7 +29,7 @@
     "directory": "packages/utils"
   },
   "dependencies": {
-    "@opencloning/store": "1.6.0",
+    "@opencloning/store": "1.7.1",
     "@teselagen/bio-parsers": "^0.4.34",
     "@teselagen/sequence-utils": "^0.3.42",
     "@zip.js/zip.js": "^2.7.62",

package/src/utils/fileParsers.js

@@ -1,7 +1,7 @@
 import { stringIsNotDNA } from '@opencloning/store/cloning_utils';
 import { readSubmittedTextFile } from './readNwrite';
 
-export async function delimitedFileToJson(fileUploaded, requiredHeaders = []) {
+export async function delimitedFileToJson(fileUploaded, requiredHeaders = [], ignoreHeaderCase = false) {
 
   const fileContent = await readSubmittedTextFile(fileUploaded);
   const allLines = fileContent.split(/\r\n|\r|\n/);
@@ -26,7 +26,10 @@ export async function delimitedFileToJson(fileUploaded, requiredHeaders = []) {
     throw new Error('File is empty');
   }
 
-  const headers = lines[0].split(delimiter);
+  let headers = lines[0].split(delimiter).map((header) => header.trim());
+  if (ignoreHeaderCase) {
+    headers = headers.map((header) => header.toLowerCase());
+  }
 
   const missingHeaders = requiredHeaders.filter(
     (header) => !headers.includes(header),
@@ -51,7 +54,7 @@ export async function delimitedFileToJson(fileUploaded, requiredHeaders = []) {
 };
 
 export const primersFromTextFile = async (fileUploaded, existingNames) => {
-  const primers = await delimitedFileToJson(fileUploaded, ['name', 'sequence']);
+  const primers = await delimitedFileToJson(fileUploaded, ['name', 'sequence'], true);
   return primers.map((primer) => {
     if (existingNames.includes(primer.name)) {
       return { ...primer, error: 'existing' };

package/src/utils/fileParsers.test.js

@@ -155,6 +155,16 @@ describe('delimitedFileToJson', () => {
       { name: 'primer1', sequence: 'ATGC' }
     ]);
   });
+
+  it('ignores header case if parameter is passed', async () => {
+    let file = createFile('Name,Sequence\nprimer1,ATGC', 'test.csv');
+    let result = await delimitedFileToJson(file, ['name', 'sequence'], true);
+    expect(result).toEqual([
+      { name: 'primer1', sequence: 'ATGC' }
+    ]);
+    file = createFile('Name,Sequence\nprimer1,ATGC', 'test.csv');
+    await expect(delimitedFileToJson(file, ['name', 'sequence'])).rejects.toThrow('Headers missing: name, sequence');
+  });
 });
 
 describe('primersFromTextFile', () => {
@@ -234,6 +244,15 @@ describe('primersFromTextFile', () => {
 
     const result = await primersFromTextFile(file, []);
     
+    expect(result).toEqual([
+      { name: 'primer1', sequence: 'ATGC', error: '' }
+    ]);
+  });
+  it('ignores header case', async () => {
+    const file = createFile('Name,Sequence\nprimer1,ATGC', 'test.csv');
+
+    const result = await primersFromTextFile(file, []);
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC', error: '' }
     ]);

package/vitest.config.js

@@ -1,5 +1,4 @@
 import { defineConfig } from 'vitest/config';
-import { resolve } from 'path';
 
 export default defineConfig({
   test: {
@@ -8,10 +7,4 @@ export default defineConfig({
     setupFiles: '../../tests/setup.js',
     include: ['src/**/*.{test,spec}.{js,jsx}'],
   },
-  resolve: {
-    alias: {
-      '@opencloning/utils': resolve(__dirname, './src/utils'),
-      '@opencloning/store': resolve(__dirname, '../store/src'),
-    },
-  },
 });