@opencloning/utils 2.1.0 → 2.2.0

package/CHANGELOG.md

@@ -1,5 +1,14 @@
 # @opencloning/utils
 
+## 2.1.1
+
+### Patch Changes
+
+- [#790](https://github.com/OpenCloning/OpenCloning_frontend/pull/790) [`0b2a21d`](https://github.com/OpenCloning/OpenCloning_frontend/commit/0b2a21dde79f5539579bee39f0de49b01cd6c10c) Thanks [@manulera](https://github.com/manulera)! - Support for fetchin sequences created by the OC mcp server
+
+- Updated dependencies []:
+  - @opencloning/store@2.1.1
+
 ## 2.1.0
 
 ### Patch Changes

package/package.json

@@ -1,7 +1,7 @@
 {
   "license": "MIT",
   "name": "@opencloning/utils",
-  "version": "2.1.0",
+  "version": "2.2.0",
   "type": "module",
   "main": "./src/utils/index.js",
   "exports": {
@@ -29,14 +29,14 @@
   },
   "repository": {
     "type": "git",
-    "url": "https://github.com/OpenCloning/OpenCloning_frontend.git",
-    "directory": "packages/utils"
+    "url": "https://github.com/OpenCloning/OpenCloning.git",
+    "directory": "js/packages/utils"
   },
   "dependencies": {
-    "@opencloning/store": "2.1.0",
+    "@opencloning/store": "2.2.0",
     "@teselagen/bio-parsers": "^0.4.38",
     "@teselagen/sequence-utils": "^0.3.42",
-    "@zip.js/zip.js": "^2.8.26",
+    "@zip.js/zip.js": "^2.24.0",
     "dom-to-svg": "^0.12.2",
     "lodash-es": "^4.18.1"
   },

package/src/config/urlWhitelist.js

@@ -20,4 +20,6 @@ export default [
   'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/taxonomy/taxon_suggest',
   'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/taxon',
   'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession',
+  // OpenCloning MCP server, set at build time
+  ...(import.meta.env.VITE_MCP_SERVER_URL ? [import.meta.env.VITE_MCP_SERVER_URL] : []),
 ];

package/src/utils/alignmentUtils.js

@@ -91,6 +91,23 @@ export function buildAlignmentConfig(id, sequenceData, alignmentTracks) {
   };
 }
 
+/**
+ * Build the alignment config of sequencing files aligned to a sequence (response of the align_sanger endpoint).
+ * @param {Object} sequenceModel - The TextFileSequence that was aligned (its id names the alignment)
+ * @param {Object} sequenceData - The reference sequence data
+ * @param {Array} parsedFiles - [{ fileName, fileContent }], fileContent is getTeselaJsonFromBase64 output
+ * @param {Array} alignedSequences - align_sanger response: the aligned reference, then one aligned string per file
+ * @returns {Object} Alignment config for addAlignment
+ */
+export function buildSequencingAlignmentConfig(sequenceModel, sequenceData, parsedFiles, alignedSequences) {
+  const referenceTrack = buildReferenceTrack(sequenceData, alignedSequences[0]);
+  const otherTracks = parsedFiles.map((f, i) => {
+    const alignmentFile = { file_name: f.fileName, alignment: [alignedSequences[0], alignedSequences[i + 1]] }; // eslint-disable-line camelcase
+    return buildAlignmentTrack(f.fileContent, alignmentFile);
+  });
+  return buildAlignmentConfig(sequenceModel.id, sequenceData, [referenceTrack, ...otherTracks]);
+}
+
 /**
  * Remove a panel from panelsShown by id.
  * @param {Array} panelsShown - Current panelsShown array (array of arrays)

package/src/utils/fileParsers.test.js

@@ -13,7 +13,7 @@ describe('delimitedFileToJson', () => {
     const file = createFile('name,sequence\nprimer1,ATGC\nprimer2,CGTG', 'test.csv');
 
     const result = await delimitedFileToJson(file);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC' },
       { name: 'primer2', sequence: 'CGTG' }
@@ -24,7 +24,7 @@ describe('delimitedFileToJson', () => {
     const file = createFile('name;sequence\nprimer1;ATGC\nprimer2;CGTG', 'test.csv');
 
     const result = await delimitedFileToJson(file);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC' },
       { name: 'primer2', sequence: 'CGTG' }
@@ -35,7 +35,7 @@ describe('delimitedFileToJson', () => {
     const file = createFile('name\tsequence\nprimer1\tATGC\nprimer2\tCGTG', 'test.tsv');
 
     const result = await delimitedFileToJson(file);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC' },
       { name: 'primer2', sequence: 'CGTG' }
@@ -70,7 +70,7 @@ describe('delimitedFileToJson', () => {
     const file = createFile('name,sequence\n\nprimer1,ATGC\n  \nprimer2,CGTG', 'test.csv');
 
     const result = await delimitedFileToJson(file);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC' },
       { name: 'primer2', sequence: 'CGTG' }
@@ -107,7 +107,7 @@ describe('delimitedFileToJson', () => {
     const file = createFile('name,sequence\r\nprimer1,ATGC\r\nprimer2,CGTG', 'test.csv');
 
     const result = await delimitedFileToJson(file);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC' },
       { name: 'primer2', sequence: 'CGTG' }
@@ -118,7 +118,7 @@ describe('delimitedFileToJson', () => {
     const file = createFile('name,sequence\rprimer1,ATGC\rprimer2,CGTG', 'test.csv');
 
     const result = await delimitedFileToJson(file);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC' },
       { name: 'primer2', sequence: 'CGTG' }
@@ -129,7 +129,7 @@ describe('delimitedFileToJson', () => {
     const file = createFile('name,sequence\nprimer1,ATGC\nprimer2,CGTG', 'test.csv');
 
     const result = await delimitedFileToJson(file);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC' },
       { name: 'primer2', sequence: 'CGTG' }
@@ -140,7 +140,7 @@ describe('delimitedFileToJson', () => {
     const file = createFile('name,sequence\nprimer1,ATGC', 'test.csv');
 
     const result = await delimitedFileToJson(file, []);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC' }
     ]);
@@ -150,7 +150,7 @@ describe('delimitedFileToJson', () => {
     const file = createFile('name,sequence\nprimer1,ATGC', 'test.csv');
 
     const result = await delimitedFileToJson(file);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC' }
     ]);
@@ -172,7 +172,7 @@ describe('primersFromTextFile', () => {
     const file = createFile('name,sequence\nprimer1,ATGC\nprimer2,CGTG', 'test.csv');
 
     const result = await primersFromTextFile(file, []);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC', error: '' },
       { name: 'primer2', sequence: 'CGTG', error: '' }
@@ -183,7 +183,7 @@ describe('primersFromTextFile', () => {
     const file = createFile('name,sequence\nprimer1,ATGC\nprimer2,CGTG', 'test.csv');
 
     const result = await primersFromTextFile(file, ['primer1']);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC', error: 'existing' },
       { name: 'primer2', sequence: 'CGTG', error: '' }
@@ -194,7 +194,7 @@ describe('primersFromTextFile', () => {
     const file = createFile('name,sequence\nprimer1,ATGC\nprimer2,XYZ', 'test.csv');
 
     const result = await primersFromTextFile(file, []);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC', error: '' },
       { name: 'primer2', sequence: 'XYZ', error: 'invalid' }
@@ -205,7 +205,7 @@ describe('primersFromTextFile', () => {
     const file = createFile('name,sequence\nprimer1,XYZ', 'test.csv');
 
     const result = await primersFromTextFile(file, ['primer1']);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'XYZ', error: 'existing' }
     ]);
@@ -215,7 +215,7 @@ describe('primersFromTextFile', () => {
     const file = createFile('name,sequence\nprimer1,ATGC\nprimer2,XYZ\nprimer3,CGTG', 'test.csv');
 
     const result = await primersFromTextFile(file, ['primer1']);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC', error: 'existing' },
       { name: 'primer2', sequence: 'XYZ', error: 'invalid' },
@@ -233,7 +233,7 @@ describe('primersFromTextFile', () => {
     const file = createFile('name,sequence\nprimer1,ATGC', 'test.csv');
 
     const result = await primersFromTextFile(file, []);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC', error: '' }
     ]);
@@ -243,7 +243,7 @@ describe('primersFromTextFile', () => {
     const file = createFile('name\tsequence\nprimer1\tATGC', 'test.tsv');
 
     const result = await primersFromTextFile(file, []);
-    
+
     expect(result).toEqual([
       { name: 'primer1', sequence: 'ATGC', error: '' }
     ]);

package/src/utils/readNwrite.js

@@ -158,6 +158,26 @@ export const downloadCloningStrategyAsSvg = async (fileName) => {
   downloadTextFile(svgString, fileName);
 };
 
+/**
+ * Extract the files of a zip whose path (e.g. 'run/A1/A1.fastq') matches filter, as Files named like the
+ * file without its folder (e.g. 'A1.fastq'). Directories, hidden files and folders, and anything in
+ * __MACOSX/ (e.g. the ._A1.fastq copies that macOS adds) are skipped.
+ */
+export async function extractFilesFromZip(zipFile, filter) {
+  const zipReader = new ZipReader(new BlobReader(zipFile));
+  try {
+    const entries = (await zipReader.getEntries()).filter((entry) => !entry.directory
+      && !entry.filename.split('/').some((part) => part.startsWith('.') || part === '__MACOSX')
+      && filter(entry.filename));
+    return await Promise.all(entries.map(async (entry) => new File(
+      [await entry.getData(new BlobWriter())],
+      entry.filename.split('/').pop(),
+    )));
+  } finally {
+    await zipReader.close();
+  }
+}
+
 export async function parseHistoryFile(file) {
   const isZipFile = file.name.endsWith('.zip');
   const isJsonFile = file.name.endsWith('.json');
@@ -279,6 +299,16 @@ export async function getTeselaJsonFromBase64(ab1Base64, fileName = null) {
   }
 }
 
+/**
+ * Read a sequencing file (ab1, fasta, genbank, fastq...) and parse it.
+ * Returns the base64 content (to store it) and the parsed teselaJson (e.g. teselaJson.sequence is the trace).
+ */
+export async function readSequencingFile(file) {
+  const base64str = await file2base64(file);
+  const teselaJson = await getTeselaJsonFromBase64(base64str, file.name);
+  return { base64str, teselaJson };
+}
+
 export function formatTemplate(data, url) {
   const newData = { ...data };
   const segments = url.split('/');