chore: eslint-fix

Author: RicardoSilvestr

docker/src/plugins/coconuts/sync/syncCoconuts.js

@@ -1,9 +1,11 @@
 import md5 from 'md5';
+
 import getLastDocumentImported from '../../../sync/http/utils/getLastDocumentImported.js';
 import getLastFileSync from '../../../sync/http/utils/getLastFileSync.js';
 import debugLibrary from '../../../utils/Debug.js';
 import createIndexes from '../../../utils/createIndexes.js';
 import { shouldUpdate } from '../../../utils/shouldUpdate.js';
+
 import { getTaxonomiesForCoconuts } from './utils/getTaxonomiesForCoconuts.js';
 import { parseCoconuts } from './utils/parseCoconuts.js';
 
@@ -39,13 +41,13 @@ export async function sync(connection) {
       options.collectionName,
     );
 
-    const isTimeToUpdate = true/*await shouldUpdate(
+    const isTimeToUpdate = await shouldUpdate(
       progress,
       sources,
       lastDocumentImported,
       process.env.COCONUT_UPDATE_INTERVAL,
       connection,
-    );*/
+    );
 
     let counter = 0;
     let imported = 0;

docker/src/plugins/coconuts/sync/utils/__tests__/syncCoconuts.test.js

@@ -1,11 +1,9 @@
-
-
 import { test, expect } from 'vitest';
+
 import { OctoChemConnection } from '../../../../../utils/OctoChemConnection.js';
 import { sync } from '../../syncCoconuts';
 
 test('syncCoconuts', async () => {
-
   const connection = new OctoChemConnection();
   const taxonomiesCollection = await connection.getCollection('taxonomies');
   while (true) {
@@ -15,7 +13,7 @@ test('syncCoconuts', async () => {
   }
   await sync(connection);
   const collection = await connection.getCollection('coconuts');
-  const collectionEntry = await collection.find({_id:'CNP0214016.1'})
+  const collectionEntry = await collection.find({ _id: 'CNP0214016.1' });
   const result = await collectionEntry.toArray();
 
   expect(result).toMatchSnapshot();

docker/src/plugins/coconuts/sync/utils/parseCoconuts.js

@@ -1,18 +1,19 @@
+import path from 'path';
+
+import csvParser from 'csv-parser';
 import { fileCollectionFromPath } from 'filelist-utils';
 import OCL from 'openchemlib';
-import csvParser from 'csv-parser';
+import unzipper from 'unzipper'; // Using unzipper to extract the contents of the ZIP
+
 import debugLibrary from '../../../../utils/Debug.js';
-import unzipper from 'unzipper';  // Using unzipper to extract the contents of the ZIP
-import fs from 'fs';
-import path from 'path';
 import { getNoStereosFromCache } from '../../../../utils/getNoStereosFromCache.js';
 
 const debug = debugLibrary('parseCoconuts');
 
 /**
  * @description Parse the coconuts CSV file from the ZIP and yield results for MongoDB
  * @param {*} zipPath path to the zip file
- * @param {*} connection MongoDB connection (for logging)
+ * @param {*} connection MongoDB connection
  * @yields {Object} yields MongoDB-ready document
  */
 export async function* parseCoconuts(zipPath, connection) {
@@ -30,23 +31,25 @@ export async function* parseCoconuts(zipPath, connection) {
     });
 
     // Sort files by last modified and select the most recent one
-    let fileToRead = fileCollection.files.sort((a, b) => b.lastModified - a.lastModified)[0];
+    let fileToRead = fileCollection.files.sort(
+      (a, b) => b.lastModified - a.lastModified,
+    )[0];
 
     // Adjust relativePath based on environment
     if (process.env.NODE_ENV === 'test') {
-      fileToRead.relativePath = folderPath.replace('data/', '') + fileToRead.relativePath;
+      fileToRead.relativePath =
+        folderPath.replace('data/', '') + fileToRead.relativePath;
     } else {
-      fileToRead.relativePath = folderPath.replace('full/', '') + fileToRead.relativePath;
+      fileToRead.relativePath =
+        folderPath.replace('full/', '') + fileToRead.relativePath;
     }
 
-   
-
     // Extract the ZIP file using unzipper
     const zipFilePath = path.resolve(fileToRead.relativePath);
     const directory = await unzipper.Open.file(zipFilePath);
-    
+
     // Find the CSV file inside the ZIP
-    const csvFile = directory.files.find(file => file.path.endsWith('.csv'));
+    const csvFile = directory.files.find((file) => file.path.endsWith('.csv'));
 
     if (!csvFile) {
       throw new Error('CSV file not found in ZIP archive');
@@ -55,36 +58,28 @@ export async function* parseCoconuts(zipPath, connection) {
     // Open the CSV file as a stream
     const csvStream = csvFile.stream().pipe(csvParser());
 
-
     // Parsing each row in the CSV stream
     for await (const row of csvStream) {
-    //  console.log('Row:', row.canonical_smiles);
-
       try {
         // Skip if required fields are missing
         if (!row.identifier || !row.canonical_smiles) continue;
         // Parse the molecule using OpenChemLib
 
-        const oclMolecule = OCL.Molecule.fromSmiles(
-          row.canonical_smiles,
-        );
+        const oclMolecule = OCL.Molecule.fromSmiles(row.canonical_smiles);
         const ocl = await getNoStereosFromCache(
           oclMolecule,
           connection,
           'coconuts',
         );
-      
 
         // Process taxonomies and comments
         const taxonomies = [];
         if (row.organisms !== '') {
           const organismsList = row.organisms.split('|');
           for (const entry of organismsList) {
-           
-              taxonomies.push({ species: entry });
-            
+            taxonomies.push({ species: entry });
           }
-        } 
+        }
 
         // Prepare the result document
         const result = {
@@ -94,25 +89,20 @@ export async function* parseCoconuts(zipPath, connection) {
           },
         };
 
-        if (row.cas!== '') result.data.cas = row.cas;
+        if (row.cas !== '') result.data.cas = row.cas;
         if (row.iupac_name) result.data.iupacName = row.iupac_name;
         if (taxonomies.length > 0) result.data.taxonomies = taxonomies;
-        if(row.name!== '') result.data.name = row.name;
+        if (row.name !== '') result.data.name = row.name;
 
-      
         yield result;
       } catch (e) {
-        debug.error(
-          `Error processing row ${row.identifier}: ${e.message}`,
-          {
-            collection: 'coconuts',
-            connection,
-            stack: e.stack,
-          },
-        );
+        debug.error(`Error processing row ${row.identifier}: ${e.message}`, {
+          collection: 'coconuts',
+          connection,
+          stack: e.stack,
+        });
       }
     }
-
   } catch (e) {
     if (connection) {
       await debug.fatal(e.message, {