Fix Biome lint errors in JS source files.

Applied safe fixes (arrow functions, node: protocol prefixes) via
`biome lint --write --unsafe`, then manually converted forEach calls
to for...of loops to satisfy the noForEach rule.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: gaurav

phyx2ontology/phyx2ontology.js

@@ -16,8 +16,8 @@ const MAX_INTERNAL_SPECIFIERS = process.env.MAX_INTERNAL_SPECIFIERS || 7;
 const MAX_EXTERNAL_SPECIFIERS = process.env.MAX_EXTERNAL_SPECIFIERS || 10;
 
 // Load necessary modules.
-const fs = require('fs');
-const path = require('path');
+const fs = require('node:fs');
+const path = require('node:path');
 const yargs = require('yargs');
 
 // Load phyx.js, our PHYX library.
@@ -111,8 +111,8 @@ const jsons = phyxFiles
 /* Convert every phyloreference (from every Phyx file) into a JSON-LD object. */
 const phylorefsByLabel = {};
 const phylorefs = [];
-jsons.forEach((phyxFile) => {
-  phyxFile.phylorefs.forEach((phyloref) => {
+for (const phyxFile of jsons) {
+  for (const phyloref of phyxFile.phylorefs) {
     // Convert phyloreference to JSON-LD.
     entityIndex += 1;
     const phylorefWrapper = new phyx.PhylorefWrapper(phyloref);
@@ -122,13 +122,13 @@ jsons.forEach((phyxFile) => {
       console.warn(`Phyloreference ${phylorefWrapper.label} has `
         + `${phylorefWrapper.internalSpecifiers.length} internal specifiers but `
         + `the limit is ${MAX_INTERNAL_SPECIFIERS}`);
-      return;
+      continue;
     }
     if (phylorefWrapper.externalSpecifiers.length > MAX_EXTERNAL_SPECIFIERS) {
       console.warn(`Phyloreference ${phylorefWrapper.label} has `
         + `${phylorefWrapper.externalSpecifiers.length} external specifiers but `
         + `the limit is ${MAX_EXTERNAL_SPECIFIERS}`);
-      return;
+      continue;
     }
 
     // Convert to OWL/JSON-LD.
@@ -143,13 +143,13 @@ jsons.forEach((phyxFile) => {
     // Set a JSON-LD context so this block can be interpreted in isolation.
     jsonld['@context'] = PHYX_CONTEXT_JSON;
     phylorefs.push(jsonld);
-  });
-});
+  }
+}
 
 /* Convert every phylogeny (from every Phyx file) into a JSON-LD object. */
 const phylogenies = [];
-jsons.forEach((phyxFile) => {
-  phyxFile.phylogenies.forEach((phylogeny) => {
+for (const phyxFile of jsons) {
+  for (const phylogeny of phyxFile.phylogenies) {
     // Convert phylogenies into JSON-LD.
     entityIndex += 1;
     const phylogenyAsJSONLD = new phyx.PhylogenyWrapper(phylogeny)
@@ -158,8 +158,8 @@ jsons.forEach((phyxFile) => {
     // Set a '@context' so it can be interpreted from other objects in the output file.
     phylogenyAsJSONLD['@context'] = PHYX_CONTEXT_JSON;
     phylogenies.push(phylogenyAsJSONLD);
-  });
-});
+  }
+}
 
 /* Construct an object to represent the Clade Ontology itself. */
 let cladeOntologyObjects = [

regnum2phyx/regnum2phyx.js

@@ -23,8 +23,8 @@ const ICN_NAME = 'http://purl.obolibrary.org/obo/NOMEN_0000109';
 // const ICTV_NAME = 'http://purl.obolibrary.org/obo/NOMEN_0000111';
 
 // Load necessary modules.
-const fs = require('fs');
-const path = require('path');
+const fs = require('node:fs');
+const path = require('node:path');
 const yargs = require('yargs');
 const {
   has, keys, pickBy, isEmpty,
@@ -161,7 +161,7 @@ function convertCitationsToBibJSON(citation) {
     });
 
     // Since we've moved pages and ISBN into journal, we don't also need it in the main entry.
-    if (has(entry, 'pages')) delete entry.pages;
+    if (has(entry, 'pages')) entry.pages = undefined;
   } else {
     process.stderr.write(`Unknown citation type: '${type}', using anyway.`);
   }
@@ -264,7 +264,7 @@ dump.forEach((entry, index) => {
   );
 
   // Convert each specifier into one
-  (entry.specifiers || []).forEach((specifier) => {
+  for (const specifier of (entry.specifiers || [])) {
     const kind = specifier.specifier_kind || '';
     let addTo = [];
     if (kind.startsWith('internal')) addTo = phylorefTemplate.internalSpecifiers;
@@ -320,7 +320,7 @@ dump.forEach((entry, index) => {
     };
 
     addTo.push(specifierTemplate);
-  });
+  }
 
   // Prepare a simple Phyx file template.
   const phyxTemplate = pickBy({

test/regnum2phyx/exec.js

@@ -3,8 +3,8 @@
  */
 
 // Javascript libraries.
-const ChildProcess = require('child_process');
-const fs = require('fs');
+const ChildProcess = require('node:child_process');
+const fs = require('node:fs');
 
 const tmp = require('tmp');
 const chai = require('chai');
@@ -19,9 +19,9 @@ function loadJSON(filename) {
   return JSON.parse(content);
 }
 
-describe('Test regnum2phyx.js', function () {
-  fs.readdirSync(`${__dirname}/examples`).forEach(function (filename) {
-    describe(`Processing example Regnum dump: ${filename}`, function () {
+describe('Test regnum2phyx.js', () => {
+  for (const filename of fs.readdirSync(`${__dirname}/examples`)) {
+    describe(`Processing example Regnum dump: ${filename}`, () => {
       const filepath = `${__dirname}/examples/${filename}`;
 
       // We only test '.json' files.
@@ -47,7 +47,7 @@ describe('Test regnum2phyx.js', function () {
         }
       );
 
-      it('could be executed by regnum2phyx.js', function () {
+      it('could be executed by regnum2phyx.js', () => {
         expect(child.stderr).to.be.empty;
         expect(child.stdout).to.match(/^(\d+) Phyx files produced successfully.\n$/);
         expect(child.status).to.equal(0);
@@ -59,17 +59,17 @@ describe('Test regnum2phyx.js', function () {
       const producedFiles = fs.readdirSync(`${tmpdirname}`);
       const expectedFiles = fs.readdirSync(`${__dirname}/expected/${basename}`);
 
-      it('should produce the expected files', function () {
+      it('should produce the expected files', () => {
         expect(producedFiles).to.deep.equal(expectedFiles);
         expect(producedFiles).to.not.be.empty;
       });
 
-      producedFiles.forEach(function (producedFile) {
-        describe(`Testing produced file ${producedFile}`, function () {
+      for (const producedFile of producedFiles) {
+        describe(`Testing produced file ${producedFile}`, () => {
           const producedPhyx = loadJSON(`${tmpdirname}/${producedFile}`);
           const expectedPhyx = loadJSON(`${__dirname}/expected/${basename}/${producedFile}`);
 
-          it('should be identical to expected', function () {
+          it('should be identical to expected', () => {
             expect(producedPhyx).to.deep.equal(expectedPhyx);
           });
 
@@ -80,14 +80,14 @@ describe('Test regnum2phyx.js', function () {
           const phyxSchema = ajvInstance.compile(phyxSchemaJSON);
           const result = phyxSchema(producedPhyx);
 
-          it('should validate against the Phyx JSON Schema', function () {
-            (phyxSchema.errors || []).forEach(function (error) {
+          it('should validate against the Phyx JSON Schema', () => {
+            for (const error of (phyxSchema.errors || [])) {
               assert.fail(ajvInstance.errorsText([error]));
-            });
+            }
             expect(result).is.true;
           });
         });
-      });
+      }
     });
-  });
+  }
 });

test/test_phyx.js

@@ -17,9 +17,9 @@ const BASE_DIR = 'phyx/';
 const phyx = require('@phyloref/phyx');
 
 // Javascript libraries.
-const ChildProcess = require('child_process');
-const fs = require('fs');
-const path = require('path');
+const ChildProcess = require('node:child_process');
+const fs = require('node:fs');
+const path = require('node:path');
 
 const Ajv = require('ajv');
 const chai = require('chai');
@@ -57,7 +57,7 @@ const phyxSchema = ajvInstance.compile(phyxSchemaJSON);
  * to get that list before we start testing.
  */
 function findPhyxFiles(dirPath) {
-  return fs.readdirSync(dirPath).map(function (filename) {
+  return fs.readdirSync(dirPath).map((filename) => {
     const filePath = path.join(dirPath, filename);
 
     if (fs.lstatSync(filePath).isDirectory()) {
@@ -72,12 +72,12 @@ function findPhyxFiles(dirPath) {
   }).reduce((x, y) => x.concat(y), []); // This flattens the list of results.
 }
 
-describe('Test Phyx files in repository', function () {
+describe('Test Phyx files in repository', () => {
   // Test each input file.
-  findPhyxFiles(BASE_DIR).forEach(function (filename) {
-    describe(`Phyx file: ${filename}`, function () {
+  for (const filename of findPhyxFiles(BASE_DIR)) {
+    describe(`Phyx file: ${filename}`, () => {
       // Make sure the file to test isn't empty.
-      it('is not empty', function () {
+      it('is not empty', () => {
         const stats = fs.lstatSync(filename);
         assert.notEqual(stats.size, 0);
       });
@@ -95,7 +95,7 @@ describe('Test Phyx files in repository', function () {
       const phyxContent = data.toString('utf-8');
       const json = JSON.parse(phyxContent);
       // Remove the .skip once the Phyx files pass validation.
-      it.skip('should validate against the Phyx JSON Schema', function () {
+      it.skip('should validate against the Phyx JSON Schema', () => {
         const result = phyxSchema(json);
         const errorStrings = (phyxSchema.errors || []).map(err => ajvInstance.errorsText([err]));
         assert.deepEqual(errorStrings, []);
@@ -108,13 +108,13 @@ describe('Test Phyx files in repository', function () {
       try {
         wrappedPhyx = new phyx.PhyxWrapper(json);
       } catch (ex) {
-        it('Exception thrown while loading Phyx to JSON-LD', function () {
+        it('Exception thrown while loading Phyx to JSON-LD', () => {
           throw ex;
         });
         return;
       }
 
-      it('has at least one Newick phylogeny', function () {
+      it('has at least one Newick phylogeny', () => {
         const phylogenies = json.phylogenies || [];
         // assert.isAbove(phylogenies.length, 0, 'No phylogenies found in file');
 
@@ -166,7 +166,7 @@ describe('Test Phyx files in repository', function () {
         const jsonld = JSON.stringify(wrappedPhyx.asJSONLD());
 
         // Make sure the produced JSON-LD is not empty.
-        it('produced a non-empty JSON-LD ontology without throwing an exception', function () {
+        it('produced a non-empty JSON-LD ontology without throwing an exception', () => {
           assert.isNotEmpty(jsonld);
         });
 
@@ -198,12 +198,12 @@ describe('Test Phyx files in repository', function () {
           // console.log(`For ${filename}: ${matches}`);
 
           // Test whether we have any failures.
-          it('did not report any failures', function () {
+          it('did not report any failures', () => {
             const failures = matches[2];
             assert.equal(failures, 0, `${failures} failures occurred during testing`);
           });
 
-          describe('test the results of resolution', function () {
+          describe('test the results of resolution', () => {
             // Look for TODOs or skipped tests.
             const successes = matches[1];
             const todos = matches[3];
@@ -226,18 +226,18 @@ describe('Test Phyx files in repository', function () {
             // We could have zero failures but also zero successes. A Phyx file
             // without any failures, TODOs or any successes in the Clade Ontology
             // should be reported as a failure.
-            it('had at least one success', function () {
+            it('had at least one success', () => {
               assert.isAbove(successes, 0, 'No successes occurred during testing');
             });
 
             // On the off chance that all of the above made sense but the exit code didn't,
             // we'll check that here.
-            it('passed testing in JPhyloRef', function () {
+            it('passed testing in JPhyloRef', () => {
               assert.equal(child.status, 0, 'Exit code from JPhyloRef was not zero');
             });
           });
         }
       }
     });
-  });
+  }
 });