Relinted source code.

.eslintrc.json

@@ -1,28 +1,31 @@
 {
-    "extends": [
-        "airbnb-base",
-        "plugin:mocha/recommended"
-    ],
-    "parserOptions": {
-        "parser": "babel-eslint",
-        "ecmaVersion": 6,
-        "sourceType": "module"
-    },
-    "env": {
-        "es6": true
-    },
-    "plugins": [
-        "mocha",
-        "json-format"
-    ],
-    "rules": {
-      "prefer-destructuring": "off",
-      "comma-dangle": ["error", {
+  "extends": [
+    "airbnb-base",
+    "plugin:mocha/recommended"
+  ],
+  "parserOptions": {
+    "parser": "babel-eslint",
+    "ecmaVersion": 6,
+    "sourceType": "module"
+  },
+  "env": {
+    "es6": true
+  },
+  "plugins": [
+    "mocha",
+    "json-format"
+  ],
+  "rules": {
+    "prefer-destructuring": "off",
+    "comma-dangle": [
+      "error",
+      {
         "arrays": "always-multiline",
         "objects": "always-multiline",
         "imports": "always-multiline",
         "exports": "always-multiline",
         "functions": "ignore"
-      }]
-    }
+      }
+    ]
+  }
 }

src/matchers/TaxonomicUnitMatcher.js

@@ -87,7 +87,7 @@ class TaxonomicUnitMatcher {
     const externalRefs2 = wrappedTUnit2.externalReferences;
 
     return externalRefs1.some(
-      extref1 => externalRefs2.some(
+      (extref1) => externalRefs2.some(
         (extref2) => {
           if (
             extref1

src/utils/owlterms.js

@@ -1,4 +1,3 @@
-
 // Some OWL constants to be used.
 module.exports = {
   // Where is our context file located?

src/wrappers/CitationWrapper.js

@@ -70,14 +70,14 @@ class CitationWrapper {
 
     // Add DOIs and URLs.
     additionalInfo += (this.citation.identifier || [])
-      .filter(id => id.type === 'doi')
-      .map(doi => ` doi: ${doi.id}`)
+      .filter((id) => id.type === 'doi')
+      .map((doi) => ` doi: ${doi.id}`)
       .join('');
-    additionalInfo += (this.citation.link || []).map(link => ` URL: ${link.url}`).join('');
+    additionalInfo += (this.citation.link || []).map((link) => ` URL: ${link.url}`).join('');
 
     additionalInfo += (this.citation.identifier || [])
-      .filter(id => id.type === 'isbn')
-      .map(isbn => ` ISBN: ${isbn.id}`)
+      .filter((id) => id.type === 'isbn')
+      .map((isbn) => ` ISBN: ${isbn.id}`)
       .join('');
 
     // A citation for a journal article should be different from others.
@@ -86,8 +86,8 @@ class CitationWrapper {
       const journalIssue = (has(journal, 'number')) ? `(${journal.number})` : '';
       const pages = (has(journal, 'pages')) ? `:${journal.pages}` : '';
       additionalInfo += (journal.identifier || [])
-        .filter(id => id.type === 'issn')
-        .map(issn => `ISSN: ${issn.id} `)
+        .filter((id) => id.type === 'issn')
+        .map((issn) => `ISSN: ${issn.id} `)
         .join('');
       return `${authorsAndTitle} ${journal.name || 'Unknown journal'} ${journal.volume || 'Unknown volume'}${journalIssue}${pages}${additionalInfo}`;
     }

src/wrappers/PhylogenyWrapper.js

@@ -136,8 +136,8 @@ class PhylogenyWrapper {
     const tunits = new Set();
 
     nodeLabels.forEach(
-      nodeLabel => this.getTaxonomicUnitsForNodeLabel(nodeLabel)
-        .forEach(tunit => tunits.add(tunit))
+      (nodeLabel) => this.getTaxonomicUnitsForNodeLabel(nodeLabel)
+        .forEach((tunit) => tunits.add(tunit))
     );
 
     return tunits;
@@ -160,8 +160,8 @@ class PhylogenyWrapper {
       return Array.from(
         new Set(
           Array.from(vertices)
-            .map(vertex => vertex.label)
-            .filter(label => label !== undefined)
+            .map((vertex) => vertex.label)
+            .filter((label) => label !== undefined)
         )
       );
     }
@@ -170,8 +170,8 @@ class PhylogenyWrapper {
       // Return the internal nodes (those with atleast one child).
       return Array.from(new Set(
         Array.from(arcs)
-          .map(arc => arc[0].label) // Retrieve the label of the parent vertex in this arc.
-          .filter(label => label !== undefined)
+          .map((arc) => arc[0].label) // Retrieve the label of the parent vertex in this arc.
+          .filter((label) => label !== undefined)
       ));
     }
 
@@ -188,7 +188,7 @@ class PhylogenyWrapper {
       const allLabels = this.getNodeLabels('both');
       const internalLabels = new Set(this.getNodeLabels('internal'));
 
-      return allLabels.filter(label => !internalLabels.has(label));
+      return allLabels.filter((label) => !internalLabels.has(label));
     }
 
     throw new Error(`Unknown nodeType: '${nodeType}'`);
@@ -241,7 +241,7 @@ class PhylogenyWrapper {
       // Attempt pairwise matches between taxonomic units in the specifier
       // and associated with the node.
       return nodeTUnits.some(
-        tunit => new TaxonomicUnitMatcher(specifier, tunit).matched
+        (tunit) => new TaxonomicUnitMatcher(specifier, tunit).matched
       );
     });
   }
@@ -399,7 +399,7 @@ class PhylogenyWrapper {
     Object.keys(nodeIdsByParentId).forEach((parentId) => {
       // What are the children of this parentId?
       const childrenIDs = Array.from(nodeIdsByParentId[parentId]);
-      const children = childrenIDs.map(childId => nodesById[childId]);
+      const children = childrenIDs.map((childId) => nodesById[childId]);
 
       // Is this the root node?
       if (has(nodesById, parentId)) {
@@ -410,7 +410,7 @@ class PhylogenyWrapper {
       children.forEach((child) => {
         const childToModify = child;
         // Add all other sibling to node.siblings, but don't add this node itself!
-        childToModify.siblings = childrenIDs.filter(childId => childId !== child['@id']);
+        childToModify.siblings = childrenIDs.filter((childId) => childId !== child['@id']);
       });
     });
 

src/wrappers/PhylorefWrapper.js

@@ -343,7 +343,7 @@ class PhylorefWrapper {
     // owlterms.UNKNOWN_CODEs, then that is still usable as a default
     // nomenclatural code for this phyloreference.
     const uniqNomenCodesNoUnknowns = this.uniqNomenCodes
-      .filter(code => code !== owlterms.UNKNOWN_CODE);
+      .filter((code) => code !== owlterms.UNKNOWN_CODE);
     if (uniqNomenCodesNoUnknowns.length === 1) return uniqNomenCodesNoUnknowns[0];
 
     return owlterms.UNKNOWN_CODE;
@@ -576,15 +576,15 @@ class PhylorefWrapper {
     // selected internals -- when there are fewer, we'll just end up with the inverses
     // of the previous comparisons, which we'll already have covered.
     if (remainingInternals.length > 1 && selected.length <= remainingInternals.length) {
-      remainingInternals.map(newlySelected => this.createClassExpressionsForInternals(
+      remainingInternals.map((newlySelected) => this.createClassExpressionsForInternals(
         jsonld,
         // The new remaining is the old remaining minus the selected TU.
-        remainingInternals.filter(i => i !== newlySelected),
+        remainingInternals.filter((i) => i !== newlySelected),
         // The new selected is the old selected plus the selected TU.
         selected.concat([newlySelected])
       ))
         .reduce((acc, val) => acc.concat(val), [])
-        .forEach(expr => classExprs.push(expr));
+        .forEach((expr) => classExprs.push(expr));
     }
 
     return classExprs;
@@ -675,7 +675,7 @@ class PhylorefWrapper {
       logicalExpressions = externalSpecifiers.map((selectedExternal) => {
         // Add the internal specifiers.
         const intersectionExprs = internalSpecifiers.map(
-          sp => this.getIncludesRestrictionForTU(sp)
+          (sp) => this.getIncludesRestrictionForTU(sp)
         );
 
         // Add the selected external specifier.
@@ -689,7 +689,7 @@ class PhylorefWrapper {
         });
 
         // Collect all of the externals that are not selected.
-        const remainingExternals = externalSpecifiers.filter(ex => ex !== selectedExternal);
+        const remainingExternals = externalSpecifiers.filter((ex) => ex !== selectedExternal);
 
         // Add the remaining externals, which we assume will resolve outside of
         // this clade.
@@ -718,9 +718,7 @@ class PhylorefWrapper {
 
       // We only have internal specifiers. We therefore need to use the algorithm in
       // this.createClassExpressionsForInternals() to create this expression.
-      logicalExpressions = this.createClassExpressionsForInternals(
-        phylorefAsJSONLD, internalSpecifiers, []
-      );
+      logicalExpressions = this.createClassExpressionsForInternals(phylorefAsJSONLD, internalSpecifiers, []);
     }
 
     // If we have a single logical expression, we set that as an equivalentClass
@@ -758,7 +756,7 @@ class PhylorefWrapper {
       //  2. We need to set each of these component classes to be a subclass of
       //     this phyloreference so that it can include instances from each of the
       //     logical expressions.
-      phylorefAsJSONLD.subClasses = logicalExpressions.map(classExpr => this.createComponentClass(
+      phylorefAsJSONLD.subClasses = logicalExpressions.map((classExpr) => this.createComponentClass(
         phylorefAsJSONLD,
         internalSpecifiers,
         externalSpecifiers,

src/wrappers/PhyxWrapper.js

@@ -45,7 +45,7 @@ class PhyxWrapper {
   get defaultNomenCode() {
     if (has(this.phyx, 'defaultNomenclaturalCodeIRI')) return this.phyx.defaultNomenclaturalCodeIRI;
     const nomenCodes = (this.phyx.phylorefs || [])
-      .map(phyloref => new PhylorefWrapper(phyloref).defaultNomenCode);
+      .map((phyloref) => new PhylorefWrapper(phyloref).defaultNomenCode);
     const uniqNomenCodes = uniq(nomenCodes);
     if (uniqNomenCodes.length === 1) return uniqNomenCodes[0];
     return owlterms.UNKNOWN_CODE;

src/wrappers/SpecimenWrapper.js

@@ -57,7 +57,7 @@ class SpecimenWrapper {
       'file://',
       'urn:',
     ];
-    if (URL_URN_PREFIXES.filter(prefix => occurID.toLowerCase().startsWith(prefix)).length > 0) {
+    if (URL_URN_PREFIXES.filter((prefix) => occurID.toLowerCase().startsWith(prefix)).length > 0) {
       return specimen;
     }
 

src/wrappers/TaxonNameWrapper.js

@@ -138,7 +138,7 @@ class TaxonNameWrapper {
 
     // Look for the entry with the same IRI as the provided IRI.
     const matchingCode = codes
-      .find(code => (code.iri || '').toLowerCase() === nomenCode.toLowerCase());
+      .find((code) => (code.iri || '').toLowerCase() === nomenCode.toLowerCase());
     if (matchingCode) return matchingCode;
     return undefined;
   }

src/wrappers/TaxonomicUnitWrapper.js

@@ -122,7 +122,7 @@ class TaxonomicUnitWrapper {
     const externalReferences = this.externalReferences;
     if (externalReferences.length > 0) {
       return externalReferences
-        .map(externalRef => `<${externalRef}>`)
+        .map((externalRef) => `<${externalRef}>`)
         .join(' and ');
     }
 
@@ -180,7 +180,7 @@ class TaxonomicUnitWrapper {
       'urn:',
     ];
 
-    if (URL_URN_PREFIXES.filter(prefix => nodeLabel.startsWith(prefix)).length > 0) {
+    if (URL_URN_PREFIXES.filter((prefix) => nodeLabel.startsWith(prefix)).length > 0) {
       // The node label starts with something that looks like a URL!
       // Treat it as an external reference.
       if (tunit === undefined) tunit = {};

test/examples.js

@@ -38,7 +38,7 @@ describe('PhyxWrapper', function () {
 
   describe('Test all correct example Phyx files', function () {
     const examples = fs.readdirSync(path.resolve(__dirname, './examples/correct'))
-      .filter(filename => filename.endsWith('.json'));
+      .filter((filename) => filename.endsWith('.json'));
 
     examples.forEach((example) => {
       const basename = path.resolve(__dirname, './examples/correct', path.parse(example).name);

test/jphyloref.js

@@ -53,7 +53,7 @@ describe('JPhyloRef', function () {
 
   describe('test example JSON-LD files using JPhyloRef', function () {
     fs.readdirSync(path.resolve(__dirname, 'examples', 'correct'))
-      .filter(filename => filename.endsWith('.nq'))
+      .filter((filename) => filename.endsWith('.nq'))
       .forEach((filename) => {
         it(`testing ${filename}`, function () {
           this.timeout(60000);

test/phylogenies.js

@@ -255,13 +255,15 @@ describe('PhylogenyWrapper', function () {
       expect(jsonld).to.have.property('@id');
       expect(jsonld['@id']).to.equal('#providedId');
     });
+
     it('should generate a new @id on input phylorefs', function () {
       const jsonld = new phyx.PhylogenyWrapper({
         newick: '((Homo_sapiens, Panthera_tigris), Mus_musculus)',
       }, owlterms.ICZN_CODE).asJSONLD('#phylogeny0');
       expect(jsonld).to.have.property('@id');
       expect(jsonld['@id']).to.equal('#phylogeny0');
     });
+
     it('should generate the phylogeny in JSON-LD as expected', function () {
       const expectedResults = [
         {

test/phylorefs.js

@@ -258,6 +258,7 @@ describe('PhylorefWrapper', function () {
       expect(jsonld).to.have.property('@id');
       expect(jsonld['@id']).to.equal('#providedId');
     });
+
     it('should generate a new @id on input phylorefs', function () {
       const jsonld = new phyx.PhylorefWrapper({
         internalSpecifiers: [specifier1],
@@ -266,6 +267,7 @@ describe('PhylorefWrapper', function () {
       expect(jsonld).to.have.property('@id');
       expect(jsonld['@id']).to.equal('#phyloref0');
     });
+
     it('should generate the expected equivClass expression for 1 int, 1 ext phyloref', function () {
       const jsonld = new phyx.PhylorefWrapper({
         internalSpecifiers: [specifier1],

test/scripts/phyx2owl.js

@@ -26,6 +26,7 @@ describe(PHYX2OWL_JS, function () {
     expect(result.stdout).to.be.empty;
     expect(result.stderr).to.contain('No input files provided.');
   });
+
   it('should support `--help`', function () {
     const result = child.spawnSync(PHYX2OWL_JS, ['--help'], {
       encoding: 'utf-8',
@@ -35,6 +36,7 @@ describe(PHYX2OWL_JS, function () {
     expect(result.stderr).to.be.empty;
     expect(result.stdout).to.contain('phyx2owl.js [files or directories to convert into OWL ontologies]');
   });
+
   it('should be able to convert `brochu_2003.json`', function () {
     const PHYX_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.json');
     const NQ_FILE = path.resolve(__dirname, '../examples/correct/brochu_2003.nq');
@@ -62,10 +64,11 @@ describe(PHYX2OWL_JS, function () {
     const nqExpected = fs.readFileSync(NQ_FILE, 'utf8');
     expect(nqGenerated).to.equal(nqExpected);
   });
+
   it('should be able to convert the entire `test/examples/correct` directory', function () {
     const EXAMPLE_DIR = path.resolve(__dirname, '../examples/correct');
     const jsonFilesInExamples = fs.readdirSync(EXAMPLE_DIR, 'utf8')
-      .filter(fileName => fileName.toLowerCase().endsWith('.json'));
+      .filter((fileName) => fileName.toLowerCase().endsWith('.json'));
 
     const result = child.spawnSync(PHYX2OWL_JS, [EXAMPLE_DIR, '--base-iri', 'http://example.org/phyx.js/example#'], {
       encoding: 'utf-8',
@@ -82,7 +85,7 @@ describe(PHYX2OWL_JS, function () {
 
     // Make sure that the generated files *look* like JSON-LD files.
     fs.readdirSync(EXAMPLE_DIR, 'utf8')
-      .filter(fileName => fileName.toLowerCase().endsWith('.owl'))
+      .filter((fileName) => fileName.toLowerCase().endsWith('.owl'))
       .forEach((owlFilename) => {
         const nqGenerated = fs.readFileSync(path.resolve(EXAMPLE_DIR, owlFilename), 'utf8');
 

test/scripts/resolve.js

@@ -27,6 +27,7 @@ describe('bin/resolve.js', function () {
     expect(result.stdout).to.be.empty;
     expect(result.stderr).to.contain('No input files provided.');
   });
+
   it('should support `--help`', function () {
     const result = child.spawnSync(RESOLVE_JS, ['--help'], {
       encoding: 'utf-8',
@@ -36,6 +37,7 @@ describe('bin/resolve.js', function () {
     expect(result.stderr).to.be.empty;
     expect(result.stdout).to.contain('resolve.js [files to resolve on the Open Tree of Life]');
   });
+
   it('should provide the expected results on the `brochu_2003.json` example file', function () {
     var resultObj; // eslint-disable-line no-var
 
@@ -77,6 +79,7 @@ describe('bin/resolve.js', function () {
       error: 'no_mrca_found:400',
     });
   });
+
   it('should correctly report errors with certain phyloreferences', function () {
     var resultObj; // eslint-disable-line no-var