sortExtractors now returns an array, tests corrected and expanded

Author: dmendelowitz

src/client/MCODEClient.js

@@ -66,7 +66,7 @@ class MCODEClient extends BaseClient {
       { type: 'CSVAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
     ];
     // Sort extractors based on order and dependencies
-    sortExtractors(this.extractorConfig, dependencyInfo);
+    this.extractorConfig = sortExtractors(this.extractorConfig, dependencyInfo);
     // Store webServiceAuthConfig if provided`
     this.authConfig = webServiceAuthConfig;
     this.commonExtractorArgs = {

src/helpers/dependencyUtils.js

@@ -14,7 +14,7 @@ const logger = require('./logger');
  */
 function sortExtractors(extractors, dependencyInfo) {
   const missing = {};
-  // Filter dependency info to onlly extractors in the config
+  // Filter dependency info to only extractors in the config
   dependencyInfo.filter((e) => extractors.map((x) => x.type).includes(e.type)).forEach((extractor) => {
     // For each extractor, check if its dependencies are present
     extractor.dependencies.forEach((dependency) => {
@@ -35,8 +35,10 @@ function sortExtractors(extractors, dependencyInfo) {
     throw new Error('Some extractors are missing dependencies, see above for details.');
   }
   // If no missing dependencies, sort extractors into correct order
+  const sortedExtractors = [...extractors];
   const order = dependencyInfo.map((x) => x.type);
-  extractors.sort((a, b) => order.indexOf(a.type) - order.indexOf(b.type));
+  sortedExtractors.sort((a, b) => order.indexOf(a.type) - order.indexOf(b.type));
+  return sortedExtractors;
 }
 
 module.exports = {

test/cli/mcodeExtraction.test.js

@@ -92,6 +92,13 @@ describe('mcodeExtraction', () => {
               filePath: path.join(__dirname, './fixtures/example-clinical-trial-info.csv'),
             },
           },
+          {
+            label: 'patient',
+            type: 'CSVPatientExtractor',
+            constructorArgs: {
+              filePath: path.join(__dirname, './fixtures/example-patient.csv'),
+            },
+          },
         ],
       };
 
@@ -105,5 +112,21 @@ describe('mcodeExtraction', () => {
       const flatErrors = flattenErrorValues(totalExtractionErrors);
       expect(flatErrors).toHaveLength(3);
     });
+    it('should throw error when initialized with missing dependencies', async () => {
+      const testConfig = {
+        extractors: [
+          // Should fail when this extractor is run without patient data in context
+          {
+            label: 'CTI',
+            type: 'CSVClinicalTrialInformationExtractor',
+            constructorArgs: {
+              filePath: path.join(__dirname, './fixtures/example-clinical-trial-info.csv'),
+            },
+          },
+        ],
+      };
+
+      expect(() => new MCODEClient(testConfig)).toThrow();
+    });
   });
 });

test/helpers/dependencyUtils.test.js

@@ -1,4 +1,3 @@
-const _ = require('lodash');
 const { sortExtractors } = require('../../src/helpers/dependencyUtils.js');
 
 const WRONG_ORDER = [
@@ -26,15 +25,14 @@ const DEPENDENCY_INFO = [
 
 describe('sortExtractors', () => {
   test('should put extractors in the correct order', () => {
-    sortExtractors(WRONG_ORDER, DEPENDENCY_INFO);
-    expect(WRONG_ORDER[0].type).toEqual('Extractor1');
-    expect(WRONG_ORDER[1].type).toEqual('Extractor2');
-    expect(WRONG_ORDER[2].type).toEqual('Extractor3');
+    const sorted = sortExtractors(WRONG_ORDER, DEPENDENCY_INFO);
+    expect(sorted[0].type).toEqual('Extractor1');
+    expect(sorted[1].type).toEqual('Extractor2');
+    expect(sorted[2].type).toEqual('Extractor3');
   });
 
   test('should change nothing if all extractors are in order with all dependencies', () => {
-    const unchanged = _.cloneDeep(NO_CHANGE);
-    sortExtractors(unchanged, DEPENDENCY_INFO);
+    const unchanged = sortExtractors(NO_CHANGE, DEPENDENCY_INFO);
     expect(unchanged).toEqual(NO_CHANGE);
   });