Cardinality matching on category attributes + AE config in example file

Author: julianxcarter

config/mcode-csv-config.example.json

@@ -74,6 +74,13 @@
       "constructorArgs": {
         "filePath": "./data/procedure-information.csv"
       }
+    },
+    {
+      "label": "adverseEvent",
+      "type": "CSVAdverseEventExtractor",
+      "constructorArgs": {
+        "filePath": "./test/sample-client-data/adverse-event-information.csv"
+      }
     }
   ]
 }

src/extractors/CSVAdverseEventExtractor.js

@@ -22,6 +22,10 @@ function formatData(adverseEventData) {
     const categorySystems = categoryCodeSystem.split('|');
     const categoryDisplays = categoryDisplayText.split('|');
 
+    if (!(categoryCodes.length === categorySystems.length && categoryCodes.length === categoryDisplays.length)) {
+      throw new Error('A category atrribute on the adverse event is missing a corresponding categoryCodeSystem or categoryDisplayText value.');
+    }
+
 
     return {
       id: adverseEventId,

test/extractors/CSVAdverseEventExtractor.test.js

@@ -34,6 +34,7 @@ describe('CSVAdverseEventExtractor', () => {
   describe('formatData', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
       const expectedErrorString = 'The adverse event is missing an expected attribute. Adverse event code, mrn, and effective date are all required.';
+      const expectedCategoryErrorString = 'A category atrribute on the adverse event is missing a corresponding categoryCodeSystem or categoryDisplayText value.';
       const localData = _.cloneDeep(exampleCSVAdverseEventModuleResponse);
 
       // Test that valid maximal data works fine
@@ -43,6 +44,20 @@ describe('CSVAdverseEventExtractor', () => {
       delete localData[0].actuality;
       expect(formatData(exampleCSVAdverseEventModuleResponse)).toEqual(expect.anything());
 
+      // Test that adding another category but not adding a corresponding categoryCodeSystem throws an error
+      localData[0].category = 'product-use-error|product-problem';
+      expect(() => formatData(localData)).toThrow(new Error(expectedCategoryErrorString));
+
+      // Test that adding another category but adding a corresponding categoryCodeSystem and categoryDisplayText works fine
+      localData[0].categoryCodeSystem = 'http://terminology.hl7.org/CodeSystem/adverse-event-category|http://snomed.info/sct';
+      localData[0].categoryDisplayText = 'Product Use Error|Product Problem';
+      expect(formatData(localData)).toEqual(expect.anything());
+
+      // Test that adding another category but including syntax for default categoryCodeSystem and categoryDisplayText values works fine
+      localData[0].categoryCodeSystem = 'http://terminology.hl7.org/CodeSystem/adverse-event-category|';
+      localData[0].categoryDisplayText = 'Product Use Error|';
+      expect(formatData(localData)).toEqual(expect.anything());
+
       // Test that deleting a mandatory value throws an error
       delete localData[0].mrn;
       expect(() => formatData(localData)).toThrow(new Error(expectedErrorString));