WIP: done with initial implementation of generic VS lookup. TODO: tests for the VS lookup and integration across repos

Author: Dtphelan1

src/helpers/conditionUtils.js

@@ -1,10 +1,5 @@
-const primaryCancerConditionVS = require('../valueSets/ValueSet-onco-core-PrimaryOrUncertainBehaviorCancerDisorderVS.json');
-const secondaryCancerConditionVS = require('../valueSets/ValueSet-onco-core-SecondaryCancerDisorderVS.json');
+const { checkCodeInVS } = require('./valueSetUtils');
 
-function checkCodeInVS(code, valueSet) {
-  // strips the period in the code since the provided value set has the periods removed
-  return valueSet.compose.include[2].concept.map((c) => c.code).includes(code.replace('.', ''));
-}
 
 /**
  * Checks for ICD-10 code
@@ -28,7 +23,8 @@ function getICD10Code(condition) {
  * @return {boolean} if primary cancer condition
  */
 function isConditionCodePrimary(code) {
-  return checkCodeInVS(code, primaryCancerConditionVS);
+  const primaryCancerConditionVSFilepath = './valueSets/ValueSet-onco-core-PrimaryOrUncertainBehaviorCancerDisorderVS.json';
+  return checkCodeInVS(code, primaryCancerConditionVSFilepath);
 }
 
 /**
@@ -37,7 +33,8 @@ function isConditionCodePrimary(code) {
  * @return {boolean} if secondary cancer condition
  */
 function isConditionCodeSecondary(code) {
-  return checkCodeInVS(code, secondaryCancerConditionVS);
+  const secondaryCancerConditionVSFilepath = './valueSets/ValueSet-onco-core-SecondaryCancerDisorderVS.json';
+  return checkCodeInVS(code, secondaryCancerConditionVSFilepath);
 }
 
 /**

src/helpers/observationUtils.js

@@ -1,4 +1,4 @@
-const tumorMarkerTestVS = require('../valueSets/ValueSet-mcode-tumor-marker-test-vs.json');
+const { checkCodeInVS } = require('./valueSetUtils');
 
 // Codes and display values for Vital Signs resources
 // Code mapping is based on http://hl7.org/fhir/R4/observation-vitalsigns.html
@@ -17,12 +17,10 @@ const vitalSignsCodeToTextLookup = {
   '8462-4': 'Diastolic blood pressure',
 };
 
-function checkCodeInVS(code, valueSet) {
-  return valueSet.compose.include[0].concept.map((c) => c.code).includes(code);
-}
 
 function isTumorMarker(code) {
-  return checkCodeInVS(code, tumorMarkerTestVS);
+  const tumorMarkerTestVSPath = './valueSets/ValueSet-mcode-tumor-marker-test-vs.json';
+  return checkCodeInVS(code, tumorMarkerTestVSPath);
 }
 
 function isVitalSign(code) {

src/helpers/valueSetUtils.js

@@ -0,0 +1,75 @@
+const fs = require('fs');
+const path = require('path');
+const logger = require('./logger');
+
+const vsTypes = {
+  json: 1,
+  xml: 2,
+  turtle: 3,
+};
+
+function loadJsonVS(filepath) {
+  try {
+    const vsData = fs.readFileSync(path.resolve(__dirname, filepath));
+    const vsJson = JSON.parse(vsData);
+    return vsJson;
+  } catch (error) {
+    logger.error(`Could not load valueSet from path ${filepath}`);
+    throw error;
+  }
+}
+
+function loadVS(filepath, typeOfVS = vsTypes.json) {
+  switch (typeOfVS) {
+    case vsTypes.json:
+      logger.info(`loading JSON valueset from ${filepath}`);
+      return loadJsonVS(filepath);
+
+    case vsTypes.xml:
+      logger.error('No defined valueset loader for `xml` type valuesets');
+      return null;
+
+    case vsTypes.turtle:
+      logger.error('No defined valueset loader for `turtle` type valuesets');
+      return null;
+
+    default:
+      logger.error(`'${typeOfVS}' is not a recognized valueset type`);
+      return null;
+  }
+}
+
+/**
+ * Check if code is in value set
+ * @param {object} code value to look for in a valueset
+ * @param {object} valueSet contains list of codes included in value set
+ * @return {boolean} true if condition is in valueSet's compose block or expansion block
+ */
+const checkCodeInVS = (code, valueSetFilePath, typeOfVS = vsTypes.json) => {
+  const valueSet = loadVS(valueSetFilePath, typeOfVS);
+  let inVSExpansion = false;
+  let inVSCompose = false;
+  if (valueSet.expansion) {
+    // If valueSet has expansion, we only need to check these codes since everything in compose is in expansion
+    inVSExpansion = valueSet.expansion.contains.some((containsItem) => {
+      if (!code || !containsItem) return false;
+      // return code.system === containsItem.system && code === containsItem.code;
+      return code === containsItem.code;
+    });
+  } else {
+    // Checks if code is in any of the valueSet.compose.include arrays
+    inVSCompose = valueSet.compose.include.some((includeItem) => {
+      if (!code || !includeItem || !includeItem.concept) return false;
+      // return c.system === includeItem.system && includeItem.concept.map((concept) => concept.code).includes(code);
+      return includeItem.concept.map((concept) => concept.code).includes(code);
+    });
+  }
+  return inVSCompose || inVSExpansion;
+};
+
+module.exports = {
+  vsTypes,
+  loadJsonVS,
+  loadVS,
+  checkCodeInVS,
+};

src/valueSets/ValueSet-mcode-tumor-marker-test-vs.json renamed to src/helpers/valueSets/ValueSet-mcode-tumor-marker-test-vs.json

@@ -11,24 +11,22 @@ const examplePrimaryCondition = require('./fixtures/primary-cancer-condition.jso
 const exampleSecondaryCondition = require('./fixtures/secondary-cancer-condition.json');
 const conditionWithICD10 = require('./fixtures/condition-with-icd10.json');
 const conditionWithoutICD10 = require('./fixtures/condition-without-icd10.json');
-const primaryCancerConditionVS = require('../../src/valueSets/ValueSet-onco-core-PrimaryOrUncertainBehaviorCancerDisorderVS.json');
-const secondaryCancerConditionVS = require('../../src/valueSets/ValueSet-onco-core-SecondaryCancerDisorderVS.json');
 const icd10 = require('./fixtures/icd10.json');
 
-const primaryCancerConditionCode = primaryCancerConditionVS.compose.include[2].concept[0].code;
-const secondaryCancerConditionCode = secondaryCancerConditionVS.compose.include[2].concept[0].code;
+const primaryCancerConditionCode = 'C50911'; // "Malignant neoplasm of unspecified site of right female breast"
+const secondaryCancerConditionCode = 'C7B1'; // "Secondary Merkel cell carcinoma" without a
 
 describe('conditionUtils', () => {
   test('isConditionCodePrimary', () => {
     expect(isConditionCodePrimary(primaryCancerConditionCode)).toBeTruthy();
     expect(isConditionCodePrimary('anything')).toBeFalsy();
-    expect(() => isConditionCodePrimary(undefined)).toThrowError(TypeError);
+    expect(isConditionCodePrimary(undefined)).toBeFalsy();
   });
 
   test('isConditionCodeSecondary', () => {
     expect(isConditionCodeSecondary(secondaryCancerConditionCode)).toBeTruthy();
     expect(isConditionCodeSecondary('anyCode')).toBeFalsy();
-    expect(() => isConditionCodeSecondary(undefined)).toThrowError(TypeError);
+    expect(isConditionCodeSecondary(undefined)).toBeFalsy();
   });
 
   test('isConditionPrimary', () => {
@@ -52,7 +50,7 @@ describe('conditionUtils', () => {
     expect(isConditionCodeCancer(primaryCancerConditionCode)).toBeTruthy();
     expect(isConditionCodeCancer(secondaryCancerConditionCode)).toBeTruthy();
     expect(isConditionCodeCancer('anything')).toBeFalsy();
-    expect(() => isConditionCodeCancer(undefined)).toThrowError(TypeError);
+    expect(isConditionCodeCancer(undefined)).toBeFalsy();
   });
 
   test('isConditionCancer', () => {

src/valueSets/ValueSet-onco-core-PrimaryOrUncertainBehaviorCancerDisorderVS.json renamed to src/helpers/valueSets/ValueSet-onco-core-PrimaryOrUncertainBehaviorCancerDisorderVS.json

@@ -1,7 +1,6 @@
 const {
   isVitalSign, isTumorMarker, isKarnofskyPerformanceStatus, isECOGPerformanceStatus, vitalSignsCodeToTextLookup,
 } = require('../../src/helpers/observationUtils.js');
-const tumorMarkerTestVS = require('../../src/valueSets/ValueSet-mcode-tumor-marker-test-vs.json');
 
 describe('observationUtils', () => {
   test('isVitalSign should return true when passed a valid Vital Sign code', () => {
@@ -14,9 +13,8 @@ describe('observationUtils', () => {
     expect(isVitalSign(code)).toEqual(false);
   });
   test('isTumorMarker should return true when passed a valid Tumor marker code', () => {
-    tumorMarkerTestVS.compose.include[0].concept.map((c) => c.code).forEach((code) => {
-      expect(isTumorMarker(code)).toEqual(true);
-    });
+    const her2InTissue = '48676-1';
+    expect(isTumorMarker(her2InTissue)).toEqual(true);
   });
   test('isTumorMarker should return false when passed a code that does not belong to a Tumor Marker', () => {
     const code = '12345';