Updated value set to use proper ICD codes; added tests for the valueSetUtils

Author: Dtphelan1

src/helpers/conditionUtils.js

@@ -1,4 +1,5 @@
-const { checkCodeInVS } = require('./valueSetUtils');
+const path = require('path');
+const { checkCodeInVs } = require('./valueSetUtils');
 
 
 /**
@@ -23,8 +24,8 @@ function getICD10Code(condition) {
  * @return {boolean} if primary cancer condition
  */
 function isConditionCodePrimary(code) {
-  const primaryCancerConditionVSFilepath = './valueSets/ValueSet-onco-core-PrimaryOrUncertainBehaviorCancerDisorderVS.json';
-  return checkCodeInVS(code, primaryCancerConditionVSFilepath);
+  const primaryCancerConditionVSFilepath = path.resolve(__dirname, './valueSets/ValueSet-mcode-primary-or-uncertain-behavior-cancer-disorder-vs.json');
+  return checkCodeInVs(code, primaryCancerConditionVSFilepath);
 }
 
 /**
@@ -33,8 +34,8 @@ function isConditionCodePrimary(code) {
  * @return {boolean} if secondary cancer condition
  */
 function isConditionCodeSecondary(code) {
-  const secondaryCancerConditionVSFilepath = './valueSets/ValueSet-onco-core-SecondaryCancerDisorderVS.json';
-  return checkCodeInVS(code, secondaryCancerConditionVSFilepath);
+  const secondaryCancerConditionVSFilepath = path.resolve(__dirname, './valueSets/ValueSet-mcode-secondary-cancer-disorder-vs.json');
+  return checkCodeInVs(code, secondaryCancerConditionVSFilepath);
 }
 
 /**

src/helpers/observationUtils.js

@@ -1,4 +1,5 @@
-const { checkCodeInVS } = require('./valueSetUtils');
+const path = require('path');
+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
@@ -19,8 +20,8 @@ const vitalSignsCodeToTextLookup = {
 
 
 function isTumorMarker(code) {
-  const tumorMarkerTestVSPath = './valueSets/ValueSet-mcode-tumor-marker-test-vs.json';
-  return checkCodeInVS(code, tumorMarkerTestVSPath);
+  const tumorMarkerTestVSPath = path.resolve(__dirname, './valueSets/ValueSet-mcode-tumor-marker-test-vs.json');
+  return checkCodeInVs(code, tumorMarkerTestVSPath);
 }
 
 function isVitalSign(code) {

src/helpers/valueSetUtils.js

@@ -1,5 +1,5 @@
 const fs = require('fs');
-const path = require('path');
+const _ = require('lodash');
 const logger = require('./logger');
 
 const vsTypes = {
@@ -8,45 +8,43 @@ const vsTypes = {
   turtle: 3,
 };
 
-function loadJsonVS(filepath) {
+function loadJsonVs(absoluteFilepath) {
   try {
-    const vsData = fs.readFileSync(path.resolve(__dirname, filepath));
+    const vsData = fs.readFileSync(absoluteFilepath);
     const vsJson = JSON.parse(vsData);
     return vsJson;
   } catch (error) {
-    logger.error(`Could not load valueSet from path ${filepath}`);
+    logger.error(`Could not load valueSet from path ${absoluteFilepath}`);
     throw error;
   }
 }
 
-function loadVS(filepath, typeOfVS = vsTypes.json) {
+function loadVs(absoluteFilepath, typeOfVS) {
   switch (typeOfVS) {
     case vsTypes.json:
-      logger.info(`loading JSON valueset from ${filepath}`);
-      return loadJsonVS(filepath);
+      logger.debug(`loading JSON valueset from ${absoluteFilepath}`);
+      return loadJsonVs(absoluteFilepath);
 
     case vsTypes.xml:
-      logger.error('No defined valueset loader for `xml` type valuesets');
-      return null;
+      throw Error('No defined valueset loader for `xml` type valuesets');
 
     case vsTypes.turtle:
-      logger.error('No defined valueset loader for `turtle` type valuesets');
-      return null;
+      throw Error('No defined valueset loader for `turtle` type valuesets');
 
     default:
-      logger.error(`'${typeOfVS}' is not a recognized valueset type`);
-      return null;
+      throw Error(`${typeOfVS}' is not a recognized valueset type`);
   }
 }
 
 /**
  * Check if code is in value set
- * @param {object} code value to look for in a valueset
+ * @param {string} 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);
+const checkCodeInVs = (code, valueSetFilePath, typeOfVS = vsTypes.json) => {
+  if (_.isUndefined(code)) throw Error('checkCodeInVs received a code of undefined');
+  const valueSet = loadVs(valueSetFilePath, typeOfVS);
   let inVSExpansion = false;
   let inVSCompose = false;
   if (valueSet.expansion) {
@@ -69,7 +67,7 @@ const checkCodeInVS = (code, valueSetFilePath, typeOfVS = vsTypes.json) => {
 
 module.exports = {
   vsTypes,
-  loadJsonVS,
-  loadVS,
-  checkCodeInVS,
+  loadJsonVs,
+  loadVs,
+  checkCodeInVs,
 };