Merge pull request #65 from mcode/generic-valueset-lookup

Generic valueSet lookup

Author: Dtphelan1

src/helpers/cancerStagingUtils.js

@@ -1,11 +1,9 @@
-const cancerStagingSystemVS = require('../valueSets/ValueSet-mcode-cancer-staging-system-vs.json');
-
-function checkCodeInVS(code, valueSet) {
-  return valueSet.compose.include[0].concept.map((c) => c.code).includes(code);
-}
+const path = require('path');
+const { checkCodeInVs } = require('./valueSetUtils');
 
 function isCancerStagingSystem(code) {
-  return checkCodeInVS(code, cancerStagingSystemVS);
+  const cancerStagingSystemVSPath = path.resolve(__dirname, 'valueSets', 'ValueSet-mcode-cancer-staging-system-vs.json');
+  return checkCodeInVs(code, cancerStagingSystemVSPath);
 }
 
 module.exports = {

src/helpers/conditionUtils.js

@@ -1,10 +1,6 @@
-const primaryCancerConditionVS = require('../valueSets/ValueSet-onco-core-PrimaryOrUncertainBehaviorCancerDisorderVS.json');
-const secondaryCancerConditionVS = require('../valueSets/ValueSet-onco-core-SecondaryCancerDisorderVS.json');
+const path = require('path');
+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 +24,8 @@ function getICD10Code(condition) {
  * @return {boolean} if primary cancer condition
  */
 function isConditionCodePrimary(code) {
-  return checkCodeInVS(code, primaryCancerConditionVS);
+  const primaryCancerConditionVSFilepath = path.resolve(__dirname, 'valueSets', 'ValueSet-mcode-primary-or-uncertain-behavior-cancer-disorder-vs.json');
+  return checkCodeInVs(code, primaryCancerConditionVSFilepath);
 }
 
 /**
@@ -37,7 +34,8 @@ function isConditionCodePrimary(code) {
  * @return {boolean} if secondary cancer condition
  */
 function isConditionCodeSecondary(code) {
-  return checkCodeInVS(code, secondaryCancerConditionVS);
+  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 tumorMarkerTestVS = require('../valueSets/ValueSet-mcode-tumor-marker-test-vs.json');
+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
@@ -17,12 +18,10 @@ 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 = path.resolve(__dirname, 'valueSets', 'ValueSet-mcode-tumor-marker-test-vs.json');
+  return checkCodeInVs(code, tumorMarkerTestVSPath);
 }
 
 function isVitalSign(code) {

src/helpers/valueSetUtils.js

@@ -0,0 +1,73 @@
+const fs = require('fs');
+const logger = require('./logger');
+
+const vsTypes = {
+  json: 1,
+  xml: 2,
+  turtle: 3,
+};
+
+function loadJsonVs(absoluteFilepath) {
+  try {
+    const vsData = fs.readFileSync(absoluteFilepath);
+    const vsJson = JSON.parse(vsData);
+    return vsJson;
+  } catch (error) {
+    logger.error(`Could not load valueSet from path ${absoluteFilepath}`);
+    throw error;
+  }
+}
+
+function loadVs(absoluteFilepath, typeOfVS) {
+  switch (typeOfVS) {
+    case vsTypes.json:
+      logger.debug(`loading JSON valueset from ${absoluteFilepath}`);
+      return loadJsonVs(absoluteFilepath);
+
+    case vsTypes.xml:
+      throw Error('No defined valueset loader for `xml` type valuesets');
+
+    case vsTypes.turtle:
+      throw Error('No defined valueset loader for `turtle` type valuesets');
+
+    default:
+      throw Error(`'${typeOfVS}' is not a recognized valueset type`);
+  }
+}
+
+/**
+ * Check if code is in value set
+ * @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);
+  let inVSExpansion = false;
+  let inVSCompose = false;
+  if (valueSet.expansion) {
+    // If valueSet has expansion, we only need to check these codes
+    inVSExpansion = valueSet.expansion.contains.some((containsItem) => {
+      if (!code || !containsItem) return false;
+      // NOTE: This is a technically incorrect interpretation of ValueSets;
+      //       this matching ought to check both code and system
+      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;
+      // NOTE: This is a technically incorrect interpretation of ValueSets;
+      //       this matching ought to check both code and system
+      return includeItem.concept.map((concept) => concept.code).includes(code);
+    });
+  }
+  return inVSCompose || inVSExpansion;
+};
+
+module.exports = {
+  vsTypes,
+  loadJsonVs,
+  loadVs,
+  checkCodeInVs,
+};