System checking added to checkCodeInVS, method system added for staging

Author: julianxcarter

docs/CSV Templates 20200806.xlsx

@@ -1,2 +1,2 @@
-mrn,conditionId,stageGroup,t,n,m,type,stagingSystem,effectiveDate
-mrn-1,example-condition-id,3C,cT3,cN3,cM0,Clinical,443830009,2020-01-01
+mrn,conditionId,stageGroup,t,n,m,type,stagingSystem,stagingCodeSystem,effectiveDate
+mrn-1,example-condition-id,3C,cT3,cN3,cM0,Clinical,443830009,'http://snomed.info/sct',2020-01-01

docs/staging.csv

@@ -10,7 +10,7 @@ function formatTNMCategoryData(stagingData) {
   logger.debug('Reformatting TNM Category data into template format');
   const formattedData = [];
   const {
-    mrn, conditionId, t, n, m, type, stagingSystem, effectiveDate,
+    mrn, conditionId, t, n, m, type, stagingSystem, stagingCodeSystem, effectiveDate,
   } = stagingData;
 
   if (!mrn || !conditionId || !effectiveDate) {
@@ -23,6 +23,7 @@ function formatTNMCategoryData(stagingData) {
     effectiveDateTime: formatDateTime(effectiveDate),
     stageType: type,
     stagingSystem,
+    stagingCodeSystem,
     subjectId: mrn,
   };
 
@@ -35,7 +36,7 @@ function formatTNMCategoryData(stagingData) {
 
 function formatStagingData(stagingData, categoryIds) {
   const {
-    mrn, conditionId, type, stageGroup, stagingSystem, effectiveDate,
+    mrn, conditionId, type, stageGroup, stagingSystem, stagingCodeSystem, effectiveDate,
   } = stagingData;
 
   return {
@@ -44,6 +45,7 @@ function formatStagingData(stagingData, categoryIds) {
     type,
     stageGroup,
     stagingSystem,
+    stagingCodeSystem,
     effectiveDateTime: formatDateTime(effectiveDate),
     categoryIds,
   };

src/extractors/CSVStagingExtractor.js

@@ -9,8 +9,7 @@ function getMCODESurgicalProcedures(fhirProcedures) {
   const surgicalProcedureVSFilepath = path.resolve(__dirname, '..', 'helpers', 'valueSets', 'ValueSet-mcode-cancer-related-surgical-procedure-vs.json');
   return fhirProcedures.filter((procedure) => {
     const coding = procedure.resource.code ? procedure.resource.code.coding : [];
-    // NOTE: Update when checkCodeInVS checks code and system (might be able to pass in the full Coding)
-    return coding.some((c) => checkCodeInVs(c.code, surgicalProcedureVSFilepath));
+    return coding.some((c) => checkCodeInVs(c.code, c.system, surgicalProcedureVSFilepath));
   });
 }
 

src/extractors/MCODESurgicalProcedureExtractor.js

@@ -1,9 +1,9 @@
 const path = require('path');
 const { checkCodeInVs } = require('./valueSetUtils');
 
-function isCancerStagingSystem(code) {
+function isCancerStagingSystem(code, system) {
   const cancerStagingSystemVSPath = path.resolve(__dirname, 'valueSets', 'ValueSet-mcode-cancer-staging-system-vs.json');
-  return checkCodeInVs(code, cancerStagingSystemVSPath);
+  return checkCodeInVs(code, system, cancerStagingSystemVSPath);
 }
 
 module.exports = {

src/helpers/cancerStagingUtils.js

@@ -20,22 +20,24 @@ function getICD10Code(condition) {
 
 /**
  * Checks if a condition code is a primary cancer condition
- * @param code ICD code, string
+ * @param {string} code ICD code
+ * @param {string} system Code system to which th code belongs
  * @return {boolean} if primary cancer condition
  */
-function isConditionCodePrimary(code) {
+function isConditionCodePrimary(code, system) {
   const primaryCancerConditionVSFilepath = path.resolve(__dirname, 'valueSets', 'ValueSet-mcode-primary-or-uncertain-behavior-cancer-disorder-vs.json');
-  return checkCodeInVs(code, primaryCancerConditionVSFilepath);
+  return checkCodeInVs(code, system, primaryCancerConditionVSFilepath);
 }
 
 /**
  * Checks if a condition code is a secondary cancer condition
- * @param code ICD code, string
+ * @param {string} code ICD code
+ * @param {string} system Code system to which th code belongs
  * @return {boolean} if secondary cancer condition
  */
-function isConditionCodeSecondary(code) {
+function isConditionCodeSecondary(code, system) {
   const secondaryCancerConditionVSFilepath = path.resolve(__dirname, 'valueSets', 'ValueSet-mcode-secondary-cancer-disorder-vs.json');
-  return checkCodeInVs(code, secondaryCancerConditionVSFilepath);
+  return checkCodeInVs(code, system, secondaryCancerConditionVSFilepath);
 }
 
 /**
@@ -45,7 +47,7 @@ function isConditionCodeSecondary(code) {
  */
 function isConditionPrimary(condition) {
   const icd10Code = getICD10Code(condition);
-  return icd10Code && isConditionCodePrimary(icd10Code.code);
+  return icd10Code && isConditionCodePrimary(icd10Code.code, icd10Code.system);
 }
 
 /**
@@ -55,16 +57,17 @@ function isConditionPrimary(condition) {
  */
 function isConditionSecondary(condition) {
   const icd10Code = getICD10Code(condition);
-  return icd10Code && isConditionCodeSecondary(icd10Code.code);
+  return icd10Code && isConditionCodeSecondary(icd10Code.code, icd10Code.system);
 }
 
 /**
  * Checks if a condition code is a cancer condition we recognize
- * @param code ICD code, string
+ * @param {string} code ICD code
+ * @param {string} system Code system to which th code belongs
  * @return {boolean} if primary or secondary cancer condition
  */
-function isConditionCodeCancer(code) {
-  return isConditionCodePrimary(code) || isConditionCodeSecondary(code);
+function isConditionCodeCancer(code, system) {
+  return isConditionCodePrimary(code, system) || isConditionCodeSecondary(code, system);
 }
 
 /**

src/helpers/conditionUtils.js

@@ -21,7 +21,7 @@ const vitalSignsCodeToTextLookup = {
 
 function isTumorMarker(code) {
   const tumorMarkerTestVSPath = path.resolve(__dirname, 'valueSets', 'ValueSet-mcode-tumor-marker-test-vs.json');
-  return checkCodeInVs(code, tumorMarkerTestVSPath);
+  return checkCodeInVs(code, 'http://loinc.org', tumorMarkerTestVSPath);
 }
 
 function isVitalSign(code) {

src/helpers/observationUtils.js

@@ -38,27 +38,31 @@ function loadVs(absoluteFilepath, typeOfVS) {
 /**
  * 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
+ * @param {string} codeSystem the system to which the code value belongs
+ * @param {string} valueSetFilePath the file path of the value set to be searched
+ * @param {string} typeOfVS the file type of the value set to be searched
  * @return {boolean} true if condition is in valueSet's compose block or expansion block
  */
-const checkCodeInVs = (code, valueSetFilePath, typeOfVS = vsTypes.json) => {
+const checkCodeInVs = (code, codeSystem, 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
+      if (containsItem.system) {
+        return code === containsItem.code && codeSystem === containsItem.codeSystem;
+      }
       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
+      if (includeItem.system) {
+        return includeItem.system === codeSystem && includeItem.concept.map((concept) => concept.code).includes(code);
+      }
       return includeItem.concept.map((concept) => concept.code).includes(code);
     });
   }

src/helpers/valueSetUtils.js

@@ -43,8 +43,9 @@ function individualCategoryTemplate(category) {
 
 function categoryArrayTemplate(array, code) {
   const category = array.map(individualCategoryTemplate);
-  const codeValue = `${code}`;
-  if (isConditionCodeCancer(codeValue)) {
+  const codeValue = `${code.code}`;
+  const codeSystem = `${code.system}`;
+  if (isConditionCodeCancer(codeValue, codeSystem)) {
     // On cancer conditions, include the fixed value for the disease category
     category.push({
       coding: [coding({
@@ -125,7 +126,7 @@ function conditionTemplate({
     ),
     ...ifAllArgsObj(clinicalStatusTemplate)({ clinicalStatus }),
     ...ifAllArgsObj(verificationStatusTemplate)({ verificationStatus }),
-    ...categoryArrayTemplate(category, code.code),
+    ...categoryArrayTemplate(category, code),
     ...codingTemplate({ code }),
     ...ifAllArgsObj(bodySiteTemplate)({ bodySite, laterality }),
     ...subjectTemplate({ subject }),

src/templates/ConditionTemplate.js

@@ -36,6 +36,7 @@ function stagingTemplate({
   id,
   stageGroup,
   stagingSystem,
+  stagingCodeSystem,
   subjectId,
   type,
 }) {
@@ -73,7 +74,7 @@ function stagingTemplate({
         }),
       ],
     },
-    ...stagingMethodTemplate({ code: stagingSystem }),
+    ...stagingMethodTemplate({ code: stagingSystem, system: stagingCodeSystem }),
     subject: reference({ id: subjectId }),
     effectiveDateTime,
     ...valueX({ code: stageGroup, system: 'http://cancerstaging.org' }, 'valueCodeableConcept'),