Merge pull request #63 from mcode/staging-method

Staging method in the form of a `stagingSystem` property

Author: Dtphelan1

docs/CSV Templates 20200806.xlsx

@@ -1,2 +1,2 @@
-mrn,conditionId,stageGroup,t,n,m,type,effectiveDate
-mrn-1,example-condition-id,3C,cT3,cN3,cM0,Clinical,2020-01-01
+mrn,conditionId,stageGroup,t,n,m,type,stagingSystem,effectiveDate
+mrn-1,example-condition-id,3C,cT3,cN3,cM0,Clinical,443830009,2020-01-01

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, effectiveDate,
+    mrn, conditionId, t, n, m, type, stagingSystem, effectiveDate,
   } = stagingData;
 
   if (!mrn || !conditionId || !effectiveDate) {
@@ -22,6 +22,7 @@ function formatTNMCategoryData(stagingData) {
     conditionId,
     effectiveDateTime: formatDateTime(effectiveDate),
     stageType: type,
+    stagingSystem,
     subjectId: mrn,
   };
 
@@ -34,14 +35,15 @@ function formatTNMCategoryData(stagingData) {
 
 function formatStagingData(stagingData, categoryIds) {
   const {
-    mrn, conditionId, type, stageGroup, effectiveDate,
+    mrn, conditionId, type, stageGroup, stagingSystem, effectiveDate,
   } = stagingData;
 
   return {
     subjectId: mrn,
     conditionId,
     type,
     stageGroup,
+    stagingSystem,
     effectiveDateTime: formatDateTime(effectiveDate),
     categoryIds,
   };

src/extractors/CSVStagingExtractor.js

@@ -0,0 +1,13 @@
+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);
+}
+
+function isCancerStagingSystem(code) {
+  return checkCodeInVS(code, cancerStagingSystemVS);
+}
+
+module.exports = {
+  isCancerStagingSystem,
+};

src/helpers/cancerStagingUtils.js

@@ -1,4 +1,4 @@
-const { coding, reference, valueX } = require('./snippets');
+const { coding, reference, stagingMethodTemplate, valueX } = require('./snippets');
 
 // Returns staging specific data based whether it is clinical or pathologic
 function getTypeSpecificData(type) {
@@ -30,13 +30,14 @@ function hasMemberTemplate(categoryIds) {
 }
 
 function stagingTemplate({
+  categoryIds,
+  conditionId,
+  effectiveDateTime,
   id,
+  stageGroup,
+  stagingSystem,
   subjectId,
-  conditionId,
   type,
-  stageGroup,
-  effectiveDateTime,
-  categoryIds,
 }) {
   if (!(id && subjectId && conditionId && effectiveDateTime && stageGroup && type)) {
     throw Error('Trying to render a StagingTemplate, but a required argument is missing;'
@@ -72,6 +73,7 @@ function stagingTemplate({
         }),
       ],
     },
+    ...stagingMethodTemplate({ code: stagingSystem }),
     subject: reference({ id: subjectId }),
     effectiveDateTime,
     ...valueX({ code: stageGroup, system: 'http://cancerstaging.org' }, 'valueCodeableConcept'),

src/templates/StagingTemplate.js

@@ -1,4 +1,4 @@
-const { coding, reference, valueX } = require('./snippets');
+const { coding, reference, stagingMethodTemplate, valueX } = require('./snippets');
 
 // Returns category specific data based on stage and category type
 function getCategorySpecificData(stageType, categoryType) {
@@ -54,7 +54,14 @@ function getCategorySpecificData(stageType, categoryType) {
 }
 
 function tnmCategoryTemplate({
-  id, subjectId, conditionId, valueCode, effectiveDateTime, categoryType, stageType,
+  categoryType,
+  conditionId,
+  effectiveDateTime,
+  id,
+  stageType,
+  stagingSystem,
+  subjectId,
+  valueCode,
 }) {
   if (!(id && subjectId && conditionId && valueCode && effectiveDateTime && categoryType && stageType)) {
     throw Error('Trying to render a TNMCategoryTemplate, but a required argument is missing;'
@@ -91,6 +98,7 @@ function tnmCategoryTemplate({
       ],
     },
     subject: reference({ id: subjectId }),
+    ...stagingMethodTemplate({ code: stagingSystem }),
     effectiveDateTime,
     ...valueX({ code: valueCode, system: 'http://cancerstaging.org' }, 'valueCodeableConcept'),
     focus: [reference({ id: conditionId })],

src/templates/TNMCategoryTemplate.js

@@ -0,0 +1,39 @@
+const _ = require('lodash');
+const logger = require('../../helpers/logger');
+const { ifSomeArgsObj } = require('../../helpers/templateUtils');
+const { isCancerStagingSystem } = require('../../helpers/cancerStagingUtils');
+const { coding } = require('./coding');
+
+function methodTemplate({ code, system }) {
+  return ifSomeArgsObj(
+    ({ code: code_, system: system_ }) => ({
+      method: {
+        coding: [
+          coding({
+            ...(code_ && { code: code_ }),
+            ...(system_ && { system: system_ }),
+          }),
+        ],
+      },
+    }),
+  )({ code, system });
+}
+
+function stagingMethodTemplate({ code }) {
+  if (isCancerStagingSystem(code)) {
+    // NOTE: our general value set lookup should probably return the associate system, since it's available at the VS level
+    return methodTemplate({ code, system: 'http://snomed.info/sct' });
+  } if (code === 'C146985') {
+    // TODO: fix this HARDCODED special case as delineated by this VS's description http://hl7.org/fhir/us/mcode/ValueSet-mcode-cancer-staging-system-vs.html
+    // System based on http://hl7.org/fhir/us/mcode/Observation-mCODETNMClinicalPrimaryTumorCategoryExample01.json.html
+    return methodTemplate({ code, system: 'http://ncimeta.nci.nih.gov' });
+  }
+  if (!_.isNull(code)) {
+    logger.debug(`stagingMethodTemplate received a code ${code} that is not recognized; code will be added without a codeSystem if possible`);
+  }
+  return methodTemplate({ code });
+}
+
+module.exports = {
+  stagingMethodTemplate,
+};

src/templates/snippets/cancerStaging.js

@@ -6,6 +6,7 @@ const { extensionArr, dataAbsentReasonExtension } = require('./extension');
 const { effectiveX } = require('./effectiveX');
 const { identifier, identifierArr } = require('./identifier');
 const { bodySiteTemplate } = require('./bodySiteTemplate');
+const { stagingMethodTemplate } = require('./cancerStaging');
 
 module.exports = {
   bodySiteTemplate,
@@ -18,5 +19,6 @@ module.exports = {
   meta,
   narrative,
   reference,
+  stagingMethodTemplate,
   valueX,
 };

src/templates/snippets/index.js

@@ -0,0 +1,52 @@
+{
+  "resourceType": "ValueSet",
+  "id": "mcode-cancer-staging-system-vs",
+  "text": {
+    "status": "generated",
+    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><h2>Cancer Staging System Value Set</h2><div><p>System used for staging. If the staging system is AJCC Version 8, use the NCI thesaurus code C146985 (AJCC Cancer Staging Manual 8th Edition) in its place. This is because SNOMED does not have an equivalent concept for AJCC Version 8 at this time.</p>\n</div><ul><li>Include these codes as defined in <a href=\"http://www.snomed.org/\"><code>http://snomed.info/sct</code></a><table class=\"none\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td></tr><tr><td><a href=\"http://browser.ihtsdotools.org/?perspective=full&amp;conceptId1=444256004\">444256004</a></td><td>American Joint Commission on Cancer, Cancer Staging Manual, 6th edition neoplasm staging system (tumor staging)</td><td/></tr><tr><td><a href=\"http://browser.ihtsdotools.org/?perspective=full&amp;conceptId1=443830009\">443830009</a></td><td>American Joint Commission on Cancer, Cancer Staging Manual, 7th edition neoplasm staging system (tumor staging)</td><td/></tr><tr><td><a href=\"http://browser.ihtsdotools.org/?perspective=full&amp;conceptId1=258235000\">258235000</a></td><td>International Union Against Cancer (tumor staging)</td><td/></tr></table></li></ul></div>"
+  },
+  "url": "http://hl7.org/fhir/us/mcode/ValueSet/mcode-cancer-staging-system-vs",
+  "version": "1.0.0",
+  "name": "CancerStagingSystemVS",
+  "title": "Cancer Staging System Value Set",
+  "status": "active",
+  "date": "2020-03-18T16:05:09+00:00",
+  "publisher": "HL7 International Clinical Interoperability Council",
+  "contact": [
+    {
+      "name": "HL7 International Clinical Interoperability Council",
+      "telecom": [
+        {
+          "system": "url",
+          "value": "http://www.hl7.org/Special/committees/cic"
+        },
+        {
+          "system": "email",
+          "value": "ciclist@lists.HL7.org"
+        }
+      ]
+    }
+  ],
+  "description": "System used for staging. If the staging system is AJCC Version 8, use the NCI thesaurus code C146985 (AJCC Cancer Staging Manual 8th Edition) in its place. This is because SNOMED does not have an equivalent concept for AJCC Version 8 at this time.",
+  "compose": {
+    "include": [
+      {
+        "system": "http://snomed.info/sct",
+        "concept": [
+          {
+            "code": "444256004",
+            "display": "American Joint Commission on Cancer, Cancer Staging Manual, 6th edition neoplasm staging system (tumor staging)"
+          },
+          {
+            "code": "443830009",
+            "display": "American Joint Commission on Cancer, Cancer Staging Manual, 7th edition neoplasm staging system (tumor staging)"
+          },
+          {
+            "code": "258235000",
+            "display": "International Union Against Cancer (tumor staging)"
+          }
+        ]
+      }
+    ]
+  }
+}

src/valueSets/ValueSet-mcode-cancer-staging-system-vs.json

@@ -28,20 +28,22 @@ describe('CSVStagingExtractor', () => {
       // Test that valid data works fine
       expect(formatTNMCategoryData(localData)).toEqual(expect.anything());
 
-      // Test all optional properties can be removed without throwing errors
-      delete localData.t;
-      delete localData.m;
-      delete localData.n;
-      delete localData.type;
-      delete localData.stageGroup;
+      // Test all optional properties can be empty without issue
+      localData.t = '';
+      localData.m = '';
+      localData.n = '';
+      localData.type = '';
+      localData.stagingSystem = '';
+      localData.stageGroup = '';
 
       // Only including required properties is valid
       expect(formatTNMCategoryData(localData)).toEqual(expect.anything());
 
       // Removing each required property should throw an error
-      Object.keys(localData).forEach((key) => {
+      const requiredKeys = ['mrn', 'conditionId', 'effectiveDate'];
+      requiredKeys.forEach((key) => {
         const clonedData = _.cloneDeep(localData);
-        delete clonedData[key];
+        clonedData[key] = '';
         expect(() => formatTNMCategoryData(clonedData)).toThrow(new Error(expectedErrorString));
       });
     });