Merge pull request #75 from mcode/careplan-extensions

Dtphelan1 · web-flow · commit 264c42e60518 · 2021-01-22T11:20:19.000-05:00
Update careplan to create multiple extensions
diff --git a/src/extractors/CSVTreatmentPlanChangeExtractor.js b/src/extractors/CSVTreatmentPlanChangeExtractor.js
@@ -1,16 +1,30 @@
 const path = require('path');
+const _ = require('lodash');
 const { Extractor } = require('./Extractor');
 const { CSVModule } = require('../modules');
-const { formatDate, formatDateTime } = require('../helpers/dateUtils');
+const { formatDate } = require('../helpers/dateUtils');
 const { generateMcodeResources } = require('../templates');
 const { getEmptyBundle } = require('../helpers/fhirUtils');
 const logger = require('../helpers/logger');
 
 // Formats data to be passed into template-friendly format
 function formatData(tpcData) {
-  logger.debug('Reformatting disease status data from CSV into template format');
-  return tpcData.map((data) => {
-    const { mrn, dateOfCarePlan, changed, reasonCode } = data;
+  logger.debug('Reformatting treatment plan change data from CSV into template format');
+
+  // Nothing to format in empty array
+  if (_.isEmpty(tpcData)) {
+    return [];
+  }
+
+  // Newly combined data has mrn and list of reviews to map to an extension
+  const combinedFormat = { mrn: tpcData[0].mrn, reviews: [] };
+
+  // If there are multiple entries, combine them into one object with multiple reviews
+  const combinedData = _.reduce(tpcData, (res, currentDataEntry) => {
+    const {
+      mrn, dateOfCarePlan, changed, reasonCode, reasonDisplayText,
+    } = currentDataEntry;
+
     if (!mrn || !dateOfCarePlan || !changed) {
       throw new Error('Treatment Plan Change Data missing an expected property: mrn, dateOfCarePlan, changed are required');
     }
@@ -20,20 +34,38 @@ function formatData(tpcData) {
       throw new Error('reasonCode is required when changed flag is true');
     }
 
+    res.reviews.push({
+      dateOfCarePlan,
+      reasonCode,
+      reasonDisplayText,
+      changed,
+    });
+    return res;
+  }, combinedFormat);
+
+  // Format each entry in the reviews array
+  combinedData.reviews = combinedData.reviews.map((review) => {
+    const { dateOfCarePlan, changed, reasonCode, reasonDisplayText } = review;
+
     const formattedData = {
       effectiveDate: formatDate(dateOfCarePlan),
-      effectiveDateTime: formatDateTime(dateOfCarePlan),
       hasChanged: changed,
-      mrn,
     };
 
     // Add reasonCode to formattedData if available
     if (reasonCode) {
       formattedData.reasonCode = reasonCode;
+
+      if (reasonDisplayText) {
+        formattedData.reasonDisplayText = reasonDisplayText;
+      }
     }
 
     return formattedData;
   });
+
+  // Array will contain one element to generate one FHIR resource with multiple extensions for reviews
+  return [combinedData];
 }
 
 class CSVTreatmentPlanChangeExtractor extends Extractor {
diff --git a/src/templates/CarePlanWithReviewTemplate.js b/src/templates/CarePlanWithReviewTemplate.js
@@ -1,7 +1,6 @@
 const {
   coding, extensionArr, meta, narrative, reference, valueX,
 } = require('./snippets');
-const { ifAllArgs } = require('../helpers/templateUtils');
 
 function metaTemplate() {
   return {
@@ -17,12 +16,6 @@ function textTemplate() {
   };
 }
 
-function createdTemplate({ effectiveDateTime }) {
-  return {
-    created: effectiveDateTime,
-  };
-}
-
 // R4 change reasons valueset: http://standardhealthrecord.org/guides/icare/ValueSet-icare-care-plan-change-reason-vs.html
 function carePlanReasonTemplate({ reasonCode, reasonDisplayText }) {
   return {
@@ -37,6 +30,12 @@ function carePlanReasonTemplate({ reasonCode, reasonDisplayText }) {
 }
 
 function carePlanChangeReasonExtensionTemplate({ hasChanged, reasonCode, reasonDisplayText, effectiveDate }) {
+  if (hasChanged === undefined || !effectiveDate) {
+    const errorMessage = 'Trying to render a CarePlanWithReviewTemplate, but a review was missing required fields; '
+      + 'ensure that hasChanged and effectiveDate are present on all reviews';
+    throw new Error(errorMessage);
+  }
+
   let hasChangedBoolean = hasChanged;
   if (hasChanged === 'true') {
     hasChangedBoolean = true;
@@ -83,12 +82,10 @@ function categoryTemplate() {
 // Treatment Plan Change modeled with CarePlanWithReview Template
 // Uses the ICARE R4 Care Plan profile which is not published yet
 // For reference, ICARE R4 Care Plan profile: http://standardhealthrecord.org/guides/icare/StructureDefinition-icare-care-plan-with-review.html
-function carePlanWithReviewTemplate({
-  id, mrn, name, effectiveDate, effectiveDateTime, hasChanged, reasonCode, reasonDisplayText,
-}) {
-  if (!(id && mrn && effectiveDate && hasChanged != null)) {
+function carePlanWithReviewTemplate({ id, mrn, name, reviews }) {
+  if (!(id && mrn && reviews)) {
     const errorMessage = 'Trying to render a CarePlanWithReviewTemplate, but a required argument was missing; '
-      + 'ensure that id, mrn, effectiveDate, hasChanged are all present';
+      + 'ensure that id, mrn, reviews are all present';
     throw new Error(errorMessage);
   }
   return {
@@ -97,12 +94,11 @@ function carePlanWithReviewTemplate({
     ...metaTemplate(),
     ...textTemplate(),
     ...extensionArr(
-      carePlanChangeReasonExtensionTemplate({ hasChanged, reasonCode, reasonDisplayText, effectiveDate }),
+      ...reviews.map(carePlanChangeReasonExtensionTemplate),
     ),
     ...subjectTemplate({ id: mrn, name }),
     status: 'draft',
     intent: 'proposal',
-    ...ifAllArgs(createdTemplate)({ effectiveDateTime }),
     ...categoryTemplate(),
   };
 }
diff --git a/test/extractors/CSVTreatmentPlanChangeExtractor.test.js b/test/extractors/CSVTreatmentPlanChangeExtractor.test.js
@@ -26,6 +26,12 @@ describe('CSVTreatmentPlanChangeExtractor', () => {
         changed: 'false',
         mrn: 'id',
       },
+      {
+        dateOfCarePlan: '2020-04-30',
+        changed: 'true',
+        reasonCode: 'example code',
+        mrn: 'id',
+      },
     ];
 
     test('should join data appropriately and throw errors when missing required properties', () => {
@@ -54,6 +60,29 @@ describe('CSVTreatmentPlanChangeExtractor', () => {
       exampleData[0].reasonCode = 'example code';
       expect(() => formatData(exampleData)).not.toThrowError();
     });
+
+    test('should join multiple entries into one', () => {
+      const expectedFormattedData = [
+        {
+          mrn: 'mrn-1',
+          reviews: [
+            {
+              effectiveDate: '2020-04-15',
+              hasChanged: 'true',
+              reasonCode: '281647001',
+              reasonDisplayText: 'Adverse reaction (disorder)',
+            },
+            {
+              effectiveDate: '2020-04-30',
+              reasonCode: '405613005',
+              hasChanged: 'true',
+            },
+          ],
+        },
+      ];
+
+      expect(formatData(exampleCSVTPCModuleResponse)).toEqual(expectedFormattedData);
+    });
   });
 
   describe('get', () => {
diff --git a/test/extractors/fixtures/csv-treatment-plan-change-bundle.json b/test/extractors/fixtures/csv-treatment-plan-change-bundle.json
@@ -3,10 +3,10 @@
   "type": "collection",
   "entry": [
     {
-      "fullUrl": "urn:uuid:4d2afb8f74b6950922b0ae5979edbcaf59cecf959ddf80cce63940b45597a29c",
+      "fullUrl": "urn:uuid:3005b559bb913fdfb23756a442645c6c37bbdafa42ad4be0bd1a6b698274f466",
       "resource": {
         "resourceType": "CarePlan",
-        "id": "4d2afb8f74b6950922b0ae5979edbcaf59cecf959ddf80cce63940b45597a29c",
+        "id": "3005b559bb913fdfb23756a442645c6c37bbdafa42ad4be0bd1a6b698274f466",
         "meta": {
           "profile": [
             "http://mcodeinitiative.org/codex/us/icare/StructureDefinition/icare-care-plan-with-review"
@@ -24,19 +24,34 @@
                 "url": "CarePlanChangeReason",
                 "valueCodeableConcept": {
                   "coding": [
-                    { "system": "http://snomed.info/sct", "code": "281647001" }
-                  ]
+                    { "system": "http://snomed.info/sct", "code": "281647001", "display": "Adverse reaction (disorder)" }
+                  ],
+                  "text": "Adverse reaction (disorder)"
                 }
               },
               { "url": "ReviewDate", "valueDate": "2020-04-15" },
               { "url": "ChangedFlag", "valueBoolean": true }
             ]
+          },
+          {
+            "url": "http://mcodeinitiative.org/codex/us/icare/StructureDefinition/icare-care-plan-review",
+            "extension": [
+              {
+                "url": "CarePlanChangeReason",
+                "valueCodeableConcept": {
+                  "coding": [
+                    { "system": "http://snomed.info/sct", "code": "405613005" }
+                  ]
+                }
+              },
+              { "url": "ReviewDate", "valueDate": "2020-04-30" },
+              { "url": "ChangedFlag", "valueBoolean": true }
+            ]
           }
         ],
         "subject": { "reference": "urn:uuid:mrn-1" },
         "status": "draft",
         "intent": "proposal",
-        "created": "2020-04-15",
         "category": [
           {
             "coding": [
diff --git a/test/extractors/fixtures/csv-treatment-plan-change-module-response.json b/test/extractors/fixtures/csv-treatment-plan-change-module-response.json
@@ -3,6 +3,13 @@
     "mrn": "mrn-1",
     "dateOfCarePlan": "2020-04-15",
     "reasonCode": "281647001",
+    "reasonDisplayText": "Adverse reaction (disorder)",
+    "changed": "true"
+  },
+  {
+    "mrn": "mrn-1",
+    "dateOfCarePlan": "2020-04-30",
+    "reasonCode": "405613005",
     "changed": "true"
   }
 ]
diff --git a/test/templates/carePlanWithReview.test.js b/test/templates/carePlanWithReview.test.js
@@ -8,13 +8,16 @@ describe('JavaScript render CarePlan template', () => {
   test('minimal required data passed into template should generate FHIR resource', () => {
     const CARE_PLAN_VALID_DATA = {
       id: 'test-id',
-      effectiveDateTime: '2020-01-23T09:07:00Z',
-      effectiveDate: '2020-01-23',
-      hasChanged: 'false',
       mrn: 'abc-def',
-      reasonCode: null,
-      reasonDisplayText: null,
       name: null,
+      reviews: [
+        {
+          effectiveDate: '2020-01-23',
+          hasChanged: 'false',
+          reasonCode: null,
+          reasonDisplayText: null,
+        },
+      ],
     };
 
     const generatedCarePlan = carePlanWithReviewTemplate(CARE_PLAN_VALID_DATA);
@@ -25,48 +28,86 @@ describe('JavaScript render CarePlan template', () => {
   test('maximal data passed into template should generate FHIR resource', () => {
     const MAX_CARE_PLAN_DATA = {
       id: 'test-id',
-      effectiveDateTime: '2020-01-23T09:07:00Z',
-      effectiveDate: '2020-01-23',
-      hasChanged: 'true',
-      reasonCode: '281647001',
-      reasonDisplayText: 'Adverse reaction (disorder)',
       mrn: 'abc-def',
       name: 'Sample Text',
+      reviews: [
+        {
+          effectiveDate: '2020-01-23',
+          hasChanged: 'true',
+          reasonCode: '281647001',
+          reasonDisplayText: 'Adverse reaction (disorder)',
+        },
+        {
+          effectiveDate: '2020-01-30',
+          hasChanged: 'true',
+          reasonCode: '405613005',
+          reasonDisplayText: 'Planned Procedure (situation)',
+        },
+      ],
     };
 
     const generatedCarePlan = carePlanWithReviewTemplate(MAX_CARE_PLAN_DATA);
     expect(generatedCarePlan).toEqual(maximalCarePlan);
     expect(isValidFHIR(generatedCarePlan)).toBeTruthy();
   });
 
-  test('missing non-required data should not throw an error', () => {
+  test('missing non-required data at care plan object level should not throw an error', () => {
     const NECESSARY_DATA = {
       id: 'test-id',
-      effectiveDateTime: '2020-01-23T09:07:00Z',
-      effectiveDate: '2020-01-23',
-      hasChanged: 'false',
       mrn: 'abc-def',
+      reviews: [],
     };
 
     const OPTIONAL_DATA = {
-      reasonCode: '281647001',
-      reasonDisplayText: 'Adverse reaction (disorder)',
       name: 'Sample Text',
     };
 
     allOptionalKeyCombinationsNotThrow(OPTIONAL_DATA, carePlanWithReviewTemplate, NECESSARY_DATA);
   });
 
+  test('missing non-required data at review object level should not throw an error', () => {
+    const NECESSARY_DATA = {
+      id: 'test-id',
+      mrn: 'abc-def',
+      reviews: [
+        {
+          effectiveDate: '2020-01-23',
+          hasChanged: 'false',
+        },
+      ],
+    };
+
+    const OPTIONAL_DATA = ['reasonCode', 'reasonDisplayText'];
+
+    // Test presence of each optional key individually
+    OPTIONAL_DATA.forEach((key) => {
+      const r = NECESSARY_DATA.reviews[0];
+      r[key] = 'sample value';
+
+      expect(() => carePlanWithReviewTemplate(NECESSARY_DATA)).not.toThrow();
+
+      delete r[key];
+    });
+  });
+
   test('missing required data should throw a reference error', () => {
     const INVALID_DATA = {
-      // Omitting 'hasChanged' field which is a required property
+      // omitting 'mrn' field which is a required property
+      id: 'test-id',
+      reviews: [],
+    };
+
+    const INVALID_REVIEW_DATA = {
+      // Omitting 'hasChanged' field on the review which is a required property
       id: 'test-id',
-      effectiveDateTime: '2020-01-23T09:07:00Z',
-      effectiveDate: '2020-01-23',
       mrn: 'abc-def',
-      haschanged: null,
+      reviews: [{
+        effectiveDate: '2020-01-23',
+        haschanged: null,
+      }],
     };
 
     expect(() => carePlanWithReviewTemplate(INVALID_DATA)).toThrow(Error);
+    expect(() => carePlanWithReviewTemplate(INVALID_REVIEW_DATA)).toThrow(Error);
   });
 });
diff --git a/test/templates/fixtures/maximal-careplan-resource.json b/test/templates/fixtures/maximal-careplan-resource.json
diff --git a/test/templates/fixtures/minimal-careplan-resource.json b/test/templates/fixtures/minimal-careplan-resource.json

Original file line number	Diff line number	Diff line change
`@@ -3,6 +3,13 @@`
`3`	`3`	`"mrn": "mrn-1",`
`4`	`4`	`"dateOfCarePlan": "2020-04-15",`
`5`	`5`	`"reasonCode": "281647001",`
	`6`	`+ "reasonDisplayText": "Adverse reaction (disorder)",`
	`7`	`+ "changed": "true"`
	`8`	`+ },`
	`9`	`+ {`
	`10`	`+ "mrn": "mrn-1",`
	`11`	`+ "dateOfCarePlan": "2020-04-30",`
	`12`	`+ "reasonCode": "405613005",`
`6`	`13`	`"changed": "true"`
`7`	`14`	`}`
`8`	`15`	`]`