Adding Timing to Medication Request Extractor

mcode · Nov 21, 2023 · c18f75a · c18f75a
1 parent 939155f
commit c18f75a
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Showing 8 changed files with 64 additions and 9 deletions.
diff --git a/src/extractors/CSVCancerRelatedMedicationRequestExtractor.js b/src/extractors/CSVCancerRelatedMedicationRequestExtractor.js
@@ -2,6 +2,7 @@ const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { generateMcodeResources } = require('../templates');
 const { getPatientFromContext } = require('../helpers/contextUtils');
 const { getEmptyBundle } = require('../helpers/fhirUtils');
+const { formatDateTime } = require('../helpers/dateUtils');
 const logger = require('../helpers/logger');
 const { CSVCancerRelatedMedicationRequestSchema } = require('../helpers/schemas/csv');
 
@@ -28,6 +29,8 @@ function formatData(medicationData, patientId) {
       doseratetype: doseRateType,
       dosequantityvalue: doseQuantityValue,
       dosequantityunit: doseQuantityUnit,
+      timingcode: timingCode,
+      timingevent: timingEvent,
     } = medication;
 
     if (!(code && codeSystem && status && intent && requesterId)) {
@@ -53,6 +56,8 @@ function formatData(medicationData, patientId) {
       doseRateType,
       doseQuantityValue,
       doseQuantityUnit,
+      timingCode,
+      timingEvent: !timingEvent ? null : formatDateTime(timingEvent),
     };
   });
 }

diff --git a/src/helpers/schemas/csv.js b/src/helpers/schemas/csv.js
@@ -122,6 +122,8 @@ const CSVCancerRelatedMedicationRequestSchema = {
     { name: 'doseRateType' },
     { name: 'doseQuantityValue' },
     { name: 'doseQuantityUnit' },
+    { name: 'timingCode' },
+    { name: 'timingEvent' },
   ],
 };
 

diff --git a/src/templates/CancerRelatedMedicationRequestTemplate.js b/src/templates/CancerRelatedMedicationRequestTemplate.js
@@ -41,14 +41,24 @@ function doseAndRateTemplate({ doseRateType, doseQuantityValue, doseQuantityUnit
   };
 }
 
+function timingTemplate({ timingCode, timingEvent }) {
+  return {
+    timing: {
+      event: [timingEvent],
+      code: { coding: [coding({ code: timingCode, system: 'http://terminology.hl7.org/CodeSystem/v3-GTSAbbreviation' })] },
+    },
+  };
+}
+
 function dosageInstructionTemplate({
-  dosageRoute, asNeededCode, doseRateType, doseQuantityValue, doseQuantityUnit,
+  dosageRoute, asNeededCode, doseRateType, doseQuantityValue, doseQuantityUnit, timingCode, timingEvent,
 }) {
   return {
     dosageInstruction: [{
       route: { coding: [coding({ code: dosageRoute, system: 'http://snomed.info/sct' })] },
       asNeededCodeableConcept: { coding: [coding({ code: asNeededCode, system: 'http://snomed.info/sct' })] },
       ...ifSomeArgsObj(doseAndRateTemplate)({ doseRateType, doseQuantityValue, doseQuantityUnit }),
+      ...ifSomeArgsObj(timingTemplate)({ timingCode, timingEvent }),
     }],
   };
 }
@@ -72,6 +82,8 @@ function cancerRelatedMedicationRequestTemplate({
   doseRateType,
   doseQuantityValue,
   doseQuantityUnit,
+  timingCode,
+  timingEvent,
 }) {
   if (!(subjectId && code && codeSystem && status && intent && requesterId)) {
     const e1 = 'Trying to render a CancerRelatedMedicationRequestTemplate, but a required argument is missing; ';
@@ -91,7 +103,7 @@ function cancerRelatedMedicationRequestTemplate({
     status,
     intent,
     ...medicationTemplate({ code, codeSystem, displayText }),
-    ...ifSomeArgsObj(dosageInstructionTemplate)({ dosageRoute, asNeededCode, doseRateType, doseQuantityValue, doseQuantityUnit }),
+    ...ifSomeArgsObj(dosageInstructionTemplate)({ dosageRoute, asNeededCode, doseRateType, doseQuantityValue, doseQuantityUnit, timingCode, timingEvent }),
     ...ifAllArgsObj(subjectTemplate)({ id: subjectId }),
     ...(authoredOn && { authoredOn: formatDateTime(authoredOn) }),
     ...ifAllArgsObj(requesterTemplate)({ id: requesterId }),

diff --git a/test/extractors/fixtures/csv-medication-request-bundle.json b/test/extractors/fixtures/csv-medication-request-bundle.json
@@ -69,7 +69,20 @@
                   "unit": "example-unit"
                 }
               }
-            ]
+            ],
+            "timing": {
+              "event": [
+                "YYYY-MM-DD"
+              ],
+              "code": {
+                "coding": [
+                  {
+                    "system": "http://terminology.hl7.org/CodeSystem/v3-GTSAbbreviation",
+                    "code": "example-code"
+                  }
+                ]
+              }
+            }
           }
         ],
         "subject": {

diff --git a/test/extractors/fixtures/csv-medication-request-module-response.json b/test/extractors/fixtures/csv-medication-request-module-response.json
@@ -17,6 +17,8 @@
     "asneededcode": "example-asneeded",
     "doseratetype": "example-type",
     "dosequantityvalue": "111",
-    "dosequantityunit": "example-unit"
+    "dosequantityunit": "example-unit",
+    "timingevent": "YYYY-MM-DD",
+    "timingcode": "example-code"
   }
 ]
diff --git a/test/sample-client-data/cancer-related-medication-request-information.csv b/test/sample-client-data/cancer-related-medication-request-information.csv
@@ -1,4 +1,4 @@
-mrn,requestId,code,codeSystem,displayText,treatmentReasonCode,treatmentReasonCodeSystem,treatmentReasonDisplayText,procedureIntent,status,intent,authoredOn,requesterId,dosageRoute,asNeededCode,doseRateType,doseQuantityValue,doseQuantityUnit
-123,requestId-1,10760,http://www.nlm.nih.gov/research/umls/rxnorm,Triamcinolone Oral Paste,999000,http://snomed.info/sct,Mixed islet cell and exocrine adenocarcinoma,373808002,active,order,2020-01-01,requester-1,26643006,1152001,calculated,100,mg
-456,requestId-2,91318,http://www.nlm.nih.gov/research/umls/rxnorm,Coal Tar Topical Solution,915007,http://snomed.info/sct,Malignant melanoma in junctional nevus,373808002,on-hold,proposal,2019-02-02,requester-2,46713006,1140008,ordered,50,mg
-789,requestId-3,91833,http://www.nlm.nih.gov/research/umls/rxnorm,Vitamin K1 Injectable Solution [Aquamephyton],900006,http://snomed.info/sct,Mucin-producing adenocarcinoma,363676003,cancelled,plan,,requester-3,,,,,
+mrn,requestId,code,codeSystem,displayText,treatmentReasonCode,treatmentReasonCodeSystem,treatmentReasonDisplayText,procedureIntent,status,intent,authoredOn,requesterId,dosageRoute,asNeededCode,doseRateType,doseQuantityValue,doseQuantityUnit,timingCode,timingEvent
+123,requestId-1,10760,http://www.nlm.nih.gov/research/umls/rxnorm,Triamcinolone Oral Paste,999000,http://snomed.info/sct,Mixed islet cell and exocrine adenocarcinoma,373808002,active,order,2020-01-01,requester-1,26643006,1152001,calculated,100,mg,QD,2023-01-01
+456,requestId-2,91318,http://www.nlm.nih.gov/research/umls/rxnorm,Coal Tar Topical Solution,915007,http://snomed.info/sct,Malignant melanoma in junctional nevus,373808002,on-hold,proposal,2019-02-02,requester-2,46713006,1140008,ordered,50,mg,AM,2023-04-04
+789,requestId-3,91833,http://www.nlm.nih.gov/research/umls/rxnorm,Vitamin K1 Injectable Solution [Aquamephyton],900006,http://snomed.info/sct,Mucin-producing adenocarcinoma,363676003,cancelled,plan,,requester-3,,,,,,,
diff --git a/test/templates/fixtures/maximal-medication-request.json b/test/templates/fixtures/maximal-medication-request.json
@@ -63,7 +63,20 @@
             "unit": "example-unit"
           }
         }
-      ]
+      ],
+      "timing": {
+        "event": [
+          "2020-01-01"
+        ],
+        "code": {
+          "coding": [
+            {
+              "system": "http://terminology.hl7.org/CodeSystem/v3-GTSAbbreviation",
+              "code": "example-code"
+            }
+          ]
+        }
+      }
     }
   ],
   "subject": {

diff --git a/test/templates/medicationRequest.test.js b/test/templates/medicationRequest.test.js
@@ -23,6 +23,8 @@ const REQUEST_VALID_DATA = {
   doseRateType: 'example-type',
   doseQuantityValue: '111',
   doseQuantityUnit: 'example-unit',
+  timingEvent: '2020-01-01',
+  timingCode: 'example-code',
 };
 
 const REQUEST_MINIMAL_DATA = {
@@ -43,6 +45,8 @@ const REQUEST_MINIMAL_DATA = {
   doseRateType: null,
   doseQuantityValue: null,
   doseQuantityUnit: null,
+  timingEvent: null,
+  timingCode: null,
 };
 
 
@@ -65,6 +69,8 @@ const REQUEST_INVALID_DATA = {
   doseRateType: 'example-type',
   doseQuantityValue: '111',
   doseQuantityUnit: 'example-unit',
+  timingEvent: '2020-01-01',
+  timingCode: 'example-code',
 };
 
 describe('test Medication Request template', () => {
@@ -96,6 +102,8 @@ describe('test Medication Request template', () => {
       doseRateType: 'example-type',
       doseQuantityValue: '111',
       doseQuantityUnit: 'example-unit',
+      timingEvent: '2020-01-01',
+      timingCode: 'example-code',
     };
 
     const NECESSARY_DATA = {