Merge pull request #153 from mcode/medication-stu2

CancerRelatedMedication STU2 Updates

Author: dmendelowitz

config/csv.config.example.json

@@ -56,10 +56,17 @@
       }
     },
     {
-      "label": "cancerRelatedMedication",
-      "type": "CSVCancerRelatedMedicationExtractor",
+      "label": "cancerRelatedMedicationAdministration",
+      "type": "CSVCancerRelatedMedicationAdministrationExtractor",
       "constructorArgs": {
-        "filePath": "./data/cancer-related-medication-information.csv"
+        "filePath": "./data/cancer-related-medication-administration-information.csv"
+      }
+    },
+    {
+      "label": "cancerRelatedMedicationRequest",
+      "type": "CSVCancerRelatedMedicationRequestExtractor",
+      "constructorArgs": {
+        "filePath": "./data/cancer-related-medication-request-information.csv"
       }
     },
     {

docs/CSV_Templates.xlsx

@@ -0,0 +1,3 @@
+mrn,requestId,code,codeSystem,displayText,treatmentReasonCode,treatmentReasonCodeSystem,treatmentReasonDisplayText,procedureIntent,status,intent,authoredOn,requesterId
+mrn-1,requestId-1,code,code-system,code-text,code,code-system,display-text,procedure-intent-code,status-code,intent-code,YYY-MM-DD,requesterId-1
+mrn-2,requestId-2,code,code-system,code-text,code,code-system,display-text,procedure-intent-code,status-code,intent-code,YYY-MM-DD,requesterId-2

docs/cancer-related-medication.csv renamed to docs/cancer-related-medication-administration.csv

@@ -2,7 +2,8 @@ const { BaseClient } = require('./BaseClient');
 const {
   CSVAdverseEventExtractor,
   CSVCancerDiseaseStatusExtractor,
-  CSVCancerRelatedMedicationExtractor,
+  CSVCancerRelatedMedicationAdministrationExtractor,
+  CSVCancerRelatedMedicationRequestExtractor,
   CSVClinicalTrialInformationExtractor,
   CSVConditionExtractor,
   CSVObservationExtractor,
@@ -30,7 +31,8 @@ class MCODEClient extends BaseClient {
     this.registerExtractors(
       CSVAdverseEventExtractor,
       CSVCancerDiseaseStatusExtractor,
-      CSVCancerRelatedMedicationExtractor,
+      CSVCancerRelatedMedicationAdministrationExtractor,
+      CSVCancerRelatedMedicationRequestExtractor,
       CSVClinicalTrialInformationExtractor,
       CSVConditionExtractor,
       CSVObservationExtractor,
@@ -60,7 +62,8 @@ class MCODEClient extends BaseClient {
       { type: 'CSVClinicalTrialInformationExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVTreatmentPlanChangeExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVStagingExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVCancerRelatedMedicationExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVCancerRelatedMedicationAdministrationExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVCancerRelatedMedicationRequestExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVProcedureExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVObservationExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },

docs/cancer-related-medication-request.csv

@@ -7,7 +7,7 @@ const logger = require('../helpers/logger');
 
 
 function formatData(medicationData, patientId) {
-  logger.debug('Reformatting cancer-related medication data from CSV into template format');
+  logger.debug('Reformatting cancer-related medication administration data from CSV into template format');
 
   return medicationData.map((medication) => {
     const {
@@ -25,7 +25,7 @@ function formatData(medicationData, patientId) {
     } = medication;
 
     if (!(code && codeSystem && status)) {
-      throw new Error('The cancer-related medication is missing an expected element; code, code system, and status are all required values.');
+      throw new Error('The cancer-related medication administration is missing an expected element; code, code system, and status are all required values.');
     }
 
     return {
@@ -45,20 +45,20 @@ function formatData(medicationData, patientId) {
   });
 }
 
-class CSVCancerRelatedMedicationExtractor extends BaseCSVExtractor {
+class CSVCancerRelatedMedicationAdministrationExtractor extends BaseCSVExtractor {
   constructor({ filePath, url }) {
     super({ filePath, url });
   }
 
   async getMedicationData(mrn) {
-    logger.debug('Getting Cancer Related Medication Data');
+    logger.debug('Getting Cancer Related Medication Administration Data');
     return this.csvModule.get('mrn', mrn);
   }
 
   async get({ mrn, context }) {
     const medicationData = await this.getMedicationData(mrn);
     if (medicationData.length === 0) {
-      logger.warn('No medication data found for patient');
+      logger.warn('No medication administration data found for patient');
       return getEmptyBundle();
     }
     const patientId = getPatientFromContext(context).id;
@@ -67,10 +67,10 @@ class CSVCancerRelatedMedicationExtractor extends BaseCSVExtractor {
     const formattedData = formatData(medicationData, patientId);
 
     // Fill templates
-    return generateMcodeResources('CancerRelatedMedication', formattedData);
+    return generateMcodeResources('CancerRelatedMedicationAdministration', formattedData);
   }
 }
 
 module.exports = {
-  CSVCancerRelatedMedicationExtractor,
+  CSVCancerRelatedMedicationAdministrationExtractor,
 };

src/client/MCODEClient.js

@@ -0,0 +1,78 @@
+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');
+
+
+function formatData(medicationData, patientId) {
+  logger.debug('Reformatting cancer-related medication request data from CSV into template format');
+
+  return medicationData.map((medication) => {
+    const {
+      requestid: requestId,
+      code,
+      codesystem: codeSystem,
+      displaytext: displayText,
+      treatmentreasoncode: treatmentReasonCode,
+      treatmentreasoncodesystem: treatmentReasonCodeSystem,
+      treatmentreasondisplaytext: treatmentReasonDisplayText,
+      procedureintent: procedureIntent,
+      status,
+      intent,
+      authoredon: authoredOn,
+      requesterid: requesterId,
+    } = medication;
+
+    if (!(code && codeSystem && status && intent && requesterId && authoredOn)) {
+      throw new Error('The cancer-related medication request is missing an expected element; code, code system, status, authoredOn, requesterId, and intent are all required values.');
+    }
+
+    return {
+      ...(requestId && { id: requestId }),
+      subjectId: patientId,
+      code,
+      codeSystem,
+      displayText,
+      treatmentReasonCode,
+      treatmentReasonCodeSystem,
+      treatmentReasonDisplayText,
+      procedureIntent,
+      status,
+      intent,
+      authoredOn: formatDateTime(authoredOn),
+      requesterId,
+    };
+  });
+}
+
+class CSVCancerRelatedMedicationRequestExtractor extends BaseCSVExtractor {
+  constructor({ filePath, url }) {
+    super({ filePath, url });
+  }
+
+  async getMedicationData(mrn) {
+    logger.debug('Getting Cancer Related Medication Request Data');
+    return this.csvModule.get('mrn', mrn);
+  }
+
+  async get({ mrn, context }) {
+    const medicationData = await this.getMedicationData(mrn);
+    if (medicationData.length === 0) {
+      logger.warn('No medication request data found for patient');
+      return getEmptyBundle();
+    }
+    const patientId = getPatientFromContext(context).id;
+
+    // Reformat data
+    const formattedData = formatData(medicationData, patientId);
+
+    // Fill templates
+    return generateMcodeResources('CancerRelatedMedicationRequest', formattedData);
+  }
+}
+
+module.exports = {
+  CSVCancerRelatedMedicationRequestExtractor,
+};

src/extractors/CSVCancerRelatedMedicationExtractor.js renamed to src/extractors/CSVCancerRelatedMedicationAdministrationExtractor.js

@@ -1,7 +1,8 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 const { CSVAdverseEventExtractor } = require('./CSVAdverseEventExtractor');
 const { CSVCancerDiseaseStatusExtractor } = require('./CSVCancerDiseaseStatusExtractor');
-const { CSVCancerRelatedMedicationExtractor } = require('./CSVCancerRelatedMedicationExtractor');
+const { CSVCancerRelatedMedicationAdministrationExtractor } = require('./CSVCancerRelatedMedicationAdministrationExtractor');
+const { CSVCancerRelatedMedicationRequestExtractor } = require('./CSVCancerRelatedMedicationRequestExtractor');
 const { CSVClinicalTrialInformationExtractor } = require('./CSVClinicalTrialInformationExtractor');
 const { CSVConditionExtractor } = require('./CSVConditionExtractor');
 const { CSVObservationExtractor } = require('./CSVObservationExtractor');
@@ -27,7 +28,8 @@ module.exports = {
   BaseFHIRExtractor,
   CSVAdverseEventExtractor,
   CSVCancerDiseaseStatusExtractor,
-  CSVCancerRelatedMedicationExtractor,
+  CSVCancerRelatedMedicationAdministrationExtractor,
+  CSVCancerRelatedMedicationRequestExtractor,
   CSVClinicalTrialInformationExtractor,
   CSVConditionExtractor,
   CSVObservationExtractor,

src/extractors/CSVCancerRelatedMedicationRequestExtractor.js

@@ -12,7 +12,8 @@ const {
   BaseFHIRExtractor,
   CSVAdverseEventExtractor,
   CSVCancerDiseaseStatusExtractor,
-  CSVCancerRelatedMedicationExtractor,
+  CSVCancerRelatedMedicationAdministrationExtractor,
+  CSVCancerRelatedMedicationRequestExtractor,
   CSVClinicalTrialInformationExtractor,
   CSVConditionExtractor,
   CSVObservationExtractor,
@@ -85,7 +86,8 @@ module.exports = {
   BaseFHIRModule,
   CSVAdverseEventExtractor,
   CSVCancerDiseaseStatusExtractor,
-  CSVCancerRelatedMedicationExtractor,
+  CSVCancerRelatedMedicationAdministrationExtractor,
+  CSVCancerRelatedMedicationRequestExtractor,
   CSVClinicalTrialInformationExtractor,
   CSVConditionExtractor,
   CSVFileModule,

src/extractors/index.js

@@ -1,9 +1,10 @@
 const {
-  coding,
   dataAbsentReasonExtension,
   extensionArr,
-  reference,
   valueX,
+  medicationTemplate,
+  subjectTemplate,
+  treatmentReasonTemplate,
 } = require('./snippets');
 const { ifAllArgsObj } = require('../helpers/templateUtils');
 
@@ -14,21 +15,6 @@ function treatmentIntentTemplate({ treatmentIntent }) {
   };
 }
 
-function medicationTemplate({ code, codeSystem, displayText }) {
-  return {
-    medicationCodeableConcept: {
-      coding: [coding({ system: codeSystem, code, display: displayText }),
-      ],
-    },
-  };
-}
-
-function subjectTemplate({ id }) {
-  return {
-    subject: reference({ id, resourceType: 'Patient' }),
-  };
-}
-
 function periodTemplate({ startDate, endDate }) {
   // If start and end date are not provided, indicate data absent with extension.
   if (!startDate && !endDate) {
@@ -45,19 +31,7 @@ function periodTemplate({ startDate, endDate }) {
   };
 }
 
-function treatmentReasonTemplate({ treatmentReasonCode, treatmentReasonCodeSystem, treatmentReasonDisplayText }) {
-  return {
-    reasonCode: [
-      {
-        coding: [coding({ system: treatmentReasonCodeSystem, code: treatmentReasonCode, display: treatmentReasonDisplayText }),
-        ],
-      },
-    ],
-  };
-}
-
-
-function cancerRelatedMedicationTemplate({
+function cancerRelatedMedicationAdministrationTemplate({
   subjectId,
   id,
   code,
@@ -72,15 +46,15 @@ function cancerRelatedMedicationTemplate({
   status,
 }) {
   if (!(subjectId && code && codeSystem && status)) {
-    throw Error('Trying to render a CancerRelatedMedicationTemplate, but a required argument is missing; ensure that subjectId, code, code system, and status are all present');
+    throw Error('Trying to render a CancerRelatedMedicationAdministrationTemplate, but a required argument is missing; ensure that subjectId, code, code system, and status are all present');
   }
 
   return {
-    resourceType: 'MedicationStatement',
+    resourceType: 'MedicationAdministration',
     id,
     meta: {
       profile: [
-        'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-related-medication-statement',
+        'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-related-medication-administration',
       ],
     },
     ...extensionArr(ifAllArgsObj(treatmentIntentTemplate)({ treatmentIntent })),
@@ -93,5 +67,5 @@ function cancerRelatedMedicationTemplate({
 }
 
 module.exports = {
-  cancerRelatedMedicationTemplate,
+  cancerRelatedMedicationAdministrationTemplate,
 };