Merge pull request #198 from mcode/appointment-extractor

Adding CSV Appointment Extractor

src/client/MCODEClient.js

@@ -1,6 +1,7 @@
 const { BaseClient } = require('./BaseClient');
 const {
   CSVAdverseEventExtractor,
+  CSVAppointmentExtractor,
   CSVCancerDiseaseStatusExtractor,
   CSVCancerRelatedMedicationAdministrationExtractor,
   CSVCancerRelatedMedicationRequestExtractor,
@@ -32,6 +33,7 @@ class MCODEClient extends BaseClient {
     super();
     this.registerExtractors(
       CSVAdverseEventExtractor,
+      CSVAppointmentExtractor,
       CSVCancerDiseaseStatusExtractor,
       CSVCancerRelatedMedicationAdministrationExtractor,
       CSVCancerRelatedMedicationRequestExtractor,
@@ -73,6 +75,7 @@ class MCODEClient extends BaseClient {
       { type: 'CSVAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVCTCAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVEncounterExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVAppointmentExtractor', dependencies: ['CSVPatientExtractor'] },
     ];
     // Sort extractors based on order and dependencies
     this.extractorConfig = sortExtractors(this.extractorConfig, dependencyInfo);

src/extractors/CSVAppointmentExtractor.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 { CSVAppointmentSchema } = require('../helpers/schemas/csv');
+const logger = require('../helpers/logger');
+
+// Formats data to be passed into template-friendly format
+function formatData(appointmentData, patientId) {
+  logger.debug('Reformatting appointment data from CSV into template format');
+  return appointmentData.map((data) => {
+    const {
+      appointmentid: appointmentId,
+      status,
+      servicecategory: serviceCategory,
+      servicetype: serviceType,
+      appointmenttype: appointmentType,
+      specialty,
+      start,
+      end,
+      cancelationcode: cancelationCode,
+      description,
+    } = data;
+
+    if (!(appointmentId && status)) {
+      throw Error('Missing required field for Appointment CSV Extraction: appointmentId or status');
+    }
+
+    return {
+      ...(appointmentId && { id: appointmentId }),
+      patientParticipant: {
+        id: patientId,
+      },
+      status,
+      serviceCategory,
+      serviceType,
+      appointmentType,
+      specialty,
+      start: !start ? null : formatDateTime(start),
+      end: !end ? null : formatDateTime(end),
+      cancelationCode,
+      description,
+    };
+  });
+}
+
+class CSVAppointmentExtractor extends BaseCSVExtractor {
+  constructor({
+    filePath, url, fileName, dataDirectory, csvParse,
+  }) {
+    super({ filePath, url, fileName, dataDirectory, csvSchema: CSVAppointmentSchema, csvParse });
+  }
+
+  async getAppointmentData(mrn) {
+    logger.debug('Getting Appointment Data');
+    return this.csvModule.get('mrn', mrn);
+  }
+
+  async get({ mrn, context }) {
+    const appointmentData = await this.getAppointmentData(mrn);
+    if (appointmentData.length === 0) {
+      logger.warn('No appointment data found for patient');
+      return getEmptyBundle();
+    }
+    const patientId = getPatientFromContext(context).id;
+
+    // Reformat data
+    const formattedData = formatData(appointmentData, patientId);
+
+    // Fill templates
+    return generateMcodeResources('Appointment', formattedData);
+  }
+}
+
+module.exports = {
+  CSVAppointmentExtractor,
+};

src/extractors/index.js

@@ -1,6 +1,7 @@
 const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 const { CSVAdverseEventExtractor } = require('./CSVAdverseEventExtractor');
+const { CSVAppointmentExtractor } = require('./CSVAppointmentExtractor');
 const { CSVCancerDiseaseStatusExtractor } = require('./CSVCancerDiseaseStatusExtractor');
 const { CSVCancerRelatedMedicationAdministrationExtractor } = require('./CSVCancerRelatedMedicationAdministrationExtractor');
 const { CSVCancerRelatedMedicationRequestExtractor } = require('./CSVCancerRelatedMedicationRequestExtractor');
@@ -31,6 +32,7 @@ module.exports = {
   BaseCSVExtractor,
   BaseFHIRExtractor,
   CSVAdverseEventExtractor,
+  CSVAppointmentExtractor,
   CSVCancerDiseaseStatusExtractor,
   CSVCancerRelatedMedicationAdministrationExtractor,
   CSVCancerRelatedMedicationRequestExtractor,

src/helpers/schemas/csv.js

@@ -221,6 +221,22 @@ const CSVEncounterSchema = {
   ],
 };
 
+const CSVAppointmentSchema = {
+  headers: [
+    { name: 'mrn', required: true },
+    { name: 'appointmentId', required: true },
+    { name: 'status', required: true },
+    { name: 'serviceCategory' },
+    { name: 'serviceType' },
+    { name: 'appointmentType' },
+    { name: 'specialty' },
+    { name: 'start' },
+    { name: 'end' },
+    { name: 'cancelationCode' },
+    { name: 'description' },
+  ],
+};
+
 module.exports = {
   CSVCancerDiseaseStatusSchema,
   CSVConditionSchema,
@@ -235,4 +251,5 @@ module.exports = {
   CSVAdverseEventSchema,
   CSVCTCAdverseEventSchema,
   CSVEncounterSchema,
+  CSVAppointmentSchema,
 };

src/index.js

@@ -11,6 +11,7 @@ const {
 const {
   BaseFHIRExtractor,
   CSVAdverseEventExtractor,
+  CSVAppointmentExtractor,
   CSVCancerDiseaseStatusExtractor,
   CSVCancerRelatedMedicationAdministrationExtractor,
   CSVCancerRelatedMedicationRequestExtractor,
@@ -95,6 +96,7 @@ module.exports = {
   BaseFHIRExtractor,
   BaseFHIRModule,
   CSVAdverseEventExtractor,
+  CSVAppointmentExtractor,
   CSVCancerDiseaseStatusExtractor,
   CSVCancerRelatedMedicationAdministrationExtractor,
   CSVCancerRelatedMedicationRequestExtractor,

src/templates/AppointmentTemplate.js

@@ -0,0 +1,82 @@
+const { ifAllArgsObj } = require('../helpers/templateUtils');
+const { reference, coding } = require('./snippets');
+
+function patientParticipantTemplate({ patientParticipant }) {
+  return {
+    participant: [
+      {
+        actor: reference({ ...patientParticipant, resourceType: 'Patient' }),
+        status: 'tentative',
+      },
+    ],
+  };
+}
+
+function cancelationReasonTemplate({ cancelationCode }) {
+  return {
+    cancelationReason: {
+      coding: [coding({ code: cancelationCode, system: 'http://terminology.hl7.org/CodeSystem/appointment-cancellation-reason' })],
+    },
+  };
+}
+
+function serviceCategoryTemplate({ serviceCategory }) {
+  return {
+    serviceCategory: [{
+      coding: [coding({ code: serviceCategory, system: 'http://terminology.hl7.org/CodeSystem/service-category' })],
+    }],
+  };
+}
+
+function serviceTypeTemplate({ serviceType }) {
+  return {
+    serviceType: [{
+      coding: [coding({ code: serviceType, system: 'http://terminology.hl7.org/CodeSystem/service-type' })],
+    }],
+  };
+}
+
+
+function appointmentTypeTemplate({ appointmentType }) {
+  return {
+    appointmentType: {
+      coding: [coding({ code: appointmentType, system: 'http://terminology.hl7.org/CodeSystem/v2-0276' })],
+    },
+  };
+}
+
+function specialtyTemplate({ specialty }) {
+  return {
+    specialty: [{
+      coding: [coding({ code: specialty, system: 'http://snomed.info/sct' })],
+    }],
+  };
+}
+
+
+function appointmentTemplate({
+  id, patientParticipant, status, serviceCategory, serviceType, appointmentType, specialty, start, end, cancelationCode, description,
+}) {
+  if (!(id && status)) {
+    throw Error('Trying to render an AppointmentTemplate, but a required argument is missing; ensure that id and status are all present');
+  }
+
+  return {
+    resourceType: 'Appointment',
+    id,
+    status,
+    ...ifAllArgsObj(serviceCategoryTemplate)({ serviceCategory }),
+    ...ifAllArgsObj(serviceTypeTemplate)({ serviceType }),
+    ...ifAllArgsObj(appointmentTypeTemplate)({ appointmentType }),
+    ...ifAllArgsObj(specialtyTemplate)({ specialty }),
+    ...patientParticipantTemplate({ patientParticipant }),
+    ...(start && { start }),
+    ...(end && { end }),
+    ...ifAllArgsObj(cancelationReasonTemplate)({ cancelationCode }),
+    ...(description && { description }),
+  };
+}
+
+module.exports = {
+  appointmentTemplate,
+};

src/templates/ResourceGenerator.js

@@ -3,6 +3,7 @@ const crypto = require('crypto');
 const logger = require('../helpers/logger');
 
 const { adverseEventTemplate } = require('./AdverseEventTemplate');
+const { appointmentTemplate } = require('./AppointmentTemplate');
 const { cancerDiseaseStatusTemplate } = require('./CancerDiseaseStatusTemplate');
 const { cancerRelatedMedicationAdministrationTemplate } = require('./CancerRelatedMedicationAdministrationTemplate');
 const { cancerRelatedMedicationRequestTemplate } = require('./CancerRelatedMedicationRequestTemplate');
@@ -20,6 +21,7 @@ const { encounterTemplate } = require('./EncounterTemplate');
 
 const fhirTemplateLookup = {
   AdverseEvent: adverseEventTemplate,
+  Appointment: appointmentTemplate,
   CancerDiseaseStatus: cancerDiseaseStatusTemplate,
   CancerRelatedMedicationAdministration: cancerRelatedMedicationAdministrationTemplate,
   CancerRelatedMedicationRequest: cancerRelatedMedicationRequestTemplate,

test/extractors/CSVAppointmentExtractor.test.js

@@ -0,0 +1,80 @@
+const path = require('path');
+const rewire = require('rewire');
+const _ = require('lodash');
+const { CSVAppointmentExtractor } = require('../../src/extractors');
+const exampleCSVAppointmentModuleResponse = require('./fixtures/csv-appointment-module-response.json');
+const exampleCSVAppointmentBundle = require('./fixtures/csv-appointment-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
+
+// Constants for tests
+const MOCK_PATIENT_MRN = 'mrn-1'; // linked to values in example-module-response and context-with-patient above
+const MOCK_CSV_PATH = path.join(__dirname, 'fixtures/example.csv'); // need a valid path/csv here to avoid parse error
+const IMPLEMENTATION = 'mcode';
+
+// Rewired extractor for helper tests
+const CSVAppointmentExtractorRewired = rewire('../../src/extractors/CSVAppointmentExtractor.js');
+
+const formatData = CSVAppointmentExtractorRewired.__get__('formatData');
+
+// Instantiate module with parameters
+const csvAppointmentExtractor = new CSVAppointmentExtractor({
+  filePath: MOCK_CSV_PATH,
+  implementation: IMPLEMENTATION,
+});
+
+// Destructure all modules
+const { csvModule } = csvAppointmentExtractor;
+
+// Spy on csvModule
+const csvModuleSpy = jest.spyOn(csvModule, 'get');
+
+
+describe('CSVAppointmentExtractor', () => {
+  describe('formatData', () => {
+    test('should format data appropriately and throw errors when missing required properties', () => {
+      const expectedErrorString = 'Missing required field for Appointment CSV Extraction: appointmentId or status';
+      const localData = _.cloneDeep(exampleCSVAppointmentModuleResponse);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
+
+      // Test that valid data works fine
+      expect(formatData(exampleCSVAppointmentModuleResponse, patientId)).toEqual(expect.anything());
+
+      localData[0].start = '';
+      localData[0].cancelationcode = '';
+
+      // Only including required properties is valid
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
+
+      const requiredProperties = ['appointmentid', 'status'];
+
+      // Removing each required property should throw an error
+      requiredProperties.forEach((key) => {
+        const clonedData = _.cloneDeep(localData);
+        clonedData[0][key] = '';
+        expect(() => formatData(clonedData, patientId)).toThrow(new Error(expectedErrorString));
+      });
+    });
+  });
+
+  describe('get', () => {
+    test('should return bundle with Appointment', async () => {
+      csvModuleSpy.mockReturnValue(exampleCSVAppointmentModuleResponse);
+      const data = await csvAppointmentExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
+      expect(data.resourceType).toEqual('Bundle');
+      expect(data.type).toEqual('collection');
+      expect(data.entry).toBeDefined();
+      expect(data.entry.length).toEqual(1);
+      expect(data.entry).toEqual(exampleCSVAppointmentBundle.entry);
+    });
+
+    test('should return empty bundle when no data available from module', async () => {
+      csvModuleSpy.mockReturnValue([]);
+      const data = await csvAppointmentExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
+      expect(data.resourceType).toEqual('Bundle');
+      expect(data.type).toEqual('collection');
+      expect(data.entry).toBeDefined();
+      expect(data.entry.length).toEqual(0);
+    });
+  });
+});