Core functionality for adverse events CSV extractor

Author: mickohanlon23

src/client/MCODEClient.js

@@ -1,5 +1,6 @@
 const { BaseClient } = require('./BaseClient');
 const {
+  CSVAdverseEventExtractor,
   CSVCancerDiseaseStatusExtractor,
   CSVCancerRelatedMedicationExtractor,
   CSVClinicalTrialInformationExtractor,
@@ -25,6 +26,7 @@ class MCODEClient extends BaseClient {
   constructor({ extractors, commonExtractorArgs, webServiceAuthConfig }) {
     super();
     this.registerExtractors(
+      CSVAdverseEventExtractor,
       CSVCancerDiseaseStatusExtractor,
       CSVCancerRelatedMedicationExtractor,
       CSVClinicalTrialInformationExtractor,

src/extractors/CSVAdverseEventExtractor.js

@@ -0,0 +1,64 @@
+const path = require('path');
+const { CSVModule } = require('../modules');
+const { generatemCODEResources } = require('../templates');
+const { Extractor } = require('./Extractor');
+const logger = require('../helpers/logger');
+const { formatDateTime } = require('../helpers/dateUtils');
+
+// Formats data to be passed into template-friendly format
+function formatData(adverseEventData) {
+  logger.debug('Reformatting adverse event data from CSV into template format');
+  return adverseEventData.map((data) => {
+    const {
+      mrn, adverseEventId, adverseEventCode, adverseEventCodeSystem, adverseEventDisplayText, suspectedCauseId, suspectedCauseType, seriousness, seriousnessCodeSystem, seriousnessDisplayText,
+      category, categoryCodeSystem, categoryDisplayText, severity, actuality, studyId, effectiveDate, recordedDate,
+    } = data;
+
+    if (!(mrn && adverseEventCode && effectiveDate)) {
+      throw new Error('The adverse event is missing an expected attribute. Adverse event code, mrn, and effective date are all required.');
+    }
+    return {
+      id: adverseEventId,
+      subjectId: mrn,
+      code: adverseEventCode,
+      system: adverseEventCodeSystem,
+      display: adverseEventDisplayText,
+      suspectedCauseId,
+      suspectedCauseType,
+      seriousnessCode: seriousness,
+      seriousnessCodeSystem,
+      seriousnessDisplayText,
+      categoryCode: category,
+      categoryCodeSystem,
+      categoryDisplayText,
+      severity,
+      actuality,
+      studyId,
+      effectiveDateTime: formatDateTime(effectiveDate),
+      recordedDateTime: formatDateTime(recordedDate),
+    };
+  });
+}
+
+class CSVAdverseEventExtractor extends Extractor {
+  constructor({ filePath }) {
+    super();
+    this.CSVModule = new CSVModule(path.resolve(filePath));
+  }
+
+  async getAdverseEventData(mrn) {
+    logger.debug('Getting Adverse Event Data');
+    return this.CSVModule.get('mrn', mrn);
+  }
+
+  async get({ mrn }) {
+    const adverseEventData = await this.getAdverseEventData(mrn);
+    const formattedData = formatData(adverseEventData);
+
+    return generatemCODEResources('AdverseEvent', formattedData);
+  }
+}
+
+module.exports = {
+  CSVAdverseEventExtractor,
+};

src/extractors/index.js

@@ -1,4 +1,5 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
+const { CSVAdverseEventExtractor } = require('./CSVAdverseEventExtractor')
 const { CSVCancerDiseaseStatusExtractor } = require('./CSVCancerDiseaseStatusExtractor');
 const { CSVCancerRelatedMedicationExtractor } = require('./CSVCancerRelatedMedicationExtractor');
 const { CSVClinicalTrialInformationExtractor } = require('./CSVClinicalTrialInformationExtractor');
@@ -24,6 +25,7 @@ const { MCODESurgicalProcedureExtractor } = require('./MCODESurgicalProcedureExt
 
 module.exports = {
   BaseFHIRExtractor,
+  CSVAdverseEventExtractor,
   CSVCancerDiseaseStatusExtractor,
   CSVCancerRelatedMedicationExtractor,
   CSVClinicalTrialInformationExtractor,

src/index.js

@@ -10,6 +10,7 @@ const {
 } = require('./cli');
 const {
   BaseFHIRExtractor,
+  CSVAdverseEventExtractor,
   CSVCancerDiseaseStatusExtractor,
   CSVCancerRelatedMedicationExtractor,
   CSVClinicalTrialInformationExtractor,
@@ -74,6 +75,7 @@ module.exports = {
   BaseClient,
   BaseFHIRExtractor,
   BaseFHIRModule,
+  CSVAdverseEventExtractor,
   CSVCancerDiseaseStatusExtractor,
   CSVCancerRelatedMedicationExtractor,
   CSVClinicalTrialInformationExtractor,

src/templates/AdverseEventTemplate.js

@@ -0,0 +1,124 @@
+const { coding, reference } = require('./snippets');
+const { ifAllArgsObj, ifSomeArgsObj } = require('../helpers/templateUtils');
+
+function eventTemplate({ eventCode, eventSystem, eventDisplay }) {
+  let codeSystem = eventSystem;
+  if (!codeSystem) {
+    codeSystem = 'http://snomed.info/sct';
+  }
+  return {
+    event: {
+      coding: [
+        coding({
+          code: eventCode,
+          system: codeSystem,
+          display: eventDisplay,
+        }),
+      ],
+    },
+  };
+}
+
+function suspectedCauseTemplate({ suspectedCauseId, suspectedCauseType }) {
+  return {
+    suspectEntity: [
+      {
+        instance:
+          reference({ id: suspectedCauseId, resourceType: suspectedCauseType }),
+      },
+    ],
+  };
+}
+
+
+function seriousnessTemplate({ seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText }) {
+  let codeSystem = seriousnessCodeSystem;
+  if (!codeSystem) {
+    codeSystem = 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness';
+  }
+  return {
+    seriousness: {
+      coding: [
+        coding({
+          code: seriousnessCode,
+          system: codeSystem,
+          display: seriousnessDisplayText,
+        }),
+      ],
+    },
+  };
+}
+
+function categoryTemplate({ categoryCode, categoryCodeSystem, categoryDisplayText }) {
+  let codeSystem = categoryCodeSystem;
+  if (!codeSystem) {
+    codeSystem = 'http://terminology.hl7.org/CodeSystem/adverse-event-category';
+  }
+  return {
+    category: {
+      coding: [
+        coding({
+          code: categoryCode,
+          system: codeSystem,
+          display: categoryDisplayText,
+        }),
+      ],
+    },
+  };
+}
+
+function severityTemplate({ severityCode }) {
+  return {
+    severity: {
+      coding: [
+        coding({
+          code: severityCode,
+        }),
+      ],
+    },
+  };
+}
+
+function actualityTemplate({ actuality }) {
+  let actualityCode = actuality;
+  if (!actualityCode) {
+    actualityCode = 'https://www.hl7.org/fhir/valueset-adverse-event-actuality.html';
+  }
+  return {
+    actuality: {
+      coding: [
+        coding({
+          code: actualityCode,
+        }),
+      ],
+    },
+  };
+}
+
+function adverseEventTemplate({
+  id, subjectId, code, system, display, suspectedCauseId, suspectedCauseType, seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText, categoryCode, categoryCodeSystem, categoryDisplayText,
+  severity, actuality, studyId, effectiveDateTime, recordedDateTime,
+}) {
+  if (!(subjectId && code && effectiveDateTime)) {
+    throw Error('Trying to render an AdverseEventTemplate, but a required argument is messing; ensure that subjectId, code and effectiveDateTime are all present');
+  }
+
+  return {
+    resourceType: 'AdverseEvent',
+    id,
+    subject: reference({ id: subjectId, resourceType: 'Patient' }),
+    ...ifSomeArgsObj(eventTemplate)({ code, system, display }),
+    ...ifAllArgsObj(suspectedCauseTemplate)({ id: suspectedCauseId, resourceType: suspectedCauseType }),
+    ...ifSomeArgsObj(seriousnessTemplate)({ seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText }),
+    ...ifSomeArgsObj(categoryTemplate)({ categoryCode, categoryCodeSystem, categoryDisplayText }),
+    ...ifAllArgsObj(severityTemplate)({ severity }),
+    ...actualityTemplate(actuality),
+    study: reference({ id: studyId, resourceType: 'ResearchStudy' }),
+    date: effectiveDateTime,
+    recordedDate: recordedDateTime,
+  };
+}
+
+module.exports = {
+  adverseEventTemplate,
+};

src/templates/ResourceGenerator.js

@@ -2,6 +2,7 @@ const _ = require('lodash');
 const shajs = require('sha.js');
 const logger = require('../helpers/logger');
 
+const { adverseEventTemplate } = require('./AdverseEventTemplate');
 const { cancerDiseaseStatusTemplate } = require('./CancerDiseaseStatusTemplate');
 const { cancerRelatedMedicationTemplate } = require('./CancerRelatedMedicationTemplate');
 const { carePlanWithReviewTemplate } = require('./CarePlanWithReviewTemplate');
@@ -15,6 +16,7 @@ const { stagingTemplate } = require('./StagingTemplate');
 const { tnmCategoryTemplate } = require('./TNMCategoryTemplate');
 
 const fhirTemplateLookup = {
+  AdverseEvent: adverseEventTemplate,
   CancerDiseaseStatus: cancerDiseaseStatusTemplate,
   CancerRelatedMedication: cancerRelatedMedicationTemplate,
   CarePlanWithReview: carePlanWithReviewTemplate,