Merge pull request #164 from mcode/duplicate-ae

Create CTC Adverse Event Extractor

Author: julianxcarter

docs/ctc-adverse-event.csv

@@ -0,0 +1,4 @@
+mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate
+mrn-full-example,example-id-1,event-code,code-system,code-display,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code,code-system,category-dislpay,mild,actual,id,1994-12-09,1994-12-09
+mrn-two-category-example,example-id-2,event-code,code-system,code-display,cause-id,resourceType,seriousness-code,code-system,seriousness-display,category-code|category-code,code-system|code-system,category-display|category-display,mild,actual,id,1994-12-09,1994-12-09
+mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,,,1994-12-09,

src/client/MCODEClient.js

@@ -6,6 +6,7 @@ const {
   CSVCancerRelatedMedicationRequestExtractor,
   CSVClinicalTrialInformationExtractor,
   CSVConditionExtractor,
+  CSVCTCAdverseEventExtractor,
   CSVObservationExtractor,
   CSVPatientExtractor,
   CSVProcedureExtractor,
@@ -35,6 +36,7 @@ class MCODEClient extends BaseClient {
       CSVCancerRelatedMedicationRequestExtractor,
       CSVClinicalTrialInformationExtractor,
       CSVConditionExtractor,
+      CSVCTCAdverseEventExtractor,
       CSVObservationExtractor,
       CSVPatientExtractor,
       CSVProcedureExtractor,
@@ -67,6 +69,7 @@ class MCODEClient extends BaseClient {
       { type: 'CSVProcedureExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVObservationExtractor', dependencies: ['CSVPatientExtractor'] },
       { type: 'CSVAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
+      { type: 'CSVCTCAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
     ];
     // Sort extractors based on order and dependencies
     this.extractorConfig = sortExtractors(this.extractorConfig, dependencyInfo);

src/extractors/CSVCTCAdverseEventExtractor.js

@@ -0,0 +1,99 @@
+const { BaseCSVExtractor } = require('./BaseCSVExtractor');
+const { generateMcodeResources } = require('../templates');
+const { getEmptyBundle } = require('../helpers/fhirUtils');
+const { getPatientFromContext } = require('../helpers/contextUtils');
+const { formatDateTime } = require('../helpers/dateUtils');
+const logger = require('../helpers/logger');
+
+// Formats data to be passed into template-friendly format
+function formatData(adverseEventData, patientId) {
+  logger.debug('Reformatting adverse event data from CSV into template format');
+  return adverseEventData.map((data) => {
+    const {
+      adverseeventid: adverseEventId,
+      adverseeventcode: adverseEventCode,
+      adverseeventcodesystem: adverseEventCodeSystem,
+      adverseeventdisplaytext: adverseEventDisplayText,
+      suspectedcauseid: suspectedCauseId,
+      suspectedcausetype: suspectedCauseType,
+      seriousness,
+      seriousnesscodesystem: seriousnessCodeSystem,
+      seriousnessdisplaytext: seriousnessDisplayText,
+      category,
+      categorycodesystem: categoryCodeSystem,
+      categorydisplaytext: categoryDisplayText,
+      severity,
+      actuality,
+      studyid: studyId,
+      effectivedate: effectiveDate,
+      recordeddate: recordedDate,
+    } = data;
+
+    if (!(adverseEventCode && effectiveDate)) {
+      throw new Error('The adverse event is missing an expected attribute. Adverse event code and effective date are all required.');
+    }
+
+    const categoryCodes = category.split('|');
+    const categorySystems = categoryCodeSystem.split('|');
+    const categoryDisplays = categoryDisplayText.split('|');
+
+    if (!(categoryCodes.length === categorySystems.length && categoryCodes.length === categoryDisplays.length)) {
+      throw new Error('A category attribute on the adverse event is missing a corresponding categoryCodeSystem or categoryDisplayText value.');
+    }
+
+
+    return {
+      ...(adverseEventId && { id: adverseEventId }),
+      subjectId: patientId,
+      code: adverseEventCode,
+      system: !adverseEventCodeSystem ? 'http://snomed.info/sct' : adverseEventCodeSystem,
+      display: adverseEventDisplayText,
+      suspectedCauseId,
+      suspectedCauseType,
+      seriousnessCode: seriousness,
+      seriousnessCodeSystem: !seriousnessCodeSystem ? 'http://terminology.hl7.org/CodeSystem/adverse-event-seriousness' : seriousnessCodeSystem,
+      seriousnessDisplayText,
+      category: categoryCodes.map((categoryCode, index) => {
+        if (!categoryCode) return null;
+        const categoryCoding = { code: categoryCode, system: categorySystems[index] ? categorySystems[index] : 'http://terminology.hl7.org/CodeSystem/adverse-event-category' };
+        if (categoryDisplays[index]) categoryCoding.display = categoryDisplays[index];
+        return categoryCoding;
+      }),
+      severity,
+      actuality: !actuality ? 'actual' : actuality,
+      studyId,
+      effectiveDateTime: formatDateTime(effectiveDate),
+      recordedDateTime: !recordedDate ? null : formatDateTime(recordedDate),
+    };
+  });
+}
+
+class CSVCTCAdverseEventExtractor extends BaseCSVExtractor {
+  constructor({ filePath, url }) {
+    super({ filePath, url });
+  }
+
+  async getAdverseEventData(mrn) {
+    logger.debug('Getting Adverse Event Data');
+    return this.csvModule.get('mrn', mrn);
+  }
+
+  async get({ mrn, context }) {
+    const adverseEventData = await this.getAdverseEventData(mrn);
+    if (adverseEventData.length === 0) {
+      logger.warn('No adverse event data found for patient');
+      return getEmptyBundle();
+    }
+    const patientId = getPatientFromContext(context).id;
+
+    // Reformat data
+    const formattedData = formatData(adverseEventData, patientId);
+
+    // Fill templates
+    return generateMcodeResources('CTCAdverseEvent', formattedData);
+  }
+}
+
+module.exports = {
+  CSVCTCAdverseEventExtractor,
+};

src/extractors/index.js

@@ -5,6 +5,7 @@ const { CSVCancerRelatedMedicationAdministrationExtractor } = require('./CSVCanc
 const { CSVCancerRelatedMedicationRequestExtractor } = require('./CSVCancerRelatedMedicationRequestExtractor');
 const { CSVClinicalTrialInformationExtractor } = require('./CSVClinicalTrialInformationExtractor');
 const { CSVConditionExtractor } = require('./CSVConditionExtractor');
+const { CSVCTCAdverseEventExtractor } = require('./CSVCTCAdverseEventExtractor');
 const { CSVObservationExtractor } = require('./CSVObservationExtractor');
 const { CSVPatientExtractor } = require('./CSVPatientExtractor');
 const { CSVProcedureExtractor } = require('./CSVProcedureExtractor');
@@ -32,6 +33,7 @@ module.exports = {
   CSVCancerRelatedMedicationRequestExtractor,
   CSVClinicalTrialInformationExtractor,
   CSVConditionExtractor,
+  CSVCTCAdverseEventExtractor,
   CSVObservationExtractor,
   CSVPatientExtractor,
   CSVProcedureExtractor,

src/templates/CTCAdverseEventTemplate.js

@@ -0,0 +1,101 @@
+const { coding, reference } = require('./snippets');
+const { ifAllArgsObj, ifSomeArgsObj, ifAllArgs, ifSomeArgsArr } = require('../helpers/templateUtils');
+
+function eventTemplate(eventCoding) {
+  return {
+    event: {
+      coding: [
+        coding(eventCoding),
+      ],
+    },
+  };
+}
+
+function suspectedCauseTemplate({ suspectedCauseId, suspectedCauseType }) {
+  return {
+    suspectEntity: [
+      {
+        instance:
+          reference({ id: suspectedCauseId, resourceType: suspectedCauseType }),
+      },
+    ],
+  };
+}
+
+
+function seriousnessTemplate(seriousnessCoding) {
+  return {
+    seriousness: {
+      coding: [
+        coding(seriousnessCoding),
+      ],
+    },
+  };
+}
+
+function individualCategoryTemplate(category) {
+  return {
+    coding: [coding(category),
+    ],
+  };
+}
+
+function categoryArrayTemplate(categoryArr) {
+  const category = categoryArr.map(individualCategoryTemplate);
+  return { category };
+}
+
+function severityTemplate(severityCode) {
+  return {
+    severity: {
+      coding: [
+        coding({
+          code: severityCode,
+          system: 'http://terminology.hl7.org/CodeSystem/adverse-event-severity',
+        }),
+      ],
+    },
+  };
+}
+
+function studyTemplate(studyId) {
+  return {
+    study: [
+      reference({ id: studyId, resourceType: 'ResearchStudy' }),
+    ],
+  };
+}
+
+function recordedDateTemplate(recordedDateTime) {
+  return {
+    recordedDate: recordedDateTime,
+  };
+}
+
+function CTCAdverseEventTemplate({
+  id, subjectId, code, system, display, suspectedCauseId, suspectedCauseType, seriousnessCode, seriousnessCodeSystem, seriousnessDisplayText, category,
+  severity, actuality, studyId, effectiveDateTime, recordedDateTime,
+}) {
+  if (!(subjectId && code && system && effectiveDateTime && actuality)) {
+    throw Error('Trying to render an AdverseEventTemplate, but a required argument is messing; ensure that subjectId, code, system, actuality, and effectiveDateTime are all present');
+  }
+
+  return {
+    resourceType: 'AdverseEvent',
+    id,
+    subject: reference({ id: subjectId, resourceType: 'Patient' }),
+    ...ifSomeArgsObj(eventTemplate)({ code, system, display }),
+    ...ifAllArgsObj(suspectedCauseTemplate)({ suspectedCauseId, suspectedCauseType }),
+    ...ifSomeArgsObj(seriousnessTemplate)({ code: seriousnessCode, system: seriousnessCodeSystem, display: seriousnessDisplayText }),
+    ...ifSomeArgsArr(categoryArrayTemplate)(category),
+    ...ifAllArgs(severityTemplate)(severity),
+    actuality,
+    ...ifAllArgs(studyTemplate)(studyId),
+    date: effectiveDateTime,
+    ...ifAllArgs(recordedDateTemplate)(recordedDateTime),
+  };
+}
+
+module.exports = {
+  CTCAdverseEventTemplate,
+};

src/templates/ResourceGenerator.js

@@ -8,6 +8,7 @@ const { cancerRelatedMedicationAdministrationTemplate } = require('./CancerRelat
 const { cancerRelatedMedicationRequestTemplate } = require('./CancerRelatedMedicationRequestTemplate');
 const { carePlanWithReviewTemplate } = require('./CarePlanWithReviewTemplate');
 const { conditionTemplate } = require('./ConditionTemplate');
+const { CTCAdverseEventTemplate } = require('./CTCAdverseEventTemplate');
 const { observationTemplate } = require('./ObservationTemplate');
 const { patientTemplate } = require('./PatientTemplate');
 const { procedureTemplate } = require('./ProcedureTemplate');
@@ -23,6 +24,7 @@ const fhirTemplateLookup = {
   CancerRelatedMedicationRequest: cancerRelatedMedicationRequestTemplate,
   CarePlanWithReview: carePlanWithReviewTemplate,
   Condition: conditionTemplate,
+  CTCAdverseEvent: CTCAdverseEventTemplate,
   Observation: observationTemplate,
   Patient: patientTemplate,
   Procedure: procedureTemplate,

test/sample-client-data/ctc-adverse-event-information.csv

@@ -0,0 +1,4 @@
+mrn,adverseEventId,adverseEventCode,adverseEventCodeSystem,adverseEventDisplayText,suspectedCauseId,suspectedCauseType,seriousness,seriousnessCodeSystem,seriousnessDisplayText,category,categoryCodeSystem,categoryDisplayText,severity,actuality,studyId,effectiveDate,recordedDate
+123,adverseEventId-1,109006,code-system,Anxiety disorder of childhood OR adolescence,procedure-id,Procedure,serious,http://terminology.hl7.org/CodeSystem/adverse-event-seriousness,Serious,product-use-error|product-quality|wrong-rate,http://terminology.hl7.org/CodeSystem/adverse-event-category|http://snomed.info/sct|http://terminology.hl7.org/CodeSystem/adverse-event-category,Product Use Error|Product Quality|Wrong Rate,severe,actual,researchId-1,12-09-1994,12-09-1994
+456,adverseEventId-2,134006,http://snomed.info/sct,Decreased hair growth,medicationId-1,Medication,non-serious,http://terminology.hl7.org/CodeSystem/adverse-event-seriousness,Non-serious,product-quality|wrong-rate,http://terminology.hl7.org/CodeSystem/adverse-event-category|,Product Quality|,mild,potential,researchId-2,12-10-1995,12-10-1995
+789,adverseEventId-3,150003,,,,,,,,product-use-error,,,,,,12-09-1994,