Merge pull request #80 from mcode/csv-adverse-event-extractor

CSV Adverse Event Extractor

Author: julianxcarter

config/mcode-csv-config.example.json

@@ -74,6 +74,13 @@
       "constructorArgs": {
         "filePath": "./data/procedure-information.csv"
       }
+    },
+    {
+      "label": "adverseEvent",
+      "type": "CSVAdverseEventExtractor",
+      "constructorArgs": {
+        "filePath": "./test/sample-client-data/adverse-event-information.csv"
+      }
     }
   ]
 }

docs/adverse-event.csv

@@ -1,3 +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,12-09-1994,12-09-1994
-mrn-minimal-example,,code-from-default-system,,,,,,,,,,,,,,12-09-1994,
+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-1,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

@@ -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 +1,77 @@
+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.');
+    }
+
+    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: mrn,
+      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 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/helpers/templateUtils.js

@@ -24,6 +24,18 @@ function ifAllArgsObj(templateFn) {
   };
 }
 
+// A decorator that modifies a template to only render
+// when all of the values on its argumentsArray are not null/empty, returning null otherwise
+// NOTE: Will not return null if the argumentsArray/elements are not defined; just checks if they're present with undefined/null values
+function ifAllArgsArr(templateFn) {
+  return (argArr) => {
+    if (_.some(argArr, (arg) => _.isUndefined(arg) || _.isNull(arg))) {
+      return null;
+    }
+    return templateFn(argArr);
+  };
+}
+
 // A decorator that modifies a template to only render
 // when some of its arguments are not null/undefined, returning null otherwise
 // NOTE: Will not return null if the arguments are not defined; just checks if they're present with undefined/null values
@@ -48,9 +60,22 @@ function ifSomeArgsObj(templateFn) {
   };
 }
 
+// A decorator that modifies a template to only render
+// when some of the values on its argumentsArray are not null/empty, returning null otherwise
+// NOTE: Will not return null if the argumentsArray/elemtns are not defined; just checks if they're present with undefined/null values
+function ifSomeArgsArr(templateFn) {
+  return (argArr) => {
+    if (_.every(argArr, (arg) => _.isUndefined(arg) || _.isNull(arg))) {
+      return null;
+    }
+    return templateFn(argArr);
+  };
+}
 module.exports = {
   ifAllArgs,
+  ifAllArgsArr,
   ifAllArgsObj,
   ifSomeArgs,
+  ifSomeArgsArr,
   ifSomeArgsObj,
 };

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 +1,101 @@
+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 adverseEventTemplate({
+  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 = {
+  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,