Merge pull request #110 from mcode/case-insensitive-csv-columns

Make CSV column headers case insensitive

Author: dmendelowitz

src/extractors/CSVAdverseEventExtractor.js

@@ -10,8 +10,23 @@ function formatData(adverseEventData, patientId) {
   logger.debug('Reformatting adverse event data from CSV into template format');
   return adverseEventData.map((data) => {
     const {
-      adverseEventId, adverseEventCode, adverseEventCodeSystem, adverseEventDisplayText, suspectedCauseId, suspectedCauseType, seriousness, seriousnessCodeSystem, seriousnessDisplayText,
-      category, categoryCodeSystem, categoryDisplayText, severity, actuality, studyId, effectiveDate, recordedDate,
+      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)) {

src/extractors/CSVCancerDiseaseStatusExtractor.js

@@ -16,31 +16,40 @@ class CSVCancerDiseaseStatusExtractor extends BaseCSVExtractor {
   joinAndReformatData(arrOfDiseaseStatusData, patientId) {
     logger.debug('Reformatting disease status data from CSV into template format');
     // Check the shape of the data
-    arrOfDiseaseStatusData.forEach((record) => {
-      if (!record.conditionId || !record.diseaseStatusCode || !record.dateOfObservation) {
+    return arrOfDiseaseStatusData.map((record) => {
+      const {
+        conditionid: conditionId,
+        diseasestatuscode: diseaseStatusCode,
+        diseasestatustext: diseaseStatusText,
+        dateofobservation: dateOfObservation,
+        observationstatus: observationStatus,
+        evidence,
+      } = record;
+
+      if (!conditionId || !diseaseStatusCode || !dateOfObservation) {
         throw new Error('DiseaseStatusData missing an expected property: conditionId, diseaseStatusCode, and dateOfObservation are required.');
       }
+
+      return {
+        status: observationStatus || 'final',
+        value: {
+          code: diseaseStatusCode,
+          system: 'http://snomed.info/sct',
+          display: diseaseStatusText || getDiseaseStatusDisplay(diseaseStatusCode, this.implementation),
+        },
+        subject: {
+          id: patientId,
+        },
+        condition: {
+          id: conditionId,
+        },
+        effectiveDateTime: formatDateTime(dateOfObservation),
+        evidence: !evidence ? null : evidence.split('|').map((evidenceCode) => ({
+          code: evidenceCode,
+          display: getDiseaseStatusEvidenceDisplay(evidenceCode),
+        })),
+      };
     });
-    const evidenceDelimiter = '|';
-    return arrOfDiseaseStatusData.map((record) => ({
-      status: record.observationStatus || 'final',
-      value: {
-        code: record.diseaseStatusCode,
-        system: 'http://snomed.info/sct',
-        display: record.diseaseStatusText ? record.diseaseStatusText : getDiseaseStatusDisplay(record.diseaseStatusCode, this.implementation),
-      },
-      subject: {
-        id: patientId,
-      },
-      condition: {
-        id: record.conditionId,
-      },
-      effectiveDateTime: formatDateTime(record.dateOfObservation),
-      evidence: !record.evidence ? null : record.evidence.split(evidenceDelimiter).map((evidenceCode) => ({
-        code: evidenceCode,
-        display: getDiseaseStatusEvidenceDisplay(evidenceCode),
-      })),
-    }));
   }
 
   async getDiseaseStatusData(mrn, fromDate, toDate) {

src/extractors/CSVCancerRelatedMedicationExtractor.js

@@ -11,7 +11,17 @@ function formatData(medicationData, patientId) {
 
   return medicationData.map((medication) => {
     const {
-      medicationId, code, codeSystem, displayText, startDate, endDate, treatmentReasonCode, treatmentReasonCodeSystem, treatmentReasonDisplayText, treatmentIntent, status,
+      medicationid: medicationId,
+      code,
+      codesystem: codeSystem,
+      displaytext: displayText,
+      startdate: startDate,
+      enddate: endDate,
+      treatmentreasoncode: treatmentReasonCode,
+      treatmentreasoncodesystem: treatmentReasonCodeSystem,
+      treatmentreasondisplaytext: treatmentReasonDisplayText,
+      treatmentintent: treatmentIntent,
+      status,
     } = medication;
 
     if (!(code && codeSystem && status)) {

src/extractors/CSVClinicalTrialInformationExtractor.js

@@ -18,7 +18,11 @@ class CSVClinicalTrialInformationExtractor extends BaseCSVExtractor {
   joinClinicalTrialData(clinicalTrialData, patientId) {
     logger.debug('Reformatting clinical trial data from CSV into template format');
     const {
-      trialSubjectID, enrollmentStatus, trialResearchID, trialStatus, trialResearchSystem,
+      trialsubjectid: trialSubjectID,
+      enrollmentstatus: enrollmentStatus,
+      trialresearchid: trialResearchID,
+      trialstatus: trialStatus,
+      trialresearchsystem: trialResearchSystem,
     } = clinicalTrialData;
     const { clinicalSiteID, clinicalSiteSystem } = this;
 

src/extractors/CSVConditionExtractor.js

@@ -11,7 +11,17 @@ function formatData(conditionData, patientId) {
   logger.debug('Reformatting condition data from CSV into template format');
   return conditionData.map((data) => {
     const {
-      conditionId, codeSystem, code, displayName, category, dateOfDiagnosis, clinicalStatus, verificationStatus, bodySite, laterality, histology,
+      conditionid: conditionId,
+      codesystem: codeSystem,
+      code,
+      displayname: displayName,
+      category,
+      dateofdiagnosis: dateOfDiagnosis,
+      clinicalstatus: clinicalStatus,
+      verificationstatus: verificationStatus,
+      bodysite: bodySite,
+      laterality,
+      histology,
     } = data;
 
     if (!(conditionId && codeSystem && code && category)) {

src/extractors/CSVObservationExtractor.js

@@ -9,7 +9,16 @@ function formatData(observationData, patientId) {
   logger.debug('Reformatting observation data from CSV into template format');
   return observationData.map((data) => {
     const {
-      observationId, status, code, codeSystem, displayName, value, valueCodeSystem, effectiveDate, bodySite, laterality,
+      observationid: observationId,
+      status,
+      code,
+      codesystem: codeSystem,
+      displayname: displayName,
+      value,
+      valuecodesystem: valueCodeSystem,
+      effectivedate: effectiveDate,
+      bodysite: bodySite,
+      laterality,
     } = data;
 
     if (!observationId || !status || !code || !codeSystem || !value || !effectiveDate) {

src/extractors/CSVPatientExtractor.js

@@ -13,7 +13,19 @@ function joinAndReformatData(patientData) {
   logger.debug('Reformatting patient data from CSV into template format');
   // No join needed, just a reformatting
   const {
-    mrn, familyName, givenName, gender, birthsex, dateOfBirth, race, ethnicity, language, addressLine, city, state, zip,
+    mrn,
+    familyname: familyName,
+    givenname: givenName,
+    gender,
+    birthsex,
+    dateofbirth: dateOfBirth,
+    race,
+    ethnicity,
+    language,
+    addressline: addressLine,
+    city,
+    state,
+    zip,
   } = patientData;
 
   if (!mrn) {

src/extractors/CSVProcedureExtractor.js

@@ -10,7 +10,19 @@ function formatData(procedureData, patientId) {
   logger.debug('Reformatting procedure data from CSV into template format');
   return procedureData.map((data) => {
     const {
-      procedureId, conditionId, status, code, codeSystem, displayName, reasonCode, reasonCodeSystem, reasonDisplayName, bodySite, laterality, effectiveDate, treatmentIntent,
+      procedureid: procedureId,
+      conditionid: conditionId,
+      status,
+      code,
+      codesystem: codeSystem,
+      displayname: displayName,
+      reasoncode: reasonCode,
+      reasoncodesystem: reasonCodeSystem,
+      reasondisplayname: reasonDisplayName,
+      bodysite: bodySite,
+      laterality,
+      effectivedate: effectiveDate,
+      treatmentintent: treatmentIntent,
     } = data;
 
     if (!(procedureId && status && code && codeSystem && effectiveDate)) {

src/extractors/CSVStagingExtractor.js

@@ -9,7 +9,14 @@ function formatTNMCategoryData(stagingData, patientId) {
   logger.debug('Reformatting TNM Category data into template format');
   const formattedData = [];
   const {
-    conditionId, t, n, m, type, stagingSystem, stagingCodeSystem, effectiveDate,
+    conditionid: conditionId,
+    t,
+    n,
+    m,
+    type,
+    stagingsystem: stagingSystem,
+    stagingcodesystem: stagingCodeSystem,
+    effectivedate: effectiveDate,
   } = stagingData;
 
   if (!conditionId || !effectiveDate) {
@@ -35,7 +42,12 @@ function formatTNMCategoryData(stagingData, patientId) {
 
 function formatStagingData(stagingData, categoryIds, patientId) {
   const {
-    conditionId, type, stageGroup, stagingSystem, stagingCodeSystem, effectiveDate,
+    conditionid: conditionId,
+    type,
+    stagegroup: stageGroup,
+    stagingsystem: stagingSystem,
+    stagingcodesystem: stagingCodeSystem,
+    effectivedate: effectiveDate,
   } = stagingData;
 
   return {

src/extractors/CSVTreatmentPlanChangeExtractor.js

@@ -21,7 +21,10 @@ function formatData(tpcData, patientId) {
 
   // If there are multiple entries, combine them into one object with multiple reviews
   const combinedData = _.reduce(tpcData, (res, currentDataEntry) => {
-    const { dateOfCarePlan, changed, reasonCode, reasonDisplayText } = currentDataEntry;
+    const { dateofcareplan: dateOfCarePlan,
+      changed,
+      reasoncode: reasonCode,
+      reasondisplaytext: reasonDisplayText } = currentDataEntry;
 
     if (!dateOfCarePlan || !changed) {
       throw new Error('Treatment Plan Change Data missing an expected property: dateOfCarePlan, changed are required');