From 68c5547f6be971314a64828ece7de7a02a92e01a Mon Sep 17 00:00:00 2001
From: Dylan Phelan <dtphelan1@gmail.com>
Date: Thu, 15 Apr 2021 13:53:31 -0400
Subject: [PATCH 01/10] All CSV extractors updated, adverseEvent tests fixed

---
 src/extractors/CSVAdverseEventExtractor.js    | 26 +++++++++-----
 .../CSVCancerDiseaseStatusExtractor.js        | 14 ++++----
 .../CSVCancerRelatedMedicationExtractor.js    | 24 +++++++++----
 .../CSVClinicalTrialInformationExtractor.js   | 24 ++++++-------
 src/extractors/CSVConditionExtractor.js       | 26 +++++++++-----
 src/extractors/CSVObservationExtractor.js     | 26 +++++++++-----
 src/extractors/CSVPatientExtractor.js         |  2 +-
 src/extractors/CSVProcedureExtractor.js       | 26 +++++++++-----
 src/extractors/CSVStagingExtractor.js         | 26 +++++++++-----
 .../CSVTreatmentPlanChangeExtractor.js        | 14 ++++----
 .../CancerRelatedMedicationTemplate.js        |  8 ++---
 src/templates/CarePlanWithReviewTemplate.js   |  8 ++---
 .../CSVAdverseEventExtractor.test.js          | 36 ++++++++++---------
 .../extractors/FHIRConditionExtractor.test.js | 12 ++-----
 .../fixtures/context-with-patient.json        | 12 +++++++
 15 files changed, 173 insertions(+), 111 deletions(-)
 create mode 100644 test/extractors/fixtures/context-with-patient.json

diff --git a/src/extractors/CSVAdverseEventExtractor.js b/src/extractors/CSVAdverseEventExtractor.js
index 09cfdd52..2f48fb61 100644
--- a/src/extractors/CSVAdverseEventExtractor.js
+++ b/src/extractors/CSVAdverseEventExtractor.js
@@ -1,19 +1,21 @@
 const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { generateMcodeResources } = require('../templates');
-const logger = require('../helpers/logger');
+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) {
+function formatData(adverseEventData, patientId) {
   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,
+      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.');
+    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('|');
@@ -27,7 +29,7 @@ function formatData(adverseEventData) {
 
     return {
       ...(adverseEventId && { id: adverseEventId }),
-      subjectId: mrn,
+      subjectId: patientId,
       code: adverseEventCode,
       system: !adverseEventCodeSystem ? 'http://snomed.info/sct' : adverseEventCodeSystem,
       display: adverseEventDisplayText,
@@ -61,10 +63,18 @@ class CSVAdverseEventExtractor extends BaseCSVExtractor {
     return this.csvModule.get('mrn', mrn);
   }
 
-  async get({ mrn }) {
+  async get({ mrn, context }) {
     const adverseEventData = await this.getAdverseEventData(mrn);
-    const formattedData = formatData(adverseEventData);
+    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('AdverseEvent', formattedData);
   }
 }
diff --git a/src/extractors/CSVCancerDiseaseStatusExtractor.js b/src/extractors/CSVCancerDiseaseStatusExtractor.js
index 69685241..166232ea 100644
--- a/src/extractors/CSVCancerDiseaseStatusExtractor.js
+++ b/src/extractors/CSVCancerDiseaseStatusExtractor.js
@@ -2,6 +2,7 @@ const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { formatDateTime } = require('../helpers/dateUtils');
 const { getDiseaseStatusDisplay, getDiseaseStatusEvidenceDisplay } = require('../helpers/diseaseStatusUtils');
 const { generateMcodeResources } = require('../templates');
+const { getPatientFromContext } = require('../helpers/contextUtils');
 const { getEmptyBundle } = require('../helpers/fhirUtils');
 const logger = require('../helpers/logger');
 const { CSVCancerDiseaseStatusSchema } = require('../helpers/schemas/csv');
@@ -12,12 +13,12 @@ class CSVCancerDiseaseStatusExtractor extends BaseCSVExtractor {
     this.implementation = implementation;
   }
 
-  joinAndReformatData(arrOfDiseaseStatusData) {
+  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.mrn || !record.conditionId || !record.diseaseStatusCode || !record.dateOfObservation) {
-        throw new Error('DiseaseStatusData missing an expected property: mrn, conditionId, diseaseStatusCode, and dateOfObservation are required.');
+      if (!record.conditionId || !record.diseaseStatusCode || !record.dateOfObservation) {
+        throw new Error('DiseaseStatusData missing an expected property: conditionId, diseaseStatusCode, and dateOfObservation are required.');
       }
     });
     const evidenceDelimiter = '|';
@@ -29,7 +30,7 @@ class CSVCancerDiseaseStatusExtractor extends BaseCSVExtractor {
         display: record.diseaseStatusText ? record.diseaseStatusText : getDiseaseStatusDisplay(record.diseaseStatusCode, this.implementation),
       },
       subject: {
-        id: record.mrn,
+        id: patientId,
       },
       condition: {
         id: record.conditionId,
@@ -47,16 +48,17 @@ class CSVCancerDiseaseStatusExtractor extends BaseCSVExtractor {
     return this.csvModule.get('mrn', mrn, fromDate, toDate);
   }
 
-  async get({ mrn, fromDate, toDate }) {
+  async get({ mrn, context, fromDate, toDate }) {
     // 1. Get all relevant data and do necessary post-processing
     const diseaseStatusData = await this.getDiseaseStatusData(mrn, fromDate, toDate);
     if (diseaseStatusData.length === 0) {
       logger.warn('No disease status data found for patient');
       return getEmptyBundle();
     }
+    const patientId = getPatientFromContext(context).id;
 
     // 2. Format data for research study and research subject
-    const packagedDiseaseStatusData = this.joinAndReformatData(diseaseStatusData);
+    const packagedDiseaseStatusData = this.joinAndReformatData(diseaseStatusData, patientId);
 
     // 3. Generate FHIR Resources
     const resources = generateMcodeResources('CancerDiseaseStatus', packagedDiseaseStatusData);
diff --git a/src/extractors/CSVCancerRelatedMedicationExtractor.js b/src/extractors/CSVCancerRelatedMedicationExtractor.js
index 259f9075..5d9e1123 100644
--- a/src/extractors/CSVCancerRelatedMedicationExtractor.js
+++ b/src/extractors/CSVCancerRelatedMedicationExtractor.js
@@ -1,24 +1,26 @@
 const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { generateMcodeResources } = require('../templates');
-const logger = require('../helpers/logger');
+const { getPatientFromContext } = require('../helpers/contextUtils');
+const { getEmptyBundle } = require('../helpers/fhirUtils');
 const { formatDateTime } = require('../helpers/dateUtils');
+const logger = require('../helpers/logger');
 
 
-function formatData(medicationData) {
+function formatData(medicationData, patientId) {
   logger.debug('Reformatting cancer-related medication data from CSV into template format');
 
   return medicationData.map((medication) => {
     const {
-      mrn, medicationId, code, codeSystem, displayText, startDate, endDate, treatmentReasonCode, treatmentReasonCodeSystem, treatmentReasonDisplayText, treatmentIntent, status,
+      medicationId, code, codeSystem, displayText, startDate, endDate, treatmentReasonCode, treatmentReasonCodeSystem, treatmentReasonDisplayText, treatmentIntent, status,
     } = medication;
 
-    if (!(mrn && code && codeSystem && status)) {
+    if (!(code && codeSystem && status)) {
       throw new Error('The cancer-related medication is missing an expected element; mrn, code, code system, and status are all required values.');
     }
 
     return {
-      mrn,
       ...(medicationId && { id: medicationId }),
+      subjectId: patientId,
       code,
       codeSystem,
       displayText,
@@ -43,10 +45,18 @@ class CSVCancerRelatedMedicationExtractor extends BaseCSVExtractor {
     return this.csvModule.get('mrn', mrn);
   }
 
-  async get({ mrn }) {
+  async get({ mrn, context }) {
     const medicationData = await this.getMedicationData(mrn);
-    const formattedData = formatData(medicationData);
+    if (medicationData.length === 0) {
+      logger.warn('No medication data found for patient');
+      return getEmptyBundle();
+    }
+    const patientId = getPatientFromContext(context).id;
+
+    // Reformat data
+    const formattedData = formatData(medicationData, patientId);
 
+    // Fill templates
     return generateMcodeResources('CancerRelatedMedication', formattedData);
   }
 }
diff --git a/src/extractors/CSVClinicalTrialInformationExtractor.js b/src/extractors/CSVClinicalTrialInformationExtractor.js
index 63331b8c..802c674a 100644
--- a/src/extractors/CSVClinicalTrialInformationExtractor.js
+++ b/src/extractors/CSVClinicalTrialInformationExtractor.js
@@ -1,19 +1,11 @@
+const _ = require('lodash');
 const { BaseCSVExtractor } = require('./BaseCSVExtractor');
-const { firstEntryInBundle, getBundleResourcesByType } = require('../helpers/fhirUtils');
+const { firstEntryInBundle, getEmptyBundle } = require('../helpers/fhirUtils');
+const { getPatientFromContext } = require('../helpers/contextUtils');
 const { generateMcodeResources } = require('../templates');
 const logger = require('../helpers/logger');
 const { CSVClinicalTrialInformationSchema } = require('../helpers/schemas/csv');
 
-function getPatientId(context) {
-  const patientInContext = getBundleResourcesByType(context, 'Patient', {}, true);
-  if (patientInContext) {
-    logger.debug('Patient resource found in context.');
-    return patientInContext.id;
-  }
-
-  logger.debug('No patient resource found in context.');
-  return undefined;
-}
 
 class CSVClinicalTrialInformationExtractor extends BaseCSVExtractor {
   constructor({ filePath, clinicalSiteID, clinicalSiteSystem }) {
@@ -23,7 +15,7 @@ class CSVClinicalTrialInformationExtractor extends BaseCSVExtractor {
     this.clinicalSiteSystem = clinicalSiteSystem;
   }
 
-  joinClinicalTrialData(patientId, clinicalTrialData) {
+  joinClinicalTrialData(clinicalTrialData, patientId) {
     logger.debug('Reformatting clinical trial data from CSV into template format');
     const {
       trialSubjectID, enrollmentStatus, trialResearchID, trialStatus, trialResearchSystem,
@@ -61,11 +53,15 @@ class CSVClinicalTrialInformationExtractor extends BaseCSVExtractor {
   }
 
   async get({ mrn, context }) {
-    const patientId = getPatientId(context) || mrn;
     const clinicalTrialData = await this.getClinicalTrialData(mrn);
+    if (_.isEmpty(clinicalTrialData)) {
+      logger.warn('No clinicalTrial record found for patient');
+      return getEmptyBundle();
+    }
+    const patientId = getPatientFromContext(context).id;
 
     // Format data for research study and research subject
-    const formattedData = this.joinClinicalTrialData(patientId, clinicalTrialData);
+    const formattedData = this.joinClinicalTrialData(clinicalTrialData, patientId);
     const { formattedDataSubject, formattedDataStudy } = formattedData;
 
     // Generate ResearchSubject and ResearchStudy resources and combine into one bundle to return
diff --git a/src/extractors/CSVConditionExtractor.js b/src/extractors/CSVConditionExtractor.js
index 4249a3c0..694059ca 100644
--- a/src/extractors/CSVConditionExtractor.js
+++ b/src/extractors/CSVConditionExtractor.js
@@ -1,24 +1,26 @@
 const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { generateMcodeResources } = require('../templates');
-const logger = require('../helpers/logger');
+const { getPatientFromContext } = require('../helpers/contextUtils');
+const { getEmptyBundle } = require('../helpers/fhirUtils');
 const { formatDateTime } = require('../helpers/dateUtils');
 const { CSVConditionSchema } = require('../helpers/schemas/csv');
+const logger = require('../helpers/logger');
 
 // Formats data to be passed into template-friendly format
-function formatData(conditionData) {
+function formatData(conditionData, patientId) {
   logger.debug('Reformatting condition data from CSV into template format');
   return conditionData.map((data) => {
     const {
-      mrn, conditionId, codeSystem, code, displayName, category, dateOfDiagnosis, clinicalStatus, verificationStatus, bodySite, laterality, histology,
+      conditionId, codeSystem, code, displayName, category, dateOfDiagnosis, clinicalStatus, verificationStatus, bodySite, laterality, histology,
     } = data;
 
-    if (!(conditionId && mrn && codeSystem && code && category)) {
-      throw new Error('The condition is missing an expected attribute. Condition id, mrn, code system, code, and category are all required.');
+    if (!(conditionId && codeSystem && code && category)) {
+      throw new Error('The condition is missing an expected attribute. Condition id, code system, code, and category are all required.');
     }
     return {
       id: conditionId,
       subject: {
-        id: mrn,
+        id: patientId,
       },
       code: {
         code,
@@ -46,10 +48,18 @@ class CSVConditionExtractor extends BaseCSVExtractor {
     return this.csvModule.get('mrn', mrn);
   }
 
-  async get({ mrn }) {
+  async get({ mrn, context }) {
     const conditionData = await this.getConditionData(mrn);
-    const formattedData = formatData(conditionData);
+    if (conditionData.length === 0) {
+      logger.warn('No condition data found for patient');
+      return getEmptyBundle();
+    }
+    const patientId = getPatientFromContext(context).id;
+
+    // Reformat data
+    const formattedData = formatData(conditionData, patientId);
 
+    // Fill templates
     return generateMcodeResources('Condition', formattedData);
   }
 }
diff --git a/src/extractors/CSVObservationExtractor.js b/src/extractors/CSVObservationExtractor.js
index c27b8d19..8b13ff74 100644
--- a/src/extractors/CSVObservationExtractor.js
+++ b/src/extractors/CSVObservationExtractor.js
@@ -1,22 +1,24 @@
 const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { generateMcodeResources } = require('../templates');
-const logger = require('../helpers/logger');
+const { getPatientFromContext } = require('../helpers/contextUtils');
+const { getEmptyBundle } = require('../helpers/fhirUtils');
 const { formatDateTime } = require('../helpers/dateUtils');
+const logger = require('../helpers/logger');
 
-function formatData(observationData) {
+function formatData(observationData, patientId) {
   logger.debug('Reformatting observation data from CSV into template format');
   return observationData.map((data) => {
     const {
-      mrn, observationId, status, code, codeSystem, displayName, value, valueCodeSystem, effectiveDate, bodySite, laterality,
+      observationId, status, code, codeSystem, displayName, value, valueCodeSystem, effectiveDate, bodySite, laterality,
     } = data;
 
-    if (!mrn || !observationId || !status || !code || !codeSystem || !value || !effectiveDate) {
-      throw new Error('The observation is missing an expected attribute. Observation id, mrn, status, code, code system, value, and effective date are all required.');
+    if (!observationId || !status || !code || !codeSystem || !value || !effectiveDate) {
+      throw new Error('The observation is missing an expected attribute. Observation id, status, code, code system, value, and effective date are all required.');
     }
 
     return {
       id: observationId,
-      subjectId: mrn,
+      subjectId: patientId,
       status,
       code,
       system: codeSystem,
@@ -40,10 +42,18 @@ class CSVObservationExtractor extends BaseCSVExtractor {
     return this.csvModule.get('mrn', mrn);
   }
 
-  async get({ mrn }) {
+  async get({ mrn, context }) {
     const observationData = await this.getObservationData(mrn);
-    const formattedData = formatData(observationData);
+    if (observationData.length === 0) {
+      logger.warn('No observation data found for patient');
+      return getEmptyBundle();
+    }
+    const patientId = getPatientFromContext(context).id;
+
+    // Reformat data
+    const formattedData = formatData(observationData, patientId);
 
+    // Fill template
     return generateMcodeResources('Observation', formattedData);
   }
 }
diff --git a/src/extractors/CSVPatientExtractor.js b/src/extractors/CSVPatientExtractor.js
index 4ec9eba0..018b0a27 100644
--- a/src/extractors/CSVPatientExtractor.js
+++ b/src/extractors/CSVPatientExtractor.js
@@ -6,8 +6,8 @@ const { getEthnicityDisplay,
   getRaceDisplay,
   maskPatientData } = require('../helpers/patientUtils');
 const { getEmptyBundle } = require('../helpers/fhirUtils');
-const logger = require('../helpers/logger');
 const { CSVPatientSchema } = require('../helpers/schemas/csv');
+const logger = require('../helpers/logger');
 
 function joinAndReformatData(patientData) {
   logger.debug('Reformatting patient data from CSV into template format');
diff --git a/src/extractors/CSVProcedureExtractor.js b/src/extractors/CSVProcedureExtractor.js
index ae3f2116..ab6909d4 100644
--- a/src/extractors/CSVProcedureExtractor.js
+++ b/src/extractors/CSVProcedureExtractor.js
@@ -1,22 +1,24 @@
 const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { generateMcodeResources } = require('../templates');
-const logger = require('../helpers/logger');
+const { getPatientFromContext } = require('../helpers/contextUtils');
+const { getEmptyBundle } = require('../helpers/fhirUtils');
 const { formatDateTime } = require('../helpers/dateUtils');
+const logger = require('../helpers/logger');
 
 // Formats data to be passed into template-friendly format
-function formatData(procedureData) {
+function formatData(procedureData, patientId) {
   logger.debug('Reformatting procedure data from CSV into template format');
   return procedureData.map((data) => {
     const {
-      mrn, procedureId, conditionId, status, code, codeSystem, displayName, reasonCode, reasonCodeSystem, reasonDisplayName, bodySite, laterality, effectiveDate, treatmentIntent,
+      procedureId, conditionId, status, code, codeSystem, displayName, reasonCode, reasonCodeSystem, reasonDisplayName, bodySite, laterality, effectiveDate, treatmentIntent,
     } = data;
 
-    if (!(mrn && procedureId && status && code && codeSystem && effectiveDate)) {
-      throw new Error('The procedure is missing an expected attribute. Procedure id, mrn, code system, code, status and effective date are all required.');
+    if (!(procedureId && status && code && codeSystem && effectiveDate)) {
+      throw new Error('The procedure is missing an expected attribute. Procedure id, code system, code, status and effective date are all required.');
     }
     return {
       id: procedureId,
-      subjectId: mrn,
+      subjectId: patientId,
       status,
       code,
       system: codeSystem,
@@ -43,10 +45,18 @@ class CSVProcedureExtractor extends BaseCSVExtractor {
     return this.csvModule.get('mrn', mrn);
   }
 
-  async get({ mrn }) {
+  async get({ mrn, context }) {
     const procedureData = await this.getProcedureData(mrn);
-    const formattedData = formatData(procedureData);
+    if (procedureData.length === 0) {
+      logger.warn('No procedure data found for patient');
+      return getEmptyBundle();
+    }
+    const patientId = getPatientFromContext(context).id;
+
+    // Reformat data
+    const formattedData = formatData(procedureData, patientId);
 
+    // Fill templates
     return generateMcodeResources('Procedure', formattedData);
   }
 }
diff --git a/src/extractors/CSVStagingExtractor.js b/src/extractors/CSVStagingExtractor.js
index 5dd77c2d..ba3cc271 100644
--- a/src/extractors/CSVStagingExtractor.js
+++ b/src/extractors/CSVStagingExtractor.js
@@ -1,18 +1,19 @@
 const { BaseCSVExtractor } = require('./BaseCSVExtractor');
-const { firstEntryInBundle } = require('../helpers/fhirUtils');
+const { firstEntryInBundle, getEmptyBundle } = require('../helpers/fhirUtils');
+const { getPatientFromContext } = require('../helpers/contextUtils');
 const { generateMcodeResources } = require('../templates');
-const logger = require('../helpers/logger');
 const { formatDateTime } = require('../helpers/dateUtils');
+const logger = require('../helpers/logger');
 
-function formatTNMCategoryData(stagingData) {
+function formatTNMCategoryData(stagingData, patientId) {
   logger.debug('Reformatting TNM Category data into template format');
   const formattedData = [];
   const {
-    mrn, conditionId, t, n, m, type, stagingSystem, stagingCodeSystem, effectiveDate,
+    conditionId, t, n, m, type, stagingSystem, stagingCodeSystem, effectiveDate,
   } = stagingData;
 
-  if (!mrn || !conditionId || !effectiveDate) {
-    throw new Error('Staging data is missing an expected property: mrn, conditionId, effectiveDate are required.');
+  if (!conditionId || !effectiveDate) {
+    throw new Error('Staging data is missing an expected property: conditionId, effectiveDate are required.');
   }
 
   // data needed for each TNM category
@@ -22,7 +23,7 @@ function formatTNMCategoryData(stagingData) {
     stageType: type,
     stagingSystem,
     stagingCodeSystem,
-    subjectId: mrn,
+    subjectId: patientId,
   };
 
   if (t) formattedData.push({ ...necessaryData, valueCode: t, categoryType: 'Tumor' });
@@ -59,11 +60,18 @@ class CSVStagingExtractor extends BaseCSVExtractor {
     return this.csvModule.get('mrn', mrn);
   }
 
-  async get({ mrn }) {
+  async get({ mrn, context }) {
     const stagingData = await this.getStagingData(mrn);
+    if (stagingData.length === 0) {
+      logger.warn('No Staging data found for patient');
+      return getEmptyBundle();
+    }
+    const patientId = getPatientFromContext(context).id;
+
+    // Iterate over the loop of staging data rows and make resources for all of them
     const entryResources = [];
     stagingData.forEach((data) => {
-      const formattedCategoryData = formatTNMCategoryData(data);
+      const formattedCategoryData = formatTNMCategoryData(data, patientId);
 
       // Generate observation for each TNM category
       const mcodeCategoryResources = formattedCategoryData.map((d) => firstEntryInBundle(generateMcodeResources('TNMCategory', d)));
diff --git a/src/extractors/CSVTreatmentPlanChangeExtractor.js b/src/extractors/CSVTreatmentPlanChangeExtractor.js
index 0e1d3bef..cc21eb7a 100644
--- a/src/extractors/CSVTreatmentPlanChangeExtractor.js
+++ b/src/extractors/CSVTreatmentPlanChangeExtractor.js
@@ -7,7 +7,7 @@ const logger = require('../helpers/logger');
 const { CSVTreatmentPlanChangeSchema } = require('../helpers/schemas/csv');
 
 // Formats data to be passed into template-friendly format
-function formatData(tpcData) {
+function formatData(tpcData, patientId) {
   logger.debug('Reformatting treatment plan change data from CSV into template format');
 
   // Nothing to format in empty array
@@ -16,16 +16,14 @@ function formatData(tpcData) {
   }
 
   // Newly combined data has mrn and list of reviews to map to an extension
-  const combinedFormat = { mrn: tpcData[0].mrn, reviews: [] };
+  const combinedFormat = { subjectId: patientId, reviews: [] };
 
   // If there are multiple entries, combine them into one object with multiple reviews
   const combinedData = _.reduce(tpcData, (res, currentDataEntry) => {
-    const {
-      mrn, dateOfCarePlan, changed, reasonCode, reasonDisplayText,
-    } = currentDataEntry;
+    const { dateOfCarePlan, changed, reasonCode, reasonDisplayText } = currentDataEntry;
 
-    if (!mrn || !dateOfCarePlan || !changed) {
-      throw new Error('Treatment Plan Change Data missing an expected property: mrn, dateOfCarePlan, changed are required');
+    if (!dateOfCarePlan || !changed) {
+      throw new Error('Treatment Plan Change Data missing an expected property: dateOfCarePlan, changed are required');
     }
 
     // reasonCode is required if changed flag is true
@@ -84,8 +82,10 @@ class CSVTreatmentPlanChangeExtractor extends BaseCSVExtractor {
       return getEmptyBundle();
     }
 
+    // Reformat data
     const formattedData = formatData(tpcData);
 
+    // Fill templates
     return generateMcodeResources('CarePlanWithReview', formattedData);
   }
 }
diff --git a/src/templates/CancerRelatedMedicationTemplate.js b/src/templates/CancerRelatedMedicationTemplate.js
index fc9de10e..f29abf59 100644
--- a/src/templates/CancerRelatedMedicationTemplate.js
+++ b/src/templates/CancerRelatedMedicationTemplate.js
@@ -58,7 +58,7 @@ function treatmentReasonTemplate({ treatmentReasonCode, treatmentReasonCodeSyste
 
 
 function cancerRelatedMedicationTemplate({
-  mrn,
+  subjectId,
   id,
   code,
   codeSystem,
@@ -71,8 +71,8 @@ function cancerRelatedMedicationTemplate({
   treatmentIntent,
   status,
 }) {
-  if (!(mrn && code && codeSystem && status)) {
-    throw Error('Trying to render a CancerRelatedMedicationTemplate, but a required argument is missing; ensure that mrn, code, code system, and status are all present');
+  if (!(subjectId && code && codeSystem && status)) {
+    throw Error('Trying to render a CancerRelatedMedicationTemplate, but a required argument is missing; ensure that subjectId, code, code system, and status are all present');
   }
 
   return {
@@ -86,7 +86,7 @@ function cancerRelatedMedicationTemplate({
     ...extensionArr(ifAllArgsObj(treatmentIntentTemplate)({ treatmentIntent })),
     status,
     ...medicationTemplate({ code, codeSystem, displayText }),
-    ...ifAllArgsObj(subjectTemplate)({ id: mrn }),
+    ...ifAllArgsObj(subjectTemplate)({ id: subjectId }),
     ...periodTemplate({ startDate, endDate }),
     ...ifAllArgsObj(treatmentReasonTemplate)({ treatmentReasonCode, treatmentReasonCodeSystem, treatmentReasonDisplayText }),
   };
diff --git a/src/templates/CarePlanWithReviewTemplate.js b/src/templates/CarePlanWithReviewTemplate.js
index 5ac7b9e0..653f11c6 100644
--- a/src/templates/CarePlanWithReviewTemplate.js
+++ b/src/templates/CarePlanWithReviewTemplate.js
@@ -82,10 +82,10 @@ function categoryTemplate() {
 // Treatment Plan Change modeled with CarePlanWithReview Template
 // Uses the ICARE R4 Care Plan profile which is not published yet
 // For reference, ICARE R4 Care Plan profile: http://standardhealthrecord.org/guides/icare/StructureDefinition-icare-care-plan-with-review.html
-function carePlanWithReviewTemplate({ id, mrn, name, reviews }) {
-  if (!(id && mrn && reviews)) {
+function carePlanWithReviewTemplate({ id, subjectId, name, reviews }) {
+  if (!(id && subjectId && reviews)) {
     const errorMessage = 'Trying to render a CarePlanWithReviewTemplate, but a required argument was missing; '
-      + 'ensure that id, mrn, reviews are all present';
+      + 'ensure that id, subjectId, reviews are all present';
     throw new Error(errorMessage);
   }
   return {
@@ -96,7 +96,7 @@ function carePlanWithReviewTemplate({ id, mrn, name, reviews }) {
     ...extensionArr(
       ...reviews.map(carePlanChangeReasonExtensionTemplate),
     ),
-    ...subjectTemplate({ id: mrn, name }),
+    ...subjectTemplate({ id: subjectId, name }),
     status: 'draft',
     intent: 'proposal',
     ...categoryTemplate(),
diff --git a/test/extractors/CSVAdverseEventExtractor.test.js b/test/extractors/CSVAdverseEventExtractor.test.js
index 4abc75e6..c36650bb 100644
--- a/test/extractors/CSVAdverseEventExtractor.test.js
+++ b/test/extractors/CSVAdverseEventExtractor.test.js
@@ -2,14 +2,13 @@ const path = require('path');
 const rewire = require('rewire');
 const _ = require('lodash');
 const { CSVAdverseEventExtractor } = require('../../src/extractors');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const exampleCSVAdverseEventModuleResponse = require('./fixtures/csv-adverse-event-module-response.json');
 const exampleCSVAdverseEventBundle = require('./fixtures/csv-adverse-event-bundle.json');
-
-// Rewired extractor for helper tests
-const CSVAdverseEventExtractorRewired = rewire('../../src/extractors/CSVAdverseEventExtractor.js');
+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 above
+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
 
 // Instantiate module with parameters
@@ -23,51 +22,54 @@ const { csvModule } = csvAdverseEventExtractor;
 // Spy on csvModule
 const csvModuleSpy = jest.spyOn(csvModule, 'get');
 
-const formatData = CSVAdverseEventExtractorRewired.__get__('formatData');
-
 // Creating an example bundle with two medication statements
 const exampleEntry = exampleCSVAdverseEventModuleResponse[0];
 const expandedExampleBundle = _.cloneDeep(exampleCSVAdverseEventBundle);
 expandedExampleBundle.entry.push(exampleCSVAdverseEventBundle.entry[0]);
 
+// Rewired extractor for helper tests
+const CSVAdverseEventExtractorRewired = rewire('../../src/extractors/CSVAdverseEventExtractor.js');
+
 describe('CSVAdverseEventExtractor', () => {
   describe('formatData', () => {
+    const formatData = CSVAdverseEventExtractorRewired.__get__('formatData');
     test('should join data appropriately and throw errors when missing required properties', () => {
-      const expectedErrorString = 'The adverse event is missing an expected attribute. Adverse event code, mrn, and effective date are all required.';
+      const expectedErrorString = 'The adverse event is missing an expected attribute. Adverse event code and effective date are all required.';
       const expectedCategoryErrorString = 'A category attribute on the adverse event is missing a corresponding categoryCodeSystem or categoryDisplayText value.';
       const localData = _.cloneDeep(exampleCSVAdverseEventModuleResponse);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
 
       // Test that valid maximal data works fine
-      expect(formatData(exampleCSVAdverseEventModuleResponse)).toEqual(expect.anything());
+      expect(formatData(exampleCSVAdverseEventModuleResponse, patientId)).toEqual(expect.anything());
 
       // Test that deleting an optional value works fine
       delete localData[0].actuality;
-      expect(formatData(exampleCSVAdverseEventModuleResponse)).toEqual(expect.anything());
+      expect(formatData(exampleCSVAdverseEventModuleResponse, patientId)).toEqual(expect.anything());
 
       // Test that adding another category but not adding a corresponding categoryCodeSystem throws an error
       localData[0].category = 'product-use-error|product-problem';
-      expect(() => formatData(localData)).toThrow(new Error(expectedCategoryErrorString));
+      expect(() => formatData(localData, patientId)).toThrow(new Error(expectedCategoryErrorString));
 
       // Test that adding another category but adding a corresponding categoryCodeSystem and categoryDisplayText works fine
       localData[0].categoryCodeSystem = 'http://terminology.hl7.org/CodeSystem/adverse-event-category|http://snomed.info/sct';
       localData[0].categoryDisplayText = 'Product Use Error|Product Problem';
-      expect(formatData(localData)).toEqual(expect.anything());
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
 
       // Test that adding another category but including syntax for default categoryCodeSystem and categoryDisplayText values works fine
       localData[0].categoryCodeSystem = 'http://terminology.hl7.org/CodeSystem/adverse-event-category|';
       localData[0].categoryDisplayText = 'Product Use Error|';
-      expect(formatData(localData)).toEqual(expect.anything());
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
 
       // Test that deleting a mandatory value throws an error
-      delete localData[0].mrn;
-      expect(() => formatData(localData)).toThrow(new Error(expectedErrorString));
+      delete localData[0].adverseEventCode;
+      expect(() => formatData(localData, patientId)).toThrow(new Error(expectedErrorString));
     });
   });
 
   describe('get', () => {
     test('should return bundle with an AdverseEvent resource', async () => {
       csvModuleSpy.mockReturnValue(exampleCSVAdverseEventModuleResponse);
-      const data = await csvAdverseEventExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvAdverseEventExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -77,7 +79,7 @@ describe('CSVAdverseEventExtractor', () => {
 
     test('should return empty bundle when no data available from module', async () => {
       csvModuleSpy.mockReturnValue([]);
-      const data = await csvAdverseEventExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvAdverseEventExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -87,7 +89,7 @@ describe('CSVAdverseEventExtractor', () => {
     test('get() should return an array of 2 when two adverse event resources are tied to a single patient', async () => {
       exampleCSVAdverseEventModuleResponse.push(exampleEntry);
       csvModuleSpy.mockReturnValue(exampleCSVAdverseEventModuleResponse);
-      const data = await csvAdverseEventExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvAdverseEventExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
 
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
diff --git a/test/extractors/FHIRConditionExtractor.test.js b/test/extractors/FHIRConditionExtractor.test.js
index 91f92172..9da357a7 100644
--- a/test/extractors/FHIRConditionExtractor.test.js
+++ b/test/extractors/FHIRConditionExtractor.test.js
@@ -1,20 +1,12 @@
 const rewire = require('rewire');
 const { FHIRConditionExtractor } = require('../../src/extractors/FHIRConditionExtractor.js');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 const FHIRConditionExtractorRewired = rewire('../../src/extractors/FHIRConditionExtractor');
 const MOCK_URL = 'http://example.com';
 const MOCK_HEADERS = {};
-const MOCK_MRN = '123456789';
 const MOCK_CATEGORIES = 'category1,category2';
-const MOCK_CONTEXT = {
-  resourceType: 'Bundle',
-  entry: [
-    {
-      fullUrl: 'context-url',
-      resource: { resourceType: 'Patient', id: MOCK_MRN },
-    },
-  ],
-};
+
 
 const extractor = new FHIRConditionExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS });
 const extractorWithCategories = new FHIRConditionExtractor({ baseFhirUrl: MOCK_URL, requestHeaders: MOCK_HEADERS, category: MOCK_CATEGORIES });
diff --git a/test/extractors/fixtures/context-with-patient.json b/test/extractors/fixtures/context-with-patient.json
new file mode 100644
index 00000000..d486da9b
--- /dev/null
+++ b/test/extractors/fixtures/context-with-patient.json
@@ -0,0 +1,12 @@
+{
+  "resourceType": "Bundle",
+  "entry": [
+    {
+      "fullUrl": "context-url",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "mrn-1"
+      }
+    }
+  ]
+}

From bf4ef147717e42462a1efac1263a12cb9a3aef37 Mon Sep 17 00:00:00 2001
From: Dylan Phelan <dtphelan1@gmail.com>
Date: Thu, 15 Apr 2021 13:56:38 -0400
Subject: [PATCH 02/10] Fixed CDS Extractor

---
 .../CSVCancerDiseaseStatusExtractor.test.js   | 10 ++++----
 .../csv-cancer-disease-status-bundle.json     | 24 +++++++++----------
 2 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/test/extractors/CSVCancerDiseaseStatusExtractor.test.js b/test/extractors/CSVCancerDiseaseStatusExtractor.test.js
index 890cd8e1..9d6656cf 100644
--- a/test/extractors/CSVCancerDiseaseStatusExtractor.test.js
+++ b/test/extractors/CSVCancerDiseaseStatusExtractor.test.js
@@ -1,8 +1,10 @@
 const path = require('path');
 const _ = require('lodash');
 const { CSVCancerDiseaseStatusExtractor } = require('../../src/extractors');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const exampleCSVDiseaseStatusModuleResponse = require('./fixtures/csv-cancer-disease-status-module-response.json');
 const exampleCSVDiseaseStatusBundle = require('./fixtures/csv-cancer-disease-status-bundle.json');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for tests
 const MOCK_PATIENT_MRN = 'pat-mrn-1'; // linked to values in example-module-response above
@@ -25,7 +27,7 @@ const csvModuleSpy = jest.spyOn(csvModule, 'get');
 describe('CSVCancerDiseaseStatusExtractor', () => {
   describe('joinAndReformatData', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
-      const expectedErrorString = 'DiseaseStatusData missing an expected property: mrn, conditionId, diseaseStatusCode, and dateOfObservation are required.';
+      const expectedErrorString = 'DiseaseStatusData missing an expected property: conditionId, diseaseStatusCode, and dateOfObservation are required.';
       const localData = _.cloneDeep(exampleCSVDiseaseStatusModuleResponse);
       // Test that valid data works fine
       expect(csvCancerDiseaseStatusExtractor.joinAndReformatData(exampleCSVDiseaseStatusModuleResponse)).toEqual(expect.anything());
@@ -36,7 +38,7 @@ describe('CSVCancerDiseaseStatusExtractor', () => {
       // Only including required properties is valid
       expect(csvCancerDiseaseStatusExtractor.joinAndReformatData(localData)).toEqual(expect.anything());
 
-      const requiredProperties = ['mrn', 'conditionId', 'diseaseStatusCode', 'dateOfObservation'];
+      const requiredProperties = ['conditionId', 'diseaseStatusCode', 'dateOfObservation'];
 
       // Removing each required property should throw an error
       requiredProperties.forEach((key) => {
@@ -50,7 +52,7 @@ describe('CSVCancerDiseaseStatusExtractor', () => {
   describe('get', () => {
     test('should return bundle with Observation', async () => {
       csvModuleSpy.mockReturnValue(exampleCSVDiseaseStatusModuleResponse);
-      const data = await csvCancerDiseaseStatusExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvCancerDiseaseStatusExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -60,7 +62,7 @@ describe('CSVCancerDiseaseStatusExtractor', () => {
 
     test('should return empty bundle when no data available from module', async () => {
       csvModuleSpy.mockReturnValue([]);
-      const data = await csvCancerDiseaseStatusExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvCancerDiseaseStatusExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
diff --git a/test/extractors/fixtures/csv-cancer-disease-status-bundle.json b/test/extractors/fixtures/csv-cancer-disease-status-bundle.json
index fcde7d2f..7ce64901 100644
--- a/test/extractors/fixtures/csv-cancer-disease-status-bundle.json
+++ b/test/extractors/fixtures/csv-cancer-disease-status-bundle.json
@@ -3,10 +3,10 @@
   "type": "collection",
   "entry": [
     {
-      "fullUrl": "urn:uuid:d1d13594c371179797ce1a58884f714624d5b1782c4775f0fa303d78e943d64c",
+      "fullUrl": "urn:uuid:4b9e9b5a8db529782cd9e89b68c6a3fac408d2195f025691a3f2850cab18057f",
       "resource": {
         "resourceType": "Observation",
-        "id": "d1d13594c371179797ce1a58884f714624d5b1782c4775f0fa303d78e943d64c",
+        "id": "4b9e9b5a8db529782cd9e89b68c6a3fac408d2195f025691a3f2850cab18057f",
         "meta": {
           "profile": [
             "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-disease-status"
@@ -40,7 +40,7 @@
           }
         ],
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1",
+          "reference": "urn:uuid:mrn-1",
           "type": "Patient"
         },
         "effectiveDateTime": "2019-12-02",
@@ -53,13 +53,13 @@
             }
           ]
         },
-        "extension" : [
+        "extension": [
           {
-            "url" : "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-evidence-type",
-            "valueCodeableConcept" : {
-              "coding" : [
+            "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-evidence-type",
+            "valueCodeableConcept": {
+              "coding": [
                 {
-                  "system" : "http://snomed.info/sct",
+                  "system": "http://snomed.info/sct",
                   "display": "imaging",
                   "code": "363679005"
                 }
@@ -67,11 +67,11 @@
             }
           },
           {
-            "url" : "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-evidence-type",
-            "valueCodeableConcept" : {
-              "coding" : [
+            "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-evidence-type",
+            "valueCodeableConcept": {
+              "coding": [
                 {
-                  "system" : "http://snomed.info/sct",
+                  "system": "http://snomed.info/sct",
                   "display": "pathology",
                   "code": "252416005"
                 }

From c4ad9c64c6774d4da17f56f12e6f2ee6cc3f682a Mon Sep 17 00:00:00 2001
From: Dylan Phelan <dtphelan1@gmail.com>
Date: Thu, 15 Apr 2021 14:14:58 -0400
Subject: [PATCH 03/10] Done CancerRelatedMeds; minor fixes to CDS and AE

---
 test/extractors/CSVAdverseEventExtractor.test.js |  2 +-
 .../CSVCancerDiseaseStatusExtractor.test.js      | 10 ++++++----
 .../CSVCancerRelatedMedicationExtractor.test.js  | 16 +++++++++-------
 3 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/test/extractors/CSVAdverseEventExtractor.test.js b/test/extractors/CSVAdverseEventExtractor.test.js
index c36650bb..a6161e85 100644
--- a/test/extractors/CSVAdverseEventExtractor.test.js
+++ b/test/extractors/CSVAdverseEventExtractor.test.js
@@ -2,9 +2,9 @@ const path = require('path');
 const rewire = require('rewire');
 const _ = require('lodash');
 const { CSVAdverseEventExtractor } = require('../../src/extractors');
-const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const exampleCSVAdverseEventModuleResponse = require('./fixtures/csv-adverse-event-module-response.json');
 const exampleCSVAdverseEventBundle = require('./fixtures/csv-adverse-event-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for tests
diff --git a/test/extractors/CSVCancerDiseaseStatusExtractor.test.js b/test/extractors/CSVCancerDiseaseStatusExtractor.test.js
index 9d6656cf..7a01dc5f 100644
--- a/test/extractors/CSVCancerDiseaseStatusExtractor.test.js
+++ b/test/extractors/CSVCancerDiseaseStatusExtractor.test.js
@@ -1,9 +1,9 @@
 const path = require('path');
 const _ = require('lodash');
 const { CSVCancerDiseaseStatusExtractor } = require('../../src/extractors');
-const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const exampleCSVDiseaseStatusModuleResponse = require('./fixtures/csv-cancer-disease-status-module-response.json');
 const exampleCSVDiseaseStatusBundle = require('./fixtures/csv-cancer-disease-status-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for tests
@@ -29,14 +29,16 @@ describe('CSVCancerDiseaseStatusExtractor', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
       const expectedErrorString = 'DiseaseStatusData missing an expected property: conditionId, diseaseStatusCode, and dateOfObservation are required.';
       const localData = _.cloneDeep(exampleCSVDiseaseStatusModuleResponse);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
+
       // Test that valid data works fine
-      expect(csvCancerDiseaseStatusExtractor.joinAndReformatData(exampleCSVDiseaseStatusModuleResponse)).toEqual(expect.anything());
+      expect(csvCancerDiseaseStatusExtractor.joinAndReformatData(exampleCSVDiseaseStatusModuleResponse, patientId)).toEqual(expect.anything());
 
       localData[0].evidence = ''; // Evidence is not required and will not throw an error
       localData[0].observationStatus = ''; // Observation Status is not required and will not throw an error
 
       // Only including required properties is valid
-      expect(csvCancerDiseaseStatusExtractor.joinAndReformatData(localData)).toEqual(expect.anything());
+      expect(csvCancerDiseaseStatusExtractor.joinAndReformatData(localData, patientId)).toEqual(expect.anything());
 
       const requiredProperties = ['conditionId', 'diseaseStatusCode', 'dateOfObservation'];
 
@@ -44,7 +46,7 @@ describe('CSVCancerDiseaseStatusExtractor', () => {
       requiredProperties.forEach((key) => {
         const clonedData = _.cloneDeep(localData);
         clonedData[0][key] = '';
-        expect(() => csvCancerDiseaseStatusExtractor.joinAndReformatData(clonedData)).toThrow(new Error(expectedErrorString));
+        expect(() => csvCancerDiseaseStatusExtractor.joinAndReformatData(clonedData, patientId)).toThrow(new Error(expectedErrorString));
       });
     });
   });
diff --git a/test/extractors/CSVCancerRelatedMedicationExtractor.test.js b/test/extractors/CSVCancerRelatedMedicationExtractor.test.js
index 500689a2..3e4ef964 100644
--- a/test/extractors/CSVCancerRelatedMedicationExtractor.test.js
+++ b/test/extractors/CSVCancerRelatedMedicationExtractor.test.js
@@ -4,6 +4,8 @@ const _ = require('lodash');
 const { CSVCancerRelatedMedicationExtractor } = require('../../src/extractors');
 const exampleCSVMedicationModuleResponse = require('./fixtures/csv-medication-module-response.json');
 const exampleCSVMedicationBundle = require('./fixtures/csv-medication-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Rewired extractor for helper tests
 const CSVCancerRelatedMedicationExtractorRewired = rewire('../../src/extractors/CSVCancerRelatedMedicationExtractor.js');
@@ -35,24 +37,25 @@ describe('CSVCancerRelatedMedicationExtractor', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
       const expectedErrorString = 'The cancer-related medication is missing an expected element; mrn, code, code system, and status are all required values.';
       const localData = _.cloneDeep(exampleCSVMedicationModuleResponse);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
 
       // Test that valid maximal data works fine
-      expect(formatData(exampleCSVMedicationModuleResponse)).toEqual(expect.anything());
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
 
       // Test that deleting an optional value works fine
       delete localData[0].treatmentIntent;
-      expect(formatData(exampleCSVMedicationModuleResponse)).toEqual(expect.anything());
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
 
       // Test that deleting a mandatory value throws an error
       delete localData[0].code;
-      expect(() => formatData(localData)).toThrow(new Error(expectedErrorString));
+      expect(() => formatData(localData, patientId)).toThrow(new Error(expectedErrorString));
     });
   });
 
   describe('get', () => {
     test('should return bundle with a CancerRelatedMedication', async () => {
       csvModuleSpy.mockReturnValue(exampleCSVMedicationModuleResponse);
-      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -62,7 +65,7 @@ describe('CSVCancerRelatedMedicationExtractor', () => {
 
     test('should return empty bundle when no data available from module', async () => {
       csvModuleSpy.mockReturnValue([]);
-      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -72,8 +75,7 @@ describe('CSVCancerRelatedMedicationExtractor', () => {
     test('get() should return an array of 2 when two medication statements are tied to a single patient', async () => {
       exampleCSVMedicationModuleResponse.push(exampleEntry);
       csvModuleSpy.mockReturnValue(exampleCSVMedicationModuleResponse);
-      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN });
-
+      const data = await csvCancerRelatedMedicationExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();

From 2a352486a419c8d94848389583cd97bc67bdae08 Mon Sep 17 00:00:00 2001
From: Dylan Phelan <dtphelan1@gmail.com>
Date: Thu, 15 Apr 2021 14:23:53 -0400
Subject: [PATCH 04/10] updates to CTI tests

---
 .../CSVClinicalTrialInformationExtractor.js   |  4 +-
 ...VClinicalTrialInformationExtractor.test.js | 48 ++++---------------
 ...csv-clinical-trial-information-bundle.json | 17 +++++--
 3 files changed, 23 insertions(+), 46 deletions(-)

diff --git a/src/extractors/CSVClinicalTrialInformationExtractor.js b/src/extractors/CSVClinicalTrialInformationExtractor.js
index 802c674a..71e0ebda 100644
--- a/src/extractors/CSVClinicalTrialInformationExtractor.js
+++ b/src/extractors/CSVClinicalTrialInformationExtractor.js
@@ -22,8 +22,8 @@ class CSVClinicalTrialInformationExtractor extends BaseCSVExtractor {
     } = clinicalTrialData;
     const { clinicalSiteID, clinicalSiteSystem } = this;
 
-    if (!(patientId && clinicalSiteID && trialSubjectID && enrollmentStatus && trialResearchID && trialStatus)) {
-      throw new Error('Clinical trial missing an expected property: patientId, clinicalSiteID, trialSubjectID, enrollmentStatus, trialResearchID, and trialStatus are required.');
+    if (!(clinicalSiteID && trialSubjectID && enrollmentStatus && trialResearchID && trialStatus)) {
+      throw new Error('Clinical trial missing an expected property: clinicalSiteID, trialSubjectID, enrollmentStatus, trialResearchID, and trialStatus are required.');
     }
 
     // Need separate data objects for ResearchSubject and ResearchStudy so that they get different resource ids
diff --git a/test/extractors/CSVClinicalTrialInformationExtractor.test.js b/test/extractors/CSVClinicalTrialInformationExtractor.test.js
index 0efd1f7d..1bea996c 100644
--- a/test/extractors/CSVClinicalTrialInformationExtractor.test.js
+++ b/test/extractors/CSVClinicalTrialInformationExtractor.test.js
@@ -1,9 +1,10 @@
 const path = require('path');
-const rewire = require('rewire');
 const _ = require('lodash');
 const { CSVClinicalTrialInformationExtractor } = require('../../src/extractors');
 const exampleClinicalTrialInformationResponse = require('./fixtures/csv-clinical-trial-information-module-response.json');
 const exampleClinicalTrialInformationBundle = require('./fixtures/csv-clinical-trial-information-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for mock tests
 const MOCK_CSV_PATH = path.join(__dirname, 'fixtures/example.csv'); // need a valid path/csv here to avoid parse error
@@ -26,34 +27,30 @@ const csvModuleSpy = jest.spyOn(csvModule, 'get');
 csvModuleSpy
   .mockReturnValue(exampleClinicalTrialInformationResponse);
 
-const getPatientId = rewire('../../src/extractors/CSVClinicalTrialInformationExtractor.js').__get__('getPatientId');
-
 describe('CSVClinicalTrialInformationExtractor', () => {
   describe('joinClinicalTrialData', () => {
     test('should join clinical trial data appropriately and throw errors when missing required properties', () => {
       const firstClinicalTrialInfoResponse = exampleClinicalTrialInformationResponse[0]; // Each patient will only have one entry per clinical trial
-      const expectedErrorString = 'Clinical trial missing an expected property: patientId, clinicalSiteID, trialSubjectID, enrollmentStatus, trialResearchID, and trialStatus are required.';
+      const expectedErrorString = 'Clinical trial missing an expected property: clinicalSiteID, trialSubjectID, enrollmentStatus, trialResearchID, and trialStatus are required.';
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
 
       // Test required properties in CSV throw error
       Object.keys(firstClinicalTrialInfoResponse).forEach((key) => {
         const clonedData = _.cloneDeep(firstClinicalTrialInfoResponse);
-        expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(MOCK_PATIENT_MRN, clonedData)).toEqual(expect.anything());
+        expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(clonedData, patientId)).toEqual(expect.anything());
         if (key === 'mrn') return; // MRN is not required from CSV
         if (key === 'trialResearchSystem') return; // trialResearchSystem is an optional field
         delete clonedData[key];
-        expect(() => csvClinicalTrialInformationExtractor.joinClinicalTrialData(MOCK_PATIENT_MRN, clonedData)).toThrow(new Error(expectedErrorString));
+        expect(() => csvClinicalTrialInformationExtractor.joinClinicalTrialData(clonedData, patientId)).toThrow(new Error(expectedErrorString));
       });
 
-      // patientId is required to be passed in
-      expect(() => csvClinicalTrialInformationExtractor.joinClinicalTrialData(undefined, firstClinicalTrialInfoResponse)).toThrow(new Error(expectedErrorString));
-
       // joinClinicalTrialData should return correct format
-      expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(MOCK_PATIENT_MRN, firstClinicalTrialInfoResponse)).toEqual({
+      expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(firstClinicalTrialInfoResponse, patientId)).toEqual({
         formattedDataSubject: {
           enrollmentStatus: firstClinicalTrialInfoResponse.enrollmentStatus,
           trialSubjectID: firstClinicalTrialInfoResponse.trialSubjectID,
           trialResearchID: firstClinicalTrialInfoResponse.trialResearchID,
-          patientId: MOCK_PATIENT_MRN,
+          patientId,
           trialResearchSystem: firstClinicalTrialInfoResponse.trialResearchSystem,
         },
         formattedDataStudy: {
@@ -67,36 +64,9 @@ describe('CSVClinicalTrialInformationExtractor', () => {
     });
   });
 
-  describe('getPatientId', () => {
-    test('should return patient id when patient resource in context', () => {
-      const contextPatient = {
-        resourceType: 'Patient',
-        id: 'context-patient-id',
-      };
-      const contextBundle = {
-        resourceType: 'Bundle',
-        type: 'collection',
-        entry: [
-          {
-            fullUrl: 'context-url',
-            resource: contextPatient,
-          },
-        ],
-      };
-
-      const patientId = getPatientId(contextBundle);
-      expect(patientId).toEqual(contextPatient.id);
-    });
-
-    test('getPatientId should return undefined when no patient resource in context', () => {
-      const patientId = getPatientId({});
-      expect(patientId).toBeUndefined();
-    });
-  });
-
   describe('get', () => {
     test('should return a bundle with the correct resources', async () => {
-      const data = await csvClinicalTrialInformationExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvClinicalTrialInformationExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
 
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
diff --git a/test/extractors/fixtures/csv-clinical-trial-information-bundle.json b/test/extractors/fixtures/csv-clinical-trial-information-bundle.json
index fe1bec3f..f583d355 100644
--- a/test/extractors/fixtures/csv-clinical-trial-information-bundle.json
+++ b/test/extractors/fixtures/csv-clinical-trial-information-bundle.json
@@ -3,14 +3,16 @@
   "type": "collection",
   "entry": [
     {
-      "fullUrl": "urn:uuid:f8acc19f44696eea31532ac9d3b658f1fea317eba9455eddc78de0857220d362",
+      "fullUrl": "urn:uuid:a9235b06dfe8c24b40b938c7a1265ed3087cf0fa43ef0f11375effbb25ecca25",
       "resource": {
         "resourceType": "ResearchSubject",
-        "id": "f8acc19f44696eea31532ac9d3b658f1fea317eba9455eddc78de0857220d362",
+        "id": "a9235b06dfe8c24b40b938c7a1265ed3087cf0fa43ef0f11375effbb25ecca25",
         "identifier": [
           {
             "system": "http://example.com/clinicaltrialsubjectids",
-            "type": { "text": "Clinical Trial Subject ID" },
+            "type": {
+              "text": "Clinical Trial Subject ID"
+            },
             "value": "example-subjectId"
           }
         ],
@@ -21,7 +23,10 @@
             "value": "example-researchId"
           }
         },
-        "individual": { "reference": "urn:uuid:EXAMPLE-MRN", "type": "Patient" }
+        "individual": {
+          "reference": "urn:uuid:mrn-1",
+          "type": "Patient"
+        }
       }
     },
     {
@@ -42,7 +47,9 @@
         "identifier": [
           {
             "system": "example-system",
-            "type": { "text": "Clinical Trial Research ID" },
+            "type": {
+              "text": "Clinical Trial Research ID"
+            },
             "value": "example-researchId"
           }
         ]

From 40a8646fba9cabc298326e7cff0ab3c88ba3e438 Mon Sep 17 00:00:00 2001
From: Dylan Phelan <dtphelan1@gmail.com>
Date: Thu, 15 Apr 2021 17:00:21 -0400
Subject: [PATCH 05/10] Consistency updates and comments; fix procedure,
 observation, condition tests

---
 .../CSVCancerDiseaseStatusExtractor.test.js   |  2 +-
 ...SVCancerRelatedMedicationExtractor.test.js |  2 +-
 ...VClinicalTrialInformationExtractor.test.js |  6 +--
 test/extractors/CSVConditionExtractor.test.js | 47 ++++++++++---------
 .../CSVObservationExtractor.test.js           | 15 +++---
 test/extractors/CSVProcedureExtractor.test.js | 18 ++++---
 ...cancer-disease-status-module-response.json |  2 +-
 ...cal-trial-information-module-response.json |  4 +-
 .../fixtures/csv-observation-bundle.json      | 15 +++---
 .../csv-observation-module-response.json      |  4 +-
 10 files changed, 62 insertions(+), 53 deletions(-)

diff --git a/test/extractors/CSVCancerDiseaseStatusExtractor.test.js b/test/extractors/CSVCancerDiseaseStatusExtractor.test.js
index 7a01dc5f..54d3d5f7 100644
--- a/test/extractors/CSVCancerDiseaseStatusExtractor.test.js
+++ b/test/extractors/CSVCancerDiseaseStatusExtractor.test.js
@@ -7,7 +7,7 @@ const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for tests
-const MOCK_PATIENT_MRN = 'pat-mrn-1'; // linked to values in example-module-response above
+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';
 
diff --git a/test/extractors/CSVCancerRelatedMedicationExtractor.test.js b/test/extractors/CSVCancerRelatedMedicationExtractor.test.js
index 3e4ef964..2473ac67 100644
--- a/test/extractors/CSVCancerRelatedMedicationExtractor.test.js
+++ b/test/extractors/CSVCancerRelatedMedicationExtractor.test.js
@@ -11,7 +11,7 @@ const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 const CSVCancerRelatedMedicationExtractorRewired = rewire('../../src/extractors/CSVCancerRelatedMedicationExtractor.js');
 
 // Constants for tests
-const MOCK_PATIENT_MRN = 'mrn-1'; // linked to values in example-module-response above
+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
 
 // Instantiate module with parameters
diff --git a/test/extractors/CSVClinicalTrialInformationExtractor.test.js b/test/extractors/CSVClinicalTrialInformationExtractor.test.js
index 1bea996c..073252d2 100644
--- a/test/extractors/CSVClinicalTrialInformationExtractor.test.js
+++ b/test/extractors/CSVClinicalTrialInformationExtractor.test.js
@@ -7,10 +7,10 @@ const { getPatientFromContext } = require('../../src/helpers/contextUtils');
 const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for mock 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 MOCK_CLINICAL_SITE_ID = 'EXAMPLE-CLINICAL-SITE-ID';
 const MOCK_CLINICAL_SITE_SYSTEM = 'EXAMPLE-CLINICAL-SITE-SYSTEM';
-const MOCK_PATIENT_MRN = 'EXAMPLE-MRN';
 
 // Instantiate module with mock parameters
 const csvClinicalTrialInformationExtractor = new CSVClinicalTrialInformationExtractor({
@@ -38,8 +38,8 @@ describe('CSVClinicalTrialInformationExtractor', () => {
       Object.keys(firstClinicalTrialInfoResponse).forEach((key) => {
         const clonedData = _.cloneDeep(firstClinicalTrialInfoResponse);
         expect(csvClinicalTrialInformationExtractor.joinClinicalTrialData(clonedData, patientId)).toEqual(expect.anything());
-        if (key === 'mrn') return; // MRN is not required from CSV
-        if (key === 'trialResearchSystem') return; // trialResearchSystem is an optional field
+        if (key === 'patientId') return; // MRN is optional
+        if (key === 'trialResearchSystem') return; // trialResearchSystem is optional
         delete clonedData[key];
         expect(() => csvClinicalTrialInformationExtractor.joinClinicalTrialData(clonedData, patientId)).toThrow(new Error(expectedErrorString));
       });
diff --git a/test/extractors/CSVConditionExtractor.test.js b/test/extractors/CSVConditionExtractor.test.js
index d0232b5c..3e7ff71d 100644
--- a/test/extractors/CSVConditionExtractor.test.js
+++ b/test/extractors/CSVConditionExtractor.test.js
@@ -3,9 +3,10 @@ const _ = require('lodash');
 const { CSVConditionExtractor } = require('../../src/extractors');
 const exampleConditionResponse = require('./fixtures/csv-condition-module-response.json');
 const exampleConditionBundle = require('./fixtures/csv-condition-bundle.json');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for mock tests
-const MOCK_PATIENT_MRN = 'mrn-1';
+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 csvConditionExtractor = new CSVConditionExtractor({
   filePath: MOCK_CSV_PATH,
@@ -23,26 +24,28 @@ expandedExampleBundle.entry.push(exampleConditionBundle.entry[0]);
 
 
 describe('CSV Condition Extractor tests', () => {
-  test('get should return a fhir bundle when MRN is known', async () => {
-    csvModuleSpy.mockReturnValue(exampleConditionResponse);
-    const data = await csvConditionExtractor.get({ mrn: MOCK_PATIENT_MRN });
-
-    expect(data.resourceType).toEqual('Bundle');
-    expect(data.type).toEqual('collection');
-    expect(data.entry).toBeDefined();
-    expect(data.entry.length).toEqual(1);
-    expect(data).toEqual(exampleConditionBundle);
-  });
-
-  test('get() should return an array of 2 when two conditions are tied to a single patient', async () => {
-    exampleConditionResponse.push(exampleEntry);
-    csvModuleSpy.mockReturnValue(exampleConditionResponse);
-    const data = await csvConditionExtractor.get({ mrn: MOCK_PATIENT_MRN });
-
-    expect(data.resourceType).toEqual('Bundle');
-    expect(data.type).toEqual('collection');
-    expect(data.entry).toBeDefined();
-    expect(data.entry.length).toEqual(2);
-    expect(data).toEqual(expandedExampleBundle);
+  describe('get', () => {
+    test('get should return a fhir bundle when MRN is known', async () => {
+      csvModuleSpy.mockReturnValue(exampleConditionResponse);
+      const data = await csvConditionExtractor.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).toEqual(exampleConditionBundle);
+    });
+
+    test('get() should return an array of 2 when two conditions are tied to a single patient', async () => {
+      exampleConditionResponse.push(exampleEntry);
+      csvModuleSpy.mockReturnValue(exampleConditionResponse);
+      const data = await csvConditionExtractor.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(2);
+      expect(data).toEqual(expandedExampleBundle);
+    });
   });
 });
diff --git a/test/extractors/CSVObservationExtractor.test.js b/test/extractors/CSVObservationExtractor.test.js
index 6f15dbdc..9922d400 100644
--- a/test/extractors/CSVObservationExtractor.test.js
+++ b/test/extractors/CSVObservationExtractor.test.js
@@ -4,12 +4,14 @@ const _ = require('lodash');
 const { CSVObservationExtractor } = require('../../src/extractors');
 const exampleCSVObservationModuleResponse = require('./fixtures/csv-observation-module-response.json');
 const exampleCSVObservationBundle = require('./fixtures/csv-observation-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Rewired extractor for helper tests
 const CSVObservationExtractorRewired = rewire('../../src/extractors/CSVObservationExtractor.js');
 
 // Constants for tests
-const MOCK_PATIENT_MRN = 'pat-mrn-1'; // linked to values in example-module-response above
+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
 
 // Instantiate module with parameters
@@ -28,15 +30,16 @@ const formatData = CSVObservationExtractorRewired.__get__('formatData');
 describe('CSVObservationExtractor', () => {
   describe('formatData', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
-      const expectedErrorString = 'The observation is missing an expected attribute. Observation id, mrn, status, code, code system, value, and effective date are all required.';
+      const expectedErrorString = 'The observation is missing an expected attribute. Observation id, status, code, code system, value, and effective date are all required.';
       const localData = _.cloneDeep(exampleCSVObservationModuleResponse);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
 
       // Test that valid maximal data works fine
-      expect(formatData(exampleCSVObservationModuleResponse)).toEqual(expect.anything());
+      expect(formatData(exampleCSVObservationModuleResponse, patientId)).toEqual(expect.anything());
 
       // Test that deleting an optional value works fine
       delete localData[0].bodySite;
-      expect(formatData(exampleCSVObservationModuleResponse)).toEqual(expect.anything());
+      expect(formatData(exampleCSVObservationModuleResponse, patientId)).toEqual(expect.anything());
 
       // Test that deleting a mandatory value throws an error
       delete localData[0].status;
@@ -47,7 +50,7 @@ describe('CSVObservationExtractor', () => {
   describe('get', () => {
     test('should return bundle with Observation', async () => {
       csvModuleSpy.mockReturnValue(exampleCSVObservationModuleResponse);
-      const data = await csvObservationExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvObservationExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -57,7 +60,7 @@ describe('CSVObservationExtractor', () => {
 
     test('should return empty bundle when no data available from module', async () => {
       csvModuleSpy.mockReturnValue([]);
-      const data = await csvObservationExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvObservationExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
diff --git a/test/extractors/CSVProcedureExtractor.test.js b/test/extractors/CSVProcedureExtractor.test.js
index 084560b2..65592c39 100644
--- a/test/extractors/CSVProcedureExtractor.test.js
+++ b/test/extractors/CSVProcedureExtractor.test.js
@@ -4,12 +4,14 @@ const _ = require('lodash');
 const { CSVProcedureExtractor } = require('../../src/extractors');
 const exampleCSVProcedureModuleResponse = require('./fixtures/csv-procedure-module-response.json');
 const exampleCSVProcedureBundle = require('./fixtures/csv-procedure-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Rewired extractor for helper tests
 const CSVProcedureExtractorRewired = rewire('../../src/extractors/CSVProcedureExtractor.js');
 
 // Constants for tests
-const MOCK_PATIENT_MRN = 'mrn-1'; // linked to values in example-module-response above
+const MOCK_PATIENT_MRN = 'mrn-1'; // linked to values in example-module-response and patient-context above
 const MOCK_CSV_PATH = path.join(__dirname, 'fixtures/example.csv'); // need a valid path/csv here to avoid parse error
 
 // Instantiate module with parameters
@@ -27,25 +29,27 @@ const formatData = CSVProcedureExtractorRewired.__get__('formatData');
 describe('CSVProcedureExtractor', () => {
   describe('formatData', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
-      const expectedErrorString = 'The procedure is missing an expected attribute. Procedure id, mrn, code system, code, status and effective date are all required.';
+      const expectedErrorString = 'The procedure is missing an expected attribute. Procedure id, code system, code, status and effective date are all required.';
       const localData = _.cloneDeep(exampleCSVProcedureModuleResponse);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
+
       // Test that valid data works fine
-      expect(formatData(localData)).toEqual(expect.anything());
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
 
       // Test that removing an optional value works
       delete localData[0].bodySite;
-      expect(formatData(localData)).toEqual(expect.anything());
+      expect(formatData(localData, patientId)).toEqual(expect.anything());
 
       // Test that removing a required value throws
       delete localData[0].procedureId;
-      expect(() => formatData(localData)).toThrow(new Error(expectedErrorString));
+      expect(() => formatData(localData, patientId)).toThrow(new Error(expectedErrorString));
     });
   });
 
   describe('get', () => {
     test('should return bundle with Procedure', async () => {
       csvModuleSpy.mockReturnValue(exampleCSVProcedureModuleResponse);
-      const data = await csvProcedureExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvProcedureExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -55,7 +59,7 @@ describe('CSVProcedureExtractor', () => {
 
     test('should return empty bundle when no data available from module', async () => {
       csvModuleSpy.mockReturnValue([]);
-      const data = await csvProcedureExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvProcedureExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
diff --git a/test/extractors/fixtures/csv-cancer-disease-status-module-response.json b/test/extractors/fixtures/csv-cancer-disease-status-module-response.json
index 67c3f854..bc5a09ad 100644
--- a/test/extractors/fixtures/csv-cancer-disease-status-module-response.json
+++ b/test/extractors/fixtures/csv-cancer-disease-status-module-response.json
@@ -1,6 +1,6 @@
 [
   {
-    "mrn": "pat-mrn-1",
+    "mrn": "mrn-1",
     "conditionId": "cond-1",
     "diseaseStatusCode": "268910001",
     "dateOfObservation": "2019-12-02",
diff --git a/test/extractors/fixtures/csv-clinical-trial-information-module-response.json b/test/extractors/fixtures/csv-clinical-trial-information-module-response.json
index 735f811c..92558480 100644
--- a/test/extractors/fixtures/csv-clinical-trial-information-module-response.json
+++ b/test/extractors/fixtures/csv-clinical-trial-information-module-response.json
@@ -1,10 +1,10 @@
 [
   {
-    "mrn": "EXAMPLE-MRN",
+    "patientId": "mrn-1",
     "trialSubjectID": "example-subjectId",
     "enrollmentStatus": "example-enrollment-status",
     "trialResearchID": "example-researchId",
     "trialStatus": "example-trialStatus",
-    "trialResearchSystem":"example-system"
+    "trialResearchSystem": "example-system"
   }
 ]
diff --git a/test/extractors/fixtures/csv-observation-bundle.json b/test/extractors/fixtures/csv-observation-bundle.json
index 6c7cebdf..b610dfb1 100644
--- a/test/extractors/fixtures/csv-observation-bundle.json
+++ b/test/extractors/fixtures/csv-observation-bundle.json
@@ -17,7 +17,7 @@
               }
             ]
           }
-        ],  
+        ],
         "code": {
           "coding": [
             {
@@ -26,11 +26,11 @@
             }
           ]
         },
-        "subject" : {
-          "reference": "urn:uuid:example-patient",
+        "subject": {
+          "reference": "urn:uuid:mrn-1",
           "type": "Patient"
         },
-        "effectiveDateTime" : "2020-01-02",
+        "effectiveDateTime": "2020-01-02",
         "valueCodeableConcept": {
           "coding": [
             {
@@ -39,7 +39,7 @@
             }
           ]
         },
-        "bodySite": { 
+        "bodySite": {
           "extension": [
             {
               "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality",
@@ -52,16 +52,15 @@
                 ]
               }
             }
-          ], 
+          ],
           "coding": [
             {
               "system": "http://snomed.info/sct",
               "code": "12345"
             }
-          ] 
+          ]
         }
       }
     }
   ]
 }
-
diff --git a/test/extractors/fixtures/csv-observation-module-response.json b/test/extractors/fixtures/csv-observation-module-response.json
index 8c64ad16..d05e251b 100644
--- a/test/extractors/fixtures/csv-observation-module-response.json
+++ b/test/extractors/fixtures/csv-observation-module-response.json
@@ -1,6 +1,6 @@
 [
   {
-    "mrn": "example-patient",
+    "mrn": "mrn-1",
     "observationId": "observation-id",
     "status": "final",
     "code": "1695-6",
@@ -12,4 +12,4 @@
     "bodySite": "12345",
     "laterality": "678910"
   }
-]
\ No newline at end of file
+]

From ff76b0b1f572aecc9573df6030a822a58d001b6d Mon Sep 17 00:00:00 2001
From: Dylan Phelan <dtphelan1@gmail.com>
Date: Thu, 15 Apr 2021 18:10:06 -0400
Subject: [PATCH 06/10] Fix all tests here

---
 .../CSVTreatmentPlanChangeExtractor.js        |  8 ++--
 test/cli/fixtures/example-patient.csv         |  4 ++
 test/cli/mcodeExtraction.test.js              |  7 +++
 test/extractors/CSVStagingExtractor.test.js   | 17 ++++---
 .../CSVTreatmentPlanChangeExtractor.test.js   | 31 ++++++++-----
 .../fixtures/csv-staging-bundle.json          | 30 ++++++-------
 .../fixtures/csv-staging-module-response.json |  2 +-
 .../csv-treatment-plan-change-bundle.json     | 45 ++++++++++++++-----
 ...treatment-plan-change-module-response.json |  4 +-
 test/templates/carePlanWithReview.test.js     | 10 ++---
 test/templates/medication.test.js             |  8 ++--
 11 files changed, 107 insertions(+), 59 deletions(-)
 create mode 100644 test/cli/fixtures/example-patient.csv

diff --git a/src/extractors/CSVTreatmentPlanChangeExtractor.js b/src/extractors/CSVTreatmentPlanChangeExtractor.js
index cc21eb7a..e7a291a5 100644
--- a/src/extractors/CSVTreatmentPlanChangeExtractor.js
+++ b/src/extractors/CSVTreatmentPlanChangeExtractor.js
@@ -3,6 +3,7 @@ const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { formatDate } = require('../helpers/dateUtils');
 const { generateMcodeResources } = require('../templates');
 const { getEmptyBundle } = require('../helpers/fhirUtils');
+const { getPatientFromContext } = require('../helpers/contextUtils');
 const logger = require('../helpers/logger');
 const { CSVTreatmentPlanChangeSchema } = require('../helpers/schemas/csv');
 
@@ -15,7 +16,7 @@ function formatData(tpcData, patientId) {
     return [];
   }
 
-  // Newly combined data has mrn and list of reviews to map to an extension
+  // Newly combined data has subjectId and list of reviews to map to an extension
   const combinedFormat = { subjectId: patientId, reviews: [] };
 
   // If there are multiple entries, combine them into one object with multiple reviews
@@ -75,15 +76,16 @@ class CSVTreatmentPlanChangeExtractor extends BaseCSVExtractor {
     return this.csvModule.get('mrn', mrn, fromDate, toDate);
   }
 
-  async get({ mrn, fromDate, toDate }) {
+  async get({ mrn, context, fromDate, toDate }) {
     const tpcData = await this.getTPCData(mrn, fromDate, toDate);
     if (tpcData.length === 0) {
       logger.warn('No treatment plan change data found for patient');
       return getEmptyBundle();
     }
+    const patientId = getPatientFromContext(context).id;
 
     // Reformat data
-    const formattedData = formatData(tpcData);
+    const formattedData = formatData(tpcData, patientId);
 
     // Fill templates
     return generateMcodeResources('CarePlanWithReview', formattedData);
diff --git a/test/cli/fixtures/example-patient.csv b/test/cli/fixtures/example-patient.csv
new file mode 100644
index 00000000..10822054
--- /dev/null
+++ b/test/cli/fixtures/example-patient.csv
@@ -0,0 +1,4 @@
+mrn,familyName,givenName,gender,birthsex,dateOfBirth,race,ethnicity,language,addressLine,city,state,zip
+123,Doe,Jane,female,F,1980-01-01,2028-9,2186-5,en,2 West Side Rd,Malden,MA,02148
+456,Doe,John,male,M,1970-01-01,2106-3,2186-5,en-US,3 East Side Rd,Brooklyn,NY,11201
+789,Doe,Jimmy,other,UNK,1980-03-01,ASKU,2186-5,ar,,,,90001
diff --git a/test/cli/mcodeExtraction.test.js b/test/cli/mcodeExtraction.test.js
index 4cc33215..42c453d7 100644
--- a/test/cli/mcodeExtraction.test.js
+++ b/test/cli/mcodeExtraction.test.js
@@ -46,6 +46,13 @@ describe('mcodeExtraction', () => {
     it('should succeed in extraction when CSV files do not have data for all patients', async () => {
       const testConfig = {
         extractors: [
+          {
+            label: 'patients',
+            type: 'CSVPatientExtractor',
+            constructorArgs: {
+              filePath: path.join(__dirname, './fixtures/example-patient.csv'),
+            },
+          },
           {
             label: 'condition',
             type: 'CSVConditionExtractor',
diff --git a/test/extractors/CSVStagingExtractor.test.js b/test/extractors/CSVStagingExtractor.test.js
index e48c0c5b..c9eae1e4 100644
--- a/test/extractors/CSVStagingExtractor.test.js
+++ b/test/extractors/CSVStagingExtractor.test.js
@@ -4,9 +4,11 @@ const _ = require('lodash');
 const { CSVStagingExtractor } = require('../../src/extractors');
 const exampleStagingModuleResponse = require('./fixtures/csv-staging-module-response.json');
 const exampleCSVStagingBundle = require('./fixtures/csv-staging-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
 // Constants for tests
-const MOCK_PATIENT_MRN = 'pat-mrn-1'; // linked to values in example-module-response above
+const MOCK_PATIENT_MRN = 'mrn-1'; // linked to values in example-module-response above
 const MOCK_CSV_PATH = path.join(__dirname, 'fixtures/example.csv'); // need a valid path/csv here to avoid parse error
 
 // Instantiate module with parameters
@@ -17,16 +19,17 @@ const { csvModule } = csvStagingExtractor;
 
 // Spy on csvModule
 const csvModuleSpy = jest.spyOn(csvModule, 'get');
-
 const formatTNMCategoryData = rewire('../../src/extractors/CSVStagingExtractor.js').__get__('formatTNMCategoryData');
 
 describe('CSVStagingExtractor', () => {
   describe('formatTNMCategoryData', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
-      const expectedErrorString = 'Staging data is missing an expected property: mrn, conditionId, effectiveDate are required.';
+      const expectedErrorString = 'Staging data is missing an expected property: conditionId, effectiveDate are required.';
       const localData = _.cloneDeep(exampleStagingModuleResponse[0]);
+      const patientId = getPatientFromContext(MOCK_CONTEXT).id;
+
       // Test that valid data works fine
-      expect(formatTNMCategoryData(localData)).toEqual(expect.anything());
+      expect(formatTNMCategoryData(localData, patientId)).toEqual(expect.anything());
 
       // Test all optional properties can be empty without issue
       localData.t = '';
@@ -41,7 +44,7 @@ describe('CSVStagingExtractor', () => {
       expect(formatTNMCategoryData(localData)).toEqual(expect.anything());
 
       // Removing each required property should throw an error
-      const requiredKeys = ['mrn', 'conditionId', 'effectiveDate'];
+      const requiredKeys = ['conditionId', 'effectiveDate'];
       requiredKeys.forEach((key) => {
         const clonedData = _.cloneDeep(localData);
         clonedData[key] = '';
@@ -53,7 +56,7 @@ describe('CSVStagingExtractor', () => {
   describe('get', () => {
     test('should return bundle with Observation', async () => {
       csvModuleSpy.mockReturnValue(exampleStagingModuleResponse);
-      const data = await csvStagingExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvStagingExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
@@ -63,7 +66,7 @@ describe('CSVStagingExtractor', () => {
 
     test('should return empty bundle when no data available from module', async () => {
       csvModuleSpy.mockReturnValue([]);
-      const data = await csvStagingExtractor.get({ mrn: MOCK_PATIENT_MRN });
+      const data = await csvStagingExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
       expect(data.entry).toBeDefined();
diff --git a/test/extractors/CSVTreatmentPlanChangeExtractor.test.js b/test/extractors/CSVTreatmentPlanChangeExtractor.test.js
index 6d920d9b..9849d208 100644
--- a/test/extractors/CSVTreatmentPlanChangeExtractor.test.js
+++ b/test/extractors/CSVTreatmentPlanChangeExtractor.test.js
@@ -4,18 +4,23 @@ const _ = require('lodash');
 const { CSVTreatmentPlanChangeExtractor } = require('../../src/extractors');
 const exampleCSVTPCModuleResponse = require('./fixtures/csv-treatment-plan-change-module-response.json');
 const exampleCSVTPCBundle = require('./fixtures/csv-treatment-plan-change-bundle.json');
+const { getPatientFromContext } = require('../../src/helpers/contextUtils');
+const MOCK_CONTEXT = require('./fixtures/context-with-patient.json');
 
-const MOCK_MRN = 'mrn-1';
+// Constants for tests
+const MOCK_PATIENT_MRN = 'mrn-1'; // linked to values in example-module-response above
 const MOCK_CSV_PATH = path.join(__dirname, 'fixtures/example.csv');
+
+// Instantiate module with parameters
 const csvTPCExtractor = new CSVTreatmentPlanChangeExtractor({
   filePath: MOCK_CSV_PATH,
 });
 
+// Destructure all modules
 const { csvModule } = csvTPCExtractor;
 
 // Spy on csvModule
 const csvModuleSpy = jest.spyOn(csvModule, 'get');
-
 const formatData = rewire('../../src/extractors/CSVTreatmentPlanChangeExtractor.js').__get__('formatData');
 
 describe('CSVTreatmentPlanChangeExtractor', () => {
@@ -33,19 +38,21 @@ describe('CSVTreatmentPlanChangeExtractor', () => {
         mrn: 'id',
       },
     ];
+    const patientId = getPatientFromContext(MOCK_CONTEXT).id;
 
     test('should join data appropriately and throw errors when missing required properties', () => {
-      const expectedErrorString = 'Treatment Plan Change Data missing an expected property: mrn, dateOfCarePlan, changed are required';
+      const expectedErrorString = 'Treatment Plan Change Data missing an expected property: dateOfCarePlan, changed are required';
 
       // formatData on example data should not throw error when changed is false
-      expect(() => formatData(exampleData)).not.toThrowError();
+      expect(() => formatData(exampleData, patientId)).not.toThrowError();
 
       // Test required properties throw error
-      Object.keys(exampleData[0]).forEach((key) => {
+      const requiredKeys = ['dateOfCarePlan', 'changed'];
+      requiredKeys.forEach((key) => {
         const clonedData = _.cloneDeep(exampleData);
 
         delete clonedData[0][key];
-        expect(() => formatData(clonedData)).toThrow(new Error(expectedErrorString));
+        expect(() => formatData(clonedData, patientId)).toThrow(new Error(expectedErrorString));
       });
     });
 
@@ -54,17 +61,17 @@ describe('CSVTreatmentPlanChangeExtractor', () => {
 
       // error should get throw when changed flag is true and there is no reasonCode provided
       exampleData[0].changed = 'true';
-      expect(() => formatData(exampleData)).toThrow(new Error(expectedErrorString));
+      expect(() => formatData(exampleData, patientId)).toThrow(new Error(expectedErrorString));
 
       // No error should be throw when reasonCode is provided
       exampleData[0].reasonCode = 'example code';
-      expect(() => formatData(exampleData)).not.toThrowError();
+      expect(() => formatData(exampleData, patientId)).not.toThrowError();
     });
 
     test('should join multiple entries into one', () => {
       const expectedFormattedData = [
         {
-          mrn: 'mrn-1',
+          subjectId: 'mrn-1',
           reviews: [
             {
               effectiveDate: '2020-04-15',
@@ -81,14 +88,14 @@ describe('CSVTreatmentPlanChangeExtractor', () => {
         },
       ];
 
-      expect(formatData(exampleCSVTPCModuleResponse)).toEqual(expectedFormattedData);
+      expect(formatData(exampleCSVTPCModuleResponse, patientId)).toEqual(expectedFormattedData);
     });
   });
 
   describe('get', () => {
     test('should return bundle with CarePlan', async () => {
       csvModuleSpy.mockReturnValue(exampleCSVTPCModuleResponse);
-      const data = await csvTPCExtractor.get({ mrn: MOCK_MRN });
+      const data = await csvTPCExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
 
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
@@ -98,7 +105,7 @@ describe('CSVTreatmentPlanChangeExtractor', () => {
 
     test('should return empty bundle with no data available from module', async () => {
       csvModuleSpy.mockReturnValue([]);
-      const data = await csvTPCExtractor.get({ mrn: MOCK_MRN });
+      const data = await csvTPCExtractor.get({ mrn: MOCK_PATIENT_MRN, context: MOCK_CONTEXT });
 
       expect(data.resourceType).toEqual('Bundle');
       expect(data.type).toEqual('collection');
diff --git a/test/extractors/fixtures/csv-staging-bundle.json b/test/extractors/fixtures/csv-staging-bundle.json
index 2dc218b9..26328b3b 100644
--- a/test/extractors/fixtures/csv-staging-bundle.json
+++ b/test/extractors/fixtures/csv-staging-bundle.json
@@ -3,10 +3,10 @@
   "type": "collection",
   "entry": [
     {
-      "fullUrl": "urn:uuid:ed5faf7f2a1cef061d7584afd463e60eb7202104700647e92fbb7c9419eb7897",
+      "fullUrl": "urn:uuid:626b61fd700d8ddc5a6a576a2e47944191b5f608e03083d00c49614f0158bb65",
       "resource": {
         "resourceType": "Observation",
-        "id": "ed5faf7f2a1cef061d7584afd463e60eb7202104700647e92fbb7c9419eb7897",
+        "id": "626b61fd700d8ddc5a6a576a2e47944191b5f608e03083d00c49614f0158bb65",
         "meta": {
           "profile": [
             "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-primary-tumor-category"
@@ -32,7 +32,7 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1",
+          "reference": "urn:uuid:mrn-1",
           "type": "Patient"
         },
         "method": {
@@ -61,10 +61,10 @@
       }
     },
     {
-      "fullUrl": "urn:uuid:88992af10e3a822f2a946628de91012d5afae49a25d1641db09e9d6ed4ca24c3",
+      "fullUrl": "urn:uuid:66e0e5f216bebeba287c3a3b0e220170bab88da95030e0c4bdba32f66628d00c",
       "resource": {
         "resourceType": "Observation",
-        "id": "88992af10e3a822f2a946628de91012d5afae49a25d1641db09e9d6ed4ca24c3",
+        "id": "66e0e5f216bebeba287c3a3b0e220170bab88da95030e0c4bdba32f66628d00c",
         "meta": {
           "profile": [
             "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-distant-metastases-category"
@@ -90,7 +90,7 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1",
+          "reference": "urn:uuid:mrn-1",
           "type": "Patient"
         },
         "method": {
@@ -119,10 +119,10 @@
       }
     },
     {
-      "fullUrl": "urn:uuid:1373d3fb234cad0b03912cfbba16bdc4eabbd6217d83b838f6d9c1343bc9b394",
+      "fullUrl": "urn:uuid:4469acab85a889d722f5b8b1cb786df8adbfc5f0b50ac23393ec42b8ecfd49e9",
       "resource": {
         "resourceType": "Observation",
-        "id": "1373d3fb234cad0b03912cfbba16bdc4eabbd6217d83b838f6d9c1343bc9b394",
+        "id": "4469acab85a889d722f5b8b1cb786df8adbfc5f0b50ac23393ec42b8ecfd49e9",
         "meta": {
           "profile": [
             "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-regional-nodes-category"
@@ -148,7 +148,7 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1",
+          "reference": "urn:uuid:mrn-1",
           "type": "Patient"
         },
         "method": {
@@ -177,10 +177,10 @@
       }
     },
     {
-      "fullUrl": "urn:uuid:23564150098c6afeb2abc712086a21ead2e9bd308929f9d290988c6921ac841b",
+      "fullUrl": "urn:uuid:8fca0c2922335ea3c92022b4b2d4de17ba0645ce72d884b1e1c71a757c300a10",
       "resource": {
         "resourceType": "Observation",
-        "id": "23564150098c6afeb2abc712086a21ead2e9bd308929f9d290988c6921ac841b",
+        "id": "8fca0c2922335ea3c92022b4b2d4de17ba0645ce72d884b1e1c71a757c300a10",
         "meta": {
           "profile": [
             "http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-stage-group"
@@ -214,7 +214,7 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1",
+          "reference": "urn:uuid:mrn-1",
           "type": "Patient"
         },
         "effectiveDateTime": "2020-01-01",
@@ -234,15 +234,15 @@
         ],
         "hasMember": [
           {
-            "reference": "urn:uuid:ed5faf7f2a1cef061d7584afd463e60eb7202104700647e92fbb7c9419eb7897",
+            "reference": "urn:uuid:626b61fd700d8ddc5a6a576a2e47944191b5f608e03083d00c49614f0158bb65",
             "type": "Observation"
           },
           {
-            "reference": "urn:uuid:88992af10e3a822f2a946628de91012d5afae49a25d1641db09e9d6ed4ca24c3",
+            "reference": "urn:uuid:66e0e5f216bebeba287c3a3b0e220170bab88da95030e0c4bdba32f66628d00c",
             "type": "Observation"
           },
           {
-            "reference": "urn:uuid:1373d3fb234cad0b03912cfbba16bdc4eabbd6217d83b838f6d9c1343bc9b394",
+            "reference": "urn:uuid:4469acab85a889d722f5b8b1cb786df8adbfc5f0b50ac23393ec42b8ecfd49e9",
             "type": "Observation"
           }
         ]
diff --git a/test/extractors/fixtures/csv-staging-module-response.json b/test/extractors/fixtures/csv-staging-module-response.json
index bfa4247a..e84c26a5 100644
--- a/test/extractors/fixtures/csv-staging-module-response.json
+++ b/test/extractors/fixtures/csv-staging-module-response.json
@@ -1,6 +1,6 @@
 [
   {
-    "mrn": "pat-mrn-1",
+    "mrn": "mrn-1",
     "conditionId": "cond-1",
     "stageGroup": "3C",
     "t": "cT3",
diff --git a/test/extractors/fixtures/csv-treatment-plan-change-bundle.json b/test/extractors/fixtures/csv-treatment-plan-change-bundle.json
index 51cec659..73974a89 100644
--- a/test/extractors/fixtures/csv-treatment-plan-change-bundle.json
+++ b/test/extractors/fixtures/csv-treatment-plan-change-bundle.json
@@ -3,10 +3,10 @@
   "type": "collection",
   "entry": [
     {
-      "fullUrl": "urn:uuid:3005b559bb913fdfb23756a442645c6c37bbdafa42ad4be0bd1a6b698274f466",
+      "fullUrl": "urn:uuid:86e98914af1979c1b3dd780ebda05a677fc05939068f587949f886f1f3de22ed",
       "resource": {
         "resourceType": "CarePlan",
-        "id": "3005b559bb913fdfb23756a442645c6c37bbdafa42ad4be0bd1a6b698274f466",
+        "id": "86e98914af1979c1b3dd780ebda05a677fc05939068f587949f886f1f3de22ed",
         "meta": {
           "profile": [
             "http://mcodeinitiative.org/codex/us/icare/StructureDefinition/icare-care-plan-with-review"
@@ -24,13 +24,23 @@
                 "url": "CarePlanChangeReason",
                 "valueCodeableConcept": {
                   "coding": [
-                    { "system": "http://snomed.info/sct", "code": "281647001", "display": "Adverse reaction (disorder)" }
+                    {
+                      "system": "http://snomed.info/sct",
+                      "code": "281647001",
+                      "display": "Adverse reaction (disorder)"
+                    }
                   ],
                   "text": "Adverse reaction (disorder)"
                 }
               },
-              { "url": "ReviewDate", "valueDate": "2020-04-15" },
-              { "url": "ChangedFlag", "valueBoolean": true }
+              {
+                "url": "ReviewDate",
+                "valueDate": "2020-04-15"
+              },
+              {
+                "url": "ChangedFlag",
+                "valueBoolean": true
+              }
             ]
           },
           {
@@ -40,22 +50,37 @@
                 "url": "CarePlanChangeReason",
                 "valueCodeableConcept": {
                   "coding": [
-                    { "system": "http://snomed.info/sct", "code": "405613005" }
+                    {
+                      "system": "http://snomed.info/sct",
+                      "code": "405613005"
+                    }
                   ]
                 }
               },
-              { "url": "ReviewDate", "valueDate": "2020-04-30" },
-              { "url": "ChangedFlag", "valueBoolean": true }
+              {
+                "url": "ReviewDate",
+                "valueDate": "2020-04-30"
+              },
+              {
+                "url": "ChangedFlag",
+                "valueBoolean": true
+              }
             ]
           }
         ],
-        "subject": { "reference": "urn:uuid:mrn-1", "type": "Patient" },
+        "subject": {
+          "reference": "urn:uuid:mrn-1",
+          "type": "Patient"
+        },
         "status": "draft",
         "intent": "proposal",
         "category": [
           {
             "coding": [
-              { "code": "assess-plan", "system": "http://argonaut.hl7.org" }
+              {
+                "code": "assess-plan",
+                "system": "http://argonaut.hl7.org"
+              }
             ]
           }
         ]
diff --git a/test/extractors/fixtures/csv-treatment-plan-change-module-response.json b/test/extractors/fixtures/csv-treatment-plan-change-module-response.json
index 51baf2e4..c049a026 100644
--- a/test/extractors/fixtures/csv-treatment-plan-change-module-response.json
+++ b/test/extractors/fixtures/csv-treatment-plan-change-module-response.json
@@ -1,13 +1,13 @@
 [
   {
-    "mrn": "mrn-1",
+    "subjectId": "mrn-1",
     "dateOfCarePlan": "2020-04-15",
     "reasonCode": "281647001",
     "reasonDisplayText": "Adverse reaction (disorder)",
     "changed": "true"
   },
   {
-    "mrn": "mrn-1",
+    "subjectId": "mrn-1",
     "dateOfCarePlan": "2020-04-30",
     "reasonCode": "405613005",
     "changed": "true"
diff --git a/test/templates/carePlanWithReview.test.js b/test/templates/carePlanWithReview.test.js
index 13dba799..ab2b9281 100644
--- a/test/templates/carePlanWithReview.test.js
+++ b/test/templates/carePlanWithReview.test.js
@@ -8,7 +8,7 @@ describe('JavaScript render CarePlan template', () => {
   test('minimal required data passed into template should generate FHIR resource', () => {
     const CARE_PLAN_VALID_DATA = {
       id: 'test-id',
-      mrn: 'abc-def',
+      subjectId: 'abc-def',
       name: null,
       reviews: [
         {
@@ -28,7 +28,7 @@ describe('JavaScript render CarePlan template', () => {
   test('maximal data passed into template should generate FHIR resource', () => {
     const MAX_CARE_PLAN_DATA = {
       id: 'test-id',
-      mrn: 'abc-def',
+      subjectId: 'abc-def',
       name: 'Sample Text',
       reviews: [
         {
@@ -54,7 +54,7 @@ describe('JavaScript render CarePlan template', () => {
   test('missing non-required data at care plan object level should not throw an error', () => {
     const NECESSARY_DATA = {
       id: 'test-id',
-      mrn: 'abc-def',
+      subjectId: 'abc-def',
       reviews: [],
     };
 
@@ -68,7 +68,7 @@ describe('JavaScript render CarePlan template', () => {
   test('missing non-required data at review object level should not throw an error', () => {
     const NECESSARY_DATA = {
       id: 'test-id',
-      mrn: 'abc-def',
+      subjectId: 'abc-def',
       reviews: [
         {
           effectiveDate: '2020-01-23',
@@ -100,7 +100,7 @@ describe('JavaScript render CarePlan template', () => {
     const INVALID_REVIEW_DATA = {
       // Omitting 'hasChanged' field on the review which is a required property
       id: 'test-id',
-      mrn: 'abc-def',
+      subjectId: 'abc-def',
       reviews: [{
         effectiveDate: '2020-01-23',
         hasChanged: null,
diff --git a/test/templates/medication.test.js b/test/templates/medication.test.js
index ca37eeb2..fad7ac7a 100644
--- a/test/templates/medication.test.js
+++ b/test/templates/medication.test.js
@@ -5,7 +5,7 @@ const { cancerRelatedMedicationTemplate } = require('../../src/templates/CancerR
 const { allOptionalKeyCombinationsNotThrow } = require('../utils');
 
 const MEDICATION_VALID_DATA = {
-  mrn: 'mrn-1',
+  subjectId: 'mrn-1',
   id: 'medicationId-1',
   code: 'example-code',
   codeSystem: 'example-code-system',
@@ -21,7 +21,7 @@ const MEDICATION_VALID_DATA = {
 
 const MEDICATION_MINIMAL_DATA = {
   // Only include 'mrn', 'code', 'codesystem', and 'status' fields which are required
-  mrn: 'mrn-1',
+  subjectId: 'mrn-1',
   code: 'example-code',
   codeSystem: 'example-code-system',
   status: 'example-status',
@@ -37,7 +37,7 @@ const MEDICATION_MINIMAL_DATA = {
 
 const MEDICATION_INVALID_DATA = {
   // Omitting 'mrn', 'code', 'codesystem', and 'status' fields which are required
-  mrn: null,
+  subjectId: null,
   code: null,
   codeSystem: null,
   status: null,
@@ -90,7 +90,7 @@ describe('test Medication template', () => {
     };
 
     const NECESSARY_DATA = {
-      mrn: 'mrn-1',
+      subjectId: 'mrn-1',
       code: 'example-code',
       codeSystem: 'example-code-system',
       status: 'example-status',

From e3b68e6a090294322971057c0bf5df5a15c590b8 Mon Sep 17 00:00:00 2001
From: Dylan Phelan <dtphelan1@gmail.com>
Date: Fri, 16 Apr 2021 11:06:03 -0400
Subject: [PATCH 07/10] staging template uses patientId instead of MRN

---
 src/extractors/CSVStagingExtractor.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/extractors/CSVStagingExtractor.js b/src/extractors/CSVStagingExtractor.js
index ba3cc271..f10cffe7 100644
--- a/src/extractors/CSVStagingExtractor.js
+++ b/src/extractors/CSVStagingExtractor.js
@@ -33,13 +33,13 @@ function formatTNMCategoryData(stagingData, patientId) {
   return formattedData;
 }
 
-function formatStagingData(stagingData, categoryIds) {
+function formatStagingData(stagingData, categoryIds, patientId) {
   const {
-    mrn, conditionId, type, stageGroup, stagingSystem, stagingCodeSystem, effectiveDate,
+    conditionId, type, stageGroup, stagingSystem, stagingCodeSystem, effectiveDate,
   } = stagingData;
 
   return {
-    subjectId: mrn,
+    subjectId: patientId,
     conditionId,
     type,
     stageGroup,
@@ -77,7 +77,7 @@ class CSVStagingExtractor extends BaseCSVExtractor {
       const mcodeCategoryResources = formattedCategoryData.map((d) => firstEntryInBundle(generateMcodeResources('TNMCategory', d)));
 
       // Pass category resource ids to formatStagingData
-      const formattedStagingData = formatStagingData(data, mcodeCategoryResources.map((r) => r.resource.id));
+      const formattedStagingData = formatStagingData(data, mcodeCategoryResources.map((r) => r.resource.id), patientId);
       const stagingResource = firstEntryInBundle(generateMcodeResources('Staging', formattedStagingData));
 
       // Push all resources into entryResources

From 65c6ff71b2c69d9329d31773031f054784afee78 Mon Sep 17 00:00:00 2001
From: Dylan Phelan <dtphelan1@gmail.com>
Date: Tue, 20 Apr 2021 09:33:12 -0400
Subject: [PATCH 08/10] Update
 src/extractors/CSVCancerRelatedMedicationExtractor.js

---
 src/extractors/CSVCancerRelatedMedicationExtractor.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/extractors/CSVCancerRelatedMedicationExtractor.js b/src/extractors/CSVCancerRelatedMedicationExtractor.js
index 5d9e1123..336d9a24 100644
--- a/src/extractors/CSVCancerRelatedMedicationExtractor.js
+++ b/src/extractors/CSVCancerRelatedMedicationExtractor.js
@@ -15,7 +15,7 @@ function formatData(medicationData, patientId) {
     } = medication;
 
     if (!(code && codeSystem && status)) {
-      throw new Error('The cancer-related medication is missing an expected element; mrn, code, code system, and status are all required values.');
+      throw new Error('The cancer-related medication is missing an expected element; code, code system, and status are all required values.');
     }
 
     return {

From 39ac9e27bf4c1cd77207057e1d9cc575328a2b11 Mon Sep 17 00:00:00 2001
From: Dylan Phelan <dtphelan1@gmail.com>
Date: Tue, 20 Apr 2021 09:45:39 -0400
Subject: [PATCH 09/10] update error message expectations

---
 test/extractors/CSVCancerRelatedMedicationExtractor.test.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/extractors/CSVCancerRelatedMedicationExtractor.test.js b/test/extractors/CSVCancerRelatedMedicationExtractor.test.js
index 2473ac67..0d65bb14 100644
--- a/test/extractors/CSVCancerRelatedMedicationExtractor.test.js
+++ b/test/extractors/CSVCancerRelatedMedicationExtractor.test.js
@@ -35,7 +35,7 @@ expandedExampleBundle.entry.push(exampleCSVMedicationBundle.entry[0]);
 describe('CSVCancerRelatedMedicationExtractor', () => {
   describe('formatData', () => {
     test('should join data appropriately and throw errors when missing required properties', () => {
-      const expectedErrorString = 'The cancer-related medication is missing an expected element; mrn, code, code system, and status are all required values.';
+      const expectedErrorString = 'The cancer-related medication is missing an expected element; code, code system, and status are all required values.';
       const localData = _.cloneDeep(exampleCSVMedicationModuleResponse);
       const patientId = getPatientFromContext(MOCK_CONTEXT).id;
 

From 98c5b37717dfdf278bb74d0da6ee97839e2b8546 Mon Sep 17 00:00:00 2001
From: Dylan Phelan <dtphelan1@gmail.com>
Date: Tue, 20 Apr 2021 13:41:39 -0400
Subject: [PATCH 10/10] udpating order of extractors

---
 config/csv.config.example.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/config/csv.config.example.json b/config/csv.config.example.json
index 9c936e9f..66862dda 100644
--- a/config/csv.config.example.json
+++ b/config/csv.config.example.json
@@ -13,17 +13,17 @@
   },
   "extractors": [
     {
-      "label": "condition",
-      "type": "CSVConditionExtractor",
+      "label": "patient",
+      "type": "CSVPatientExtractor",
       "constructorArgs": {
-        "filePath": "./data/condition-information.csv"
+        "filePath": "./data/patient-information.csv"
       }
     },
     {
-      "label": "patient",
-      "type": "CSVPatientExtractor",
+      "label": "condition",
+      "type": "CSVConditionExtractor",
       "constructorArgs": {
-        "filePath": "./data/patient-information.csv"
+        "filePath": "./data/condition-information.csv"
       }
     },
     {