Adding post-extraction mapping and importing extractor list from MEF

.github/CODEOWNERS

@@ -1 +1 @@
-*   @julianxcarter @dmendelowitz @dtphelan1
+*   @dmendelowitz

.gitignore

@@ -4,5 +4,5 @@ node_modules/
 output/
 logs/
 *.p12
-config/*.json
+config/*
 !config/csv.config.example.json

package.json

@@ -28,10 +28,11 @@
     "commander": "^4.1.1",
     "cross-env": "^7.0.1",
     "csv-parse": "^4.8.9",
+    "fhir-mapper": "git+https://github.com/standardhealth/fhir-mapper.git#old-fhirpath",
     "fhir-messaging-client": "git+https://github.com/ICAREdata/fhir-messaging-client.git",
     "fhirpath": "^2.3.0",
     "lodash": "^4.17.21",
-    "mcode-extraction-framework": "git+https://github.com/mcode/mcode-extraction-framework.git",
+    "mcode-extraction-framework": "git+https://github.com/mcode/mcode-extraction-framework.git#export-extractor-list",
     "moment": "^2.29.4",
     "nodemailer": "^6.7.2",
     "uuid": "^7.0.2"

src/ICARECSVClient.js

@@ -1,58 +1,12 @@
-const {
-  BaseClient,
-  CSVAdverseEventExtractor,
-  CSVCancerDiseaseStatusExtractor,
-  CSVCancerRelatedMedicationAdministrationExtractor,
-  CSVCancerRelatedMedicationRequestExtractor,
-  CSVClinicalTrialInformationExtractor,
-  CSVConditionExtractor,
-  CSVCTCAdverseEventExtractor,
-  CSVEncounterExtractor,
-  CSVObservationExtractor,
-  CSVPatientExtractor,
-  CSVProcedureExtractor,
-  CSVStagingExtractor,
-  CSVTreatmentPlanChangeExtractor,
-  sortExtractors,
-} = require('mcode-extraction-framework');
+const { CSVExtractors, dependencyInfo, BaseClient, sortExtractors } = require('mcode-extraction-framework');
 const { generateNewMessageBundle } = require('./icareFhirMessaging');
 
 class ICARECSVClient extends BaseClient {
   constructor({ extractors, commonExtractorArgs }) {
     super();
-    this.registerExtractors(
-      CSVAdverseEventExtractor,
-      CSVCancerDiseaseStatusExtractor,
-      CSVCancerRelatedMedicationAdministrationExtractor,
-      CSVCancerRelatedMedicationRequestExtractor,
-      CSVClinicalTrialInformationExtractor,
-      CSVConditionExtractor,
-      CSVCTCAdverseEventExtractor,
-      CSVEncounterExtractor,
-      CSVObservationExtractor,
-      CSVPatientExtractor,
-      CSVProcedureExtractor,
-      CSVStagingExtractor,
-      CSVTreatmentPlanChangeExtractor,
-    );
+    this.registerExtractors(...CSVExtractors);
     // Store the extractors defined by the configuration file as local state
     this.extractorConfig = extractors;
-    // Define information about the order and dependencies of extractors
-    const dependencyInfo = [
-      { type: 'CSVPatientExtractor', dependencies: [] },
-      { type: 'CSVConditionExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVCancerDiseaseStatusExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVClinicalTrialInformationExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVTreatmentPlanChangeExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVStagingExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVCancerRelatedMedicationAdministrationExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVCancerRelatedMedicationRequestExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVProcedureExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVObservationExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVCTCAdverseEventExtractor', dependencies: ['CSVPatientExtractor'] },
-      { type: 'CSVEncounterExtractor', dependencies: ['CSVPatientExtractor'] },
-    ];
     // Sort extractors based on order and dependencies
     this.extractorConfig = sortExtractors(this.extractorConfig, dependencyInfo);
     this.commonExtractorArgs = {

src/app.js

@@ -1,4 +1,7 @@
 const moment = require('moment');
+const fs = require('fs');
+const path = require('path');
+const { AggregateMapper } = require('fhir-mapper');
 const {
   logger,
   sendEmailNotification,
@@ -81,6 +84,19 @@ async function icareApp(
   logger.info(`Extracting data for ${patientIds.length} patients`);
   const { extractedData, successfulExtraction, totalExtractionErrors } = await extractDataForPatients(patientIds, icareClient, effectiveFromDate, effectiveToDate);
 
+  // Post-extraction mapping
+  if (fs.existsSync('./config/mapper.js')) {
+    logger.info('Applying post-extraction mapping');
+    // eslint-disable-next-line global-require, import/no-dynamic-require
+    const { resourceMapping, variables } = require(path.resolve('../../config/mapper.js'));
+    const mapper = new AggregateMapper(resourceMapping, variables);
+    extractedData.map((bundle) => {
+      const mappedBundle = bundle;
+      mappedBundle.entry = mapper.execute(bundle.entry);
+      return bundle;
+    });
+  }
+
   // Post the data using the messagingClient
   let successfulMessagePost = true;
   let messagingErrors = {};