Merge pull request #199 from mcode/fhir-mapper-filtering

Post-extraction mapper

.gitignore

@@ -3,5 +3,5 @@ node_modules/
 .DS_Store
 output/
 logs/
-config/*.json
+config/*
 !config/csv.config.example.json

package.json

@@ -27,6 +27,7 @@
     "commander": "^6.2.0",
     "csv-parse": "^4.8.8",
     "fhir-crud-client": "^1.2.2",
+    "fhir-mapper": "git+https://github.com/standardhealth/fhir-mapper.git",
     "fhirpath": "2.1.5",
     "lodash": "^4.17.21",
     "moment": "^2.29.4",

src/application/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 = require('../helpers/logger');
 const { RunInstanceLogger } = require('./tools/RunInstanceLogger');
 const { sendEmailNotification, zipErrors } = require('./tools/emailNotifications');
@@ -43,6 +46,19 @@ async function mcodeApp(Client, fromDate, toDate, config, pathToRunLogs, debug,
   logger.info(`Extracting data for ${patientIds.length} patients`);
   const { extractedData, successfulExtraction, totalExtractionErrors } = await extractDataForPatients(patientIds, mcodeClient, 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;
+    });
+  }
+
   // If we have notification information, send an emailNotification
   const { notificationInfo } = config;
   if (notificationInfo && Object.keys(notificationInfo).length > 0) {