Adding post-extraction filtering

src/application/app.js

@@ -5,6 +5,7 @@ const { sendEmailNotification, zipErrors } = require('./tools/emailNotifications
 const { extractDataForPatients } = require('./tools/mcodeExtraction');
 const { parsePatientIds } = require('../helpers/appUtils');
 const { validateConfig } = require('../helpers/configUtils');
+const { postExtractionFilter } = require('../helpers/filterUtils');
 
 function checkInputAndConfig(config, fromDate, toDate) {
   // Check input args and needed config variables based on client being used
@@ -43,6 +44,12 @@ 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);
 
+  // Perform post-extraction processes
+  if (config.postExtractionFilter) {
+    logger.info('Applying post-extraction filter to bundle');
+    postExtractionFilter(extractedData, config.postExtractionFilter);
+  }
+
   // If we have notification information, send an emailNotification
   const { notificationInfo } = config;
   if (notificationInfo && Object.keys(notificationInfo).length > 0) {

src/helpers/filterUtils.js

@@ -0,0 +1,16 @@
+const fhirpath = require('fhirpath');
+
+function postExtractionFilter(extractedData, filter) {
+  extractedData.map((bundle) => {
+    const filteredBundle = bundle;
+    filteredBundle.entry = fhirpath.evaluate(
+      bundle,
+      `Bundle.entry.where(${filter})`,
+    );
+    return filteredBundle;
+  });
+}
+
+module.exports = {
+  postExtractionFilter,
+};

src/helpers/schemas/config.schema.json

@@ -8,6 +8,10 @@
       "title": "Patient ID CSV File",
       "type": "string"
     },
+    "postExtractionFilter": {
+      "title": "Post-Extraction Filter",
+      "type": "string"
+    },
     "commonExtractorArgs": {
       "$ref": "#/$defs/commonExtractorArgs"
     },

src/index.js

@@ -79,6 +79,7 @@ const { parsePatientIds } = require('./helpers/appUtils');
 const { getConfig, validateConfig } = require('./helpers/configUtils');
 const configSchema = require('./helpers/schemas/config.schema.json');
 const { sortExtractors } = require('./helpers/dependencyUtils');
+const { postExtractionFilter } = require('./helpers/filterUtils');
 
 module.exports = {
   // CLI Related utilities
@@ -156,6 +157,7 @@ module.exports = {
   lowercaseLookupQuery,
   mEpochToDate,
   sortExtractors,
+  postExtractionFilter,
   // Context operations
   getConditionEntriesFromContext,
   getConditionsFromContext,