added ability to load a directory of directories of patients

src/cli.ts

@@ -148,9 +148,8 @@ async function populatePatientBundles() {
  }
 
  if (program.patientsDirectory) {
- patientBundles = fs
- .readdirSync(program.patientsDirectory)
- .map(p => parseBundle(path.join(program.patientsDirectory, p)));
+ const patientBundlePaths = findPatientBundlePathsInDirectory(program.patientsDirectory);
+ patientBundles = patientBundlePaths.map(p => parseBundle(path.join(program.patientsDirectory, p)));
  } else {
  patientBundles = program.patientBundles.map((bundlePath: string) => parseBundle(path.resolve(bundlePath)));
  }
@@ -167,6 +166,24 @@ async function populatePatientBundles() {
  return patientBundles;
 }
 
+function findPatientBundlePathsInDirectory(patientDir: string): string[] {
+ const paths: string[] = [];
+ // iterate over the given directory
+ fs.readdirSync(patientDir, { withFileTypes: true }).forEach(ent => {
+ // if this item is a directory, look for .json files under it
+ if (ent.isDirectory()) {
+ fs.readdirSync(path.join(patientDir, ent.name), { withFileTypes: true }).forEach(subEnt => {
+ if (!subEnt.isDirectory() && subEnt.name.endsWith('.json')) {
+ paths.push(path.join(ent.name, subEnt.name));
+ }
+ });
+ } else if (ent.name.endsWith('.json')) {
+ paths.push(ent.name);
+ }
+ });
+ return paths;
+}
+
 const measureBundle = parseBundle(path.resolve(program.measureBundle));
 
 // Only cache valuesets retreived from service

test/unit/queryFilters/interpretIn.test.ts

@@ -1,7 +1,7 @@
 import { getELMFixture } from '../helpers/testHelpers';
 import { DateTime, Interval } from 'cql-execution';
 import * as QueryFilter from '../../../src/gaps/QueryFilterParser';
-import { ELMIn, ELMIncludedIn } from '../../../src/types/ELMTypes';
+import { ELMIn } from '../../../src/types/ELMTypes';
 import { DuringFilter } from '../../../src/types/QueryFilterTypes';
 
 // to use as a library parameter for tests