Merge pull request #104 from mcode/fhir-validation-errors

Added fn to find all invalid resources in a bundle

Author: Dtphelan1

src/client/BaseClient.js

@@ -1,4 +1,4 @@
-const { isValidFHIR } = require('../helpers/fhirUtils');
+const { isValidFHIR, invalidResourcesFromBundle } = require('../helpers/fhirUtils');
 const logger = require('../helpers/logger');
 
 class BaseClient {
@@ -97,7 +97,7 @@ class BaseClient {
     }, Promise.resolve(contextBundle));
 
     if (!isValidFHIR(contextBundle)) {
-      logger.error('Extracted bundle is not valid FHIR.');
+      logger.warn(`Extracted bundle is not valid FHIR, the following resources failed validation: ${invalidResourcesFromBundle(contextBundle).join(',')}`);
     }
 
     return { bundle: contextBundle, extractionErrors };

src/helpers/fhirUtils.js

@@ -163,8 +163,22 @@ const logOperationOutcomeInfo = (operationOutcome) => {
   });
 };
 
-const isValidFHIR = (resource) => validator.validate('FHIR', resource);
-
+function isValidFHIR(resource) {
+  return validator.validate('FHIR', resource);
+}
+function invalidResourcesFromBundle(bundle) {
+  // Bundle is assumed to have all resources in bundle.entry[x].resource
+  const failingResources = [];
+  bundle.entry.forEach((e) => {
+    const { resource } = e;
+    const { id, resourceType } = resource;
+    if (!validator.validate('FHIR', resource)) {
+      const failureId = `${resourceType}-${id}`;
+      failingResources.push(failureId);
+    }
+  });
+  return failingResources;
+}
 
 module.exports = {
   allResourcesInBundle,
@@ -182,4 +196,5 @@ module.exports = {
   mapFHIRVersions,
   quantityCodeToUnitLookup,
   isValidFHIR,
+  invalidResourcesFromBundle,
 };

test/client/BaseClient.test.js

@@ -76,8 +76,8 @@ describe('BaseClient', () => {
     });
     it('should iterate over all extractors gets, aggregating resultant entries in a bundle', async () => {
       const extractorClassesWithEntryGets = [
-        class Ext1 { get() { return { entry: [{ data: 'here' }] }; }},
-        class Ext2 { get() { return { entry: [{ data: 'alsoHere' }] }; }},
+        class Ext1 { get() { return { entry: [{ resource: 'here' }] }; }},
+        class Ext2 { get() { return { entry: [{ resource: 'alsoHere' }] }; }},
         class Ext3 { get() { throw new Error('Error'); }},
       ];
       engine.registerExtractors(...extractorClassesWithEntryGets);

test/helpers/fhirUtils.test.js

@@ -7,13 +7,17 @@ const {
   allResourcesInBundle,
   quantityCodeToUnitLookup,
   getResourceCountInBundle,
+  isValidFHIR,
+  invalidResourcesFromBundle,
 } = require('../../src/helpers/fhirUtils.js');
 const emptyBundle = require('./fixtures/emptyBundle.json');
 const bundleWithOneEntry = require('./fixtures/searchsetBundleWithOneEntry.json');
 const bundleWithMultipleEntries = require('./fixtures/searchsetBundleWithMultipleEntries.json');
 const countBundle5Unique = require('./fixtures/count-bundle-5-unique.json');
 const countBundle5Same = require('./fixtures/count-bundle-5-same.json');
 const countBundle5Nested = require('./fixtures/count-bundle-5-nested.json');
+const validResource = require('./fixtures/valid-resource');
+const invalidResource = require('./fixtures/invalid-resource');
 
 describe('getQuantityUnit', () => {
   test('Should return unit text if provided in lookup table', () => {
@@ -137,3 +141,25 @@ describe('getResourceCountInBundle', () => {
     expect(getResourceCountInBundle(countBundle5Nested)).toEqual(counts);
   });
 });
+
+describe('isValidFHIR', () => {
+  test('Should return true when provided valid FHIR resources', () => {
+    expect(isValidFHIR(validResource)).toEqual(true);
+  });
+  test('Should return false when provided invalid FHIR resources', () => {
+    expect(isValidFHIR(invalidResource)).toEqual(false);
+  });
+});
+
+describe('invalidResourcesFromBundle', () => {
+  test('Should return an empty array when all resources are valid', () => {
+    expect(invalidResourcesFromBundle(emptyBundle)).toEqual([]);
+  });
+  test('Should return an array of all invalid resources when they exist', () => {
+    const invalidBundle = { ...bundleWithOneEntry };
+    invalidBundle.entry[0].resource = invalidResource;
+    // This is dependent on implementation details intrinsic to invalidResourcesFromBundle
+    const invalidResourceId = `${invalidResource.resourceType}-${invalidResource.id}`;
+    expect(invalidResourcesFromBundle(invalidBundle)).toEqual([invalidResourceId]);
+  });
+});

test/helpers/fixtures/invalid-resource.json

@@ -0,0 +1,14 @@
+{
+  "resourceType": "Patient",
+  "id": "invalid-patient",
+  "name": [
+    {
+      "family": "Godel",
+      "given": [
+        "Kurt"
+      ]
+    }
+  ],
+  "gender": "invalid-enum-value",
+  "birthDate": "1906-04-28"
+}

test/helpers/fixtures/valid-resource.json

@@ -0,0 +1,14 @@
+{
+  "resourceType": "Patient",
+  "id": "valid-patient",
+  "name": [
+    {
+      "family": "Frege",
+      "given": [
+        "Gottlob"
+      ]
+    }
+  ],
+  "gender": "male",
+  "birthDate": "1848-11-08"
+}