Add more granular resource-level validation and logging

Author: Matthew Gramigna

src/client/BaseClient.js

@@ -96,8 +96,25 @@ class BaseClient {
       }
     }, Promise.resolve(contextBundle));
 
+    // Report detailed validation errors
     if (!isValidFHIR(contextBundle)) {
-      logger.warn(`Extracted bundle is not valid FHIR, the following resources failed validation: ${invalidResourcesFromBundle(contextBundle).join(',')}`);
+      const invalidResources = invalidResourcesFromBundle(contextBundle);
+      const baseWarningMessage = 'Extracted bundle is not valid FHIR, the following resources failed validation: ';
+
+      const warnMessages = [];
+      const debugMessages = [];
+      invalidResources.forEach(({ failureId, errors }) => {
+        warnMessages.push(`${failureId} at ${errors.map((e) => e.dataPath).join(',')}`);
+
+        errors.forEach((e) => {
+          debugMessages.push(`${failureId} at ${e.dataPath} - ${e.message}`);
+        });
+      });
+
+      logger.warn(`${baseWarningMessage}${warnMessages.join(', ')}`);
+      debugMessages.forEach((m) => {
+        logger.debug(m);
+      });
     }
 
     return { bundle: contextBundle, extractionErrors };

src/helpers/fhirUtils.js

@@ -7,7 +7,7 @@ const logger = require('./logger');
 
 const ajv = new Ajv({ logger: false });
 ajv.addMetaSchema(metaSchema);
-const validator = ajv.addSchema(schema, 'FHIR');
+const validate = ajv.compile(schema);
 
 // Unit codes and display values fo Vital Signs values
 // Code mapping is based on http://hl7.org/fhir/R4/observation-vitalsigns.html
@@ -164,17 +164,29 @@ const logOperationOutcomeInfo = (operationOutcome) => {
 };
 
 function isValidFHIR(resource) {
-  return validator.validate('FHIR', resource);
+  return validate(resource);
 }
+
+function errorFilter(error) {
+  return error.message !== 'should NOT have additional properties' && error.keyword !== 'oneOf' && error.keyword !== 'const';
+}
+
 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)) {
+
+    // Validate only this resource to get more scoped errors
+    const subSchema = schema;
+    subSchema.oneOf = [{ $ref: `#/definitions/${resourceType}` }];
+
+    const validateResource = ajv.compile(subSchema);
+
+    if (!validateResource(resource)) {
       const failureId = `${resourceType}-${id}`;
-      failingResources.push(failureId);
+      failingResources.push({ failureId, errors: validateResource.errors.filter(errorFilter) });
     }
   });
   return failingResources;

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: [{ resource: 'here' }] }; }},
-        class Ext2 { get() { return { entry: [{ resource: 'alsoHere' }] }; }},
+        class Ext1 { get() { return { entry: [{ resource: { resourceType: 'Patient' } }] }; }},
+        class Ext2 { get() { return { entry: [{ resource: { resourceType: 'Patient' } }] }; }},
         class Ext3 { get() { throw new Error('Error'); }},
       ];
       engine.registerExtractors(...extractorClassesWithEntryGets);

test/helpers/fhirUtils.test.js

@@ -160,6 +160,26 @@ describe('invalidResourcesFromBundle', () => {
     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]);
+    expect(invalidResourcesFromBundle(invalidBundle)).toEqual([
+      {
+        failureId: invalidResourceId,
+        errors: [
+          {
+            keyword: 'enum',
+            dataPath: '.gender',
+            schemaPath: '#/properties/gender/enum',
+            params: {
+              allowedValues: [
+                'male',
+                'female',
+                'other',
+                'unknown',
+              ],
+            },
+            message: 'should be equal to one of the allowed values',
+          },
+        ],
+      },
+    ]);
   });
 });