Merge pull request #57 from mcode/validate

Validate against FHIR in BaseClient after extraction is complete

Author: danlee1025

package-lock.json

@@ -19,6 +19,7 @@
   },
   "license": "Apache-2.0",
   "dependencies": {
+    "ajv": "^6.12.6",
     "axios": "^0.19.0",
     "commander": "^6.2.0",
     "csv-parse": "^4.8.8",
@@ -32,7 +33,6 @@
   },
   "devDependencies": {
     "@types/jest": "^26.0.14",
-    "ajv": "^6.12.6",
     "cross-env": "^7.0.0",
     "eslint": "^6.6.0",
     "eslint-config-airbnb-base": "^14.0.0",

package.json

@@ -1,3 +1,4 @@
+const { isValidFHIR } = require('../helpers/fhirUtils');
 const logger = require('../helpers/logger');
 
 class BaseClient {
@@ -69,6 +70,10 @@ class BaseClient {
       }
     }, Promise.resolve(contextBundle));
 
+    if (!isValidFHIR(contextBundle)) {
+      logger.error('Extracted bundle is not valid FHIR.');
+    }
+
     return { bundle: contextBundle, extractionErrors };
   }
 }

src/client/BaseClient.js

@@ -1,7 +1,14 @@
 const _ = require('lodash');
 const fhirpath = require('fhirpath');
+const Ajv = require('ajv');
+const metaSchema = require('ajv/lib/refs/json-schema-draft-06.json');
+const schema = require('./schemas/fhir.schema.json');
 const logger = require('./logger');
 
+const ajv = new Ajv({ logger: false });
+ajv.addMetaSchema(metaSchema);
+const validator = ajv.addSchema(schema, 'FHIR');
+
 // Unit codes and display values fo Vital Signs values
 // Code mapping is based on http://hl7.org/fhir/R4/observation-vitalsigns.html
 // and inferred from manually referencing display values of codes in
@@ -149,6 +156,8 @@ const logOperationOutcomeInfo = (operationOutcome) => {
   });
 };
 
+const isValidFHIR = (resource) => validator.validate('FHIR', resource);
+
 module.exports = {
   allResourcesInBundle,
   determineVersion,
@@ -163,4 +172,5 @@ module.exports = {
   logOperationOutcomeInfo,
   mapFHIRVersions,
   quantityCodeToUnitLookup,
+  isValidFHIR,
 };

src/helpers/fhirUtils.js

@@ -1,4 +1,4 @@
-const { isValidFHIR } = require('../utils');
+const { isValidFHIR } = require('../../src/helpers/fhirUtils');
 const maximalCancerDiseaseStatus = require('./fixtures/disease-status-resource.json');
 const minimalCancerDiseaseStatus = require('./fixtures/minimal-disease-status-resource.json');
 const { cancerDiseaseStatusTemplate } = require('../../src/templates/CancerDiseaseStatusTemplate');

test/helpers/fixtures/fhir.schema.json renamed to src/helpers/schemas/fhir.schema.json

@@ -1,4 +1,4 @@
-const { isValidFHIR } = require('../utils');
+const { isValidFHIR } = require('../../src/helpers/fhirUtils');
 const minimalCarePlan = require('./fixtures/minimal-careplan-resource.json');
 const maximalCarePlan = require('./fixtures/maximal-careplan-resource.json');
 const { carePlanWithReviewTemplate } = require('../../src/templates/CarePlanWithReviewTemplate');

test/templates/cancerDiseaseStatus.test.js

@@ -1,4 +1,4 @@
-const { isValidFHIR } = require('../utils');
+const { isValidFHIR } = require('../../src/helpers/fhirUtils');
 const maximalValidExampleCondition = require('./fixtures/maximal-condition-resource.json');
 const minimalValidExampleCondition = require('./fixtures/minimal-condition-resource.json');
 const cancerValidExampleCondition = require('./fixtures/cancer-condition-resource.json');

test/templates/carePlanWithReview.test.js

@@ -1,4 +1,4 @@
-const { isValidFHIR } = require('../utils');
+const { isValidFHIR } = require('../../src/helpers/fhirUtils');
 const maximalValidExampleMedication = require('./fixtures/maximal-medication-resource.json');
 const minimalValidExampleMedication = require('./fixtures/minimal-medication-resource.json');
 const { cancerRelatedMedicationTemplate } = require('../../src/templates/CancerRelatedMedicationTemplate.js');

test/templates/condition.test.js

@@ -1,4 +1,4 @@
-const { isValidFHIR } = require('../utils');
+const { isValidFHIR } = require('../../src/helpers/fhirUtils');
 const maximalObservationResource = require('./fixtures/maximal-observation-resource.json');
 const minimalObservationResource = require('./fixtures/minimal-observation-resource.json');
 const { observationTemplate } = require('../../src/templates/ObservationTemplate');