Assigning a code with an invalid code system should only warn when as…

…signing to a primitive code/string/uri

src/fhirtypes/ElementDefinition.ts

@@ -2102,18 +2102,34 @@ export class ElementDefinition {
    * @throws {InvalidUriError} when the system being assigned is not a valid uri
    */
   private assignFshCode(code: FshCode, exactly = false, fisher?: Fishable): void {
+    const type = this.type[0].code;
+
     if (code.system) {
       const csURI = code.system.split('|')[0];
       const vsURI = fishForMetadataBestVersion(fisher, code.system, Type.ValueSet)?.url ?? '';
       if (vsURI) {
-        throw new MismatchedBindingTypeError(code.system, this.path, 'CodeSystem');
+        if (type === 'code' || type === 'string' || type === 'uri') {
+          logger.warn(
+            `The fully qualified code ${code.system}#${code.code} is invalid because the specified system is a ValueSet. ` +
+              `Since ${this.path} is a ${type}, the system will not be used, but this issue should be corrected by ` +
+              `updating the system to refer to a proper CodeSystem or by specifying a code only (e.g., #${code.code}).`
+          );
+        } else {
+          throw new MismatchedBindingTypeError(code.system, this.path, 'CodeSystem');
+        }
       } else if (!isUri(csURI)) {
-        throw new InvalidUriError(code.system);
+        if (type === 'code' || type === 'string' || type === 'uri') {
+          logger.warn(
+            `The fully qualified code ${code.system}#${code.code} is invalid because the specified system is not a URI. ` +
+              `Since ${this.path} is a ${type}, the system will not be used, but this issue should be corrected by ` +
+              `updating the system to refer to a proper CodeSystem or by specifying a code only (e.g., #${code.code}).`
+          );
+        } else {
+          throw new InvalidUriError(code.system);
+        }
       }
     }
 
-    const type = this.type[0].code;
-
     if (type === 'code' || type === 'string' || type === 'uri') {
       this.assignFHIRValue(code.toString(), code.code, exactly, type);
     } else if (type === 'CodeableConcept') {

test/fhirtypes/ElementDefinition.assignFshCode.test.ts

@@ -1,7 +1,7 @@
 import path from 'path';
 import cloneDeep from 'lodash/cloneDeep';
 import { loadFromPath } from 'fhir-package-loader';
-import { TestFisher } from '../testhelpers';
+import { TestFisher, loggerSpy } from '../testhelpers';
 import { FHIRDefinitions } from '../../src/fhirdefs/FHIRDefinitions';
 import { StructureDefinition } from '../../src/fhirtypes/StructureDefinition';
 import { FshCode } from '../../src/fshtypes/FshCode';
@@ -28,6 +28,7 @@ describe('ElementDefinition', () => {
     barFooCode = new FshCode('foo', 'http://bar.com');
     versionedCode = new FshCode('versioned', 'http://versioned.com|7.6.5');
     codeWithDisplay = new FshCode('bar', 'http://foo.com', 'Foo Bar');
+    loggerSpy.reset();
   });
 
   describe('#assignFshCode()', () => {
@@ -167,7 +168,7 @@ describe('ElementDefinition', () => {
       expect(clone).toEqual(concept);
     });
 
-    it('should throw InvalidUriError when binding with a non-URI value', () => {
+    it('should throw InvalidUriError when assigning a code with a non-URI value', () => {
       const category = observation.elements.find(e => e.id === 'Observation.category');
       const clone = cloneDeep(category);
       expect(() => {
@@ -178,7 +179,30 @@ describe('ElementDefinition', () => {
       }).toThrow(/notAUri/);
     });
 
-    it('should throw MismatchedBindingTypeError when binding with a ValueSet as a system', () => {
+    it('should NOT throw InvalidUriError when assigning a code with a non-URI value to a primitive code', () => {
+      const status = observation.elements.find(e => e.id === 'Observation.status');
+      const clone = cloneDeep(status);
+      clone.assignValue(new FshCode('code', 'notAUri'));
+      expect(loggerSpy.getAllLogs('warn')).toHaveLength(1);
+      expect(loggerSpy.getLastMessage('warn')).toMatch(
+        /code notAUri#code is invalid.*specified system is not a URI/
+      );
+      expect(loggerSpy.getLastMessage('warn')).toMatch(/Observation.status is a code/);
+      expect(loggerSpy.getLastMessage('warn')).toMatch(
+        /specifying a code only \(e\.g\., #code\)\./
+      );
+      clone.assignValue(new FshCode('code', 'notAUri'), true);
+      expect(loggerSpy.getAllLogs('warn')).toHaveLength(2);
+      expect(loggerSpy.getLastMessage('warn')).toMatch(
+        /code notAUri#code is invalid.*specified system is not a URI/
+      );
+      expect(loggerSpy.getLastMessage('warn')).toMatch(/Observation.status is a code/);
+      expect(loggerSpy.getLastMessage('warn')).toMatch(
+        /specifying a code only \(e\.g\., #code\)\./
+      );
+    });
+
+    it('should throw MismatchedBindingTypeError when assigning a code with a ValueSet as a system', () => {
       const category = observation.elements.find(e => e.id === 'Observation.category');
       const clone = cloneDeep(category);
       expect(() => {
@@ -197,7 +221,7 @@ describe('ElementDefinition', () => {
       }).toThrow(/CodeSystem/);
     });
 
-    it('should throw MismatchedBindingTypeError when binding with a ValueSet as a system when provided with a version', () => {
+    it('should throw MismatchedBindingTypeError when assigning a code with a ValueSet as a system when provided with a version', () => {
       const category = observation.elements.find(e => e.id === 'Observation.category');
       const clone = cloneDeep(category);
       expect(() => {
@@ -216,6 +240,37 @@ describe('ElementDefinition', () => {
       }).toThrow(/CodeSystem/);
     });
 
+    it('should NOT throw MismatchedBindingTypeError when assigning a code with a ValueSet as a system to a primitive code', () => {
+      const status = observation.elements.find(e => e.id === 'Observation.status');
+      const clone = cloneDeep(status);
+      clone.assignValue(
+        new FshCode('final', 'http://hl7.org/fhir/ValueSet/observation-status'),
+        false,
+        fisher
+      );
+      expect(loggerSpy.getAllLogs('warn')).toHaveLength(1);
+      expect(loggerSpy.getLastMessage('warn')).toMatch(
+        /code http:\/\/hl7\.org\/fhir\/ValueSet\/observation-status#final is invalid.*specified system is a ValueSet/
+      );
+      expect(loggerSpy.getLastMessage('warn')).toMatch(/Observation.status is a code/);
+      expect(loggerSpy.getLastMessage('warn')).toMatch(
+        /specifying a code only \(e\.g\., #final\)\./
+      );
+      clone.assignValue(
+        new FshCode('final', 'http://hl7.org/fhir/ValueSet/observation-status'),
+        true,
+        fisher
+      );
+      expect(loggerSpy.getAllLogs('warn')).toHaveLength(2);
+      expect(loggerSpy.getLastMessage('warn')).toMatch(
+        /code http:\/\/hl7\.org\/fhir\/ValueSet\/observation-status#final is invalid.*specified system is a ValueSet/
+      );
+      expect(loggerSpy.getLastMessage('warn')).toMatch(/Observation.status is a code/);
+      expect(loggerSpy.getLastMessage('warn')).toMatch(
+        /specifying a code only \(e\.g\., #final\)\./
+      );
+    });
+
     it('should assign a code to a Coding', () => {
       const concept = observation.elements.find(e => e.id === 'Observation.code');
       concept.unfold(fisher);

test/testhelpers/testdefs/r4-definitions/package/ValueSet-observation-status.json

@@ -0,0 +1 @@
+{"resourceType":"ValueSet","id":"observation-status","meta":{"lastUpdated":"2019-11-01T09:29:23.356+11:00","profile":["http://hl7.org/fhir/StructureDefinition/shareablevalueset"]},"extension":[{"url":"http://hl7.org/fhir/StructureDefinition/structuredefinition-wg","valueCode":"oo"},{"url":"http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status","valueCode":"normative"},{"url":"http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm","valueInteger":5},{"url":"http://hl7.org/fhir/StructureDefinition/structuredefinition-normative-version","valueCode":"4.0.0"}],"url":"http://hl7.org/fhir/ValueSet/observation-status","identifier":[{"system":"urn:ietf:rfc:3986","value":"urn:oid:2.16.840.1.113883.4.642.3.400"}],"version":"4.0.1","name":"ObservationStatus","title":"ObservationStatus","status":"active","experimental":false,"date":"2019-11-01T09:29:23+11:00","publisher":"HL7 (FHIR Project)","contact":[{"telecom":[{"system":"url","value":"http://hl7.org/fhir"},{"system":"email","value":"[email protected]"}]}],"description":"Codes providing the status of an observation.","immutable":true,"compose":{"include":[{"system":"http://hl7.org/fhir/observation-status"}]}}