Fix regression in validator when validating codesystems explicitly

defined in the JPA database

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/JpaValidationSupportDstu3.java

@@ -167,7 +167,7 @@ public class JpaValidationSupportDstu3 implements IJpaValidationSupportDstu3, Ap
 	@Override
 	@Transactional(value = TxType.SUPPORTS)
 	public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
-		return false;
+		return fetchCodeSystem(theCtx, theSystem) != null;
 	}
 
 	@Override

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/JpaValidationSupportR4.java

@@ -161,7 +161,7 @@ public class JpaValidationSupportR4 implements IJpaValidationSupportR4, Applicat
 	@Override
 	@Transactional(value = TxType.SUPPORTS)
 	public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
-		return false;
+		return fetchCodeSystem(theCtx, theSystem) != null;
 	}
 
 	@Override

hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/FhirInstanceValidatorDstu3Test.java

@@ -53,13 +53,7 @@ import org.mockito.stubbing.Answer;
 
 import java.io.IOException;
 import java.io.InputStream;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
 import java.util.zip.GZIPInputStream;
 
 public class FhirInstanceValidatorDstu3Test {
@@ -122,8 +116,12 @@ public class FhirInstanceValidatorDstu3Test {
 		when(myMockSupport.isCodeSystemSupported(nullable(FhirContext.class), nullable(String.class))).thenAnswer(new Answer<Boolean>() {
 			@Override
 			public Boolean answer(InvocationOnMock theInvocation) {
-				boolean retVal = myValidSystems.contains(theInvocation.getArguments()[1]);
+				String url = (String) theInvocation.getArguments()[1];
-				ourLog.debug("isCodeSystemSupported({}) : {}", new Object[] {theInvocation.getArguments()[1], retVal});
+				boolean retVal = myValidSystems.contains(url);
+				ourLog.debug("isCodeSystemSupported({}) : {}", new Object[] {url, retVal});
+				if (retVal == false) {
+					retVal = myCodeSystems.containsKey(url);
+				}
 				return retVal;
 			}
 		});
@@ -169,6 +167,10 @@ public class FhirInstanceValidatorDstu3Test {
 				CodeValidationResult retVal;
 				if (myValidConcepts.contains(system + "___" + code)) {
 					retVal = new CodeValidationResult(new ConceptDefinitionComponent(new CodeType(code)));
+				} else if (myCodeSystems.containsKey(system)) {
+					CodeSystem cs = myCodeSystems.get(system);
+					Optional<ConceptDefinitionComponent> found = cs.getConcept().stream().filter(t -> t.getCode().equals(code)).findFirst();
+					retVal = found.map(t->new CodeValidationResult(t)).orElse(null);
 				} else {
 					retVal = myDefaultValidationSupport.validateCode(ctx, system, code, (String) theInvocation.getArguments()[2]);
 				}
@@ -342,6 +344,29 @@ public class FhirInstanceValidatorDstu3Test {
 
 	}
 
+	@Test
+	public void testValidateQuestionnaire03() throws IOException {
+		CodeSystem csYesNo = loadResource("/dstu3/fmc01-cs-yesnounk.json", CodeSystem.class);
+		myCodeSystems.put(csYesNo.getUrl(), csYesNo);
+		CodeSystem csBinderRecommended = loadResource("/dstu3/fmc03-cs-binderrecommend.json", CodeSystem.class);
+		myCodeSystems.put(csBinderRecommended.getUrl(), csBinderRecommended);
+
+		ValueSet vsBinderRequired = loadResource("/dstu3/fmc03-vs-binderrecommend.json", ValueSet.class);
+		myValueSets.put(vsBinderRequired.getUrl(), vsBinderRequired);
+		myValueSets.put("ValueSet/" +vsBinderRequired.getIdElement().getIdPart(), vsBinderRequired);
+		ValueSet vsYesNo = loadResource("/dstu3/fmc03-vs-fmcyesno.json", ValueSet.class);
+		myValueSets.put(vsYesNo.getUrl(), vsYesNo);
+		myValueSets.put("ValueSet/" + vsYesNo.getIdElement().getIdPart(), vsYesNo);
+		Questionnaire q = loadResource("/dstu3/fmc03-questionnaire.json", Questionnaire.class);
+		myQuestionnaires.put("Questionnaire/" + q.getIdElement().getIdPart(), q);
+
+		QuestionnaireResponse qr = loadResource("/dstu3/fmc03-questionnaireresponse.json", QuestionnaireResponse.class);
+		ValidationResult result = myVal.validateWithResult(qr);
+		List<SingleValidationMessage> errors = logResultsAndReturnAll(result);
+		assertThat(errors, empty());
+
+	}
+
 	@Test
 	public void testValidateQuestionnaireWithEnableWhenAndSubItems_ShouldNotBeEnabled() throws IOException {
 		CodeSystem csYesNo = loadResource("/dstu3/fmc01-cs-yesnounk.json", CodeSystem.class);

hapi-fhir-validation/src/test/resources/dstu3/fmc03-cs-binderrecommend.json

@@ -0,0 +1,41 @@
+{
+	"resourceType": "CodeSystem",
+	"id": "FMCBinderRecommendation",
+	"meta": {
+		"versionId": "1",
+		"lastUpdated": "2019-05-02T16:57:22.705+00:00"
+	},
+	"url": "http://fkcfhir.org/fhir/cs/FMCBinderRecommendation",
+	"identifier": {
+		"value": "FMCBinderRecommendation"
+	},
+	"name": "FMCBinderRecommendation",
+	"title": "Binder recommendation",
+	"status": "active",
+	"publisher": "FMCNA",
+	"description": "CodeSystem for Binder recommendation.",
+	"hierarchyMeaning": "grouped-by",
+	"content": "complete",
+	"concept": [
+		{
+			"code": "Velphoro",
+			"display": "Velphoro"
+		},
+		{
+			"code": "Fosrenal",
+			"display": "Fosrenal"
+		},
+		{
+			"code": "Auryxia",
+			"display": "Auryxia"
+		},
+		{
+			"code": "Renvela",
+			"display": "Renvela"
+		},
+		{
+			"code": "Maintain current binder",
+			"display": "Maintain current binder"
+		}
+	]
+}

hapi-fhir-validation/src/test/resources/dstu3/fmc03-questionnaire.json

@@ -0,0 +1,188 @@
+{
+	"resourceType": "Questionnaire",
+	"id": "FMCBinderOptimizationAssessmentTest",
+	"meta": {
+		"versionId": "8",
+		"lastUpdated": "2019-05-07T18:55:20.151+00:00"
+	},
+	"url": "http://fkcfhir.org/fhir/Questionnaire/FMCBinderOptimizationAssessmentTest",
+	"status": "active",
+	"item": [
+		{
+			"linkId": "Binder Optimization Assessment Test",
+			"text": "Binder Optimization Assessment Test",
+			"type": "group",
+			"item": [
+				{
+					"linkId": "BINDER OPTIMIZATION ASSESSMENT TEST",
+					"text": "BINDER OPTIMIZATION ASSESSMENT TEST",
+					"type": "group",
+					"item": [
+						{
+							"linkId": "CLINICID",
+							"text": "CLINICID",
+							"type": "reference"
+						},
+						{
+							"linkId": "Home Medications",
+							"text": "Home Medications",
+							"type": "group",
+							"item": [
+								{
+									"linkId": "BO_ConsPharm",
+									"text": "Pharmacist consult",
+									"type": "choice",
+									"options": {
+										"reference": "ValueSet/FMCYesNo"
+									}
+								},
+								{
+									"linkId": "BO_ConsTxt",
+									"text": "Pharmacy consult notes",
+									"type": "text"
+								},
+								{
+									"linkId": "BO_RecCons",
+									"text": "Recommendation consistent with binder optimization guidelines",
+									"type": "choice",
+									"enableWhen": [
+										{
+											"question": "BO_RecNotCons",
+											"hasAnswer": false
+										}
+									],
+									"options": {
+										"reference": "ValueSet/FMCYesNo"
+									},
+									"item": [
+										{
+											"linkId": "BO_ConsDrop",
+											"text": "Binder recommended",
+											"type": "choice",
+											"enableWhen": [
+												{
+													"question": "BO_RecCons",
+													"answerCoding": {
+														"system": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+														"code": "Yes"
+													}
+												}
+											],
+											"options": {
+												"reference": "ValueSet/FMCBinderRecommended"
+											}
+										}
+									]
+								},
+								{
+									"linkId": "BO_RecNotCons",
+									"text": "Recommendation not consistent with binder optimization guidelines",
+									"type": "choice",
+									"enableWhen": [
+										{
+											"question": "BO_RecCons",
+											"hasAnswer": false
+										}
+									],
+									"options": {
+										"reference": "ValueSet/FMCYesNo"
+									},
+									"item": [
+										{
+											"linkId": "BO_NotConsDrop",
+											"text": "Recommendation not consistent with binder optimization guidelines",
+											"type": "text",
+											"enableWhen": [
+												{
+													"question": "BO_RecNotCons",
+													"answerCoding": {
+														"system": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+														"code": "Yes"
+													}
+												}
+											],
+											"item": [
+												{
+													"linkId": "BO_OtherTxt",
+													"text": "Other",
+													"type": "text",
+													"enableWhen": [
+														{
+															"question": "BO_NotConsDrop",
+															"hasAnswer": true
+														}
+													]
+												}
+											]
+										},
+										{
+											"linkId": "BO_Recommend",
+											"text": "What is your recommendation",
+											"type": "choice",
+											"enableWhen": [
+												{
+													"question": "BO_RecNotCons",
+													"answerCoding": {
+														"system": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+														"code": "Yes"
+													}
+												}
+											],
+											"options": {
+												"reference": "ValueSet/FMCBinderRecommendation"
+											}
+										}
+									]
+								}
+							]
+						},
+						{
+							"linkId": "Plan",
+							"text": "Plan",
+							"type": "group",
+							"item": [
+								{
+									"linkId": "BO_CommPres",
+									"text": "Binder recommendation communicated to prescriber",
+									"type": "choice",
+									"options": {
+										"reference": "ValueSet/FMCYesNo"
+									}
+								},
+								{
+									"linkId": "BO_ComAssmt",
+									"text": "Referred to MSW for expressed co-pay concerns",
+									"type": "choice",
+									"options": {
+										"reference": "ValueSet/FMCYesNo"
+									}
+								},
+								{
+									"linkId": "BO_RefMSW",
+									"text": "Referred to MSW for potential medication adherence issues",
+									"type": "choice",
+									"options": {
+										"reference": "ValueSet/FMCYesNo"
+									}
+								},
+								{
+									"linkId": "BO_AdjHyp",
+									"text": "Continue adjustments per CMAB Hyperphosphatemia Algorithm",
+									"type": "choice",
+									"options": {
+										"reference": "ValueSet/FMCYesNo"
+									}
+								},
+								{
+									"linkId": "BO_AdjTxt",
+									"text": "Adjustment Text",
+									"type": "text"
+								}
+							]
+						}
+					]
+				}
+			]
+		}
+	]
+}

hapi-fhir-validation/src/test/resources/dstu3/fmc03-questionnaireresponse.json

@@ -0,0 +1,147 @@
+{
+	"resourceType": "QuestionnaireResponse",
+	"id": "QRsfId",
+	"identifier": {
+		"system": "urn:oid:2.16.840.1.113883.3.7418.21.1",
+		"value": "sfId"
+	},
+	"questionnaire": {
+		"reference": "Questionnaire/FMCBinderOptimizationAssessmentTest"
+	},
+	"status": "completed",
+	"subject": {
+		"reference": "Patient/P123456"
+	},
+	"context": {
+		"reference": "EpisodeOfCare/EC12345"
+	},
+	"authored": "2019-05-02T10:41:00-04:00",
+	"author": {
+		"reference": "Practitioner/PRLoginID"
+	},
+	"item": [{
+		"linkId": "Binder Optimization Assessment Test",
+		"text": "Binder Optimization Assessment Test",
+		"item": [{
+			"linkId": "BINDER OPTIMIZATION ASSESSMENT TEST",
+			"text": "BINDER OPTIMIZATION ASSESSMENT TEST",
+			"item": [{
+				"linkId": "Home Medications",
+				"text": "Home Medications",
+				"item": [{
+					"linkId": "BO_ConsPharm",
+					"text": "Pharmacist consult",
+					"answer": [{
+						"valueCoding": {
+							"system": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+							"code": "Yes",
+							"display": "Yes"
+						}
+					}]
+				},
+					{
+						"linkId": "BO_ConsTxt",
+						"text": "Pharmacy consult notes",
+						"answer": [{
+							"valueString": "Pharmacy consult notes comes here"
+						}]
+					},
+					{
+						"linkId": "BO_RecNotCons",
+						"text": "Recommendation not consistent with binder optimization guidelines",
+						"answer": [{
+							"valueCoding": {
+								"system": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+								"code": "Yes",
+								"display": "Yes"
+							}
+						}],
+						"item": [{
+							"linkId": "BO_NotConsDrop",
+							"text": "Recommendation not consistent with binder optimization guidelines",
+							"answer": [{
+								"valueString": "Chewing difficulty,Other"
+							}],
+							"item": [{
+								"linkId": "BO_OtherTxt",
+								"text": "Other",
+								"answer": [{
+									"valueString": "Other difficulty"
+								}]
+							}]
+						},
+							{
+								"linkId": "BO_Recommend",
+								"text": "What is your recommendation",
+								"answer": [{
+									"valueCoding": {
+										"system": "http://fkcfhir.org/fhir/cs/FMCBinderRecommendation",
+										"code": "Renvela",
+										"display": "Renvela"
+									}
+								}]
+							}
+						]
+					}
+				]
+			},
+				{
+					"linkId": "Plan",
+					"text": "Plan",
+					"item": [{
+						"linkId": "BO_CommPres",
+						"text": "Binder recommendation communicated to prescriber",
+						"answer": [{
+							"valueCoding": {
+								"system": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+								"code": "No",
+								"display": "No"
+							}
+						}]
+					},
+						{
+							"linkId": "BO_ComAssmt",
+							"text": "Referred to MSW for expressed co-pay concerns",
+							"answer": [{
+								"valueCoding": {
+									"system": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+									"code": "No",
+									"display": "No"
+								}
+							}]
+						},
+						{
+							"linkId": "BO_RefMSW",
+							"text": "Referred to MSW for potential medication adherence issues",
+							"answer": [{
+								"valueCoding": {
+									"system": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+									"code": "No",
+									"display": "No"
+								}
+							}]
+						},
+						{
+							"linkId": "BO_AdjHyp",
+							"text": "Continue adjustments per CMAB Hyperphosphatemia Algorithm",
+							"answer": [{
+								"valueCoding": {
+									"system": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+									"code": "No",
+									"display": "No"
+								}
+							}]
+						},
+						{
+							"linkId": "BO_AdjTxt",
+							"text": "Adjustment Text",
+							"answer": [{
+								"valueString": "Adjustment Text comes here"
+							}]
+						}
+					]
+				}
+			]
+		}]
+	}]
+}

hapi-fhir-validation/src/test/resources/dstu3/fmc03-vs-binderrecommend.json

@@ -0,0 +1,26 @@
+{
+	"resourceType": "ValueSet",
+	"id": "FMCBinderRecommendation",
+	"meta": {
+		"versionId": "1",
+		"lastUpdated": "2019-05-02T16:58:46.423+00:00"
+	},
+	"url": "http://fkcfhir.org/fhir/vs/FMCBinderRecommendation",
+	"identifier": [
+		{
+			"value": "FMCBinderRecommendation"
+		}
+	],
+	"name": "FMCBinderRecommendation",
+	"title": "Binder recommendation",
+	"status": "active",
+	"publisher": "FMCNA",
+	"description": "ValueSet for Binder recommendation.",
+	"compose": {
+		"include": [
+			{
+				"system": "http://fkcfhir.org/fhir/cs/FMCBinderRecommendation"
+			}
+		]
+	}
+}

hapi-fhir-validation/src/test/resources/dstu3/fmc03-vs-fmcyesno.json

@@ -0,0 +1,36 @@
+{
+	"resourceType": "ValueSet",
+	"id": "FMCYesNo",
+	"meta": {
+		"versionId": "3",
+		"lastUpdated": "2019-05-03T16:50:45.195+00:00"
+	},
+	"url": "http://fkcfhir.org/fhir/vs/FMCYesNo",
+	"identifier": [
+		{
+			"value": "FMCYesNo"
+		}
+	],
+	"name": "FMCYesNo",
+	"title": "Yes or No Choice",
+	"status": "active",
+	"publisher": "FMCNA",
+	"description": "ValueSet for Yes or No Choice",
+	"compose": {
+		"include": [
+			{
+				"system": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+				"concept": [
+					{
+						"code": "Yes",
+						"display": "Yes"
+					},
+					{
+						"code": "No",
+						"display": "No"
+					}
+				]
+			}
+		]
+	}
+}