Fix an NPE in validation

hapi-fhir-jpaserver-base/pom.xml

@@ -401,11 +401,11 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
-<!--		<dependency>-->
+		<dependency>
-<!--			<groupId>com.sun.activation</groupId>-->
+			<groupId>com.sun.activation</groupId>
-<!--			<artifactId>javax.activation</artifactId>-->
+			<artifactId>javax.activation</artifactId>
-<!--			<version>1.2.0</version>-->
+			<version>1.2.0</version>
-<!--		</dependency>-->
+		</dependency>
 		<!--<dependency>-->
 			<!--<groupId>javax.transaction</groupId>-->
 			<!--<artifactId>javax.transaction-api</artifactId>-->

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3CodeSystemTest.java

@@ -1,10 +1,15 @@
 package ca.uhn.fhir.jpa.provider.dstu3;
 
+import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.TestUtil;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.dstu3.model.*;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Before;
@@ -12,11 +17,14 @@ import org.junit.Test;
 import org.springframework.transaction.annotation.Transactional;
 
 import java.io.IOException;
+import java.io.InputStream;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
 
 public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDstu3Test {
 
+	public static FhirContext ourCtx = FhirContext.forDstu3();
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu3CodeSystemTest.class);
 	private IIdType myExtensionalVsId;
 
@@ -254,6 +262,42 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
 		assertEquals(false, ((BooleanType) respParam.getParameter().get(2).getValue()).booleanValue());
 	}
 
+	@Test
+	public void testValidationOfUploadedCodeSystems() throws IOException {
+		CodeSystem csYesNo = loadResource("/dstu3/fmc01-cs-yesnounk.json", CodeSystem.class);
+		ourClient.update().resource(csYesNo).execute();
+
+		CodeSystem csBinderRecommended = loadResource("/dstu3/fmc03-cs-binderrecommend.json", CodeSystem.class);
+		ourClient.update().resource(csBinderRecommended).execute();
+
+		ValueSet vsBinderRequired = loadResource("/dstu3/fmc03-vs-binderrecommend.json", ValueSet.class);
+		ourClient.update().resource(vsBinderRequired);
+
+		ValueSet vsYesNo = loadResource("/dstu3/fmc03-vs-fmcyesno.json", ValueSet.class);
+		ourClient.update().resource(vsYesNo).execute();
+
+		Questionnaire q = loadResource("/dstu3/fmc03-questionnaire.json", Questionnaire.class);
+		ourClient.update().resource(q).execute();
+
+		QuestionnaireResponse qr = loadResource("/dstu3/fmc03-questionnaireresponse.json", QuestionnaireResponse.class);
+		IBaseOperationOutcome oo = ourClient.validate().resource(qr).execute().getOperationOutcome();
+
+		String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
+		ourLog.info("Encoded:\n{}", encoded);
+	}
+
+	private String loadResource(String theFileName) throws IOException {
+		InputStream resourceAsStream = ResourceProviderDstu3CodeSystemTest.class.getResourceAsStream(theFileName);
+		if (resourceAsStream == null) {
+			resourceAsStream = ResourceProviderDstu3CodeSystemTest.class.getResourceAsStream(theFileName.substring(1));
+		}
+		return IOUtils.toString(resourceAsStream, Charsets.UTF_8);
+	}
+
+	private <T extends IBaseResource> T loadResource(String theFilename, Class<T> theType) throws IOException {
+		return ourCtx.newJsonParser().parseResource(theType, loadResource(theFilename));
+	}
+
 	@AfterClass
 	public static void afterClassClearContext() {
 		TestUtil.clearAllStaticFieldsForUnitTest();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/util/jsonpatch/JsonPatchUtilsTest.java

@@ -15,7 +15,7 @@ import static org.junit.Assert.*;
 
 public class JsonPatchUtilsTest extends BaseJpaTest {
 
-	public static final FhirContext ourCtx = FhirContext.forR4();
+	private static final FhirContext ourCtx = FhirContext.forR4();
 	private static final Logger ourLog = LoggerFactory.getLogger(JsonPatchUtilsTest.class);
 
 	@Test

hapi-fhir-jpaserver-base/src/test/resources/dstu3/fmc01-cs-yesnounk.json

@@ -0,0 +1,36 @@
+{
+	"resourceType": "CodeSystem",
+	"id": "FMCYesNoUnk",
+	"meta": {
+		"versionId": "1",
+		"lastUpdated": "2019-04-17T12:50:19.996+00:00"
+	},
+	"url": "http://fkcfhir.org/fhir/cs/FMCYesNoUnk",
+	"identifier": {
+		"value": "FMCYesNoUnk"
+	},
+	"name": "FMCYesNoUnk",
+	"status": "active",
+	"publisher": "FMCNA",
+	"description": "CodeSystem for  Yes or No or Unknown",
+	"hierarchyMeaning": "grouped-by",
+	"content": "complete",
+	"concept": [
+		{
+			"code": "Yes",
+			"display": "Yes"
+		},
+		{
+			"code": "No",
+			"display": "No"
+		},
+		{
+			"code": "UnKnown",
+			"display": "UnKnown"
+		},
+		{
+			"code": "Pending",
+			"display": "Pending"
+		}
+	]
+}

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

@@ -0,0 +1,146 @@
+{
+	"resourceType": "QuestionnaireResponse",
+	"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-jpaserver-base/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-jpaserver-base/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"
+					}
+				]
+			}
+		]
+	}
+}

hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/ValidationSupportChain.java

@@ -155,8 +155,10 @@ public class ValidationSupportChain implements IValidationSupport {
 		for (IValidationSupport next : myChain) {
 			if (next.isCodeSystemSupported(theCtx, theCodeSystem)) {
 				CodeValidationResult result = next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
-				ourLog.debug("Chain item {} returned outcome {}", next, result.isOk());
+				if (result != null) {
-				return result;
+					ourLog.debug("Chain item {} returned outcome {}", next, result.isOk());
+					return result;
+				}
 			} else {
 				ourLog.debug("Chain item {} does not support code system {}", next, theCodeSystem);
 			}

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/ValidationSupportChain.java

@@ -134,8 +134,10 @@ public class ValidationSupportChain implements IValidationSupport {
 		for (IValidationSupport next : myChain) {
 			if (next.isCodeSystemSupported(theCtx, theCodeSystem)) {
 				CodeValidationResult result = next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
-				ourLog.debug("Chain item {} returned outcome {}", next, result.isOk());
+				if (result != null) {
-				return result;
+					ourLog.debug("Chain item {} returned outcome {}", next, result.isOk());
+					return result;
+				}
 			} else {
 				ourLog.debug("Chain item {} does not support code system {}", next, theCodeSystem);
 			}

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

@@ -153,7 +153,7 @@ public class FhirInstanceValidatorDstu3Test {
 					}
 				}
 				if (retVal == null) {
-					ourLog.info("fetchResource({}, {}) : {}", new Object[] {type, id, retVal});
+					ourLog.info("fetchResource({}, {}) : {}", type, id, retVal);
 				}
 				return retVal;
 			}