Merge branch 'master' of github.com:jamesagnew/hapi-fhir

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

@@ -1266,7 +1266,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 		IIdType resourceId;
 		if (isNotBlank(theMatchUrl)) {
-			StopWatch sw = new StopWatch();
 			Set<Long> match = myMatchResourceUrlService.processMatchUrl(theMatchUrl, myResourceType);
 			if (match.size() > 1) {
 				String msg = getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "transactionOperationWithMultipleMatchFailure", "UPDATE", theMatchUrl, match.size());
@@ -1315,6 +1314,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		 * See SystemProviderR4Test#testTransactionReSavesPreviouslyDeletedResources
 		 * for a test that needs this.
 		 */
+		boolean wasDeleted = entity.getDeleted() != null;
 		entity.setDeleted(null);
 
 		/*
@@ -1325,7 +1325,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		 */
 		if (!thePerformIndexing) {
 			theResource.setId(entity.getIdDt().getValue());
-			DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, entity, theResource).setCreated(false);
+			DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, entity, theResource).setCreated(wasDeleted);
 			outcome.setPreviousResource(oldResource);
 			return outcome;
 		}
@@ -1334,7 +1334,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		 * Otherwise, we're not in a transaction
 		 */
 		ResourceTable savedEntity = updateInternal(theRequestDetails, theResource, thePerformIndexing, theForceUpdateVersion, entity, resourceId, oldResource);
-		DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, savedEntity, theResource).setCreated(false);
+		DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, savedEntity, theResource).setCreated(wasDeleted);
 
 		if (!thePerformIndexing) {
 			outcome.setId(theResource.getIdElement());

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/JpaConformanceProviderR4.java

@@ -154,7 +154,7 @@ public class JpaConformanceProviderR4 extends org.hl7.fhir.r4.hapi.rest.server.S
 			if (isNotBlank(myDaoConfig.getWebsocketContextPath())) {
 				Extension websocketExtension = new Extension();
 				websocketExtension.setUrl(Constants.CAPABILITYSTATEMENT_WEBSOCKET_URL);
-				websocketExtension.setValue(new org.hl7.fhir.dstu3.model.UriType(myDaoConfig.getWebsocketContextPath()));
+				websocketExtension.setValue(new UriType(myDaoConfig.getWebsocketContextPath()));
 				retVal.getRestFirstRep().addExtension(websocketExtension);
 			}
 		}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java

@@ -1,9 +1,5 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
-import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.fail;
-
 import ca.uhn.fhir.jpa.util.TestUtil;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -12,21 +8,33 @@ import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.StopWatch;
+import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.utils.IResourceValidator;
+import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.util.AopTestUtils;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
+
 public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3ValidateTest.class);
+	@Autowired
+	private IValidatorModule myValidatorModule;
 
 	@Test
 	public void testValidateChangedQuestionnaire() {
@@ -73,6 +81,77 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
 
 	}
 
+	@After
+	public void after() {
+		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
+		val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
+	}
+
+
+	@Test
+	public void testValidateWithCanonicalReference() {
+		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
+		IResourceValidator.BestPracticeWarningLevel a = IResourceValidator.BestPracticeWarningLevel.Ignore;
+		val.setBestPracticeWarningLevel(a);
+
+		ValueSet vs = new ValueSet();
+		vs.setId("MYVS");
+		vs.setUrl("http://myvs");
+		vs.getCompose()
+			.addInclude()
+			.setSystem("http://hl7.org/fhir/administrative-gender")
+			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("male"))
+			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("female"));
+		myValueSetDao.update(vs);
+
+		Questionnaire q = new Questionnaire();
+		q.setId("MYQ");
+		q.setUrl("http://hl7.org/fhir/Questionnaire/myq");
+		q.addItem()
+			.setLinkId("LINKID")
+			.setType(Questionnaire.QuestionnaireItemType.CHOICE)
+			.setOptions(new Reference().setReference("ValueSet/MYVS"));
+		myQuestionnaireDao.update(q);
+
+		// Validate with matching code
+		QuestionnaireResponse qr = new QuestionnaireResponse();
+		qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
+		qr.setQuestionnaire(new Reference("Questionnaire/MYQ"));
+		qr.addItem()
+			.setLinkId("LINKID")
+			.addAnswer()
+			.setValue(new Coding().setSystem("http://hl7.org/fhir/administrative-gender").setCode("aaa").setDisplay("AAAA"));
+
+		// Validate as resource
+		try {
+			MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
+			OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
+			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
+			fail();
+		} catch (PreconditionFailedException e) {
+			OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
+			String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
+			ourLog.info(encoded);
+			assertThat(encoded, containsString("is not in the options value set"));
+		}
+
+		// Validate as string
+		try {
+			String raw = myFhirCtx.newJsonParser().encodeResourceToString(qr);
+			MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, raw, EncodingEnum.JSON, ValidationModeEnum.CREATE, null, mySrd);
+			OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
+			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
+			fail();
+		} catch (PreconditionFailedException e) {
+			OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
+			String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
+			ourLog.info(encoded);
+			assertThat(encoded, containsString("is not in the options value set"));
+		}
+
+	}
+
+
 	@Test
 	public void testValidateStructureDefinition() throws Exception {
 		String input = IOUtils.toString(getClass().getResourceAsStream("/sd-david-dhtest7.json"), StandardCharsets.UTF_8);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -1,9 +1,5 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.fail;
-
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
@@ -13,34 +9,33 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.TestUtil;
+import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
+import org.hl7.fhir.r4.model.*;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
-import org.hl7.fhir.r4.model.CanonicalType;
-import org.hl7.fhir.r4.model.IdType;
-import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Observation.ObservationStatus;
-import org.hl7.fhir.r4.model.OperationOutcome;
+import org.hl7.fhir.r4.utils.IResourceValidator;
-import org.hl7.fhir.r4.model.Organization;
+import org.junit.After;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.StructureDefinition;
-import org.hl7.fhir.r4.model.ValueSet;
 import org.junit.AfterClass;
 import org.junit.Ignore;
 import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.util.AopTestUtils;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 
+import static org.hamcrest.Matchers.containsString;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
+
 public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ValidateTest.class);
-
+	@Autowired
-	@AfterClass
+	private IValidatorModule myValidatorModule;
-	public static void afterClassClearContext() {
-		TestUtil.clearAllStaticFieldsForUnitTest();
-	}
 
 	@Test
 	public void testValidateStructureDefinition() throws Exception {
@@ -139,24 +134,24 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		MethodOutcome outcome = null;
 		ValidationModeEnum mode = ValidationModeEnum.CREATE;
 		switch (enc) {
-		case JSON:
+			case JSON:
-			encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
+				encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
-			try {
+				try {
-				myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
+					myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
-				fail();
+					fail();
-			} catch (PreconditionFailedException e) {
+				} catch (PreconditionFailedException e) {
-				return (OperationOutcome) e.getOperationOutcome();
+					return (OperationOutcome) e.getOperationOutcome();
-			}
+				}
-			break;
+				break;
-		case XML:
+			case XML:
-			encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
+				encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
-			try {
+				try {
-				myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
+					myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
-				fail();
+					fail();
-			} catch (PreconditionFailedException e) {
+				} catch (PreconditionFailedException e) {
-				return (OperationOutcome) e.getOperationOutcome();
+					return (OperationOutcome) e.getOperationOutcome();
-			}
+				}
-			break;
+				break;
 		}
 
 		throw new IllegalStateException(); // shouldn't get here
@@ -185,6 +180,57 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	public void testValidateWithCanonicalReference() {
+		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
+		val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Ignore);
+
+		ValueSet vs = new ValueSet();
+		vs.setId("MYVS");
+		vs.setUrl("http://myvs");
+		vs.getCompose()
+			.addInclude()
+			.setSystem("http://hl7.org/fhir/administrative-gender")
+			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("male"))
+			.addConcept(new ValueSet.ConceptReferenceComponent().setCode("female"));
+		myValueSetDao.update(vs);
+
+		Questionnaire q = new Questionnaire();
+		q.setId("MYQ");
+		q.setUrl("http://myquestionnaire");
+		q.addItem()
+			.setLinkId("LINKID")
+			.setType(Questionnaire.QuestionnaireItemType.CHOICE)
+			.setAnswerValueSet("ValueSet/MYVS");
+		myQuestionnaireDao.update(q);
+
+		// Validate with matching code
+		QuestionnaireResponse qr = new QuestionnaireResponse();
+		qr.setStatus(QuestionnaireResponse.QuestionnaireResponseStatus.COMPLETED);
+		qr.setQuestionnaire("Questionnaire/MYQ");
+		qr.addItem()
+			.setLinkId("LINKID")
+			.addAnswer()
+			.setValue(new Coding().setSystem("http://hl7.org/fhir/administrative-gender").setCode("aaa"));
+		try {
+			MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
+			OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
+			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
+			fail();
+		} catch (PreconditionFailedException e) {
+			OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
+			String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
+			ourLog.info(encoded);
+			assertThat(encoded, containsString("is not in the options value set"));
+		}
+	}
+
+	@After
+	public void after() {
+		FhirInstanceValidator val = AopTestUtils.getTargetObject(myValidatorModule);
+		val.setBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Warning);
+	}
+
 	@Test
 	public void testValidateForCreate() {
 		String methodName = "testValidateForCreate";
@@ -344,11 +390,11 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 	@Test
 	@Ignore
 	public void testValidateNewQuestionnaireFormat() throws Exception {
-		String input =IOUtils.toString(FhirResourceDaoR4ValidateTest.class.getResourceAsStream("/questionnaire_r4.xml"));
+		String input = IOUtils.toString(FhirResourceDaoR4ValidateTest.class.getResourceAsStream("/questionnaire_r4.xml"));
 		try {
-		MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
+			MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
-		OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
+			OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
-		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
+			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
 		} catch (PreconditionFailedException e) {
 			// this is a failure of the test
 			ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
@@ -356,4 +402,9 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		}
 	}
 
+	@AfterClass
+	public static void afterClassClearContext() {
+		TestUtil.clearAllStaticFieldsForUnitTest();
+	}
+
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -391,6 +391,50 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
 
 	}
 
+	@Test
+	public void testCreateWithClientAssignedId() throws IOException {
+
+		// Create with client assigned ID
+		Patient p = new Patient();
+		p.setActive(true);
+		p.setId("AAA");
+		String encoded = myFhirCtx.newJsonParser().encodeResourceToString(p);
+		HttpPut httpPut = new HttpPut(ourServerBase + "/Patient/AAA");
+		httpPut.setEntity(new StringEntity(encoded, ContentType.parse("application/json+fhir")));
+		try (CloseableHttpResponse status = ourHttpClient.execute(httpPut)) {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(status.getStatusLine().toString());
+			ourLog.info(responseContent);
+
+			assertEquals(201, status.getStatusLine().getStatusCode());
+			assertThat(responseContent, containsString("true"));
+		}
+
+		// Delete
+		HttpDelete httpDelete = new HttpDelete(ourServerBase + "/Patient/AAA");
+		try (CloseableHttpResponse status = ourHttpClient.execute(httpDelete)) {
+			assertEquals(200, status.getStatusLine().getStatusCode());
+		}
+
+		// Create it again
+		p = new Patient();
+		p.setActive(true);
+		p.setId("AAA");
+		encoded = myFhirCtx.newJsonParser().encodeResourceToString(p);
+		httpPut = new HttpPut(ourServerBase + "/Patient/AAA");
+		httpPut.setEntity(new StringEntity(encoded, ContentType.parse("application/json+fhir")));
+		try (CloseableHttpResponse status = ourHttpClient.execute(httpPut)) {
+			String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(status.getStatusLine().toString());
+			ourLog.info(responseContent);
+
+			assertEquals(201, status.getStatusLine().getStatusCode());
+			assertThat(responseContent, containsString("true"));
+		}
+
+
+
+	}
 
 
 	@Before

hapi-fhir-testpage-overlay/src/main/java/ca/uhn/fhir/to/BaseController.java

@@ -63,7 +63,6 @@ public class BaseController {
 		final String serverName = theRequest.getServerName(myConfig);
 		final String apiKey = theRequest.getApiKey(theServletRequest, myConfig);
 		theModel.put("serverId", sanitizeInput(serverId));
-		theModel.put("base", sanitizeInput(serverBase));
 		theModel.put("baseName", sanitizeInput(serverName));
 		theModel.put("apiKey", sanitizeInput(apiKey));
 		theModel.put("resourceName", sanitizeInput(defaultString(theRequest.getResource())));
@@ -72,6 +71,9 @@ public class BaseController {
 		theModel.put("_summary", sanitizeInput(theRequest.get_summary()));
 		theModel.put("serverEntries", myConfig.getIdToServerName());
 
+		// doesn't need sanitizing
+		theModel.put("base", serverBase);
+
 		return loadAndAddConf(theServletRequest, theRequest, theModel);
 	}
 

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

@@ -2371,10 +2371,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         return null;
       } else {
         long t = System.nanoTime();
-        if (!Utilities.isAbsoluteUrl(reference))
+			ValueSet fr = context.fetchResource(ValueSet.class, reference);
-          reference = resolve(uri, reference);
+			if (fr == null) {
-        ValueSet fr = context.fetchResource(ValueSet.class, reference);
+				if (!Utilities.isAbsoluteUrl(reference)) {
-        txTime = txTime + (System.nanoTime() - t);
+					reference = resolve(uri, reference);
+					fr = context.fetchResource(ValueSet.class, reference);
+				}
+			}
+			txTime = txTime + (System.nanoTime() - t);
         return fr;
       }
     } else

src/changes/changes.xml

@@ -208,6 +208,11 @@
 				calling fetchCodeSystem() in order to reduce the work required by chain entries. Thanks to 
 				Anders Havn for the suggestion!
 			</action>
+			<action type="fix" issue="1299">
+				In JPA server when updating a resource using a client assigned ID, if the resource was previously
+				deleted (meaning that the operation is actually a create), the server will now return
+				an HTTP 201 instead of an HTTP 200. Thanks to Mario Hyland for reporting!
+			</action>
 		</release>
 		<release version="3.7.0" date="2019-02-06" description="Gale">
 			<action type="add">