Correctly handle custom types in programatic access to JPA

hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java

@@ -694,12 +694,15 @@ public void setAddProfileTagWhenEncoding(AddProfileTagEnum theAddProfileTagWhenE
 	 *           The profile string, e.g. <code>"http://example.com/some_patient_profile"</code>. Must not be
 	 *           <code>null</code> or empty.
 	 * @param theClass
-	 *           The resource type. Must not be <code>null</code> or empty.
+	 *           The resource type, or <code>null</code> to clear any existing type
 	 */
 	public void setDefaultTypeForProfile(String theProfile, Class<? extends IBaseResource> theClass) {
 		Validate.notBlank(theProfile, "theProfile must not be null or empty");
-		Validate.notNull(theClass, "theProfile must not be null");
-		myDefaultTypeForProfile.put(theProfile, theClass);
+		if (theClass == null) {
+			myDefaultTypeForProfile.remove(theProfile);
+		} else {
+			myDefaultTypeForProfile.put(theProfile, theClass);
+		}
 	}
 
 	/**

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

@@ -733,6 +733,17 @@ protected void populateResourceIntoEntity(IBaseResource theResource, ResourceTab
 			extractTagsRi((IAnyResource) theResource, theEntity, allDefs);
 		}
 
+		RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
+		if (def.isStandardType() == false) {
+			String profile = def.getResourceProfile("");
+			if (isNotBlank(profile)) {
+				TagDefinition tag = getTag(TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null);
+				allDefs.add(tag);
+				theEntity.addTag(tag);
+				theEntity.setHasTags(true);
+			}
+		}
+
 		ArrayList<ResourceTag> existingTags = new ArrayList<ResourceTag>();
 		if (theEntity.isHasTags()) {
 			existingTags.addAll(theEntity.getTags());
@@ -1003,9 +1014,11 @@ protected ResourceTable toEntity(IResource theResource) {
 	@Override
 	public IBaseResource toResource(BaseHasResource theEntity, boolean theForHistoryOperation) {
 		RuntimeResourceDefinition type = myContext.getResourceDefinition(theEntity.getResourceType());
-		return toResource(type.getImplementingClass(), theEntity, theForHistoryOperation);
+		Class<? extends IBaseResource> resourceType = type.getImplementingClass();
+		return toResource(resourceType, theEntity, theForHistoryOperation);
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity, boolean theForHistoryOperation) {
 		String resourceText = null;
@@ -1022,14 +1035,34 @@ public <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasR
 			break;
 		}
 
+		/*
+		 * Use the appropriate custom type if one is specified in the context
+		 */
+		Class<R> resourceType = theResourceType;
+		if (myContext.hasDefaultTypeForProfile()) {
+			for (BaseTag nextTag : theEntity.getTags()) {
+				if (nextTag.getTag().getTagType() == TagTypeEnum.PROFILE) {
+					String profile = nextTag.getTag().getCode();
+					if (isNotBlank(profile)) {
+						Class<? extends IBaseResource> newType = myContext.getDefaultTypeForProfile(profile);
+						if (newType != null && theResourceType.isAssignableFrom(newType)) {
+							ourLog.debug("Using custom type {} for profile: {}", newType.getName(), profile);
+							resourceType = (Class<R>) newType;
+							break;
+						}
+					}
+				}
+			}
+		}
+
 		IParser parser = theEntity.getEncoding().newParser(getContext(theEntity.getFhirVersion()));
 		R retVal;
 		try {
-			retVal = parser.parseResource(theResourceType, resourceText);
+			retVal = parser.parseResource(resourceType, resourceText);
 		} catch (Exception e) {
 			StringBuilder b = new StringBuilder();
 			b.append("Failed to parse database resource[");
-			b.append(theResourceType);
+			b.append(resourceType);
 			b.append("/");
 			b.append(theEntity.getIdDt().getIdPart());
 			b.append(" (pid ");
@@ -1045,10 +1078,10 @@ public <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasR
 
 		if (retVal instanceof IResource) {
 			IResource res = (IResource) retVal;
-			retVal = populateResourceMetadataHapi(theResourceType, theEntity, theForHistoryOperation, res);
+			retVal = populateResourceMetadataHapi(resourceType, theEntity, theForHistoryOperation, res);
 		} else {
 			IAnyResource res = (IAnyResource) retVal;
-			retVal = populateResourceMetadataRi(theResourceType, theEntity, theForHistoryOperation, res);
+			retVal = populateResourceMetadataRi(resourceType, theEntity, theForHistoryOperation, res);
 		}
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/CustomObservationDstu3.java

@@ -0,0 +1,29 @@
+package ca.uhn.fhir.jpa.dao.dstu3;
+
+import org.hl7.fhir.dstu3.model.Observation;
+import org.hl7.fhir.dstu3.model.StringType;
+
+import ca.uhn.fhir.model.api.annotation.Child;
+import ca.uhn.fhir.model.api.annotation.Extension;
+import ca.uhn.fhir.model.api.annotation.ResourceDef;
+
+@ResourceDef(name = "Observation", profile = CustomObservationDstu3.PROFILE)
+public class CustomObservationDstu3 extends Observation {
+
+	public static final String PROFILE = "http://custom_ObservationDstu3";
+
+	private static final long serialVersionUID = 1L;
+
+	@Extension(definedLocally = false, isModifier = false, url = "http://eyeColour")
+	@Child(name = "eyeColour")
+	private StringType myEyeColour;
+
+	public StringType getEyeColour() {
+		return myEyeColour;
+	}
+
+	public void setEyeColour(StringType theEyeColour) {
+		myEyeColour = theEyeColour;
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCustomTypeDstu3Test.java

@@ -0,0 +1,45 @@
+package ca.uhn.fhir.jpa.dao.dstu3;
+
+import static org.junit.Assert.assertEquals;
+
+import org.hl7.fhir.dstu3.model.StringType;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import ca.uhn.fhir.rest.server.IBundleProvider;
+
+@SuppressWarnings({ })
+public class FhirResourceDaoCustomTypeDstu3Test extends BaseJpaDstu3Test {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoCustomTypeDstu3Test.class);
+
+	@Before
+	public void before() {
+		myFhirCtx.setDefaultTypeForProfile(CustomObservationDstu3.PROFILE, CustomObservationDstu3.class);
+	}
+
+	@Test
+	public void testSaveAndRestore() {
+		CustomObservationDstu3 obs = new CustomObservationDstu3();
+		obs.setEyeColour(new StringType("blue"));
+
+		IIdType id = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+
+		CustomObservationDstu3 read = (CustomObservationDstu3) myObservationDao.read(id);
+		assertEquals("blue", read.getEyeColour().getValue());
+
+		IBundleProvider found = myObservationDao.search(new SearchParameterMap());
+		assertEquals(1, found.size());
+		CustomObservationDstu3 search = (CustomObservationDstu3) found.getResources(0, 1).get(0);
+		assertEquals("blue", search.getEyeColour().getValue());
+
+	}
+
+	@After
+	public void after() {
+		myFhirCtx.setDefaultTypeForProfile(CustomObservationDstu3.PROFILE, null);
+	}
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDocumentDstu3Test.java

@@ -1,5 +1,7 @@
 package ca.uhn.fhir.jpa.dao.dstu3;
 
+import java.nio.charset.StandardCharsets;
+
 import org.apache.commons.io.IOUtils;
 import org.hl7.fhir.dstu3.model.Bundle;
 import org.junit.AfterClass;
@@ -8,7 +10,6 @@
 import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
 import ca.uhn.fhir.util.TestUtil;
 
-@SuppressWarnings("unchecked")
 public class FhirResourceDaoDocumentDstu3Test extends BaseJpaDstu3Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDocumentDstu3Test.class);
@@ -21,7 +22,7 @@ public static void afterClassClearContext() {
 
 	@Test
 	public void testPostDocument() throws Exception {
-		String input = IOUtils.toString(getClass().getResourceAsStream("/sample-document.xml"));
+		String input = IOUtils.toString(getClass().getResourceAsStream("/sample-document.xml"), StandardCharsets.UTF_8);
 		Bundle inputBundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
 		DaoMethodOutcome responseBundle = myBundleDao.create(inputBundle, mySrd);
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java

@@ -13,11 +13,14 @@
 import static org.junit.Assert.fail;
 import static org.mockito.Mockito.mock;
 
+import java.io.IOException;
 import java.math.BigDecimal;
+import java.nio.charset.StandardCharsets;
 import java.util.*;
 
 import javax.servlet.http.HttpServletRequest;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.dstu3.model.*;
 import org.hl7.fhir.dstu3.model.ContactPoint.ContactPointSystem;
@@ -81,6 +84,18 @@ public IIdType doInTransaction(TransactionStatus theStatus) {
 		assertEquals(Patient.class, foundResources.get(0).getClass());
 		assertEquals(Condition.class, foundResources.get(1).getClass());
 	}
+
+	/**
+	 * #454
+	 */
+	@Test
+	public void testIndexWithUtf8Chars() throws IOException {
+		String input = IOUtils.toString(getClass().getResourceAsStream("/bug454_utf8.json"), StandardCharsets.UTF_8);
+
+		CodeSystem cs = (CodeSystem) myFhirCtx.newJsonParser().parseResource(input);
+		myCodeSystemDao.create(cs);
+	}
+
 
 	@Test
 	public void testCodeSearch() {

hapi-fhir-jpaserver-base/src/test/resources/bug454_utf8.json

@@ -0,0 +1,16 @@
+{
+	"resourceType": "CodeSystem",
+	"url": "http://nestvision.com/fhir/myexample-yh",
+	"name": "NestVision Restful Interactions",
+	"status": "active",
+	"publisher": "杨浩",
+	"description": "this is a codesystem example.",
+	"caseSensitive": true,
+	"concept": [
+		{
+			"code": "mygod",
+			"display": "wodetian",
+			"definition": "this is a translate."
+		}
+	]
+}

hapi-fhir-jpaserver-uhnfhirtest/derby_maintenance.txt

@@ -1,3 +1,5 @@
 call SYSCS_UTIL.SYSCS_COMPRESS_TABLE('SA', 'HFJ_SEARCH_RESULT', 1);
 CALL SYSCS_UTIL.SYSCS_INPLACE_COMPRESS_TABLE( 'SA', 'HFJ_SEARCH_RESULT', 0, 0, 1 );
 
+
+dd if=/dev/urandom of=/opt/glassfish/tmp.tmp bs=1M count=500

src/changes/changes.xml

@@ -102,6 +102,11 @@
 				JAX-RS server was not able to handle the new mime types defined
 				in STU3
 			</action>
+			<action type="fix">
+				JPA server did not handle custom types when being called
+				programatically (I.e. not through HTTP interface). Thanks to
+				Anthony Mei for pointing this out!
+			</action>
 		</release>
 		<release version="2.0" date="2016-08-30">
 			<action type="fix">