Remove warning

hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties

@@ -54,6 +54,7 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao.transactionInvalidUrl=Unable to perfor
 
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.duplicateCreateForcedId=Can not create entity with ID[{0}], a resource with this ID already exists
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.failedToCreateWithInvalidId=Can not process entity with ID[{0}], this is not a valid FHIR ID
+ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.incorrectResourceType=Incorrect resource type detected for endpoint, found {0} but expected {1}
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.failedToCreateWithClientAssignedNumericId=Can not create resource with ID[{0}], no resource with this ID exists and clients may only assign IDs which contain at least one non-numeric character
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.failedToCreateWithClientAssignedId=Can not create resource with ID[{0}], ID must not be supplied on a create (POST) operation
 ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.invalidParameterChain=Invalid parameter chain: {0}

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

@@ -754,6 +754,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	 *           The resource that is about to be stored
 	 */
 	protected void preProcessResourceForStorage(T theResource) {
+		String type = getContext().getResourceDefinition(theResource).getName();
+		if (!getResourceName().equals(type)) {
+			throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "incorrectResourceType", type, getResourceName()));
+		}
+		
 		if (theResource.getIdElement().hasIdPart()) {
 			if (!theResource.getIdElement().isIdPartValid()) {
 				throw new InvalidRequestException(getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "failedToCreateWithInvalidId", theResource.getIdElement().getIdPart()));

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu21Config.java

@@ -49,7 +49,6 @@ public class TestDstu21Config extends BaseJavaConfigDstu21 {
 		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
 		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
-		retVal.afterPropertiesSet();
 		return retVal;
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java

@@ -51,7 +51,6 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
 		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
-		retVal.afterPropertiesSet();
 		return retVal;
 	}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu21/BaseJpaDstu21Test.java

@@ -26,6 +26,7 @@ import org.hl7.fhir.dstu21.model.Media;
 import org.hl7.fhir.dstu21.model.Medication;
 import org.hl7.fhir.dstu21.model.MedicationOrder;
 import org.hl7.fhir.dstu21.model.Meta;
+import org.hl7.fhir.dstu21.model.NamingSystem;
 import org.hl7.fhir.dstu21.model.Observation;
 import org.hl7.fhir.dstu21.model.Organization;
 import org.hl7.fhir.dstu21.model.Patient;
@@ -142,6 +143,9 @@ public abstract class BaseJpaDstu21Test extends BaseJpaTest {
 	@Qualifier("myPatientDaoDstu21")
 	protected IFhirResourceDaoPatient<Patient> myPatientDao;
 	@Autowired
+	@Qualifier("myNamingSystemDaoDstu21")
+	protected IFhirResourceDao<NamingSystem> myNamingSystemDao;
+	@Autowired
 	@Qualifier("myMediaDaoDstu21")
 	protected IFhirResourceDao<Media> myMediaDao;
 	@Autowired

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu21/FhirResourceDaoDstu21Test.java

@@ -49,6 +49,7 @@ import org.hl7.fhir.dstu21.model.Encounter;
 import org.hl7.fhir.dstu21.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.dstu21.model.IdType;
 import org.hl7.fhir.dstu21.model.Meta;
+import org.hl7.fhir.dstu21.model.NamingSystem;
 import org.hl7.fhir.dstu21.model.Observation;
 import org.hl7.fhir.dstu21.model.OperationOutcome;
 import org.hl7.fhir.dstu21.model.OperationOutcome.IssueSeverity;
@@ -71,6 +72,8 @@ import org.mockito.ArgumentCaptor;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
 import ca.uhn.fhir.jpa.dao.FhirResourceDaoDstu21;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoPatient;
 import ca.uhn.fhir.jpa.dao.SearchParameterMap;
 import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
 import ca.uhn.fhir.jpa.entity.TagTypeEnum;
@@ -326,6 +329,51 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 		}
 	}
 
+	@Test
+	public void testCreateLongString() {
+		//@formatter:off
+		String input = "<NamingSystem>\n" + 
+				"        <name value=\"NDF-RT (National Drug File – Reference Terminology)\"/>\n" + 
+				"        <status value=\"draft\"/>\n" + 
+				"        <kind value=\"codesystem\"/>\n" + 
+				"        <publisher value=\"HL7, Inc\"/>\n" + 
+				"        <date value=\"2015-08-21\"/>\n" + 
+				"        <uniqueId>\n" + 
+				"          <type value=\"uri\"/>\n" + 
+				"          <value value=\"http://hl7.org/fhir/ndfrt\"/>\n" + 
+				"          <preferred value=\"true\"/>\n" + 
+				"        </uniqueId>\n" + 
+				"        <uniqueId>\n" + 
+				"          <type value=\"oid\"/>\n" + 
+				"          <value value=\"2.16.840.1.113883.6.209\"/>\n" + 
+				"          <preferred value=\"false\"/>\n" + 
+				"        </uniqueId>\n" + 
+				"      </NamingSystem>";
+		//@formatter:on
+
+		NamingSystem res = myFhirCtx.newXmlParser().parseResource(NamingSystem.class, input);
+		IIdType id = myNamingSystemDao.create(res).getId().toUnqualifiedVersionless();
+		
+		assertThat(toUnqualifiedVersionlessIdValues(myNamingSystemDao.search(NamingSystem.SP_NAME, new StringParam("NDF"))), contains(id.getValue()));
+	}
+
+	@Test
+	public void testCreateWrongType() {
+
+		// Lose typing so we can put the wrong type in
+		@SuppressWarnings("rawtypes")
+		IFhirResourceDao dao = myNamingSystemDao;
+		
+		Patient resource = new Patient();
+		resource.addName().addFamily("My Name");
+		try {
+			dao.create(resource);
+			fail();
+		} catch (InvalidRequestException e) {
+			assertEquals("Incorrect resource type detected for endpoint, found Patient but expected NamingSystem", e.getMessage());
+		}
+	}
+	
 	@Test
 	public void testCreateTextIdFails() {
 		Patient p = new Patient();
@@ -829,8 +877,7 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 
 		assertGone(id);
 	}
-	
+
-	
 	@Test
 	public void testDeleteWithMatchUrlChainedIdentifier() {
 		String methodName = "testDeleteWithMatchUrlChainedIdentifer";
@@ -850,13 +897,12 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 		myPatientDao.deleteByUrl("Patient?organization.identifier=http://example.com|" + methodName);
 		assertGone(id);
 		assertNotGone(orgId);
-		
+
 		myOrganizationDao.deleteByUrl("Organization?identifier=http://example.com|" + methodName);
 		assertGone(id);
 		assertGone(orgId);
 
 	}
-	
 
 	@Test
 	public void testDeleteWithMatchUrlChainedTag() {
@@ -864,9 +910,9 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 
 		Organization org = new Organization();
 		org.getMeta().addTag().setSystem("http://foo").setCode("term");
-		
+
 		org.setName(methodName);
-		
+
 		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
 
 		Patient p = new Patient();
@@ -878,7 +924,7 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 
 		myPatientDao.deleteByUrl("Patient?organization._tag=http://foo|term");
 		assertGone(id);
-		
+
 		myOrganizationDao.deleteByUrl("Organization?_tag=http://foo|term");
 		try {
 			myOrganizationDao.read(orgId);
@@ -903,7 +949,6 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 
 	}
 
-	
 	@Test
 	public void testDeleteWithMatchUrlQualifierMissing() {
 		String methodName = "testDeleteWithMatchUrlChainedProfile";
@@ -924,9 +969,9 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 		/*
 		 * Org 2 has a name
 		 */
-		
+
 		Organization org2 = new Organization();
-		org2.setName(methodName);		
+		org2.setName(methodName);
 		org2.addIdentifier().setValue(methodName);
 		IIdType org2Id = myOrganizationDao.create(org2).getId().toUnqualifiedVersionless();
 
@@ -939,13 +984,13 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 		ourLog.info("Org ID 1 : {}", org1Id);
 		ourLog.info("Pat ID 2 : {}", patId2);
 		ourLog.info("Org ID 2 : {}", org2Id);
-		
+
 		myPatientDao.deleteByUrl("Patient?organization.name:missing=true");
 		assertGone(patId1);
 		assertNotGone(patId2);
 		assertNotGone(org1Id);
 		assertNotGone(org2Id);
-		
+
 		myOrganizationDao.deleteByUrl("Organization?name:missing=true");
 		assertGone(patId1);
 		assertNotGone(patId2);
@@ -957,7 +1002,7 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 		assertGone(patId2);
 		assertGone(org1Id);
 		assertNotGone(org2Id);
-		
+
 		myOrganizationDao.deleteByUrl("Organization?name:missing=false");
 		assertGone(patId1);
 		assertGone(patId2);
@@ -971,12 +1016,13 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 	private void assertNotGone(IIdType theId) {
 		if ("Patient".equals(theId.getResourceType())) {
 			myPatientDao.read(theId);
-		} else if ("Organization".equals(theId.getResourceType())){
+		} else if ("Organization".equals(theId.getResourceType())) {
 			myOrganizationDao.read(theId);
 		} else {
 			fail("No type");
 		}
 	}
+
 	private void assertGone(IIdType theId) {
 		try {
 			assertNotGone(theId);
@@ -986,19 +1032,17 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 		}
 	}
 
-	
-	
 	@Test
 	public void testDeleteWithMatchUrlChainedProfile() {
 		String methodName = "testDeleteWithMatchUrlChainedProfile";
 
 		List<IdType> profileList = new ArrayList<IdType>();
-		
+
 		Organization org = new Organization();
-		
+
-		org.getMeta().getProfile().add(new IdType("http://foo"));		
+		org.getMeta().getProfile().add(new IdType("http://foo"));
 		org.setName(methodName);
-		
+
 		IIdType orgId = myOrganizationDao.create(org).getId().toUnqualifiedVersionless();
 
 		Patient p = new Patient();
@@ -1010,7 +1054,7 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 
 		myPatientDao.deleteByUrl("Patient?organization._profile=http://foo");
 		assertGone(id);
-		
+
 		myOrganizationDao.deleteByUrl("Organization?_profile=http://foo");
 		try {
 			myOrganizationDao.read(orgId);
@@ -1995,7 +2039,7 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 			patient.getMeta().addTag(null, "Dog", "Puppies");
 
 			patient.getMeta().addSecurity().setSystem("seclabel:sys:1").setCode("seclabel:code:1").setDisplay("seclabel:dis:1");
-			
+
 			patient.getMeta().addProfile(("http://profile/1"));
 
 			id1 = myPatientDao.create(patient).getId();
@@ -2741,7 +2785,7 @@ public class FhirResourceDaoDstu21Test extends BaseJpaDstu21Test {
 		assertEquals("http://profile/1", profiles.get(0).getValue());
 		assertEquals("http://profile/2", profiles.get(1).getValue());
 
-		List<Patient> search = toList(myPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam(patient.getIdentifier().get(0).getSystem(),patient.getIdentifier().get(0).getValue())));
+		List<Patient> search = toList(myPatientDao.search(Patient.SP_IDENTIFIER, new TokenParam(patient.getIdentifier().get(0).getSystem(), patient.getIdentifier().get(0).getValue())));
 		assertEquals(1, search.size());
 		retrieved = search.get(0);
 

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java

@@ -63,7 +63,6 @@ public class FhirServerConfig extends BaseJavaConfigDstu2 {
 		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
 		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
-		retVal.afterPropertiesSet();
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu1Config.java

@@ -70,7 +70,6 @@ public class TestDstu1Config extends BaseJavaConfigDstu1 {
 		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
 		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
-		retVal.afterPropertiesSet();
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu21Config.java

@@ -69,7 +69,6 @@ public class TestDstu21Config extends BaseJavaConfigDstu21 {
 		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
 		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
-		retVal.afterPropertiesSet();
 		return retVal;
 	}
 

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java

@@ -80,7 +80,6 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
 		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
-		retVal.afterPropertiesSet();
 		return retVal;
 	}
 

src/changes/changes.xml

@@ -139,6 +139,12 @@
 				implementations and wasn't compatible
 				with coming changes to that API.
 			</action>
+			<action type="fix">
+				Remove afterPropertiesSet() call in Java config for JPA
+				server's EntityManagerFactory. This doesn't need to be called
+				manually, the the manual call led to a warning about
+				the EntityManager being created twice.
+			</action>
 		</release>
 		<release version="1.3" date="2015-11-14">
 			<action type="add">

src/site/fml/hapi-fhir-faq.fml

@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<faqs xmlns="http://maven.apache.org/FML/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/FML/1.0.1 http://maven.apache.org/xsd/fml-1.0.1.xsd"
+	title="Frequently Asked Questions" toplink="false">
+	<part id="JPA Server">
+		<title>JPA Server</title>
+		<faq id="access_underlying_derby_database">
+			<question>
+				I would like to connect to the Derby database using a JDBC database browser (e.g. Squirrel, Toad, DBVisualizer)
+				so that I can access the underlying tables. How do I do that?
+			</question>
+			<answer>
+				<p>
+					By default Derby doesn't actually open any TCP ports for you to connect externally to it. 
+					Being an embedded database, it works a bit differently than other databases in that the 
+					client actually is the database and there's no outside communication with it possible.
+				</p>
+				<p>
+					There are a few options available to work around this fact:
+					<ul>
+						<li>
+							The easiest thing is to just load your data using the FHIR API. E.g. you can 
+							use HTTP/REST creates, transactions, etc to load data into your database directly.
+						</li>
+						<li>
+							If you want to access the underlying database, the next easiest thing is to configure 
+							the database to use a filesystem directory, e.g. 
+							"<code>jdbc:derby:directory:target/jpaserver_derby_files;create=true</code>". You can 
+							then shut the server down and use that same URL to connect a derby client (e.g. 
+							Squirrel or DBVisualizer) to the same path. You may need to use a fully qualified 
+							path instead of a relative one though.
+						</li>
+						<li>
+							Another option is to use a different database (e.g. MySQL, Postgres, Oracle, etc.). 
+							HAPI's JPA server is based on JPA/Hibernate so it will support any database platform 
+							that hibernate supports.
+						</li>
+						<li>
+							A final option is to start up Derby in network mode. Doing this is a bit more 
+							involved since you need to start the derby server separately, and then use a special
+							URL to connect to it. You can find an example of how to start network Derby 
+							<a href="https://github.com/jamesagnew/hapi-fhir/blob/master/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/DerbyNetworkServer.java">here</a> 
+							and
+							an example of setting up a datasource 
+							<a href="https://github.com/jamesagnew/hapi-fhir/blob/master/hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu21Config.java">here</a>.
+						</li>
+					</ul>
+				</p>
+			</answer>
+		</faq>
+	</part>
+</faqs>