Improve the error message thrown by JPA server

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

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.cds.example;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
+import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
@@ -59,18 +60,16 @@ public class FhirServerConfig extends BaseJavaConfigDstu3 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
 
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
-		extraProperties.put("hibernate.dialect", org.hibernate.dialect.DerbyTenSevenDialect.class.getName());
+		extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
 		extraProperties.put("hibernate.format_sql", "true");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");

example-projects/hapi-fhir-jpaserver-dynamic/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigCommon.java

@@ -6,6 +6,9 @@ import java.util.Properties;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.config.BaseConfig;
+import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.jpa.HibernatePersistenceProvider;
@@ -84,14 +87,14 @@ public class FhirServerConfigCommon {
 		return dataSource;
 	}
 
-	public static LocalContainerEntityManagerFactoryBean getEntityManagerFactory(Environment env, DataSource dataSource) {
+	public static LocalContainerEntityManagerFactoryBean getEntityManagerFactory(Environment env, DataSource dataSource, FhirContext theCtx) {
 		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		BaseConfig.configureEntityManagerFactory(retVal, theCtx);
+
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(dataSource);
-		
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties(env));
+
 		return retVal;
 	}
 
@@ -134,7 +137,7 @@ public class FhirServerConfigCommon {
 			extraProperties.put("hibernate.dialect", org.hibernate.dialect.PostgreSQL9Dialect.class.getName());
 		} 
 		else if(dbUrl != null && dbUrl.indexOf("derby") > -1) {
-			extraProperties.put("hibernate.dialect", org.hibernate.dialect.DerbyTenSevenDialect.class.getName());
+			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
 		} 
 		boolean hibernateCreate = new Boolean(env.getProperty(Utils.HIBERNATE_CREATE));
 		logger.info("------DB hibernateCreate: " + hibernateCreate);

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

@@ -57,6 +57,8 @@ ca.uhn.fhir.validation.ValidationResult.noIssuesDetected=No issues detected duri
 
 # JPA Messages
 
+ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceVersionConstraintFailure=The operation has failed with a version constraint failure. This generally means that two clients/threads were trying to update the same resource at the same time, and this request was chosen as the failing request.
+
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.externalReferenceNotAllowed=Resource contains external reference to URL "{0}" but this server is not configured to allow external references
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request
 ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlInvalidResourceType=Invalid match URL "{0}" - Unknown resource type: "{1}"

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseCommand.java

@@ -26,10 +26,7 @@ import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
 import com.google.common.base.Charsets;
-import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.*;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
 import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
@@ -57,9 +54,6 @@ import java.util.zip.GZIPInputStream;
 import static org.apache.commons.lang3.StringUtils.*;
 
 public abstract class BaseCommand implements Comparable<BaseCommand> {
-	// TODO: Don't use qualified names for loggers in HAPI CLI.
-	private static final Logger ourLog = LoggerFactory.getLogger(BaseCommand.class);
-
 	protected static final String BASE_URL_PARAM = "t";
 	protected static final String BASE_URL_PARAM_LONGOPT = "target";
 	protected static final String BASE_URL_PARAM_NAME = "target";
@@ -78,8 +72,8 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 	protected static final String VERBOSE_LOGGING_PARAM = "l";
 	protected static final String VERBOSE_LOGGING_PARAM_LONGOPT = "logging";
 	protected static final String VERBOSE_LOGGING_PARAM_DESC = "If specified, verbose logging will be used.";
-
+	// TODO: Don't use qualified names for loggers in HAPI CLI.
-
+	private static final Logger ourLog = LoggerFactory.getLogger(BaseCommand.class);
 	protected FhirContext myFhirCtx;
 
 	public BaseCommand() {
@@ -104,13 +98,8 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 		addRequiredOption(theOptions, FHIR_VERSION_PARAM, FHIR_VERSION_PARAM_LONGOPT, FHIR_VERSION_PARAM_NAME, FHIR_VERSION_PARAM_DESC + versions);
 	}
 
-	protected void addVerboseLoggingOption(Options theOptions) {
+	private void addOption(Options theOptions, OptionGroup theOptionGroup, boolean theRequired, String theOpt, String theLongOpt, boolean theHasArgument, String theArgumentName, String theDescription) {
-		addOptionalOption(theOptions, VERBOSE_LOGGING_PARAM, VERBOSE_LOGGING_PARAM_LONGOPT, false, VERBOSE_LOGGING_PARAM_DESC);
+		Option option = createOption(theRequired, theOpt, theLongOpt, theHasArgument, theDescription);
-	}
-
-	private void addOption(Options theOptions, boolean theRequired, String theOpt, String theLong, boolean theHasArgument, String theArgumentName, String theDescription) {
-		Option option = new Option(theOpt, theLong, theHasArgument, theDescription);
-		option.setRequired(theRequired);
 		if (theHasArgument && isNotBlank(theArgumentName)) {
 			option.setArgName(theArgumentName);
 		}
@@ -119,30 +108,48 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 			if (theOptions.getOption(theOpt) != null) {
 				throw new IllegalStateException("Duplicate option: " + theOpt);
 			}
+			if (theOptionGroup != null && theOptionGroup.getOptions().stream().anyMatch(t-> theOpt.equals(t.getOpt()))) {
+				throw new IllegalStateException("Duplicate option: " + theOpt);
+			}
 		}
-		if (isNotBlank(theLong)) {
+		if (isNotBlank(theLongOpt)) {
-			if (theOptions.getOption(theLong) != null) {
+			if (theOptions.getOption(theLongOpt) != null) {
-				throw new IllegalStateException("Duplicate option: " + theLong);
+				throw new IllegalStateException("Duplicate option: " + theLongOpt);
+			}
+			if (theOptionGroup != null && theOptionGroup.getOptions().stream().anyMatch(t-> theLongOpt.equals(t.getLongOpt()))) {
+				throw new IllegalStateException("Duplicate option: " + theOpt);
 			}
 		}
 
-		theOptions.addOption(option);
+		if (theOptionGroup != null) {
+			theOptionGroup.addOption(option);
+		} else {
+			theOptions.addOption(option);
+		}
 	}
 
 	protected void addOptionalOption(Options theOptions, String theOpt, String theLong, boolean theTakesArgument, String theDescription) {
-		addOption(theOptions, false, theOpt, theLong, theTakesArgument, null, theDescription);
+		addOption(theOptions, null, false, theOpt, theLong, theTakesArgument, null, theDescription);
 	}
 
 	protected void addOptionalOption(Options theOptions, String theOpt, String theLong, String theArgumentName, String theDescription) {
-		addOption(theOptions, false, theOpt, theLong, isNotBlank(theArgumentName), theArgumentName, theDescription);
+		addOption(theOptions, null, false, theOpt, theLong, isNotBlank(theArgumentName), theArgumentName, theDescription);
+	}
+
+	protected void addOptionalOption(Options theOptions, OptionGroup theOptionGroup, String theOpt, String theLong, String theArgumentName, String theDescription) {
+		addOption(theOptions, theOptionGroup, false, theOpt, theLong, isNotBlank(theArgumentName), theArgumentName, theDescription);
 	}
 
 	protected void addRequiredOption(Options theOptions, String theOpt, String theLong, boolean theTakesArgument, String theDescription) {
-		addOption(theOptions, true, theOpt, theLong, theTakesArgument, null, theDescription);
+		addOption(theOptions, null, true, theOpt, theLong, theTakesArgument, null, theDescription);
 	}
 
 	protected void addRequiredOption(Options theOptions, String theOpt, String theLong, String theArgumentName, String theDescription) {
-		addOption(theOptions, true, theOpt, theLong, isNotBlank(theArgumentName), theArgumentName, theDescription);
+		addOption(theOptions, null, true, theOpt, theLong, isNotBlank(theArgumentName), theArgumentName, theDescription);
+	}
+
+	protected void addVerboseLoggingOption(Options theOptions) {
+		addOptionalOption(theOptions, VERBOSE_LOGGING_PARAM, VERBOSE_LOGGING_PARAM_LONGOPT, false, VERBOSE_LOGGING_PARAM_DESC);
 	}
 
 	@Override
@@ -150,6 +157,12 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
 		return getCommandName().compareTo(theO.getCommandName());
 	}
 
+	private Option createOption(boolean theRequired, String theOpt, String theLong, boolean theHasArgument, String theDescription) {
+		Option option = new Option(theOpt, theLong, theHasArgument, theDescription);
+		option.setRequired(theRequired);
+		return option;
+	}
+
 	protected Reader createReader(File theInputFile) throws IOException {
 		InputStream inputStream = new FileInputStream(theInputFile);
 		if (theInputFile.getName().toLowerCase().endsWith(".gz")) {

hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ValidateCommand.java

@@ -68,18 +68,18 @@ public class ValidateCommand extends BaseCommand {
 		addFhirVersionOption(retVal);
 
 		OptionGroup source = new OptionGroup();
-		addOptionalOption(source, "n", "file", true, "filename", "The name of the file to validate");
+		addOptionalOption(retVal, source, "n", "file", "filename", "The name of the file to validate");
-		addOptionalOption(source, "d", "data", true, "text", "The text to validate");
+		addOptionalOption(retVal, source, "d", "data", "text", "The text to validate");
 		retVal.addOptionGroup(source);
 
 		retVal.addOption("p", "profile", false, "Validate using Profiles (StructureDefinition / ValueSet)");
 		retVal.addOption("r", "fetch-remote", false,
 			"Allow fetching remote resources (in other words, if a resource being validated refers to an external StructureDefinition, Questionnaire, etc. this flag allows the validator to access the internet to try and fetch this resource)");
-		addOptionalOption(retVal, "l", "fetch-local", true, "filename", "Fetch a profile locally and use it if referenced"));
+		addOptionalOption(retVal, "l", "fetch-local", "filename", "Fetch a profile locally and use it if referenced");
 		addOptionalOption(retVal, null, "igpack", true, "If specified, provides the filename of an IGPack file to include in validation");
 		addOptionalOption(retVal, "x", "xsd", false, "Validate using Schemas");
 		addOptionalOption(retVal, "s", "sch", false, "Validate using Schematrons");
-		addOptionalOption(retVal, "e", "encoding", true, "encoding", "File encoding (default is UTF-8)");
+		addOptionalOption(retVal, "e", "encoding","encoding", "File encoding (default is UTF-8)");
 		return retVal;
 	}
 

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirDbConfig.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.demo;
 import java.util.Properties;
 
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
+import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
@@ -15,7 +16,7 @@ public class FhirDbConfig {
 	@Bean()
 	public Properties jpaProperties() {
 		Properties extraProperties = new Properties();
-		extraProperties.put("hibernate.dialect", org.hibernate.dialect.DerbyTenSevenDialect.class.getName());
+		extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
 		extraProperties.put("hibernate.format_sql", "true");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");

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

@@ -65,7 +65,7 @@ public class FhirServerConfig extends BaseJavaConfigDstu2 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(dataSource());
 		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu3.java

@@ -68,11 +68,9 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(myJpaProperties);
 		return retVal;
 	}

hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigR4.java

@@ -68,11 +68,9 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(myJpaProperties);
 		return retVal;
 	}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java

@@ -20,12 +20,15 @@ package ca.uhn.fhir.jpa.config;
  * #L%
  */
 
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.i18n.HapiLocalizer;
 import ca.uhn.fhir.jpa.search.*;
 import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
 import ca.uhn.fhir.jpa.sp.SearchParamPresenceSvcImpl;
 import ca.uhn.fhir.jpa.subscription.email.SubscriptionEmailInterceptor;
 import ca.uhn.fhir.jpa.subscription.resthook.SubscriptionRestHookInterceptor;
 import ca.uhn.fhir.jpa.subscription.websocket.SubscriptionWebsocketInterceptor;
+import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
@@ -35,6 +38,9 @@ import org.springframework.context.annotation.Lazy;
 import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
 import org.springframework.core.env.Environment;
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
+import org.springframework.orm.hibernate5.HibernateExceptionTranslator;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+import org.springframework.orm.jpa.vendor.HibernateJpaDialect;
 import org.springframework.scheduling.TaskScheduler;
 import org.springframework.scheduling.annotation.EnableScheduling;
 import org.springframework.scheduling.annotation.SchedulingConfigurer;
@@ -47,7 +53,7 @@ import javax.annotation.Resource;
 @Configuration
 @EnableScheduling
 @EnableJpaRepositories(basePackages = "ca.uhn.fhir.jpa.dao.data")
-public class BaseConfig implements SchedulingConfigurer {
+public abstract class BaseConfig implements SchedulingConfigurer {
 
 	public static final String TASK_EXECUTOR_NAME = "hapiJpaTaskExecutor";
 
@@ -67,6 +73,29 @@ public class BaseConfig implements SchedulingConfigurer {
 		return retVal;
 	}
 
+	/**
+	 * This method should be overridden to provide an actual completed
+	 * bean, but it provides a partially completed entity manager
+	 * factory with HAPI FHIR customizations
+	 */
+	protected LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		configureEntityManagerFactory(retVal, fhirContext());
+		return retVal;
+	}
+
+	public abstract FhirContext fhirContext();
+
+	@Bean
+	public HibernateExceptionTranslator hibernateExceptionTranslator() {
+		return new HibernateExceptionTranslator();
+	}
+
+	@Bean
+	public HibernateJpaDialect hibernateJpaDialectIntance() {
+		return new HibernateJpaDialect();
+	}
+
 	@Bean()
 	public ScheduledExecutorFactoryBean scheduledExecutorService() {
 		ScheduledExecutorFactoryBean b = new ScheduledExecutorFactoryBean();
@@ -112,7 +141,7 @@ public class BaseConfig implements SchedulingConfigurer {
 		return new SubscriptionWebsocketInterceptor();
 	}
 
-	@Bean(name=TASK_EXECUTOR_NAME)
+	@Bean(name = TASK_EXECUTOR_NAME)
 	public TaskScheduler taskScheduler() {
 		ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
 		retVal.setConcurrentExecutor(scheduledExecutorService().getObject());
@@ -120,6 +149,16 @@ public class BaseConfig implements SchedulingConfigurer {
 		return retVal;
 	}
 
+	public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) {
+		theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer()));
+		theFactory.setPackagesToScan("ca.uhn.fhir.jpa.entity");
+		theFactory.setPersistenceProvider(new HibernatePersistenceProvider());
+	}
+
+	private static HibernateJpaDialect hibernateJpaDialect(HapiLocalizer theLocalizer) {
+		return new HapiFhirHibernateJpaDialect(theLocalizer);
+	}
+
 	/**
 	 * This lets the "@Value" fields reference properties from the properties file
 	 */

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java

@@ -53,6 +53,11 @@ public class BaseDstu2Config extends BaseConfig {
 		return fhirContextDstu2();
 	}
 
+	@Override
+	public FhirContext fhirContext() {
+		return fhirContextDstu2();
+	}
+
 	@Bean(name = "myFhirContextDstu2")
 	@Lazy
 	public FhirContext fhirContextDstu2() {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HapiFhirHibernateJpaDialect.java

@@ -0,0 +1,33 @@
+package ca.uhn.fhir.jpa.config;
+
+import ca.uhn.fhir.i18n.HapiLocalizer;
+import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
+import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
+import org.hibernate.HibernateException;
+import org.hibernate.exception.ConstraintViolationException;
+import org.springframework.dao.DataAccessException;
+import org.springframework.orm.jpa.vendor.HibernateJpaDialect;
+
+public class HapiFhirHibernateJpaDialect extends HibernateJpaDialect {
+
+	private HapiLocalizer myLocalizer;
+
+	/**
+	 * Constructor
+	 */
+	public HapiFhirHibernateJpaDialect(HapiLocalizer theLocalizer) {
+		myLocalizer = theLocalizer;
+	}
+
+	@Override
+	protected DataAccessException convertHibernateAccessException(HibernateException theException) {
+		if (theException instanceof ConstraintViolationException) {
+			if (ResourceHistoryTable.IDX_RESVER_ID_VER.equals(((ConstraintViolationException) theException).getConstraintName())) {
+				throw new PreconditionFailedException(myLocalizer.getMessage(HapiFhirHibernateJpaDialect.class, "resourceVersionConstraintFailure"));
+			}
+		}
+
+		return super.convertHibernateAccessException(theException);
+	}
+
+}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java

@@ -15,7 +15,6 @@ import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvcDstu3;
 import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
-import ca.uhn.fhir.jpa.util.SingleItemLoadingCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.lang3.time.DateUtils;
@@ -29,8 +28,6 @@ import org.springframework.context.annotation.Lazy;
 import org.springframework.context.annotation.Primary;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import java.util.Map;
-
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -55,6 +52,11 @@ import java.util.Map;
 @EnableTransactionManagement
 public class BaseDstu3Config extends BaseConfig {
 
+	@Override
+	public FhirContext fhirContext() {
+		return fhirContextDstu3();
+	}
+
 	@Bean
 	@Primary
 	public FhirContext fhirContextDstu3() {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java

@@ -16,7 +16,6 @@ import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
 import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
 import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
 import ca.uhn.fhir.jpa.util.ResourceCountCache;
-import ca.uhn.fhir.jpa.util.SingleItemLoadingCache;
 import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR4;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.lang3.time.DateUtils;
@@ -32,8 +31,6 @@ import org.springframework.context.annotation.Lazy;
 import org.springframework.context.annotation.Primary;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import java.util.Map;
-
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -58,6 +55,11 @@ import java.util.Map;
 @EnableTransactionManagement
 public class BaseR4Config extends BaseConfig {
 
+	@Override
+	public FhirContext fhirContext() {
+		return fhirContextR4();
+	}
+
 	@Bean
 	@Primary
 	public FhirContext fhirContextR4() {

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

@@ -78,6 +78,7 @@ import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Slice;
 import org.springframework.data.domain.SliceImpl;
+import org.springframework.stereotype.Repository;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.support.TransactionTemplate;
 
@@ -98,6 +99,7 @@ import java.util.concurrent.atomic.AtomicInteger;
 import static org.apache.commons.lang3.StringUtils.*;
 
 @SuppressWarnings("WeakerAccess")
+@Repository
 public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 	public static final long INDEX_STATUS_INDEXED = 1L;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTable.java

@@ -32,7 +32,7 @@ import java.util.Collection;
 //@formatter:off
 @Entity
 @Table(name = "HFJ_RES_VER", uniqueConstraints = {
-	@UniqueConstraint(name = "IDX_RESVER_ID_VER", columnNames = {"RES_ID", "RES_VER"})
+	@UniqueConstraint(name = ResourceHistoryTable.IDX_RESVER_ID_VER, columnNames = {"RES_ID", "RES_VER"})
 }, indexes = {
 	@Index(name = "IDX_RESVER_TYPE_DATE", columnList = "RES_TYPE,RES_UPDATED"),
 	@Index(name = "IDX_RESVER_ID_DATE", columnList = "RES_ID,RES_UPDATED"),
@@ -42,6 +42,7 @@ import java.util.Collection;
 public class ResourceHistoryTable extends BaseHasResource implements Serializable {
 
 	private static final long serialVersionUID = 1L;
+	public static final String IDX_RESVER_ID_VER = "IDX_RESVER_ID_VER";
 
 	@Id
 	@SequenceGenerator(name = "SEQ_RESOURCE_HISTORY_ID", sequenceName = "SEQ_RESOURCE_HISTORY_ID")

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/DerbyTenSevenHapiFhirDialect.java

@@ -0,0 +1,30 @@
+package ca.uhn.fhir.jpa.util;
+
+import org.hibernate.dialect.DerbyTenSevenDialect;
+import org.hibernate.exception.spi.TemplatedViolatedConstraintNameExtracter;
+import org.hibernate.exception.spi.ViolatedConstraintNameExtracter;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+
+public class DerbyTenSevenHapiFhirDialect extends DerbyTenSevenDialect {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(DerbyTenSevenHapiFhirDialect.class);
+
+	@Override
+	public ViolatedConstraintNameExtracter getViolatedConstraintNameExtracter() {
+		return new TemplatedViolatedConstraintNameExtracter() {
+			@Override
+			protected String doExtractConstraintName(SQLException theSqlException) throws NumberFormatException {
+				switch (theSqlException.getSQLState()) {
+					case "23505":
+						return this.extractUsingTemplate("unique or primary key constraint or unique index identified by '", "'", theSqlException.getMessage());
+					default:
+						return null;
+				}
+			}
+		};
+	}
+
+}

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

@@ -45,11 +45,9 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu2");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
@@ -59,7 +57,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 		extraProperties.put("hibernate.format_sql", "true");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");
-		extraProperties.put("hibernate.dialect", "org.hibernate.dialect.DerbyTenSevenDialect");
+		extraProperties.put("hibernate.dialect", "ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect");
 		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "ram");
 		extraProperties.put("hibernate.search.lucene_version","LUCENE_CURRENT");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java

@@ -135,10 +135,9 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu3");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
 		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
@@ -150,7 +149,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");
-		extraProperties.put("hibernate.dialect", "org.hibernate.dialect.DerbyTenSevenDialect");
+		extraProperties.put("hibernate.dialect", "ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect");
 		extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "ram");
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3WithoutLuceneConfig.java

@@ -27,11 +27,7 @@ public class TestDstu3WithoutLuceneConfig extends TestDstu3Config {
 	@Override
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
-		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu3");
-		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
@@ -41,7 +37,7 @@ public class TestDstu3WithoutLuceneConfig extends TestDstu3Config {
 		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");
-		extraProperties.put("hibernate.dialect", "org.hibernate.dialect.DerbyTenSevenDialect");
+		extraProperties.put("hibernate.dialect", "ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect");
 		extraProperties.put("hibernate.search.autoregister_listeners", "false");
 		return extraProperties;
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java

@@ -12,8 +12,10 @@ import org.hibernate.query.criteria.LiteralHandlingMode;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Lazy;
+import org.springframework.orm.hibernate5.HibernateExceptionTranslator;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+import org.springframework.orm.jpa.vendor.HibernateJpaDialect;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 import javax.persistence.EntityManagerFactory;
@@ -115,11 +117,9 @@ public class TestR4Config extends BaseJavaConfigR4 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaR4");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
@@ -130,7 +130,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");
-		extraProperties.put("hibernate.dialect", "org.hibernate.dialect.DerbyTenSevenDialect");
+		extraProperties.put("hibernate.dialect", "ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect");
 		extraProperties.put("hibernate.search.model_mapping", ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory.class.getName());
 		extraProperties.put("hibernate.search.default.directory_provider", "ram");
 		extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4WithoutLuceneConfig.java

@@ -27,11 +27,8 @@ public class TestR4WithoutLuceneConfig extends TestR4Config {
 	@Override
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
-		retVal.setPersistenceUnitName("PU_HapiFhirJpaR4");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
@@ -41,7 +38,7 @@ public class TestR4WithoutLuceneConfig extends TestR4Config {
 		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");
-		extraProperties.put("hibernate.dialect", "org.hibernate.dialect.DerbyTenSevenDialect");
+		extraProperties.put("hibernate.dialect", "ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect");
 		extraProperties.put("hibernate.search.autoregister_listeners", "false");
 		return extraProperties;
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java

@@ -1,27 +1,41 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
-import static org.apache.commons.lang3.StringUtils.defaultString;
+import ca.uhn.fhir.jpa.dao.*;
-import static org.hamcrest.Matchers.*;
+import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
-import static org.junit.Assert.*;
+import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
-import static org.mockito.Matchers.eq;
+import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
-import static org.mockito.Mockito.*;
+import ca.uhn.fhir.jpa.entity.TagTypeEnum;
-
+import ca.uhn.fhir.model.api.Include;
-import java.io.IOException;
+import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
-import java.util.*;
+import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
-
+import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.*;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.*;
+import ca.uhn.fhir.rest.server.exceptions.*;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
+import ca.uhn.fhir.util.TestUtil;
+import com.google.common.base.Charsets;
+import com.google.common.collect.Lists;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.RandomStringUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.hamcrest.Matchers;
 import org.hamcrest.core.StringContains;
+import org.hl7.fhir.instance.model.api.IAnyResource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.Bundle.*;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Bundle.BundleType;
+import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
 import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
 import org.hl7.fhir.r4.model.Observation.ObservationStatus;
 import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
 import org.hl7.fhir.r4.model.OperationOutcome.IssueType;
 import org.hl7.fhir.r4.model.Quantity.QuantityComparator;
-import org.hl7.fhir.instance.model.api.*;
 import org.junit.*;
 import org.mockito.ArgumentCaptor;
 import org.springframework.transaction.TransactionDefinition;
@@ -29,24 +43,21 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import com.google.common.base.Charsets;
+import java.io.IOException;
-import com.google.common.collect.Lists;
+import java.util.*;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
 
-import ca.uhn.fhir.jpa.dao.*;
+import static org.apache.commons.lang3.StringUtils.defaultString;
-import ca.uhn.fhir.jpa.entity.*;
+import static org.hamcrest.Matchers.contains;
-import ca.uhn.fhir.model.api.Include;
+import static org.hamcrest.Matchers.*;
-import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
+import static org.junit.Assert.*;
-import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
+import static org.mockito.Matchers.eq;
-import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
+import static org.mockito.Mockito.*;
-import ca.uhn.fhir.rest.api.*;
-import ca.uhn.fhir.rest.api.Constants;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.param.*;
-import ca.uhn.fhir.rest.server.exceptions.*;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
-import ca.uhn.fhir.util.TestUtil;
 
-@SuppressWarnings({ "unchecked", "deprecation" })
+@SuppressWarnings({"unchecked", "deprecation"})
 public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4Test.class);
@@ -82,47 +93,6 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		}
 	}
 
-
-	@Test
-	public void testSaveAndReturnCollectionBundle() throws IOException {
-		String input = IOUtils.toString(FhirResourceDaoR4Test.class.getResourceAsStream("/r4/collection-bundle.json"));
-		Bundle inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
-
-		myBundleDao.update(inputBundle);
-
-		Bundle outputBundle = myBundleDao.read(new IdType("cftest"));
-		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
-
-		for (BundleEntryComponent next : outputBundle.getEntry()) {
-			assertTrue(next.getResource().getIdElement().hasIdPart());
-		}
-	}
-
-
-	/**
-	 * See #773
-	 */
-	@Test
-	public void testDeleteResourceWithOutboundDeletedResources() {
-		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
-
-		Organization org = new Organization();
-		org.setId("ORG");
-		org.setName("ORG");
-		myOrganizationDao.update(org);
-
-		Patient pat = new Patient();
-		pat.setId("PAT");
-		pat.setActive(true);
-		pat.setManagingOrganization(new Reference("Organization/ORG"));
-		myPatientDao.update(pat);
-
-		myOrganizationDao.delete(new IdType("Organization/ORG"));
-
-		myPatientDao.delete(new IdType("Patient/PAT"));
-	}
-
-
 	@Before
 	public void beforeDisableResultReuse() {
 		myDaoConfig.setReuseCachedSearchResultsForMillis(null);
@@ -161,7 +131,6 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		}
 	}
 
-	
 	private void sortCodings(List<Coding> theSecLabels) {
 		Collections.sort(theSecLabels, new Comparator<Coding>() {
 			@Override
@@ -453,6 +422,54 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		assertGone(id.toUnqualifiedVersionless());
 	}
 
+	@Test
+	public void testConflictingUpdates() throws ExecutionException, InterruptedException {
+		ExecutorService pool = Executors.newFixedThreadPool(5);
+		try {
+
+			Patient p = new Patient();
+			p.setActive(true);
+			IIdType id = myPatientDao.create(p).getId();
+
+			List<Future<String>> futures = new ArrayList<>();
+			for (int i = 0; i < 50; i++) {
+				Patient updatePatient = new Patient();
+				updatePatient.setId(id.toUnqualifiedVersionless());
+				updatePatient.addIdentifier().setSystem("" + i);
+				updatePatient.setActive(true);
+
+				int finalI = i;
+				Future<String> future = pool.submit(() -> {
+					ourLog.info("Starting update {}", finalI);
+					try {
+						try {
+							myPatientDao.update(updatePatient);
+						} catch (PreconditionFailedException e) {
+							assertEquals("The operation has failed with a version constraint failure. This generally means that two clients/threads were trying to update the same resource at the same time, and this request was chosen as the failing request.", e.getMessage());
+						}
+					} catch (Exception e) {
+						ourLog.error("Failure", e);
+						return e.toString();
+					}
+					ourLog.info("Finished update {}", finalI);
+					return null;
+				});
+				futures.add(future);
+			}
+
+			for (Future<String> next : futures) {
+				String nextError = next.get();
+				if (StringUtils.isNotBlank(nextError)) {
+					fail(nextError);
+				}
+			}
+
+
+		} finally {
+			pool.shutdown();
+		}
+	}
+
 	@Test
 	@Ignore
 	public void testCreateBuiltInProfiles() throws Exception {
@@ -523,7 +540,6 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 	}
 
-	
 	@Test
 	public void testCreateDifferentTypesWithSameForcedId() {
 		String idName = "forcedId";
@@ -544,7 +560,6 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		obs = myObservationDao.read(obsId.toUnqualifiedVersionless(), mySrd);
 	}
 
-
 	@Test
 	public void testCreateDuplicateTagsDoesNotCauseDuplicates() {
 		Patient p = new Patient();
@@ -599,22 +614,22 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 	public void testCreateLongString() {
 		//@formatter:off
 		String input = "<NamingSystem>\n" +
-				"        <name value=\"NDF-RT (National Drug File – Reference Terminology)\"/>\n" + 
+			"        <name value=\"NDF-RT (National Drug File – Reference Terminology)\"/>\n" +
-				"        <status value=\"draft\"/>\n" + 
+			"        <status value=\"draft\"/>\n" +
-				"        <kind value=\"codesystem\"/>\n" + 
+			"        <kind value=\"codesystem\"/>\n" +
-				"        <publisher value=\"HL7, Inc\"/>\n" + 
+			"        <publisher value=\"HL7, Inc\"/>\n" +
-				"        <date value=\"2015-08-21\"/>\n" + 
+			"        <date value=\"2015-08-21\"/>\n" +
-				"        <uniqueId>\n" + 
+			"        <uniqueId>\n" +
-				"          <type value=\"uri\"/>\n" + 
+			"          <type value=\"uri\"/>\n" +
-				"          <value value=\"http://hl7.org/fhir/ndfrt\"/>\n" + 
+			"          <value value=\"http://hl7.org/fhir/ndfrt\"/>\n" +
-				"          <preferred value=\"true\"/>\n" + 
+			"          <preferred value=\"true\"/>\n" +
-				"        </uniqueId>\n" + 
+			"        </uniqueId>\n" +
-				"        <uniqueId>\n" + 
+			"        <uniqueId>\n" +
-				"          <type value=\"oid\"/>\n" + 
+			"          <type value=\"oid\"/>\n" +
-				"          <value value=\"2.16.840.1.113883.6.209\"/>\n" + 
+			"          <value value=\"2.16.840.1.113883.6.209\"/>\n" +
-				"          <preferred value=\"false\"/>\n" + 
+			"          <preferred value=\"false\"/>\n" +
-				"        </uniqueId>\n" + 
+			"        </uniqueId>\n" +
-				"      </NamingSystem>";
+			"      </NamingSystem>";
 		//@formatter:on
 
 		NamingSystem res = myFhirCtx.newXmlParser().parseResource(NamingSystem.class, input);
@@ -853,7 +868,6 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		}
 	}
 
-
 	@Test
 	public void testCreateWithInvalidReferenceFailsGracefully() {
 		Patient patient = new Patient();
@@ -1108,49 +1122,6 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 	}
 
-	@Test
-	public void testDeleteTwicePerformsNoOp() {
-		Patient patient = new Patient();
-		patient.setActive(true);
-
-		IIdType id = myPatientDao.create(patient, mySrd).getId();
-		assertNotNull(id.getIdPartAsLong());
-		assertEquals("1", id.getVersionIdPart());
-
-		IIdType id2 = myPatientDao.delete(id.toUnqualifiedVersionless()).getId();
-		assertEquals(id.getIdPart(), id2.getIdPart());
-		assertEquals("2", id2.getVersionIdPart());
-
-		IIdType id3 = myPatientDao.delete(id.toUnqualifiedVersionless()).getId();
-		assertEquals(id.getIdPart(), id3.getIdPart());
-		assertEquals("2", id3.getVersionIdPart());
-
-		IIdType id4 = myPatientDao.delete(id.toUnqualifiedVersionless()).getId();
-		assertEquals(id.getIdPart(), id4.getIdPart());
-		assertEquals("2", id4.getVersionIdPart());
-
-		patient = new Patient();
-		patient.setId(id.getIdPart());
-		patient.setActive(false);
-		IIdType id5 = myPatientDao.update(patient).getId();
-		assertEquals(id.getIdPart(), id5.getIdPart());
-		assertEquals("3", id5.getVersionIdPart());
-
-		patient = myPatientDao.read(id.withVersion("1"));
-		assertEquals(true, patient.getActive());
-
-		try {
-			myPatientDao.read(id.withVersion("2"));
-			fail();
-		} catch (ResourceGoneException e) {
-			// good
-		}
-
-		patient = myPatientDao.read(id.withVersion("3"));
-		assertEquals(false, patient.getActive());
-
-	}
-
 	@Test
 	public void testDeleteResource() {
 		int initialHistory = myPatientDao.history(null, null, mySrd).size();
@@ -1215,6 +1186,29 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 	}
 
+	/**
+	 * See #773
+	 */
+	@Test
+	public void testDeleteResourceWithOutboundDeletedResources() {
+		myDaoConfig.setEnforceReferentialIntegrityOnDelete(false);
+
+		Organization org = new Organization();
+		org.setId("ORG");
+		org.setName("ORG");
+		myOrganizationDao.update(org);
+
+		Patient pat = new Patient();
+		pat.setId("PAT");
+		pat.setActive(true);
+		pat.setManagingOrganization(new Reference("Organization/ORG"));
+		myPatientDao.update(pat);
+
+		myOrganizationDao.delete(new IdType("Organization/ORG"));
+
+		myPatientDao.delete(new IdType("Patient/PAT"));
+	}
+
 	@Test
 	public void testDeleteThenUndelete() {
 		Patient patient = new Patient();
@@ -1248,6 +1242,49 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		assertEquals(id2, gotId);
 	}
 
+	@Test
+	public void testDeleteTwicePerformsNoOp() {
+		Patient patient = new Patient();
+		patient.setActive(true);
+
+		IIdType id = myPatientDao.create(patient, mySrd).getId();
+		assertNotNull(id.getIdPartAsLong());
+		assertEquals("1", id.getVersionIdPart());
+
+		IIdType id2 = myPatientDao.delete(id.toUnqualifiedVersionless()).getId();
+		assertEquals(id.getIdPart(), id2.getIdPart());
+		assertEquals("2", id2.getVersionIdPart());
+
+		IIdType id3 = myPatientDao.delete(id.toUnqualifiedVersionless()).getId();
+		assertEquals(id.getIdPart(), id3.getIdPart());
+		assertEquals("2", id3.getVersionIdPart());
+
+		IIdType id4 = myPatientDao.delete(id.toUnqualifiedVersionless()).getId();
+		assertEquals(id.getIdPart(), id4.getIdPart());
+		assertEquals("2", id4.getVersionIdPart());
+
+		patient = new Patient();
+		patient.setId(id.getIdPart());
+		patient.setActive(false);
+		IIdType id5 = myPatientDao.update(patient).getId();
+		assertEquals(id.getIdPart(), id5.getIdPart());
+		assertEquals("3", id5.getVersionIdPart());
+
+		patient = myPatientDao.read(id.withVersion("1"));
+		assertEquals(true, patient.getActive());
+
+		try {
+			myPatientDao.read(id.withVersion("2"));
+			fail();
+		} catch (ResourceGoneException e) {
+			// good
+		}
+
+		patient = myPatientDao.read(id.withVersion("3"));
+		assertEquals(false, patient.getActive());
+
+	}
+
 	@Test
 	public void testDeleteWithHas() {
 		Observation obs1 = new Observation();
@@ -1784,7 +1821,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 			preDates.add(new Date());
 			Thread.sleep(100);
 			patient.setId(id);
-			patient.getName().get(0).getFamilyElement().setValue(methodName + "_i"+i);
+			patient.getName().get(0).getFamilyElement().setValue(methodName + "_i" + i);
 			ids.add(myPatientDao.update(patient, mySrd).getId().toUnqualified().getValue());
 		}
 
@@ -2144,7 +2181,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 		//@formatter:off
 		String inputStr =
-				"{" +
+			"{" +
 				"  \"resourceType\":\"Organization\",\n" +
 				"  \"extension\":[\n" +
 				"     {\n" +
@@ -2851,6 +2888,21 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		assertEquals(BundleEntrySearchModeEnum.INCLUDE.getCode(), ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get((IAnyResource) results.get(1)));
 	}
 
+	@Test
+	public void testSaveAndReturnCollectionBundle() throws IOException {
+		String input = IOUtils.toString(FhirResourceDaoR4Test.class.getResourceAsStream("/r4/collection-bundle.json"));
+		Bundle inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
+
+		myBundleDao.update(inputBundle);
+
+		Bundle outputBundle = myBundleDao.read(new IdType("cftest"));
+		ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
+
+		for (BundleEntryComponent next : outputBundle.getEntry()) {
+			assertTrue(next.getResource().getIdElement().hasIdPart());
+		}
+	}
+
 	@Test()
 	public void testSortByComposite() {
 		Observation o = new Observation();
@@ -2920,6 +2972,40 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 	}
 
+	@Test
+	@Ignore
+	public void testSortByEncounterLength() {
+		String methodName = "testSortByNumber";
+
+		Encounter e1 = new Encounter();
+		e1.addIdentifier().setSystem("foo").setValue(methodName);
+		e1.getLength().setSystem(BaseHapiFhirDao.UCUM_NS).setCode("min").setValue(4.0 * 24 * 60);
+		IIdType id1 = myEncounterDao.create(e1, mySrd).getId().toUnqualifiedVersionless();
+
+		Encounter e3 = new Encounter();
+		e3.addIdentifier().setSystem("foo").setValue(methodName);
+		e3.getLength().setSystem(BaseHapiFhirDao.UCUM_NS).setCode("year").setValue(3.0);
+		IIdType id3 = myEncounterDao.create(e3, mySrd).getId().toUnqualifiedVersionless();
+
+		Encounter e2 = new Encounter();
+		e2.addIdentifier().setSystem("foo").setValue(methodName);
+		e2.getLength().setSystem(BaseHapiFhirDao.UCUM_NS).setCode("year").setValue(2.0);
+		IIdType id2 = myEncounterDao.create(e2, mySrd).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap pm;
+		List<String> actual;
+
+		pm = new SearchParameterMap();
+		pm.setSort(new SortSpec(Encounter.SP_LENGTH));
+		actual = toUnqualifiedVersionlessIdValues(myEncounterDao.search(pm));
+		assertThat(actual, contains(toValues(id1, id2, id3)));
+
+		pm = new SearchParameterMap();
+		pm.setSort(new SortSpec(Encounter.SP_LENGTH, SortOrderEnum.DESC));
+		actual = toUnqualifiedVersionlessIdValues(myEncounterDao.search(pm));
+		assertThat(actual, contains(toValues(id3, id2, id1)));
+	}
+
 	@Test
 	public void testSortById() {
 		String methodName = "testSortBTyId";
@@ -3053,41 +3139,6 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 		assertThat(actual, contains(toValues(id3, id2, id1)));
 	}
 
-
-	@Test
-	@Ignore
-	public void testSortByEncounterLength() {
-		String methodName = "testSortByNumber";
-
-		Encounter e1 = new Encounter();
-		e1.addIdentifier().setSystem("foo").setValue(methodName);
-		e1.getLength().setSystem(BaseHapiFhirDao.UCUM_NS).setCode("min").setValue(4.0 * 24 * 60);
-		IIdType id1 = myEncounterDao.create(e1, mySrd).getId().toUnqualifiedVersionless();
-
-		Encounter e3 = new Encounter();
-		e3.addIdentifier().setSystem("foo").setValue(methodName);
-		e3.getLength().setSystem(BaseHapiFhirDao.UCUM_NS).setCode("year").setValue(3.0);
-		IIdType id3 = myEncounterDao.create(e3, mySrd).getId().toUnqualifiedVersionless();
-
-		Encounter e2 = new Encounter();
-		e2.addIdentifier().setSystem("foo").setValue(methodName);
-		e2.getLength().setSystem(BaseHapiFhirDao.UCUM_NS).setCode("year").setValue(2.0);
-		IIdType id2 = myEncounterDao.create(e2, mySrd).getId().toUnqualifiedVersionless();
-
-		SearchParameterMap pm;
-		List<String> actual;
-
-		pm = new SearchParameterMap();
-		pm.setSort(new SortSpec(Encounter.SP_LENGTH));
-		actual = toUnqualifiedVersionlessIdValues(myEncounterDao.search(pm));
-		assertThat(actual, contains(toValues(id1, id2, id3)));
-
-		pm = new SearchParameterMap();
-		pm.setSort(new SortSpec(Encounter.SP_LENGTH, SortOrderEnum.DESC));
-		actual = toUnqualifiedVersionlessIdValues(myEncounterDao.search(pm));
-		assertThat(actual, contains(toValues(id3, id2, id1)));
-	}
-
 	public void testSortByQuantity() {
 		Observation res;
 
@@ -3694,7 +3745,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
 
 	public static void assertConflictException(ResourceVersionConflictException e) {
 		assertThat(e.getMessage(), matchesPattern(
-				"Unable to delete [a-zA-Z]+/[0-9]+ because at least one resource has a reference to this resource. First reference found was resource [a-zA-Z]+/[0-9]+ in path [a-zA-Z]+.[a-zA-Z]+"));
+			"Unable to delete [a-zA-Z]+/[0-9]+ because at least one resource has a reference to this resource. First reference found was resource [a-zA-Z]+/[0-9]+ in path [a-zA-Z]+.[a-zA-Z]+"));
 	}
 
 	private static List<String> toStringList(List<CanonicalType> theUriType) {

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

@@ -6,6 +6,7 @@ import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
+import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
 import org.hibernate.jpa.HibernatePersistenceProvider;
@@ -58,18 +59,16 @@ public class FhirServerConfig extends BaseJavaConfigDstu3 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
 
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
-		extraProperties.put("hibernate.dialect", org.hibernate.dialect.DerbyTenSevenDialect.class.getName());
+		extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
 		extraProperties.put("hibernate.format_sql", "true");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");

hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu2.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.demo;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
+import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
@@ -59,18 +60,16 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
 
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
-		extraProperties.put("hibernate.dialect", org.hibernate.dialect.DerbyTenSevenDialect.class.getName());
+		extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
 		extraProperties.put("hibernate.format_sql", "true");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");

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

@@ -55,18 +55,16 @@ public class FhirServerConfig extends BaseJavaConfigDstu3 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("HAPI_PU");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
 
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
-		extraProperties.put("hibernate.dialect", org.hibernate.dialect.DerbyTenSevenDialect.class.getName());
+		extraProperties.put("hibernate.dialect", ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect.class.getName());
 		extraProperties.put("hibernate.format_sql", "true");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu2Config.java

@@ -3,6 +3,7 @@ package ca.uhn.fhirtest.config;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
+import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
 import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
@@ -12,7 +13,6 @@ import ca.uhn.fhir.validation.ResultSeverityEnum;
 import ca.uhn.fhirtest.interceptor.TdlSecurityInterceptor;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
-import org.hibernate.dialect.DerbyTenSevenDialect;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Value;
@@ -92,7 +92,7 @@ public class TdlDstu2Config extends BaseJavaConfigDstu2 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu2");
 		retVal.setDataSource(dataSource());
 		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
@@ -103,7 +103,7 @@ public class TdlDstu2Config extends BaseJavaConfigDstu2 {
 
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
-		extraProperties.put("hibernate.dialect", DerbyTenSevenDialect.class.getName());
+		extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
 		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu3Config.java

@@ -1,14 +1,18 @@
 package ca.uhn.fhirtest.config;
 
-import java.util.Properties;
+import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
-
+import ca.uhn.fhir.jpa.dao.DaoConfig;
-import javax.persistence.EntityManagerFactory;
-import javax.sql.DataSource;
-
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
+import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
+import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
+import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import ca.uhn.fhirtest.interceptor.TdlSecurityInterceptor;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
-import org.hibernate.dialect.DerbyTenSevenDialect;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Value;
@@ -21,15 +25,9 @@ import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
+import javax.persistence.EntityManagerFactory;
-import ca.uhn.fhir.jpa.dao.DaoConfig;
+import javax.sql.DataSource;
-import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
+import java.util.Properties;
-import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
-import ca.uhn.fhir.validation.ResultSeverityEnum;
-import ca.uhn.fhirtest.interceptor.TdlSecurityInterceptor;
 
 @Configuration
 @Import(CommonConfig.class)
@@ -74,18 +72,16 @@ public class TdlDstu3Config extends BaseJavaConfigDstu3 {
 	
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu3");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
 
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
-		extraProperties.put("hibernate.dialect", DerbyTenSevenDialect.class.getName());
+		extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
 		extraProperties.put("hibernate.format_sql", "false");
 		extraProperties.put("hibernate.show_sql", "false");
 		extraProperties.put("hibernate.hbm2ddl.auto", "update");

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

@@ -3,15 +3,14 @@ package ca.uhn.fhirtest.config;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
+import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
-import org.hibernate.dialect.DerbyTenSevenDialect;
 import org.hibernate.dialect.PostgreSQL94Dialect;
-import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -95,11 +94,9 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu2");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
@@ -107,7 +104,7 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenDialect.class.getName());
+			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", PostgreSQL94Dialect.class.getName());
 		}

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java

@@ -1,31 +1,32 @@
 package ca.uhn.fhirtest.config;
 
-import java.util.Properties;
+import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
-
+import ca.uhn.fhir.jpa.dao.DaoConfig;
-import javax.persistence.EntityManagerFactory;
+import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
-import javax.sql.DataSource;
-
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
+import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
-import org.hibernate.dialect.DerbyTenSevenDialect;
 import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Value;
-import org.springframework.context.annotation.*;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.Lazy;
 import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
+import javax.persistence.EntityManagerFactory;
-import ca.uhn.fhir.jpa.dao.DaoConfig;
+import javax.sql.DataSource;
-import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import java.util.Properties;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
-import ca.uhn.fhir.validation.ResultSeverityEnum;
-import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
 
 @Configuration
 @Import(CommonConfig.class)
@@ -92,11 +93,9 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu3");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
@@ -104,7 +103,7 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenDialect.class.getName());
+			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", PostgreSQL94Dialect.class.getName());
 		}

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java

@@ -1,31 +1,32 @@
 package ca.uhn.fhirtest.config;
 
-import java.util.Properties;
+import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
-
+import ca.uhn.fhir.jpa.dao.DaoConfig;
-import javax.persistence.EntityManagerFactory;
+import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
-import javax.sql.DataSource;
-
 import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
+import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.apache.commons.lang3.time.DateUtils;
-import org.hibernate.dialect.DerbyTenSevenDialect;
 import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hibernate.jpa.HibernatePersistenceProvider;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.beans.factory.annotation.Value;
-import org.springframework.context.annotation.*;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.Lazy;
 import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
-import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
+import javax.persistence.EntityManagerFactory;
-import ca.uhn.fhir.jpa.dao.DaoConfig;
+import javax.sql.DataSource;
-import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import java.util.Properties;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
-import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
-import ca.uhn.fhir.validation.ResultSeverityEnum;
-import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
 
 @Configuration
 @Import(CommonConfig.class)
@@ -87,11 +88,9 @@ public class TestR4Config extends BaseJavaConfigR4 {
 
 	@Bean()
 	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
 		retVal.setPersistenceUnitName("PU_HapiFhirJpaR4");
 		retVal.setDataSource(dataSource());
-		retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
-		retVal.setPersistenceProvider(new HibernatePersistenceProvider());
 		retVal.setJpaProperties(jpaProperties());
 		return retVal;
 	}
@@ -99,7 +98,7 @@ public class TestR4Config extends BaseJavaConfigR4 {
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenDialect.class.getName());
+			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", PostgreSQL94Dialect.class.getName());
 		}

hapi-fhir-tutorial/jpaserver-example-with-custom/src/main/webapp/WEB-INF/hapi-fhir-server-database-config.xml

@@ -48,7 +48,7 @@
 			<bean class="org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter">
 				<property name="showSql" value="false" />
 				<property name="generateDdl" value="true" />
-				<property name="databasePlatform" value="org.hibernate.dialect.DerbyTenSevenDialect" />
+				<property name="databasePlatform" value="ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect" />
 			</bean>
 		</property>
 	</bean>

src/changes/changes.xml

@@ -145,6 +145,11 @@
 				The HAPI FHIR CLI now supports importing an IGPack file as an import
 				to the validation process.
 			</action>
+			<action type="add">
+				When two threads attempt to update the same resource at the same time, previously
+				an unspecified error was thrown by the JPA server. An HTTP 412
+				(Precondition Failed) with an informative error message is now thrown.
+			</action>
 		</release>
 		<release version="3.3.0" date="2018-03-29">
 			<action type="add">