Cleanup

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

@@ -654,16 +654,6 @@ public static void beforeClassRandomizeLocale() {
 		doRandomizeLocaleAndTimezone();
 	}
 
-	@AfterAll
-	public static void afterClassShutdownDerby() {
-		// DriverManager.getConnection("jdbc:derby:;shutdown=true");
-		// try {
-		// DriverManager.getConnection("jdbc:derby:memory:myUnitTestDB;drop=true");
-		// } catch (SQLNonTransientConnectionException e) {
-		// // expected.. for some reason....
-		// }
-	}
-
 	public static String loadClasspath(String resource) throws IOException {
 		return new String(loadClasspathBytes(resource), Constants.CHARSET_UTF8);
 	}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java

@@ -16,6 +16,7 @@
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.param.QuantityParam;
+import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
@@ -102,6 +103,10 @@ public void testCreateLinkCreatesAppropriatePaths() {
 				.collect(Collectors.toList());
 			assertThat(paths.toString(), paths, contains("Observation.subject", "Observation.subject.where(resolve() is Patient)"));
 		});
+
+		myCaptureQueriesListener.clear();
+		assertEquals(1, myObservationDao.search(SearchParameterMap.newSynchronous("patient", new ReferenceParam("Patient/A"))).sizeOrThrowNpe());
+		myCaptureQueriesListener.logSelectQueries();
 	}
 
 	@Test

hapi-fhir-jpaserver-uhnfhirtest/pom.xml

@@ -19,6 +19,7 @@
 			<groupId>org.postgresql</groupId>
 			<artifactId>postgresql</artifactId>
 		</dependency>
+
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-jpaserver-base</artifactId>
@@ -102,6 +103,12 @@
 		</dependency>
 
 		<!-- TEST DEPS -->
+		<dependency>
+			<groupId>com.h2database</groupId>
+			<artifactId>h2</artifactId>
+			<scope>test</scope>
+		</dependency>
+
 		<dependency>
 			<groupId>org.eclipse.jetty</groupId>
 			<artifactId>jetty-servlets</artifactId>

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

@@ -35,6 +35,7 @@
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
+import ca.uhn.fhirtest.config.SqlCaptureInterceptor;
 import ca.uhn.fhirtest.config.TestDstu2Config;
 import ca.uhn.fhirtest.config.TestDstu3Config;
 import ca.uhn.fhirtest.config.TestR4Config;
@@ -282,6 +283,8 @@ protected void initialize() throws ServletException {
 		loggingInterceptor.setMessageFormat("${operationType} Content-Type: ${requestHeader.content-type} - Accept: ${responseEncodingNoDefault} \"${requestHeader.accept}\" - Agent: ${requestHeader.user-agent}");
 		registerInterceptor(loggingInterceptor);
 
+		// SQL Capturing
+		registerInterceptor(myAppCtx.getBean(SqlCaptureInterceptor.class));
 	}
 
 	/**

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

@@ -1,29 +1,24 @@
 package ca.uhn.fhirtest.config;
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
-import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
 import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
 import org.apache.commons.dbcp2.BasicDataSource;
-import org.apache.commons.lang3.time.DateUtils;
-import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
 import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
 import org.hibernate.search.engine.cfg.BackendSettings;
-import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -102,7 +97,7 @@ public ValidationSettings validationSettings() {
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 		if (CommonConfig.isLocalTestMode()) {
-			retVal.setUrl("jdbc:derby:memory:fhirtest_dstu2;create=true");
+			retVal.setUrl("jdbc:h2:mem:fhirtest_dstu2");
 		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_dstu2");
@@ -144,7 +139,7 @@ public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableL
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
+			extraProperties.put("hibernate.dialect", HapiFhirH2Dialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
 		}
@@ -168,6 +163,7 @@ private Properties jpaProperties() {
 
 	/**
 	 * Bean which validates incoming requests
+	 *
 	 * @param theInstanceValidator
 	 */
 	@Bean

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

@@ -2,28 +2,24 @@
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
-import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
 import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
 import org.apache.commons.dbcp2.BasicDataSource;
-import org.apache.commons.lang3.time.DateUtils;
-import org.hibernate.dialect.PostgreSQL94Dialect;
 import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
 import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
 import org.hibernate.search.engine.cfg.BackendSettings;
-import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
 import org.springframework.beans.factory.annotation.Autowire;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -92,8 +88,6 @@ public ValidationSettings validationSettings() {
 	}
 
 
-
-
 	@Override
 	@Bean(autowire = Autowire.BY_TYPE)
 	public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
@@ -103,8 +97,8 @@ public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
 		return retVal;
 	}
 
-	
-	@Bean 
+
+	@Bean
 	public PublicSecurityInterceptor securityInterceptor() {
 		return new PublicSecurityInterceptor();
 	}
@@ -113,7 +107,7 @@ public PublicSecurityInterceptor securityInterceptor() {
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 		if (CommonConfig.isLocalTestMode()) {
-			retVal.setUrl("jdbc:derby:memory:fhirtest_dstu3;create=true");
+			retVal.setUrl("jdbc:h2:mem:fhirtest_dstu3");
 		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_dstu3");
@@ -147,7 +141,7 @@ public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableL
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
+			extraProperties.put("hibernate.dialect", HapiFhirH2Dialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
 		}

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

@@ -2,12 +2,12 @@
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
 import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
-import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
 import ca.uhn.fhir.jpa.validation.ValidationSettings;
 import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
@@ -20,7 +20,6 @@
 import org.hl7.fhir.dstu2.model.Subscription;
 import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
 import org.springframework.beans.factory.annotation.Autowire;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -94,7 +93,7 @@ public ValidationSettings validationSettings() {
 	public DataSource dataSource() {
 		BasicDataSource retVal = new BasicDataSource();
 		if (CommonConfig.isLocalTestMode()) {
-			retVal.setUrl("jdbc:derby:memory:fhirtest_r4;create=true");
+			retVal.setUrl("jdbc:h2:mem:fhirtest_r4");
 		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_r4");
@@ -137,7 +136,7 @@ public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableL
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
+			extraProperties.put("hibernate.dialect", HapiFhirH2Dialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
 		}
@@ -196,5 +195,4 @@ public static PropertySourcesPlaceholderConfigurer propertySourcesPlaceholderCon
 	}
 
 
-
 }

hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR5Config.java

@@ -2,6 +2,7 @@
 
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigR5;
+import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
 import ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
@@ -99,7 +100,7 @@ public DataSource dataSource() {
 
 		BasicDataSource retVal = new BasicDataSource();
 		if (CommonConfig.isLocalTestMode()) {
-			retVal.setUrl("jdbc:derby:memory:fhirtest_r5;create=true");
+			retVal.setUrl("jdbc:h2:mem:fhirtest_r5");
 		} else {
 			retVal.setDriver(new org.postgresql.Driver());
 			retVal.setUrl("jdbc:postgresql://localhost/fhirtest_r5");
@@ -142,7 +143,7 @@ public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableL
 	private Properties jpaProperties() {
 		Properties extraProperties = new Properties();
 		if (CommonConfig.isLocalTestMode()) {
-			extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
+			extraProperties.put("hibernate.dialect", HapiFhirH2Dialect.class.getName());
 		} else {
 			extraProperties.put("hibernate.dialect", HapiFhirPostgres94Dialect.class.getName());
 		}

hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/AuthorizedList.java

@@ -107,7 +107,7 @@ public AuthorizedList addCodeInValueSet(String theResourceName, String theSearch
 		Validate.notBlank(theSearchParameterName, "theSearchParameterName must not be missing or null");
 		Validate.notBlank(theValueSetUrl, "theResourceUrl must not be missing or null");
 
-		myAllowedCodeInValueSets.add(new AllowedCodeInValueSet(theResourceName, theSearchParameterName, theValueSetUrl))
+//		myAllowedCodeInValueSets.add(new AllowedCodeInValueSet(theResourceName, theSearchParameterName, theValueSetUrl))
 
 		return this;
 	}

hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProvider.java

@@ -56,7 +56,7 @@
 import java.util.function.Supplier;
 
 public class GraphQLProvider {
-	private Logger ourLog = LoggerFactory.getLogger(GraphQLProvider.class);
+	private static final Logger ourLog = LoggerFactory.getLogger(GraphQLProvider.class);
 
 	private final Supplier<IGraphQLEngine> myEngineFactory;
 	private final IGraphQLStorageServices myStorageServices;
@@ -137,7 +137,7 @@ public String processGraphQLRequest(ServletRequestDetails theRequestDetails, IId
 		try {
 			parsedGraphQLRequest = Parser.parse(theQuery);
 		} catch (Exception e) {
-			throw new InvalidRequestException("Unable to parse GraphQL Expression: " + e);
+			throw new InvalidRequestException(Msg.code(1146) + "Unable to parse GraphQL Expression: " + e);
 		}
 
 		return processGraphQLRequest(theRequestDetails, theId, parsedGraphQLRequest);
@@ -147,15 +147,7 @@ protected String processGraphQLRequest(ServletRequestDetails theRequestDetails,
 		IGraphQLEngine engine = myEngineFactory.get();
 		engine.setAppInfo(theRequestDetails);
 		engine.setServices(myStorageServices);
-<<<<<<< HEAD
 		engine.setGraphQL(parsedGraphQLRequest);
-=======
-		try {
-			engine.setGraphQL(Parser.parse(theQuery));
-		} catch (Exception theE) {
-			throw new InvalidRequestException(Msg.code(1146) + "Unable to parse GraphQL Expression: " + theE.toString());
-		}
->>>>>>> master
 
 		try {
 
@@ -185,7 +177,7 @@ protected String processGraphQLRequest(ServletRequestDetails theRequestDetails,
 				ourLog.error("Failure during GraphQL processing", e);
 			}
 			b.append(e.getMessage());
-			throw new UnclassifiedServerFailureException(statusCode, Msg.code(1147) + b.toString());
+			throw new UnclassifiedServerFailureException(statusCode, Msg.code(1147) + b);
 		}
 	}