Merge pull request #171 from jvitrifork/spring-pr

Spring pr

src/main/java/ca/uhn/fhir/jpa/starter/Application.java

@@ -1,6 +1,7 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.jpa.empi.EmpiConfig;
+import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
 import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
 import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
@@ -15,6 +16,7 @@ import org.springframework.boot.web.servlet.ServletComponentScan;
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
 import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Import;
 import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
 import org.springframework.web.servlet.DispatcherServlet;
@@ -44,6 +46,7 @@ public class Application extends SpringBootServletInitializer {
   AutowireCapableBeanFactory beanFactory;
 
   @Bean
+  @Conditional(OnEitherVersion.class)
   public ServletRegistrationBean hapiServletRegistration() {
     ServletRegistrationBean servletRegistrationBean = new ServletRegistrationBean();
     JpaRestfulServer jpaRestfulServer = new JpaRestfulServer();

src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java

@@ -13,11 +13,7 @@ import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
 import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
 import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
 import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
-import ca.uhn.fhir.jpa.provider.GraphQLProvider;
-import ca.uhn.fhir.jpa.provider.IJpaSystemProvider;
-import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
-import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
-import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
+import ca.uhn.fhir.jpa.provider.*;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
 import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
 import ca.uhn.fhir.jpa.provider.r5.JpaConformanceProviderR5;

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java

@@ -16,6 +16,7 @@ import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Lazy;
 import org.springframework.context.annotation.Primary;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 import java.util.Optional;
@@ -133,8 +134,8 @@ public class FhirServerConfigCommon {
 
   @Primary
   @Bean
-  public HibernateDialectProvider jpaStarterDialectProvider() {
-    return new JpaHibernateDialectProvider();
+  public HibernateDialectProvider jpaStarterDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
+    return new JpaHibernateDialectProvider(myEntityManagerFactory);
   }
 
   @Bean

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java

@@ -3,24 +3,21 @@ package ca.uhn.fhir.jpa.starter;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import ca.uhn.fhir.jpa.starter.annotations.OnDSTU2Condition;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
-import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.ConfigurableEnvironment;
-import org.springframework.core.env.Environment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Properties;
 
 @Configuration
-@Profile("dstu2")
+@Conditional(OnDSTU2Condition.class)
 public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
 
   @Autowired

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java

@@ -3,11 +3,9 @@ package ca.uhn.fhir.jpa.starter;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Primary;
-import org.springframework.context.annotation.Profile;
+import org.springframework.context.annotation.*;
 import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -16,7 +14,7 @@ import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 @Configuration
-@Profile("dstu3")
+@Conditional(OnDSTU3Condition.class)
 public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 
   @Autowired

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java

@@ -3,23 +3,21 @@ package ca.uhn.fhir.jpa.starter;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
-import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.ConfigurableEnvironment;
-import org.springframework.core.env.Environment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
-import java.util.Arrays;
-import java.util.Properties;
 
 @Configuration
-@Profile("r4")
+@Conditional(OnR4Condition.class)
 public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
   @Autowired

src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java

@@ -3,11 +3,12 @@ package ca.uhn.fhir.jpa.starter;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.jpa.config.BaseJavaConfigR5;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
+import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Conditional;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Primary;
-import org.springframework.context.annotation.Profile;
 import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -16,7 +17,7 @@ import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
 @Configuration
-@Profile("r5")
+@Conditional(OnR5Condition.class)
 public class FhirServerConfigR5 extends BaseJavaConfigR5 {
 
   @Autowired

src/main/java/ca/uhn/fhir/jpa/starter/JpaHibernateDialectProvider.java

@@ -3,20 +3,29 @@ package ca.uhn.fhir.jpa.starter;
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.jpa.config.HibernateDialectProvider;
 import org.hibernate.dialect.Dialect;
-import org.springframework.beans.factory.annotation.Value;
+import org.hibernate.engine.jdbc.dialect.internal.StandardDialectResolver;
+import org.hibernate.engine.jdbc.dialect.spi.DatabaseMetaDataDialectResolutionInfoAdapter;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+
+import javax.sql.DataSource;
+import java.sql.SQLException;
 
 public class JpaHibernateDialectProvider extends HibernateDialectProvider {
 
-  @Value("${spring.jpa.properties.hibernate.dialect}")
-  public String myDialectClass;
+  private final Dialect dialect;
 
+  public JpaHibernateDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) {
+    DataSource connection = myEntityManagerFactory.getDataSource();
+    try {
+      dialect = new StandardDialectResolver()
+        .resolveDialect(new DatabaseMetaDataDialectResolutionInfoAdapter(connection.getConnection().getMetaData()));
+    } catch (SQLException sqlException) {
+      throw new ConfigurationException(sqlException.getMessage(), sqlException);
+    }
+  }
 
   @Override
   public Dialect getDialect() {
-    try {
-      return (Dialect) Class.forName(myDialectClass).newInstance();
-    } catch (ClassNotFoundException | InstantiationException | IllegalAccessException e) {
-      throw new ConfigurationException("Can not load dialect: " + myDialectClass);
-    }
+    return dialect;
   }
 }

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU2Condition.java

@@ -0,0 +1,19 @@
+package ca.uhn.fhir.jpa.starter.annotations;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.springframework.context.annotation.Condition;
+import org.springframework.context.annotation.ConditionContext;
+import org.springframework.core.type.AnnotatedTypeMetadata;
+
+public class OnDSTU2Condition implements Condition {
+  @Override
+  public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+    FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
+      getEnvironment()
+      .getProperty("hapi.fhir.fhir_version")
+      .toUpperCase());
+
+    return version == FhirVersionEnum.DSTU2;
+
+  }
+}

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU3Condition.java

@@ -0,0 +1,19 @@
+package ca.uhn.fhir.jpa.starter.annotations;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.springframework.context.annotation.Condition;
+import org.springframework.context.annotation.ConditionContext;
+import org.springframework.core.type.AnnotatedTypeMetadata;
+
+public class OnDSTU3Condition implements Condition {
+  @Override
+  public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+    FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
+      getEnvironment()
+      .getProperty("hapi.fhir.fhir_version")
+      .toUpperCase());
+
+    return version == FhirVersionEnum.DSTU3;
+
+  }
+}

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnEitherVersion.java

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.jpa.starter.annotations;
+
+import org.springframework.boot.autoconfigure.condition.AnyNestedCondition;
+import org.springframework.boot.autoconfigure.condition.ConditionOutcome;
+import org.springframework.context.annotation.Conditional;
+
+public class OnEitherVersion extends AnyNestedCondition {
+
+  OnEitherVersion() {
+    super(ConfigurationPhase.REGISTER_BEAN);
+  }
+
+  @Override
+  protected ConditionOutcome getFinalMatchOutcome(MemberMatchOutcomes memberOutcomes) {
+    ConditionOutcome result = super.getFinalMatchOutcome(memberOutcomes);
+    return result;
+  }
+
+  @Conditional(OnDSTU2Condition.class)
+  static class OnDSTU2 {
+  }
+
+  @Conditional(OnDSTU3Condition.class)
+  static class OnDSTU3 {
+  }
+
+  @Conditional(OnR4Condition.class)
+  static class OnR4 {
+  }
+
+  @Conditional(OnR5Condition.class)
+  static class OnR5 {
+  }
+
+}

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR4Condition.java

@@ -0,0 +1,19 @@
+package ca.uhn.fhir.jpa.starter.annotations;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.springframework.context.annotation.Condition;
+import org.springframework.context.annotation.ConditionContext;
+import org.springframework.core.type.AnnotatedTypeMetadata;
+
+public class OnR4Condition implements Condition {
+  @Override
+  public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+    FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
+      getEnvironment()
+      .getProperty("hapi.fhir.fhir_version")
+      .toUpperCase());
+
+    return version == FhirVersionEnum.R4;
+
+  }
+}

src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR5Condition.java

@@ -0,0 +1,19 @@
+package ca.uhn.fhir.jpa.starter.annotations;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.springframework.context.annotation.Condition;
+import org.springframework.context.annotation.ConditionContext;
+import org.springframework.core.type.AnnotatedTypeMetadata;
+
+public class OnR5Condition implements Condition {
+  @Override
+  public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) {
+    FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext.
+      getEnvironment()
+      .getProperty("hapi.fhir.fhir_version")
+      .toUpperCase());
+
+    return version == FhirVersionEnum.R5;
+
+  }
+}

src/main/resources/application.yaml

@@ -5,24 +5,21 @@ spring:
     password: null
     driverClassName: org.h2.Driver
     max-active: 15
-  profiles:
-    ### This is the FHIR version. Choose between, dstu2, dstu3, r4 or r5
-    active: r4
-  jpa:
-    properties:
-      hibernate.dialect: org.hibernate.dialect.H2Dialect
-      hibernate.search.model_mapping: ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory
-      hibernate.format_sql: false
-      hibernate.show_sql: false
-      hibernate.hbm2ddl.auto: update
-      hibernate.jdbc.batch_size: 20
-      hibernate.cache.use_query_cache: false
-      hibernate.cache.use_second_level_cache: false
-      hibernate.cache.use_structured_entries: false
-      hibernate.cache.use_minimal_puts: false
-      hibernate.search.default.directory_provider: filesystem
-      hibernate.search.default.indexBase: target/lucenefiles
-      hibernate.search.lucene_version: LUCENE_CURRENT
+#  jpa:
+#    properties:
+#      hibernate.dialect: org.hibernate.dialect.h2dialect
+#      hibernate.search.model_mapping: ca.uhn.fhir.jpa.search.lucenesearchmappingfactory
+#      hibernate.format_sql: false
+#      hibernate.show_sql: false
+#      hibernate.hbm2ddl.auto: update
+#      hibernate.jdbc.batch_size: 20
+#      hibernate.cache.use_query_cache: false
+#      hibernate.cache.use_second_level_cache: false
+#      hibernate.cache.use_structured_entries: false
+#      hibernate.cache.use_minimal_puts: false
+#      hibernate.search.default.directory_provider: filesystem
+#      hibernate.search.default.indexbase: target/lucenefiles
+#      hibernate.search.lucene_version: lucene_current
 
   batch:
     job:
@@ -30,7 +27,9 @@ spring:
 
 hapi:
   fhir:
-    defer_indexing_for_codesystems_of_size: 101
+    ### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5
+    fhir_version: R4
+#    defer_indexing_for_codesystems_of_size: 101
 #    implementationguides:
 #      -
 #        url: https://build.fhir.org/ig/hl7dk/dk-medcom/branches/corrections/package.tgz

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java

@@ -19,7 +19,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
   {
     "spring.batch.job.enabled=false",
-    "spring.profiles.active=dstu2",
+    "hapi.fhir.fhir_version=dstu2",
     "spring.datasource.url=jdbc:h2:mem:dbr2"
   })
 public class ExampleServerDstu2IT {

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java

@@ -33,8 +33,8 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
   {
     "spring.batch.job.enabled=false",
-    "spring.profiles.active=dstu3",
     "spring.datasource.url=jdbc:h2:mem:dbr3",
+    "hapi.fhir.fhir_version=dstu3",
     "hapi.fhir.subscription.websocket_enabled=true",
     "hapi.fhir.allow_external_references=true",
     "hapi.fhir.allow_placeholder_references=true",

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java

@@ -36,8 +36,8 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
   {
     "spring.batch.job.enabled=false",
-    "spring.profiles.active=r4",
     "spring.datasource.url=jdbc:h2:mem:dbr4",
+    "hapi.fhir.fhir_version=r4",
     "hapi.fhir.subscription.websocket_enabled=true",
     "hapi.fhir.empi_enabled=true",
     //Override is currently required when using Empi as the construction of the Empi beans are ambiguous as they are constructed multiple places. This is evident when running in a spring boot environment

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java

@@ -35,8 +35,8 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
   {
     "spring.batch.job.enabled=false",
-    "spring.profiles.active=r5",
     "spring.datasource.url=jdbc:h2:mem:dbr5",
+    "hapi.fhir.fhir_version=r5",
     "hapi.fhir.subscription.websocket_enabled=true"
   })
 public class ExampleServerR5IT {

src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java

@@ -21,8 +21,8 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
   {
     "spring.batch.job.enabled=false",
-    "spring.profiles.active=r4",
     "spring.datasource.url=jdbc:h2:mem:dbr4-mt",
+    "hapi.fhir.fhir_version=r4",
     "hapi.fhir.subscription.websocket_enabled=true",
     "hapi.fhir.partitioning.partitioning_include_in_search_hashes=false"