Unit tests are starting to work again ...

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

@@ -0,0 +1,92 @@
+package ca.uhn.fhir.jpa.starter;
+
+import org.springframework.core.env.CompositePropertySource;
+import org.springframework.core.env.ConfigurableEnvironment;
+import org.springframework.core.env.EnumerablePropertySource;
+import org.springframework.core.env.PropertySource;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+
+public class EnvironmentHelper {
+
+  public static Properties getHibernateProperties(ConfigurableEnvironment environment) {
+    Properties properties = new Properties();
+    if (environment.getProperty("spring.jpa.properties", String.class) == null) {
+      properties.put("hibernate.dialect", "org.hibernate.dialect.H2Dialect");
+      properties.put("hibernate.search.model_mapping", "ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory");
+      properties.put("hibernate.format_sql", "false");
+      properties.put("hibernate.show_sql", "false");
+      properties.put("hibernate.hbm2ddl.auto", "update");
+      properties.put("hibernate.jdbc.batch_size", "20");
+      properties.put("hibernate.cache.use_query_cache", "false");
+      properties.put("hibernate.cache.use_second_level_cache", "false");
+      properties.put("hibernate.cache.use_structured_entries", "false");
+      properties.put("hibernate.cache.use_minimal_puts", "false");
+      properties.put("hibernate.search.default.directory_provider", "filesystem");
+      properties.put("hibernate.search.default.indexBase", "target/lucenefiles");
+      properties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
+    } else {
+      Arrays.asList(environment.getProperty("spring.jpa.properties", String.class).split(" ")).stream().forEach(s ->
+      {
+        String[] values = s.split("=");
+        properties.put(values[0], values[1]);
+      });
+    }
+    return properties;
+  }
+
+  public static Map<String, Object> getPropertiesStartingWith(ConfigurableEnvironment aEnv,
+                                                              String aKeyPrefix) {
+    Map<String, Object> result = new HashMap<>();
+
+    Map<String, Object> map = getAllProperties(aEnv);
+
+    for (Map.Entry<String, Object> entry : map.entrySet()) {
+      String key = entry.getKey();
+
+      if (key.startsWith(aKeyPrefix)) {
+        result.put(key, entry.getValue());
+      }
+    }
+
+    return result;
+  }
+
+  public static Map<String, Object> getAllProperties(ConfigurableEnvironment aEnv) {
+    Map<String, Object> result = new HashMap<>();
+    aEnv.getPropertySources().forEach(ps -> addAll(result, getAllProperties(ps)));
+    return result;
+  }
+
+  public static Map<String, Object> getAllProperties(PropertySource<?> aPropSource) {
+    Map<String, Object> result = new HashMap<>();
+
+    if (aPropSource instanceof CompositePropertySource) {
+      CompositePropertySource cps = (CompositePropertySource) aPropSource;
+      cps.getPropertySources().forEach(ps -> addAll(result, getAllProperties(ps)));
+      return result;
+    }
+
+    if (aPropSource instanceof EnumerablePropertySource<?>) {
+      EnumerablePropertySource<?> ps = (EnumerablePropertySource<?>) aPropSource;
+      Arrays.asList(ps.getPropertyNames()).forEach(key -> result.put(key, ps.getProperty(key)));
+      return result;
+    }
+
+    return result;
+
+  }
+
+  private static void addAll(Map<String, Object> aBase, Map<String, Object> aToBeAdded) {
+    for (Map.Entry<String, Object> entry : aToBeAdded.entrySet()) {
+      if (aBase.containsKey(entry.getKey())) {
+        continue;
+      }
+
+      aBase.put(entry.getKey(), entry.getValue());
+    }
+  }
+}

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

@@ -8,26 +8,31 @@ 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.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")
 public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
 
-    @Autowired
+  @Autowired
-    private DataSource myDataSource;
+  private DataSource myDataSource;
 
-    /**
+  /**
-     * We override the paging provider definition so that we can customize
+   * We override the paging provider definition so that we can customize
-     * the default/max page sizes for search results. You can set these however
+   * the default/max page sizes for search results. You can set these however
-     * you want, although very large page sizes will require a lot of RAM.
+   * you want, although very large page sizes will require a lot of RAM.
-     */
+   */
-    @Autowired
+  @Autowired
-    AppProperties appProperties;
+  AppProperties appProperties;
 
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
@@ -37,28 +42,31 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
     return pagingProvider;
   }
 
-    @Override
+  @Autowired
-    @Bean()
+  private ConfigurableEnvironment configurableEnvironment;
-    public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-        LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
-        retVal.setPersistenceUnitName("HAPI_PU");
 
-        try {
+  @Override
-            retVal.setDataSource(myDataSource);
+  @Bean()
-        } catch (Exception e) {
+  public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-            throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
+    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
-        }
+    retVal.setPersistenceUnitName("HAPI_PU");
 
-
+    try {
-        return retVal;
+      retVal.setDataSource(myDataSource);
+    } catch (Exception e) {
+      throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
+    return retVal;
+  }
 
   @Bean
   @Primary
   public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
-        JpaTransactionManager retVal = new JpaTransactionManager();
+    JpaTransactionManager retVal = new JpaTransactionManager();
-        retVal.setEntityManagerFactory(entityManagerFactory);
+    retVal.setEntityManagerFactory(entityManagerFactory);
-        return retVal;
+    return retVal;
-    }
+  }
+
 
 }

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

@@ -8,6 +8,7 @@ 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.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -18,47 +19,50 @@ import javax.sql.DataSource;
 @Profile("dstu3")
 public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
 
-    @Autowired
+  @Autowired
-    private DataSource myDataSource;
+  private DataSource myDataSource;
 
-    /**
+  /**
-     * We override the paging provider definition so that we can customize
+   * We override the paging provider definition so that we can customize
-     * the default/max page sizes for search results. You can set these however
+   * the default/max page sizes for search results. You can set these however
-     * you want, although very large page sizes will require a lot of RAM.
+   * you want, although very large page sizes will require a lot of RAM.
-     */
+   */
-    @Autowired
+  @Autowired
-    AppProperties appProperties;
+  AppProperties appProperties;
 
-    @Override
+  @Override
-    public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
+  public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
-      DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
+    DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
-      pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
+    pagingProvider.setDefaultPageSize(appProperties.getDefault_page_size());
-      pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
+    pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
-      return pagingProvider;
+    return pagingProvider;
+  }
+
+  @Autowired
+  private ConfigurableEnvironment configurableEnvironment;
+  
+  @Override
+  @Bean
+  public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+    retVal.setPersistenceUnitName("HAPI_PU");
+
+    try {
+      retVal.setDataSource(myDataSource);
+    } catch (Exception e) {
+      throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
 
-    @Override
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
-    @Bean
+    return retVal;
-    public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+  }
-        LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
-        retVal.setPersistenceUnitName("HAPI_PU");
 
-        try {
+  @Bean
-            retVal.setDataSource(myDataSource);
+  @Primary
-        } catch (Exception e) {
+  public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
-            throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
+    JpaTransactionManager retVal = new JpaTransactionManager();
-        }
+    retVal.setEntityManagerFactory(entityManagerFactory);
-
+    return retVal;
-
+  }
-        return retVal;
-    }
-
-    @Bean
-    @Primary
-    public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
-        JpaTransactionManager retVal = new JpaTransactionManager();
-        retVal.setEntityManagerFactory(entityManagerFactory);
-        return retVal;
-    }
 
 }

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

@@ -8,26 +8,30 @@ 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.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")
 public class FhirServerConfigR4 extends BaseJavaConfigR4 {
 
-    @Autowired
+  @Autowired
-    private DataSource myDataSource;
+  private DataSource myDataSource;
 
-    /**
+  /**
-     * We override the paging provider definition so that we can customize
+   * We override the paging provider definition so that we can customize
-     * the default/max page sizes for search results. You can set these however
+   * the default/max page sizes for search results. You can set these however
-     * you want, although very large page sizes will require a lot of RAM.
+   * you want, although very large page sizes will require a lot of RAM.
-     */
+   */
-    @Autowired
+  @Autowired
-    AppProperties appProperties;
+  AppProperties appProperties;
 
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
@@ -37,28 +41,31 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
     return pagingProvider;
   }
 
-    @Override
+  @Autowired
-    @Bean()
+  private ConfigurableEnvironment configurableEnvironment;
-    public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-        LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
-        retVal.setPersistenceUnitName("HAPI_PU");
 
-        try {
+  @Override
-            retVal.setDataSource(myDataSource);
+  @Bean()
-        } catch (Exception e) {
+  public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-            throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
+    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
-        }
+    retVal.setPersistenceUnitName("HAPI_PU");
 
-
+    try {
-        return retVal;
+      retVal.setDataSource(myDataSource);
+    } catch (Exception e) {
+      throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
 
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
+    return retVal;
+  }
+
   @Bean
   @Primary
   public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
-        JpaTransactionManager retVal = new JpaTransactionManager();
+    JpaTransactionManager retVal = new JpaTransactionManager();
-        retVal.setEntityManagerFactory(entityManagerFactory);
+    retVal.setEntityManagerFactory(entityManagerFactory);
-        return retVal;
+    return retVal;
-    }
+  }
 
 }

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

@@ -8,6 +8,7 @@ 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.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
@@ -18,16 +19,16 @@ import javax.sql.DataSource;
 @Profile("r5")
 public class FhirServerConfigR5 extends BaseJavaConfigR5 {
 
-    @Autowired
+  @Autowired
-    private DataSource myDataSource;
+  private DataSource myDataSource;
 
-    /**
+  /**
-     * We override the paging provider definition so that we can customize
+   * We override the paging provider definition so that we can customize
-     * the default/max page sizes for search results. You can set these however
+   * the default/max page sizes for search results. You can set these however
-     * you want, although very large page sizes will require a lot of RAM.
+   * you want, although very large page sizes will require a lot of RAM.
-     */
+   */
-    @Autowired
+  @Autowired
-    AppProperties appProperties;
+  AppProperties appProperties;
 
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
@@ -36,28 +37,32 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
     pagingProvider.setMaximumPageSize(appProperties.getMax_page_size());
     return pagingProvider;
   }
-    @Override
-    @Bean()
-    public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
-        LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
-        retVal.setPersistenceUnitName("HAPI_PU");
 
-        try {
+  @Autowired
-            retVal.setDataSource(myDataSource);
+  private ConfigurableEnvironment configurableEnvironment;
-        } catch (Exception e) {
-            throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
-        }
 
-        retVal.setJpaProperties(HapiProperties.getJpaProperties());
+  @Override
-        return retVal;
+  @Bean()
+  public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+    LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
+    retVal.setPersistenceUnitName("HAPI_PU");
+
+    try {
+      retVal.setDataSource(myDataSource);
+    } catch (Exception e) {
+      throw new ConfigurationException("Could not set the data source due to a configuration issue", e);
     }
 
+    retVal.setJpaProperties(EnvironmentHelper.getHibernateProperties(configurableEnvironment));
+    return retVal;
+  }
+
   @Bean
   @Primary
   public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
-        JpaTransactionManager retVal = new JpaTransactionManager();
+    JpaTransactionManager retVal = new JpaTransactionManager();
-        retVal.setEntityManagerFactory(entityManagerFactory);
+    retVal.setEntityManagerFactory(entityManagerFactory);
-        return retVal;
+    return retVal;
-    }
+  }
 
 }

src/main/resources/application.yaml

@@ -7,7 +7,23 @@ spring:
     max-active: 15
   profiles:
     ### This is the FHIR version. Choose between, dstu2, dstu3, r4 or r5
-    active: r4
+    active: dstu2
+  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
+
 hapi:
   fhir:
     #supported_resource_types:

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

@@ -12,11 +12,13 @@ import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.web.server.LocalServerPort;
 import org.springframework.context.annotation.Import;
+import org.springframework.test.context.TestPropertySource;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 @ExtendWith(SpringExtension.class)
+@TestPropertySource(locations = "/application-integrationtest.yaml")
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties =
   {
     "spring.batch.job.enabled=false",

src/test/resources/application-integrationtest.yaml

@@ -7,7 +7,8 @@ spring:
     max-active: 15
   profiles:
     ### This is the FHIR version. Choose between, dstu2, dstu3, r4 or r5
-    active: r4
+    active: dstu2
+
 hapi:
   fhir:
     #supported_resource_types: