Merge pull request #220 from hapifhir/rel_5_4_0

Release 5.4.0

pom.xml

@@ -14,8 +14,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <!-- FIMXME KBD Change this to 5.3.0 BEFORE merging this code to master !  -->
+		  <version>5.4.0</version>
-        <version>5.3.0</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>

src/main/java/ca/uhn/fhir/jpa/mdm/MdmConfig.java

@@ -7,7 +7,7 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
 import ca.uhn.fhir.mdm.api.IMdmSettings;
 import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
 import ca.uhn.fhir.mdm.rules.config.MdmSettings;
-import ca.uhn.fhir.rest.server.util.ISearchParamRetriever;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import com.google.common.base.Charsets;
 import org.apache.commons.io.IOUtils;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -30,8 +30,8 @@ import java.io.IOException;
 public class MdmConfig {
 
 	@Bean
-  MdmRuleValidator mdmRuleValidator(FhirContext theFhirContext, ISearchParamRetriever theSearchParamRetriever) {
+	MdmRuleValidator mdmRuleValidator(FhirContext theFhirContext, ISearchParamRegistry theSearchParamRegistry) {
-    return new MdmRuleValidator(theFhirContext, theSearchParamRetriever);
+		return new MdmRuleValidator(theFhirContext, theSearchParamRegistry);
 	}
 
 	@Bean

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

@@ -31,6 +31,7 @@ public class AppProperties {
   private Boolean allow_placeholder_references = true;
   private Boolean auto_create_placeholder_reference_targets = false;
   private Boolean enable_index_missing_fields = false;
+  private Boolean enable_index_contained_resource = false;
   private Boolean enable_repository_validating_interceptor = false;
   private Boolean enforce_referential_integrity_on_delete = true;
   private Boolean enforce_referential_integrity_on_write = true;
@@ -67,6 +68,9 @@ public class AppProperties {
   private Boolean lastn_enabled = false;
   private NormalizedQuantitySearchLevel normalized_quantity_search_level = NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED;
 
+  private Integer search_coord_core_pool_size = 20;
+  private Integer search_coord_max_pool_size = 100;
+  private Integer search_coord_queue_capacity = 200;
   private Boolean use_apache_address_strategy = false;
   private Boolean use_apache_address_strategy_https = false;
 
@@ -273,6 +277,14 @@ public class AppProperties {
     this.enable_index_missing_fields = enable_index_missing_fields;
   }
 
+	public Boolean getEnable_index_contained_resource() {
+		return enable_index_contained_resource;
+	}
+
+	public void setEnable_index_contained_resource(Boolean enable_index_contained_resource) {
+		this.enable_index_contained_resource = enable_index_contained_resource;
+	}
+
 	public Boolean getEnable_repository_validating_interceptor() {
 		return enable_repository_validating_interceptor;
 	}
@@ -441,6 +453,23 @@ public class AppProperties {
 	this.normalized_quantity_search_level = normalized_quantity_search_level;
   }
 
+  public Integer getSearch_coord_core_pool_size() { return search_coord_core_pool_size; }
+
+  public void setSearch_coord_core_pool_size(Integer search_coord_core_pool_size) {
+    this.search_coord_core_pool_size = search_coord_core_pool_size;
+  }
+
+  public Integer getSearch_coord_max_pool_size() { return search_coord_max_pool_size; }
+
+  public void setSearch_coord_max_pool_size(Integer search_coord_max_pool_size) {
+    this.search_coord_max_pool_size = search_coord_max_pool_size;
+  }
+
+  public Integer getSearch_coord_queue_capacity() { return search_coord_queue_capacity; }
+
+  public void setSearch_coord_queue_capacity(Integer search_coord_queue_capacity) {
+  	 this.search_coord_queue_capacity = search_coord_queue_capacity;
+  }
 
 public static class Cors {
     private Boolean allow_Credentials = true;

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

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.context.support.IValidationSupport;
 import ca.uhn.fhir.cql.common.provider.CqlProviderLoader;
 import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
 import ca.uhn.fhir.interceptor.api.IInterceptorService;
@@ -9,31 +10,38 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
 import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
-import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
+import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
 import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
 import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
-import ca.uhn.fhir.jpa.packages.PackageInstallOutcomeJson;
 import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
 import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
-import ca.uhn.fhir.jpa.provider.*;
+import ca.uhn.fhir.jpa.provider.GraphQLProvider;
+import ca.uhn.fhir.jpa.provider.IJpaSystemProvider;
+import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
+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.dstu3.JpaConformanceProviderDstu3;
-import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
-import ca.uhn.fhir.jpa.provider.r5.JpaConformanceProviderR5;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
-import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
 import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
+import ca.uhn.fhir.rest.server.ApacheProxyAddressStrategy;
 import ca.uhn.fhir.rest.server.ETagSupportEnum;
 import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
-import ca.uhn.fhir.rest.server.ApacheProxyAddressStrategy;
 import ca.uhn.fhir.rest.server.IncomingRequestAddressStrategy;
 import ca.uhn.fhir.rest.server.RestfulServer;
-import ca.uhn.fhir.rest.server.interceptor.*;
+import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.FhirPathFilterInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
 import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import ca.uhn.fhir.validation.IValidatorModule;
 import ca.uhn.fhir.validation.ResultSeverityEnum;
 import com.google.common.base.Strings;
@@ -44,67 +52,56 @@ import org.springframework.http.HttpHeaders;
 import org.springframework.web.cors.CorsConfiguration;
 
 import javax.servlet.ServletException;
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
 import java.util.stream.Collectors;
 
 public class BaseJpaRestfulServer extends RestfulServer {
 
+	private static final long serialVersionUID = 1L;
   @Autowired
   DaoRegistry daoRegistry;
-
   @Autowired
   DaoConfig daoConfig;
-
   @Autowired
   ISearchParamRegistry searchParamRegistry;
-
   @Autowired
   IFhirSystemDao fhirSystemDao;
-
   @Autowired
   ResourceProviderFactory resourceProviders;
-
   @Autowired
   IJpaSystemProvider jpaSystemProvider;
-
   @Autowired
   IInterceptorBroadcaster interceptorBroadcaster;
-
   @Autowired
   DatabaseBackedPagingProvider databaseBackedPagingProvider;
-
   @Autowired
   IInterceptorService interceptorService;
-
   @Autowired
   IValidatorModule validatorModule;
-
   @Autowired
   Optional<GraphQLProvider> graphQLProvider;
-
   @Autowired
   BulkDataExportProvider bulkDataExportProvider;
-
   @Autowired
   PartitionManagementProvider partitionManagementProvider;
-
   @Autowired
   BinaryStorageInterceptor binaryStorageInterceptor;
-
   @Autowired
   IPackageInstallerSvc packageInstallerSvc;
-
   @Autowired
   AppProperties appProperties;
-
   @Autowired
   ApplicationContext myApplicationContext;
-
   @Autowired(required = false)
   IRepositoryValidationInterceptorFactory factory;
-
   // These are set only if the features are enabled
   private CqlProviderLoader cqlProviderLoader;
+	@Autowired
+	private IValidationSupport myValidationSupport;
 
   public BaseJpaRestfulServer() {
   }
@@ -158,14 +155,14 @@ public class BaseJpaRestfulServer extends RestfulServer {
         setServerConformanceProvider(confProvider);
       } else if (fhirVersion == FhirVersionEnum.R4) {
 
-        JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, fhirSystemDao,
+				JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(this, fhirSystemDao,
-          daoConfig, searchParamRegistry);
+					daoConfig, searchParamRegistry, myValidationSupport);
         confProvider.setImplementationDescription("HAPI FHIR R4 Server");
         setServerConformanceProvider(confProvider);
       } else if (fhirVersion == FhirVersionEnum.R5) {
 
-        JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, fhirSystemDao,
+				JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(this, fhirSystemDao,
-          daoConfig, searchParamRegistry);
+					daoConfig, searchParamRegistry, myValidationSupport);
         confProvider.setImplementationDescription("HAPI FHIR R5 Server");
         setServerConformanceProvider(confProvider);
       } else {
@@ -384,5 +381,7 @@ public class BaseJpaRestfulServer extends RestfulServer {
     }
 
     daoConfig.getModelConfig().setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
+
+		daoConfig.getModelConfig().setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
   }
 }

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

@@ -61,6 +61,10 @@ public class FhirServerConfigCommon {
     if (appProperties.getSubscription().getEmail() != null) {
       ourLog.info("Email subscriptions enabled");
     }
+    
+    if (appProperties.getEnable_index_contained_resource() == Boolean.TRUE) {
+        ourLog.info("Indexed on contained resource enabled");
+      }
   }
 
   /**
@@ -163,6 +167,8 @@ public class FhirServerConfigCommon {
     }
 
     modelConfig.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
+    
+    modelConfig.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
     return modelConfig;
   }
 

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

@@ -13,6 +13,7 @@ import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
+import javax.annotation.PostConstruct;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
@@ -31,6 +32,19 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
   @Autowired
   AppProperties appProperties;
 
+  @PostConstruct
+  public void initSettings() {
+    if(appProperties.getSearch_coord_core_pool_size() != null) {
+		 setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
+	 }
+	  if(appProperties.getSearch_coord_max_pool_size() != null) {
+		  setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
+	  }
+	  if(appProperties.getSearch_coord_queue_capacity() != null) {
+		  setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
+	  }
+  }
+
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
     DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();

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

@@ -11,6 +11,7 @@ import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
+import javax.annotation.PostConstruct;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
@@ -29,6 +30,20 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
   @Autowired
   AppProperties appProperties;
 
+  @PostConstruct
+  public void initSettings() {
+    if(appProperties.getSearch_coord_core_pool_size() != null) {
+		 setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
+	 }
+	  if(appProperties.getSearch_coord_max_pool_size() != null) {
+		  setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
+	  }
+	  if(appProperties.getSearch_coord_queue_capacity() != null) {
+		  setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
+	  }
+  }
+
+
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
     DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
@@ -68,7 +83,12 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
   public ElasticsearchSvcImpl elasticsearchSvc() {
     if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
       String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
-      String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":"));
+      String elasticsearchHost;
+      if (elasticsearchUrl.startsWith("http")) {
+        elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://") + 3, elasticsearchUrl.lastIndexOf(":"));
+      } else {
+        elasticsearchHost = elasticsearchUrl.substring(0, elasticsearchUrl.indexOf(":"));
+      }
       String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
       String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
       int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));

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

@@ -12,6 +12,7 @@ import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
+import javax.annotation.PostConstruct;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
@@ -31,6 +32,19 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
   @Autowired
   AppProperties appProperties;
 
+  @PostConstruct
+  public void initSettings() {
+    if(appProperties.getSearch_coord_core_pool_size() != null) {
+		 setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
+	 }
+	  if(appProperties.getSearch_coord_max_pool_size() != null) {
+		  setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
+	  }
+	  if(appProperties.getSearch_coord_queue_capacity() != null) {
+		  setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
+	  }
+  }
+
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
     DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();

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

@@ -14,6 +14,7 @@ import org.springframework.core.env.ConfigurableEnvironment;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
 
+import javax.annotation.PostConstruct;
 import javax.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
@@ -32,6 +33,19 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
   @Autowired
   AppProperties appProperties;
 
+  @PostConstruct
+  public void initSettings() {
+    if(appProperties.getSearch_coord_core_pool_size() != null) {
+		 setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
+	 }
+	  if(appProperties.getSearch_coord_max_pool_size() != null) {
+		  setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
+	  }
+	  if(appProperties.getSearch_coord_queue_capacity() != null) {
+		  setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
+	  }
+  }
+
   @Override
   public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
     DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
@@ -71,7 +85,12 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
   public ElasticsearchSvcImpl elasticsearchSvc() {
     if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
       String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
-      String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":"));
+      String elasticsearchHost;
+      if (elasticsearchUrl.startsWith("http")) {
+        elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://") + 3, elasticsearchUrl.lastIndexOf(":"));
+      } else {
+        elasticsearchHost = elasticsearchUrl.substring(0, elasticsearchUrl.indexOf(":"));
+      }
       String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
       String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
       int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));

src/main/resources/application.yaml

@@ -6,6 +6,10 @@ spring:
     password: null
     driverClassName: org.h2.Driver
     max-active: 15
+
+    # database connection pool size
+    hikari:
+      maximum-pool-size: 10
   jpa:
     properties:
       hibernate.format_sql: false
@@ -66,6 +70,7 @@ hapi:
 #    default_page_size: 20
 #    enable_repository_validating_interceptor: false
 #    enable_index_missing_fields: false
+#    enable_index_contained_resource: false
 #    enforce_referential_integrity_on_delete: false
 #    enforce_referential_integrity_on_write: false
 #    etag_support_enabled: true
@@ -84,6 +89,12 @@ hapi:
        # These are allowed_origin patterns, see: https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/cors/CorsConfiguration.html#setAllowedOriginPatterns-java.util.List-
        allowed_origin:
        - '*'
+
+    # Search coordinator thread pool sizes
+    search-coord-core-pool-size: 20
+    search-coord-max-pool-size: 100
+    search-coord-queue-capacity: 200
+
 #    logger:
 #      error_format: 'ERROR - ${requestVerb} ${requestUrl}'
 #      format: >-

src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java

@@ -60,7 +60,7 @@ public class ElasticsearchLastNR4IT {
   private IGenericClient ourClient;
   private FhirContext ourCtx;
 
-  private static final String ELASTIC_VERSION = "7.10.1";
+  private static final String ELASTIC_VERSION = "7.10.2";
 	private static final String ELASTIC_IMAGE = "docker.elastic.co/elasticsearch/elasticsearch:" + ELASTIC_VERSION;
 
 	private static ElasticsearchContainer embeddedElastic;

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

@@ -67,16 +67,18 @@ public class ExampleServerR5IT {
   public void testWebsocketSubscription() throws Exception {
 
     /*
-     * Create topic
+     * Create topic (will be contained in subscription)
      */
     SubscriptionTopic topic = new SubscriptionTopic();
-    topic.getResourceTrigger().getQueryCriteria().setCurrent("Observation?status=final");
+    topic.setId("#1");
+    topic.getResourceTriggerFirstRep().getQueryCriteria().setCurrent("Observation?status=final");
 
     /*
      * Create subscription
      */
     Subscription subscription = new Subscription();
-    subscription.getTopic().setResource(topic);
+    subscription.getContained().add(topic);
+    subscription.setTopic("#1");
     subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
     subscription.setStatus(Enumerations.SubscriptionState.REQUESTED);
     subscription.getChannelType()