Merge pull request #798 from honestica/elasticsearch-mapping

Elasticsearch mapping for Jpa Server

hapi-fhir-jpaserver-elasticsearch/pom.xml

@@ -0,0 +1,23 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>ca.uhn.hapi.fhir</groupId>
+		<artifactId>hapi-deployable-pom</artifactId>
+		<version>3.2.0-SNAPSHOT</version>
+		<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
+	</parent>
+
+	<artifactId>hapi-fhir-jpaserver-elasticsearch</artifactId>
+	<packaging>jar</packaging>
+
+	<name>HAPI FHIR JPA Server - ElasticSearch Integration</name>
+
+	<dependencies>
+		<dependency>
+			<groupId>org.hibernate</groupId>
+			<artifactId>hibernate-search-elasticsearch</artifactId>
+		</dependency>
+	</dependencies>
+
+</project>

hapi-fhir-jpaserver-elasticsearch/src/main/java/ca/uhn/fhir/jpa/search/ElasticsearchMappingProvider.java

@@ -0,0 +1,41 @@
+package ca.uhn.fhir.jpa.search;
+
+import org.hibernate.search.elasticsearch.analyzer.definition.ElasticsearchAnalysisDefinitionRegistryBuilder;
+import org.hibernate.search.elasticsearch.analyzer.definition.spi.ElasticsearchAnalysisDefinitionProvider;
+
+public class ElasticsearchMappingProvider implements ElasticsearchAnalysisDefinitionProvider {
+
+	@Override
+	public void register(ElasticsearchAnalysisDefinitionRegistryBuilder builder) {
+		builder.analyzer("autocompleteEdgeAnalyzer")
+			.withTokenizer("pattern_all")
+			.withTokenFilters("lowercase", "stop", "edgengram_3_50");
+		builder.tokenizer("pattern_all").type("pattern").param("pattern", "(.*)").param("group", "1");
+		builder.tokenFilter("edgengram_3_50")
+			.type("edgeNGram")
+			.param("min_gram", "3")
+			.param("max_gram", "50");
+
+		builder.analyzer("autocompletePhoneticAnalyzer")
+			.withTokenizer("standard")
+			.withTokenFilters("standard", "stop", "snowball_english", "phonetic_doublemetaphone");
+		builder.tokenFilter("phonetic_doublemetaphone")
+			.type("phonetic")
+			.param("encoder", "double_metaphone");
+		builder.tokenFilter("snowball_english").type("snowball").param("language", "English");
+
+		builder.analyzer("autocompleteNGramAnalyzer")
+			.withTokenizer("standard")
+			.withTokenFilters("word_delimiter", "lowercase", "ngram_3_20");
+		builder.tokenFilter("ngram_3_20")
+			.type("nGram")
+			.param("min_gram", "3")
+			.param("max_gram", "20");
+
+		builder.analyzer("standardAnalyzer").withTokenizer("standard").withTokenFilters("lowercase");
+
+		builder.analyzer("exactAnalyzer").withTokenizer("standard");
+
+		builder.analyzer("conceptParentPidsAnalyzer").withTokenizer("whitespace");
+	}
+}

hapi-fhir-jpaserver-example/README.md

@@ -41,3 +41,17 @@ Use this command to start the container:
   `docker run -d --name hapi-fhir-jpaserver-example -p 8080:8080 hapi-fhir/hapi-fhir-jpaserver-example`
 
 Note: with this command data is persisted across container restarts, but not after removal of the container. Use a docker volume mapping on /var/lib/jetty/target to achieve this.
+
+#### Using ElasticSearch as the search engine instead of the default Apache Lucene
+1. Install ElasticSearch server and the phonetic plugin
+    * Download ElasticSearch from https://www.elastic.co/downloads/elasticsearch
+    * ```cd {your elasticsearch directory}```
+    * ```bin/plugin install analysis-phonetic```
+    * start ElasticSearch server: ```./bin/elasticsearch```
+2. Replace configuration in web.xml
+    * replace the configuration class ```ca.uhn.fhir.jpa.demo.FhirServerConfig``` in web.xml by ```ca.uhn.fhir.jpa.demo.elasticsearch.FhirServerConfig```
+3. Start server by runing: ```mvn jetty:run```
+4. Limitations:
+    * Hibernate search are not compatible with all ElasticSearch version. If you are using Hibernate search: 5.6 or 5.7, the compatible ElasticSearch version is 2.0 - 2.4. If you are using Hibernate search: 5.8 or 5.9, the compatible ElasticSearch version is
+    2.0 - 5.6.
+    * Please check all the limitations in the reference documentation: https://docs.jboss.org/hibernate/search/5.7/reference/en-US/html_single/#elasticsearch-limitations before use the integration.

hapi-fhir-jpaserver-example/pom.xml

@@ -74,6 +74,12 @@
 			<version>${project.version}</version>
 		</dependency>
 
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-elasticsearch</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+
 		<!-- This dependency is used for the "FHIR Tester" web app overlay -->
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>

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

@@ -0,0 +1,110 @@
+package ca.uhn.fhir.jpa.demo.elasticsearch;
+
+import java.util.Properties;
+import javax.persistence.EntityManagerFactory;
+import javax.sql.DataSource;
+
+import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.search.ElasticsearchMappingProvider;
+import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
+import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
+import org.apache.commons.dbcp2.BasicDataSource;
+import org.hibernate.jpa.HibernatePersistenceProvider;
+import org.springframework.beans.factory.annotation.Autowire;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.orm.jpa.JpaTransactionManager;
+import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
+
+/**
+ * This is the configuration file for the example server integrating the ElasticSearch engine.
+ */
+@Configuration
+@EnableTransactionManagement()
+public class FhirServerConfig extends BaseJavaConfigDstu3 {
+
+	/**
+	 * Configure FHIR properties around the the JPA server via this bean
+	 */
+	@Bean()
+	public DaoConfig daoConfig() {
+		DaoConfig retVal = new DaoConfig();
+		retVal.setAllowMultipleDelete(true);
+		return retVal;
+	}
+
+	/**
+	 * The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
+	 * directory called "jpaserver_derby_files".
+	 *
+	 * A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
+	 */
+	@Bean(destroyMethod = "close")
+	public DataSource dataSource() {
+		BasicDataSource retVal = new BasicDataSource();
+		retVal.setDriver(new org.apache.derby.jdbc.EmbeddedDriver());
+		retVal.setUrl("jdbc:derby:directory:target/jpaserver_derby_files;create=true");
+		retVal.setUsername("");
+		retVal.setPassword("");
+		return retVal;
+	}
+
+	@Bean()
+	public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
+		LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
+		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.format_sql", "true");
+		extraProperties.put("hibernate.show_sql", "false");
+		extraProperties.put("hibernate.hbm2ddl.auto", "update");
+		extraProperties.put("hibernate.jdbc.batch_size", "20");
+		extraProperties.put("hibernate.cache.use_query_cache", "false");
+		extraProperties.put("hibernate.cache.use_second_level_cache", "false");
+		extraProperties.put("hibernate.cache.use_structured_entries", "false");
+		extraProperties.put("hibernate.cache.use_minimal_puts", "false");
+
+		// the belowing properties are used for ElasticSearch integration
+		extraProperties.put("hibernate.search.elasticsearch.analyzer_definition_provider", ElasticsearchMappingProvider.class.getName());
+		extraProperties.put("hibernate.search.default.indexmanager", "elasticsearch");
+		extraProperties.put("hibernate.search.default.elasticsearch.host", "http://127.0.0.1:9200");
+		extraProperties.put("hibernate.search.default.elasticsearch.index_schema_management_strategy", "CREATE");
+		extraProperties.put("hibernate.search.default.elasticsearch.index_management_wait_timeout", "10000");
+		extraProperties.put("hibernate.search.default.elasticsearch.required_index_status", "yellow");
+		return extraProperties;
+	}
+
+	/**
+	 * This interceptor adds some pretty syntax highlighting in responses when a browser is detected
+	 */
+	@Bean(autowire = Autowire.BY_TYPE)
+	public IServerInterceptor responseHighlighterInterceptor() {
+		ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
+		return retVal;
+	}
+
+	@Bean(autowire = Autowire.BY_TYPE)
+	public IServerInterceptor subscriptionSecurityInterceptor() {
+		SubscriptionsRequireManualActivationInterceptorDstu3 retVal = new SubscriptionsRequireManualActivationInterceptorDstu3();
+		return retVal;
+	}
+
+	@Bean()
+	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
+		JpaTransactionManager retVal = new JpaTransactionManager();
+		retVal.setEntityManagerFactory(entityManagerFactory);
+		return retVal;
+	}
+
+}

pom.xml

@@ -958,6 +958,11 @@
 				<artifactId>hibernate-search-orm</artifactId>
 				<version>${hibernate_search_version}</version>
 			</dependency>
+			<dependency>
+				<groupId>org.hibernate</groupId>
+				<artifactId>hibernate-search-elasticsearch</artifactId>
+				<version>${hibernate_search_version}</version>
+			</dependency>
 			<dependency>
 				<groupId>org.javassist</groupId>
 				<artifactId>javassist</artifactId>
@@ -1958,6 +1963,7 @@
 				<module>hapi-fhir-jaxrsserver-base</module>
 				<module>hapi-fhir-jaxrsserver-example</module>
 				<module>hapi-fhir-jpaserver-base</module>
+				<module>hapi-fhir-jpaserver-elasticsearch</module>
 				<module>hapi-fhir-jpaserver-example</module>
 				<module>restful-server-example</module>
 				<module>restful-server-example-test</module>