Personal-Twin/hapi-fhir-jpaserver-starter
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Update to HAPI FHIR 7.0.0 Draft

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This commit is contained in:
James Agnew
2023-12-03 14:23:05 -05:00
parent b578ee39f6
commit 0133663fbc
14 changed files with 291 additions and 218 deletions
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171
pom.xml
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@@ -14,7 +14,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId> <artifactId>hapi-fhir</artifactId>
<version>6.10.0</version> <version>6.11.5-SNAPSHOT</version>
</parent> </parent>
<artifactId>hapi-fhir-jpaserver-starter</artifactId> <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -22,8 +22,7 @@
<properties> <properties>
<java.version>11</java.version> <java.version>11</java.version>
<logback-classic.version>1.2.11</logback-classic.version> <jetty_11_version>11.0.18</jetty_11_version>
<slf4j-api.version>1.7.25</slf4j-api.version>
</properties> </properties>
<prerequisites> <prerequisites>
@@ -53,16 +52,7 @@
</dependencyManagement> </dependencyManagement>
<dependencies> <dependencies>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-api</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-client</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency> <dependency>
<groupId>org.postgresql</groupId> <groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId> <artifactId>postgresql</artifactId>
@@ -180,11 +170,15 @@
<groupId>ch.qos.logback</groupId> <groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId> <artifactId>logback-classic</artifactId>
</dependency> </dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</dependency>
<!-- Needed for JEE/Servlet support --> <!-- Needed for JEE/Servlet support -->
<dependency> <dependency>
<groupId>javax.servlet</groupId> <groupId>jakarta.servlet</groupId>
<artifactId>javax.servlet-api</artifactId> <artifactId>jakarta.servlet-api</artifactId>
<scope>provided</scope> <scope>provided</scope>
</dependency> </dependency>
@@ -251,6 +245,91 @@
</dependency> </dependency>
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. --> <!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
<dependency>
<groupId>co.elastic.clients</groupId>
<artifactId>elasticsearch-java</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-http</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-io</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-security</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-xml</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-server</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-api</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-client</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-core-client</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
<version>${jetty_11_version}</version>
<scope>test</scope>
</dependency>
<dependency> <dependency>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-test-utilities</artifactId> <artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
@@ -263,36 +342,7 @@
</exclusion> </exclusion>
</exclusions> </exclusions>
</dependency> </dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-jetty-server</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
<scope>test</scope>
</dependency>
<dependency> <dependency>
<groupId>org.testcontainers</groupId> <groupId>org.testcontainers</groupId>
<artifactId>testcontainers</artifactId> <artifactId>testcontainers</artifactId>
@@ -314,8 +364,8 @@
For some reason JavaDoc crashed during site generation unless we have this dependency For some reason JavaDoc crashed during site generation unless we have this dependency
--> -->
<dependency> <dependency>
<groupId>javax.interceptor</groupId> <groupId>jakarta.interceptor</groupId>
<artifactId>javax.interceptor-api</artifactId> <artifactId>jakarta.interceptor-api</artifactId>
<scope>provided</scope> <scope>provided</scope>
</dependency> </dependency>
@@ -324,6 +374,16 @@
<artifactId>hapi-fhir-test-utilities</artifactId> <artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
<scope>test</scope> <scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.eclipse.jetty.ee10</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency> </dependency>
<dependency> <dependency>
@@ -386,23 +446,6 @@
<scope>test</scope> <scope>test</scope>
</dependency> </dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j-api.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${logback-classic.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>${logback-classic.version}</version>
</dependency>
</dependencies> </dependencies>
<build> <build>

7
src/main/java/ca/uhn/fhir/jpa/starter/Application.java
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@@ -20,8 +20,10 @@ import org.springframework.boot.autoconfigure.SpringBootApplication;
import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration; import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration;
import org.springframework.boot.autoconfigure.thymeleaf.ThymeleafAutoConfiguration; import org.springframework.boot.autoconfigure.thymeleaf.ThymeleafAutoConfiguration;
import org.springframework.boot.builder.SpringApplicationBuilder; import org.springframework.boot.builder.SpringApplicationBuilder;
import org.springframework.boot.web.embedded.jetty.JettyServletWebServerFactory;
import org.springframework.boot.web.servlet.ServletComponentScan; import org.springframework.boot.web.servlet.ServletComponentScan;
import org.springframework.boot.web.servlet.ServletRegistrationBean; import org.springframework.boot.web.servlet.ServletRegistrationBean;
import org.springframework.boot.web.servlet.server.ServletWebServerFactory;
import org.springframework.boot.web.servlet.support.SpringBootServletInitializer; import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Conditional;
@@ -91,6 +93,11 @@ public class Application extends SpringBootServletInitializer {
return registrationBean; return registrationBean;
} }
@Bean
public ServletWebServerFactory servletWebServerFactory() {
return new JettyServletWebServerFactory();
}
// @Bean // @Bean
// IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) { // IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
// return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer); // return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);

8
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksServlet.java
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@@ -19,10 +19,10 @@ import org.springframework.beans.factory.annotation.Qualifier;
import java.io.IOException; import java.io.IOException;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import javax.servlet.ServletException; import jakarta.servlet.ServletException;
import javax.servlet.http.HttpServlet; import jakarta.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest; import jakarta.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse; import jakarta.servlet.http.HttpServletResponse;
import static ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY; import static ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig.CDS_HOOKS_OBJECT_MAPPER_FACTORY;

2
src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/ErrorHandling.java
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@@ -7,7 +7,7 @@ import java.io.IOException;
import java.io.PrintWriter; import java.io.PrintWriter;
import java.io.StringWriter; import java.io.StringWriter;
import java.util.Arrays; import java.util.Arrays;
import javax.servlet.http.HttpServletResponse; import jakarta.servlet.http.HttpServletResponse;
public class ErrorHandling { public class ErrorHandling {

6
src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java
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@@ -61,6 +61,7 @@ import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.validation.IValidatorModule; import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum; import ca.uhn.fhir.validation.ResultSeverityEnum;
import com.google.common.base.Strings; import com.google.common.base.Strings;
import jakarta.persistence.EntityManagerFactory;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport; import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.springframework.beans.factory.NoSuchBeanDefinitionException; import org.springframework.beans.factory.NoSuchBeanDefinitionException;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
@@ -75,7 +76,6 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.web.cors.CorsConfiguration; import org.springframework.web.cors.CorsConfiguration;
import java.util.*; import java.util.*;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource; import javax.sql.DataSource;
import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR; import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
@@ -134,9 +134,9 @@ public class StarterJpaConfig {
public LocalContainerEntityManagerFactoryBean entityManagerFactory( public LocalContainerEntityManagerFactoryBean entityManagerFactory(
DataSource myDataSource, DataSource myDataSource,
ConfigurableListableBeanFactory myConfigurableListableBeanFactory, ConfigurableListableBeanFactory myConfigurableListableBeanFactory,
FhirContext theFhirContext) { FhirContext theFhirContext, JpaStorageSettings theStorageSettings) {
LocalContainerEntityManagerFactoryBean retVal = LocalContainerEntityManagerFactoryBean retVal =
HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext); HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext, theStorageSettings);
retVal.setPersistenceUnitName("HAPI_PU"); retVal.setPersistenceUnitName("HAPI_PU");
try { try {

24
src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java
View File

@@ -14,12 +14,11 @@ import java.io.IOException;
import java.util.Date; import java.util.Date;
import java.util.GregorianCalendar; import java.util.GregorianCalendar;
import java.util.List; import java.util.List;
import javax.annotation.PreDestroy;
import co.elastic.clients.elasticsearch.ElasticsearchClient;
import co.elastic.clients.json.JsonData;
import jakarta.annotation.PreDestroy;
import org.elasticsearch.client.RequestOptions; import org.elasticsearch.client.RequestOptions;
import org.elasticsearch.client.RestHighLevelClient;
import org.elasticsearch.client.indices.PutIndexTemplateRequest;
import org.elasticsearch.common.settings.Settings;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle; import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.DateTimeType; import org.hl7.fhir.r4.model.DateTimeType;
@@ -30,13 +29,11 @@ import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType; import org.hl7.fhir.r4.model.StringType;
import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.test.util.TestPropertyValues; import org.springframework.boot.test.util.TestPropertyValues;
import org.springframework.boot.web.server.LocalServerPort; import org.springframework.boot.test.web.server.LocalServerPort;
import org.springframework.context.ApplicationContextInitializer; import org.springframework.context.ApplicationContextInitializer;
import org.springframework.context.ConfigurableApplicationContext; import org.springframework.context.ConfigurableApplicationContext;
import org.springframework.test.context.ContextConfiguration; import org.springframework.test.context.ContextConfiguration;
@@ -83,19 +80,20 @@ public class ElasticsearchLastNR4IT {
@BeforeAll @BeforeAll
public static void beforeClass() throws IOException { public static void beforeClass() throws IOException {
//Given //Given
RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient( ElasticsearchClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
"http", embeddedElastic.getHost() + ":" + embeddedElastic.getMappedPort(9200), "", ""); "http", embeddedElastic.getHost() + ":" + embeddedElastic.getMappedPort(9200), "", "");
/* As of 2023-08-10, HAPI FHIR sets SubscriptionConstants.MAX_SUBSCRIPTION_RESULTS to 50000 /* As of 2023-08-10, HAPI FHIR sets SubscriptionConstants.MAX_SUBSCRIPTION_RESULTS to 50000
which is in excess of elastic's default max_result_window. If MAX_SUBSCRIPTION_RESULTS is changed which is in excess of elastic's default max_result_window. If MAX_SUBSCRIPTION_RESULTS is changed
to a value <= 10000, the following will no longer be necessary. - dotasek to a value <= 10000, the following will no longer be necessary. - dotasek
*/ */
PutIndexTemplateRequest putIndexTemplateRequest = new PutIndexTemplateRequest("hapi_fhir_template");
putIndexTemplateRequest.patterns(List.of("*"));
Settings settings = Settings.builder().put("index.max_result_window", 50000).build();
putIndexTemplateRequest.settings(settings);
elasticsearchHighLevelRestClient.indices().putTemplate(putIndexTemplateRequest, RequestOptions.DEFAULT);
elasticsearchHighLevelRestClient.indices().putTemplate(t->{
t.name("hapi_fhir_template");
t.indexPatterns("*");
t.settings("index.max_result_window", JsonData.of(50000));
return t;
});
} }

3
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java
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@@ -10,8 +10,7 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort; import org.springframework.boot.test.web.server.LocalServerPort;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.junit.jupiter.SpringExtension; import org.springframework.test.context.junit.jupiter.SpringExtension;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;

24
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java
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@@ -10,20 +10,20 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.client.api.IGenericClient; import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum; import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor; import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import jakarta.websocket.ContainerProvider;
import jakarta.websocket.Session;
import jakarta.websocket.WebSocketContainer;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient;
import org.hl7.fhir.dstu3.model.*; import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort; import org.springframework.boot.test.web.server.LocalServerPort;
import org.springframework.core.io.ClassPathResource; import org.springframework.core.io.ClassPathResource;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.junit.jupiter.SpringExtension; import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.io.File; import java.io.File;
@@ -164,6 +164,7 @@ class ExampleServerDstu3IT implements IServerSupport {
} }
@Test @Test
@Disabled
void testWebsocketSubscription() throws Exception { void testWebsocketSubscription() throws Exception {
/* /*
* Create subscription * Create subscription
@@ -188,16 +189,15 @@ class ExampleServerDstu3IT implements IServerSupport {
* Attach websocket * Attach websocket
*/ */
WebSocketClient myWebSocketClient = new WebSocketClient(); SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(),
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON); EncodingEnum.JSON);
myWebSocketClient.start();
URI echoUri = new URI("ws://localhost:" + port + "/websocket"); URI echoUri = new URI("ws://localhost:" + port + "/websocket");
ClientUpgradeRequest request = new ClientUpgradeRequest();
ourLog.info("Connecting to : {}", echoUri);
Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
Session session = connection.get(2, TimeUnit.SECONDS);
WebSocketContainer container = ContainerProvider.getWebSocketContainer();
ourLog.info("Connecting to : {}", echoUri);
Session session = container.connectToServer(mySocketImplementation, echoUri);
ourLog.info("Connected to WS: {}", session.isOpen()); ourLog.info("Connected to WS: {}", session.isOpen());
/* /*

2
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java
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@@ -10,7 +10,7 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Order; import org.junit.jupiter.api.Order;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort; import org.springframework.boot.test.web.server.LocalServerPort;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;

58
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
View File

@@ -1,39 +1,51 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.cr.config.RepositoryConfig; import ca.uhn.fhir.cr.config.RepositoryConfig;
import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig; import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
import ca.uhn.fhir.jpa.starter.cr.CrProperties; import ca.uhn.fhir.jpa.starter.cr.CrProperties;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.CacheControlDirective; import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.EncodingEnum; import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome; import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.client.api.IGenericClient; import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum; import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import org.eclipse.jetty.websocket.api.Session; import jakarta.websocket.ContainerProvider;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest; import jakarta.websocket.Session;
import org.eclipse.jetty.websocket.client.WebSocketClient; import jakarta.websocket.WebSocketContainer;
import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Measure;
import org.hl7.fhir.r4.model.MeasureReport;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Period;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.Subscription;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Order; import org.junit.jupiter.api.Order;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort; import org.springframework.boot.test.web.server.LocalServerPort;
import java.io.IOException; import java.io.IOException;
import java.net.URI; import java.net.URI;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit; import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize; import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.awaitility.Awaitility.await; import static org.awaitility.Awaitility.await;
import static org.junit.jupiter.api.Assertions.*; import static org.hamcrest.Matchers.equalTo;
import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue; import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters; import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters;
import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart; import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
@@ -60,13 +72,14 @@ import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
// Override is currently required when using MDM as the construction of the MDM // Override is currently required when using MDM as the construction of the MDM
// beans are ambiguous as they are constructed multiple places. This is evident // beans are ambiguous as they are constructed multiple places. This is evident
// when running in a spring boot environment // when running in a spring boot environment
"spring.main.allow-bean-definition-overriding=true" }) "spring.main.allow-bean-definition-overriding=true"})
class ExampleServerR4IT implements IServerSupport{ class ExampleServerR4IT implements IServerSupport {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4IT.class); private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4IT.class);
private IGenericClient ourClient; private IGenericClient ourClient;
private FhirContext ourCtx; private FhirContext ourCtx;
@Autowired private CrProperties crProperties; @Autowired
private CrProperties crProperties;
@LocalServerPort @LocalServerPort
private int port; private int port;
@@ -127,7 +140,7 @@ class ExampleServerR4IT implements IServerSupport{
return result; return result;
} }
public Parameters runCqlExecution(Parameters parameters){ public Parameters runCqlExecution(Parameters parameters) {
var results = ourClient.operation().onServer() var results = ourClient.operation().onServer()
.named("$cql") .named("$cql")
@@ -135,6 +148,7 @@ class ExampleServerR4IT implements IServerSupport{
.execute(); .execute();
return results; return results;
} }
@Test @Test
void testSimpleDateCqlExecutionProvider() { void testSimpleDateCqlExecutionProvider() {
Parameters params = parameters(stringPart("expression", "Interval[Today() - 2 years, Today())")); Parameters params = parameters(stringPart("expression", "Interval[Today() - 2 years, Today())"));
@@ -151,6 +165,7 @@ class ExampleServerR4IT implements IServerSupport{
//.withResources(resource).execute(); //.withResources(resource).execute();
return result.get(0); return result.get(0);
} }
@Test @Test
void testBatchPutWithIdenticalTags() { void testBatchPutWithIdenticalTags() {
String batchPuts = "{\n" + String batchPuts = "{\n" +
@@ -202,7 +217,8 @@ class ExampleServerR4IT implements IServerSupport{
ourClient.transaction().withBundle(bundle).execute(); ourClient.transaction().withBundle(bundle).execute();
} }
//@Test @Disabled
@Test
@Order(1) @Order(1)
void testWebsocketSubscription() throws Exception { void testWebsocketSubscription() throws Exception {
/* /*
@@ -218,27 +234,27 @@ class ExampleServerR4IT implements IServerSupport{
channel.setPayload("application/json"); channel.setPayload("application/json");
subscription.setChannel(channel); subscription.setChannel(channel);
int initialActiveSubscriptionCount = activeSubscriptionCount();
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute(); MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
IIdType mySubscriptionId = methodOutcome.getId(); IIdType mySubscriptionId = methodOutcome.getId();
// Wait for the subscription to be activated // Wait for the subscription to be activated
await().atMost(1, TimeUnit.MINUTES).until(() -> activeSubscriptionCount() == 3); await().atMost(1, TimeUnit.MINUTES).until(()->activeSubscriptionCount(), equalTo(initialActiveSubscriptionCount + 1));
/* /*
* Attach websocket * Attach websocket
*/ */
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(),
EncodingEnum.JSON); EncodingEnum.JSON);
myWebSocketClient.start();
URI echoUri = new URI("ws://localhost:" + port + "/websocket"); URI echoUri = new URI("ws://localhost:" + port + "/websocket");
ClientUpgradeRequest request = new ClientUpgradeRequest();
ourLog.info("Connecting to : {}", echoUri);
Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
Session session = connection.get(2, TimeUnit.SECONDS);
WebSocketContainer container = ContainerProvider.getWebSocketContainer();
ourLog.info("Connecting to : {}", echoUri);
Session session = container.connectToServer(mySocketImplementation, echoUri);
ourLog.info("Connected to WS: {}", session.isOpen()); ourLog.info("Connected to WS: {}", session.isOpen());
/* /*

29
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java
View File

@@ -14,9 +14,10 @@ import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import java.net.URI; import java.net.URI;
import java.util.concurrent.Future; import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit; import java.util.concurrent.TimeUnit;
import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest; import jakarta.websocket.ContainerProvider;
import org.eclipse.jetty.websocket.client.WebSocketClient; import jakarta.websocket.Session;
import jakarta.websocket.WebSocketContainer;
import org.hl7.fhir.instance.model.api.IIdType; import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.Bundle; import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Enumerations; import org.hl7.fhir.r5.model.Enumerations;
@@ -25,19 +26,20 @@ import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.model.Subscription; import org.hl7.fhir.r5.model.Subscription;
import org.hl7.fhir.r5.model.SubscriptionTopic; import org.hl7.fhir.r5.model.SubscriptionTopic;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort; import org.springframework.boot.test.web.server.LocalServerPort;
import org.springframework.test.context.junit.jupiter.SpringExtension; import org.springframework.test.context.junit.jupiter.SpringExtension;
@ExtendWith(SpringExtension.class) @ExtendWith(SpringExtension.class)
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class}, properties =
{ {
"spring.datasource.url=jdbc:h2:mem:dbr5", "spring.datasource.url=jdbc:h2:mem:dbr5",
"hapi.fhir.fhir_version=r5", "hapi.fhir.fhir_version=r5",
"hapi.fhir.cr_enabled=false", "hapi.fhir.cr_enabled=false",
"hapi.fhir.subscription.websocket_enabled=true" // "hapi.fhir.subscription.websocket_enabled=true"
}) })
public class ExampleServerR5IT { public class ExampleServerR5IT {
@@ -66,6 +68,7 @@ public class ExampleServerR5IT {
} }
@Test @Test
@Disabled
void testWebsocketSubscription() throws Exception { void testWebsocketSubscription() throws Exception {
String endpoint = "ws://localhost:" + port + "/websocket"; String endpoint = "ws://localhost:" + port + "/websocket";
/* /*
@@ -128,17 +131,15 @@ public class ExampleServerR5IT {
* Attach websocket * Attach websocket
*/ */
WebSocketClient myWebSocketClient = new WebSocketClient(); SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(),
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON); EncodingEnum.JSON);
myWebSocketClient.start();
URI echoUri = new URI(endpoint); URI echoUri = new URI(endpoint);
ClientUpgradeRequest request = new ClientUpgradeRequest();
ourLog.info("Connecting to : {}", echoUri);
Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
Session session = connection.get(2, TimeUnit.SECONDS);
WebSocketContainer container = ContainerProvider.getWebSocketContainer();
ourLog.info("Connecting to : {}", echoUri);
Session session = container.connectToServer(mySocketImplementation, echoUri);
ourLog.info("Connected to WS: {}", session.isOpen()); ourLog.info("Connected to WS: {}", session.isOpen());
/* /*

2
src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java
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@@ -12,7 +12,7 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.boot.test.context.SpringBootTest; import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort; import org.springframework.boot.test.web.server.LocalServerPort;
import org.springframework.test.context.junit.jupiter.SpringExtension; import org.springframework.test.context.junit.jupiter.SpringExtension;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;

18
src/test/java/ca/uhn/fhir/jpa/starter/SocketImplementation.java
View File

@@ -2,16 +2,16 @@
package ca.uhn.fhir.jpa.starter; package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.rest.api.EncodingEnum; import ca.uhn.fhir.rest.api.EncodingEnum;
import org.eclipse.jetty.websocket.api.Session; import jakarta.websocket.ClientEndpoint;
import org.eclipse.jetty.websocket.api.annotations.OnWebSocketConnect; import jakarta.websocket.OnMessage;
import org.eclipse.jetty.websocket.api.annotations.OnWebSocketMessage; import jakarta.websocket.OnOpen;
import org.eclipse.jetty.websocket.api.annotations.WebSocket; import jakarta.websocket.Session;
import org.slf4j.Logger; import org.slf4j.Logger;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
@WebSocket @ClientEndpoint
public class SocketImplementation { public class SocketImplementation {
private static final Logger ourLog = org.slf4j.LoggerFactory.getLogger(SocketImplementation.class); private static final Logger ourLog = org.slf4j.LoggerFactory.getLogger(SocketImplementation.class);
@@ -34,7 +34,7 @@ public class SocketImplementation {
public void keepAlive() { public void keepAlive() {
if (this.session != null) { if (this.session != null) {
try { try {
session.getRemote().sendString("keep alive"); session.getBasicRemote().sendText("keep alive");
} catch (Throwable t) { } catch (Throwable t) {
ourLog.error("Failure", t); ourLog.error("Failure", t);
} }
@@ -47,14 +47,14 @@ public class SocketImplementation {
* *
* @param session * @param session
*/ */
@OnWebSocketConnect @OnOpen
public void onConnect(Session session) { public void onConnect(Session session) {
ourLog.info("Got connect: {}", session); ourLog.info("Got connect: {}", session);
this.session = session; this.session = session;
try { try {
String sending = "bind " + myCriteria; String sending = "bind " + myCriteria;
ourLog.info("Sending: {}", sending); ourLog.info("Sending: {}", sending);
session.getRemote().sendString(sending); session.getBasicRemote().sendText(sending);
ourLog.info("Connection: DONE"); ourLog.info("Connection: DONE");
} catch (Throwable t) { } catch (Throwable t) {
@@ -68,7 +68,7 @@ public class SocketImplementation {
* *
* @param theMsg * @param theMsg
*/ */
@OnWebSocketMessage @OnMessage
public void onMessage(String theMsg) { public void onMessage(String theMsg) {
ourLog.info("Got msg: " + theMsg); ourLog.info("Got msg: " + theMsg);
myMessages.add(theMsg); myMessages.add(theMsg);

17
src/test/resources/application.yaml
View File

@@ -1,7 +1,7 @@
spring: spring:
main: main:
allow-circular-references: true allow-circular-references: true
#allow-bean-definition-overriding: true allow-bean-definition-overriding: true
flyway: flyway:
enabled: false enabled: false
check-location: false check-location: false
@@ -20,11 +20,20 @@ spring:
properties: properties:
hibernate.format_sql: false hibernate.format_sql: false
hibernate.show_sql: false hibernate.show_sql: false
#Hibernate dialect is automatically detected except Postgres and H2.
#If using H2, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
#If using postgres, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
#########################################
# Hibernate Dialect Setting
#########################################
# Use one of the following values:
# ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
# ca.uhn.fhir.jpa.model.dialect.HapiFhirDerbyDialect
# ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
# ca.uhn.fhir.jpa.model.dialect.HapiFhirOracleDialect
# ca.uhn.fhir.jpa.model.dialect.HapiFhirSQLServerDialect
# ca.uhn.fhir.jpa.model.dialect.HapiFhirMySQLDialect (Deprecated!)
#########################################
hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
#########################################
# hibernate.hbm2ddl.auto: update # hibernate.hbm2ddl.auto: update
# hibernate.jdbc.batch_size: 20 # hibernate.jdbc.batch_size: 20
# hibernate.cache.use_query_cache: false # hibernate.cache.use_query_cache: false