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Merge pull request #618 from hapifhir/ja_20231203_hapi_7_0

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Update to HAPI FHIR 7.0.0
This commit is contained in:
dotasek
2024-02-27 14:53:35 -05:00
committed by GitHub
parent 9e21d8062e 71715476b1
commit 4ad7c3cbb7
18 changed files with 238 additions and 276 deletions
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2
.github/workflows/smoke-tests.yml vendored
View File

@@ -33,7 +33,7 @@ jobs:
run: docker pull jetbrains/intellij-http-client
- name: Start server with jetty
run: |
mvn -Pjetty jetty:run & export JPA_PROCESS=$!
mvn -P jetty spring-boot:run & export JPA_PROCESS=$!
sleep 80
- name: Execute smoke tests
run: docker run --rm -v $PWD:/workdir --add-host host.docker.internal:host-gateway jetbrains/intellij-http-client -D src/test/smoketest/plain_server.http --env-file src/test/smoketest/http-client.env.json --env default

123
pom.xml
View File

@@ -14,7 +14,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.10.0</version>
<version>7.0.0</version>
</parent>
<artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -22,8 +22,6 @@
<properties>
<java.version>11</java.version>
<logback-classic.version>1.2.11</logback-classic.version>
<slf4j-api.version>1.7.25</slf4j-api.version>
</properties>
<prerequisites>
@@ -53,16 +51,7 @@
</dependencyManagement>
<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>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
@@ -180,11 +169,15 @@
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</dependency>
<!-- Needed for JEE/Servlet support -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<groupId>jakarta.servlet</groupId>
<artifactId>jakarta.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
@@ -201,6 +194,14 @@
<artifactId>spring-web</artifactId>
</dependency>
<!-- commons-logging is provided by jcl-over-slf4j, and the jar often shows up because of transitive dependencies; this dependency should avoid it -->
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.2</version>
<scope>provided</scope>
</dependency>
<!-- You may not need this if you are deploying to an application server which provides database connection pools itself. -->
<dependency>
<groupId>org.apache.commons</groupId>
@@ -251,6 +252,12 @@
</dependency>
<!-- 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>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
@@ -263,36 +270,7 @@
</exclusion>
</exclusions>
</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>
<groupId>org.testcontainers</groupId>
<artifactId>testcontainers</artifactId>
@@ -314,8 +292,8 @@
For some reason JavaDoc crashed during site generation unless we have this dependency
-->
<dependency>
<groupId>javax.interceptor</groupId>
<artifactId>javax.interceptor-api</artifactId>
<groupId>jakarta.interceptor</groupId>
<artifactId>jakarta.interceptor-api</artifactId>
<scope>provided</scope>
</dependency>
@@ -324,6 +302,24 @@
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.eclipse.jetty.ee10</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty.ee10.websocket</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
@@ -369,40 +365,20 @@
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<version>5.7.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>5.7.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<version>${spring_boot_version}</version>
<scope>test</scope>
</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>${logback-classic.version}</version>
</dependency>
</dependencies>
<build>
@@ -429,6 +405,14 @@
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<!--
java -jar ROOT.war doesn't work; there is a bug in spring-boot-3.2.0 due to hibernate search,
probably solved in 3.2.1 https://github.com/spring-projects/spring-boot/issues/38585
(at the moment only tomcat works)
-->
<loaderImplementation>CLASSIC</loaderImplementation>
</configuration>
<executions>
<execution>
<goals>
@@ -629,6 +613,11 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-jetty</artifactId>
<version>${spring_boot_version}</version>
</dependency>
</dependencies>
</profile>
<profile>

4
src/main/java/ca/uhn/fhir/jpa/starter/Application.java
View File

@@ -4,7 +4,6 @@ import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
import ca.uhn.fhir.jpa.starter.cdshooks.StarterCdsHooksConfig;
import ca.uhn.fhir.jpa.starter.common.FhirTesterConfig;
import ca.uhn.fhir.jpa.starter.cr.StarterCrDstu3Config;
import ca.uhn.fhir.jpa.starter.cr.StarterCrR4Config;
import ca.uhn.fhir.jpa.starter.mdm.MdmConfig;
@@ -19,15 +18,12 @@ import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration;
import org.springframework.boot.autoconfigure.thymeleaf.ThymeleafAutoConfiguration;
import org.springframework.boot.builder.SpringApplicationBuilder;
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;
@ServletComponentScan(basePackageClasses = {RestfulServer.class})
@SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class, ThymeleafAutoConfiguration.class})

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.util.stream.Collectors;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import jakarta.servlet.ServletException;
import jakarta.servlet.http.HttpServlet;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
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.StringWriter;
import java.util.Arrays;
import javax.servlet.http.HttpServletResponse;
import jakarta.servlet.http.HttpServletResponse;
public class ErrorHandling {

10
src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java
View File

@@ -62,6 +62,7 @@ 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;
import jakarta.persistence.EntityManagerFactory;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.springframework.beans.factory.NoSuchBeanDefinitionException;
import org.springframework.beans.factory.annotation.Autowired;
@@ -76,7 +77,6 @@ import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.web.cors.CorsConfiguration;
import java.util.*;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import static ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory.ENABLE_REPOSITORY_VALIDATING_INTERCEPTOR;
@@ -133,11 +133,11 @@ public class StarterJpaConfig {
@Primary
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(
DataSource myDataSource,
ConfigurableListableBeanFactory myConfigurableListableBeanFactory,
FhirContext theFhirContext) {
DataSource myDataSource,
ConfigurableListableBeanFactory myConfigurableListableBeanFactory,
FhirContext theFhirContext, JpaStorageSettings theStorageSettings) {
LocalContainerEntityManagerFactoryBean retVal =
HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext);
HapiEntityManagerFactoryUtil.newEntityManagerFactory(myConfigurableListableBeanFactory, theFhirContext, theStorageSettings);
retVal.setPersistenceUnitName("HAPI_PU");
try {

2
src/test/java/ca/uhn/fhir/jpa/starter/CustomBeanTest.java
View File

@@ -5,7 +5,7 @@ import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = {
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class}, properties = {
"hapi.fhir.custom-bean-packages=some.custom.pkg1,some.custom.pkg2",
"spring.datasource.url=jdbc:h2:mem:dbr4",
"hapi.fhir.enable_repository_validating_interceptor=true",

2
src/test/java/ca/uhn/fhir/jpa/starter/CustomInterceptorTest.java
View File

@@ -13,7 +13,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = {
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class}, properties = {
"hapi.fhir.custom-bean-packages=some.custom.pkg1",
"hapi.fhir.custom-interceptor-classes=some.custom.pkg1.CustomInterceptorBean,some.custom.pkg1.CustomInterceptorPojo",
"spring.datasource.url=jdbc:h2:mem:dbr4",

26
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.GregorianCalendar;
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.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.r4.model.Bundle;
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.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
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.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.ConfigurableApplicationContext;
import org.springframework.test.context.ContextConfiguration;
@@ -47,7 +44,7 @@ import org.testcontainers.junit.jupiter.Testcontainers;
@ExtendWith(SpringExtension.class)
@Testcontainers
@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:dbr4",
"hapi.fhir.fhir_version=r4",
@@ -83,19 +80,20 @@ public class ElasticsearchLastNR4IT {
@BeforeAll
public static void beforeClass() throws IOException {
//Given
RestHighLevelClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
ElasticsearchClient elasticsearchHighLevelRestClient = ElasticsearchRestClientFactory.createElasticsearchHighLevelRestClient(
"http", embeddedElastic.getHost() + ":" + embeddedElastic.getMappedPort(9200), "", "");
/* 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
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;
});
}

5
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java
View File

@@ -10,14 +10,13 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.boot.web.server.LocalServerPort;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.boot.test.web.server.LocalServerPort;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import static org.junit.jupiter.api.Assertions.assertEquals;
@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 =
{
"hapi.fhir.fhir_version=dstu2",
"spring.datasource.url=jdbc:h2:mem:dbr2",

29
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java
View File

@@ -10,10 +10,10 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
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.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.instance.model.api.IIdType;
import org.junit.jupiter.api.BeforeEach;
@@ -21,9 +21,8 @@ import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired;
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.test.annotation.DirtiesContext;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import java.io.File;
@@ -31,8 +30,6 @@ import java.io.IOException;
import java.net.URI;
import java.util.Collection;
import java.util.List;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -43,7 +40,6 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
classes = {
Application.class,
JpaStarterWebsocketDispatcherConfig.class,
RepositoryConfig.class
}, properties =
{
@@ -188,17 +184,16 @@ class ExampleServerDstu3IT implements IServerSupport {
* Attach websocket
*/
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(),
EncodingEnum.JSON);
myWebSocketClient.start();
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);
URI echoUri = new URI("ws://localhost:" + port + "/websocket");
ourLog.info("Connected to WS: {}", session.isOpen());
WebSocketContainer container = ContainerProvider.getWebSocketContainer();
ourLog.info("Connecting to : {}", echoUri);
Session session = container.connectToServer(mySocketImplementation, echoUri);
ourLog.info("Connected to WS: {}", session.isOpen());
/*
* Create a matching resource

4
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4BIT.java
View File

@@ -10,12 +10,12 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Order;
import org.junit.jupiter.api.Test;
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;
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class},
classes = {Application.class},
properties = {
"spring.datasource.url=jdbc:h2:mem:dbr4b",
"hapi.fhir.enable_repository_validating_interceptor=true",

185
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
View File

@@ -1,39 +1,50 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.cr.config.RepositoryConfig;
import ca.uhn.fhir.jpa.searchparam.config.NicknameServiceConfig;
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.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient;
import jakarta.websocket.ContainerProvider;
import jakarta.websocket.Session;
import jakarta.websocket.WebSocketContainer;
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.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.Order;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
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.net.URI;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
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.opencds.cqf.fhir.utility.r4.Parameters.parameters;
import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
@@ -41,32 +52,32 @@ import static org.opencds.cqf.fhir.utility.r4.Parameters.stringPart;
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
classes = {
Application.class,
JpaStarterWebsocketDispatcherConfig.class,
NicknameServiceConfig.class,
RepositoryConfig.class
}, properties = {
"spring.profiles.include=storageSettingsTest",
"spring.datasource.url=jdbc:h2:mem:dbr4",
"hapi.fhir.enable_repository_validating_interceptor=true",
"hapi.fhir.fhir_version=r4",
//"hapi.fhir.subscription.websocket_enabled=true",
//"hapi.fhir.mdm_enabled=true",
"hapi.fhir.cr.enabled=true",
"hapi.fhir.cr.caregaps_section_author=Organization/alphora-author",
"hapi.fhir.cr.caregaps_reporter=Organization/alphora",
"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
"hapi.fhir.implementationguides.dk-core.version=1.1.0",
"hapi.fhir.auto_create_placeholder_reference_targets=true",
// 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
// when running in a spring boot environment
"spring.main.allow-bean-definition-overriding=true" })
class ExampleServerR4IT implements IServerSupport{
"spring.datasource.url=jdbc:h2:mem:dbr4",
"hapi.fhir.enable_repository_validating_interceptor=true",
"hapi.fhir.fhir_version=r4",
//"hapi.fhir.subscription.websocket_enabled=true",
//"hapi.fhir.mdm_enabled=true",
"hapi.fhir.cr.enabled=true",
"hapi.fhir.cr.caregaps_section_author=Organization/alphora-author",
"hapi.fhir.cr.caregaps_reporter=Organization/alphora",
"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
"hapi.fhir.implementationguides.dk-core.version=1.1.0",
"hapi.fhir.auto_create_placeholder_reference_targets=true",
// 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
// when running in a spring boot environment
"spring.main.allow-bean-definition-overriding=true"})
class ExampleServerR4IT implements IServerSupport {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4IT.class);
private IGenericClient ourClient;
private FhirContext ourCtx;
@Autowired private CrProperties crProperties;
@Autowired
private CrProperties crProperties;
@LocalServerPort
private int port;
@@ -127,7 +138,7 @@ class ExampleServerR4IT implements IServerSupport{
return result;
}
public Parameters runCqlExecution(Parameters parameters){
public Parameters runCqlExecution(Parameters parameters) {
var results = ourClient.operation().onServer()
.named("$cql")
@@ -135,6 +146,7 @@ class ExampleServerR4IT implements IServerSupport{
.execute();
return results;
}
@Test
void testSimpleDateCqlExecutionProvider() {
Parameters params = parameters(stringPart("expression", "Interval[Today() - 2 years, Today())"));
@@ -148,61 +160,62 @@ class ExampleServerR4IT implements IServerSupport{
IBaseResource resource = (IBaseResource) theCtx.newJsonParser().parseResource(json);
resList.add(resource);
var result = theClient.transaction().withResources(resList).execute();
//.withResources(resource).execute();
//.withResources(resource).execute();
return result.get(0);
}
@Test
void testBatchPutWithIdenticalTags() {
String batchPuts = "{\n" +
"\t\"resourceType\": \"Bundle\",\n" +
"\t\"id\": \"patients\",\n" +
"\t\"type\": \"batch\",\n" +
"\t\"entry\": [\n" +
"\t\t{\n" +
"\t\t\t\"request\": {\n" +
"\t\t\t\t\"method\": \"PUT\",\n" +
"\t\t\t\t\"url\": \"Patient/pat-1\"\n" +
"\t\t\t},\n" +
"\t\t\t\"resource\": {\n" +
"\t\t\t\t\"resourceType\": \"Patient\",\n" +
"\t\t\t\t\"id\": \"pat-1\",\n" +
"\t\t\t\t\"meta\": {\n" +
"\t\t\t\t\t\"tag\": [\n" +
"\t\t\t\t\t\t{\n" +
"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
"\t\t\t\t\t\t}\n" +
"\t\t\t\t\t]\n" +
"\t\t\t\t}\n" +
"\t\t\t},\n" +
"\t\t\t\"fullUrl\": \"/Patient/pat-1\"\n" +
"\t\t},\n" +
"\t\t{\n" +
"\t\t\t\"request\": {\n" +
"\t\t\t\t\"method\": \"PUT\",\n" +
"\t\t\t\t\"url\": \"Patient/pat-2\"\n" +
"\t\t\t},\n" +
"\t\t\t\"resource\": {\n" +
"\t\t\t\t\"resourceType\": \"Patient\",\n" +
"\t\t\t\t\"id\": \"pat-2\",\n" +
"\t\t\t\t\"meta\": {\n" +
"\t\t\t\t\t\"tag\": [\n" +
"\t\t\t\t\t\t{\n" +
"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
"\t\t\t\t\t\t}\n" +
"\t\t\t\t\t]\n" +
"\t\t\t\t}\n" +
"\t\t\t},\n" +
"\t\t\t\"fullUrl\": \"/Patient/pat-2\"\n" +
"\t\t}\n" +
"\t]\n" +
"}";
"\t\"resourceType\": \"Bundle\",\n" +
"\t\"id\": \"patients\",\n" +
"\t\"type\": \"batch\",\n" +
"\t\"entry\": [\n" +
"\t\t{\n" +
"\t\t\t\"request\": {\n" +
"\t\t\t\t\"method\": \"PUT\",\n" +
"\t\t\t\t\"url\": \"Patient/pat-1\"\n" +
"\t\t\t},\n" +
"\t\t\t\"resource\": {\n" +
"\t\t\t\t\"resourceType\": \"Patient\",\n" +
"\t\t\t\t\"id\": \"pat-1\",\n" +
"\t\t\t\t\"meta\": {\n" +
"\t\t\t\t\t\"tag\": [\n" +
"\t\t\t\t\t\t{\n" +
"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
"\t\t\t\t\t\t}\n" +
"\t\t\t\t\t]\n" +
"\t\t\t\t}\n" +
"\t\t\t},\n" +
"\t\t\t\"fullUrl\": \"/Patient/pat-1\"\n" +
"\t\t},\n" +
"\t\t{\n" +
"\t\t\t\"request\": {\n" +
"\t\t\t\t\"method\": \"PUT\",\n" +
"\t\t\t\t\"url\": \"Patient/pat-2\"\n" +
"\t\t\t},\n" +
"\t\t\t\"resource\": {\n" +
"\t\t\t\t\"resourceType\": \"Patient\",\n" +
"\t\t\t\t\"id\": \"pat-2\",\n" +
"\t\t\t\t\"meta\": {\n" +
"\t\t\t\t\t\"tag\": [\n" +
"\t\t\t\t\t\t{\n" +
"\t\t\t\t\t\t\t\"system\": \"http://mysystem.org\",\n" +
"\t\t\t\t\t\t\t\"code\": \"value2\"\n" +
"\t\t\t\t\t\t}\n" +
"\t\t\t\t\t]\n" +
"\t\t\t\t}\n" +
"\t\t\t},\n" +
"\t\t\t\"fullUrl\": \"/Patient/pat-2\"\n" +
"\t\t}\n" +
"\t]\n" +
"}";
Bundle bundle = FhirContext.forR4().newJsonParser().parseResource(Bundle.class, batchPuts);
ourClient.transaction().withBundle(bundle).execute();
}
//@Test
@Test
@Order(1)
void testWebsocketSubscription() throws Exception {
/*
@@ -218,27 +231,27 @@ class ExampleServerR4IT implements IServerSupport{
channel.setPayload("application/json");
subscription.setChannel(channel);
int initialActiveSubscriptionCount = activeSubscriptionCount();
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
IIdType mySubscriptionId = methodOutcome.getId();
// 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
*/
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(),
EncodingEnum.JSON);
myWebSocketClient.start();
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());
/*
@@ -268,11 +281,11 @@ class ExampleServerR4IT implements IServerSupport{
assertTrue(reporter.equals("Organization/alphora"));
assertTrue(author.equals("Organization/alphora-author"));
String periodStartValid = "2019-01-01";
String periodEndValid = "2019-12-31";
String subjectPatientValid = "Patient/numer-EXM125";
String statusValid = "open-gap";
String measureIdValid = "BreastCancerScreeningFHIR";
String periodStartValid = "2019-01-01";
String periodEndValid = "2019-12-31";
String subjectPatientValid = "Patient/numer-EXM125";
String statusValid = "open-gap";
String measureIdValid = "BreastCancerScreeningFHIR";
loadBundle("r4/CareGaps/authreporter-bundle.json", ourCtx, ourClient);
loadBundle("r4/CareGaps/BreastCancerScreeningFHIR-bundle.json", ourCtx, ourClient);

39
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java
View File

@@ -1,9 +1,5 @@
package ca.uhn.fhir.jpa.starter;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.awaitility.Awaitility.await;
import static org.junit.jupiter.api.Assertions.assertEquals;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.CacheControlDirective;
import ca.uhn.fhir.rest.api.EncodingEnum;
@@ -11,12 +7,9 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import java.net.URI;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import org.eclipse.jetty.websocket.api.Session;
import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
import org.eclipse.jetty.websocket.client.WebSocketClient;
import jakarta.websocket.ContainerProvider;
import jakarta.websocket.Session;
import jakarta.websocket.WebSocketContainer;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Enumerations;
@@ -28,11 +21,17 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
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 java.net.URI;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.awaitility.Awaitility.await;
import static org.junit.jupiter.api.Assertions.assertEquals;
@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",
"hapi.fhir.fhir_version=r5",
@@ -128,18 +127,16 @@ public class ExampleServerR5IT {
* Attach websocket
*/
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(),
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("Connected to WS: {}", session.isOpen());
ourLog.info("Connecting to : {}", echoUri);
Session session = container.connectToServer(mySocketImplementation, echoUri);
ourLog.info("Connected to WS: {}", session.isOpen());
/*
* Create a matching resource

34
src/test/java/ca/uhn/fhir/jpa/starter/JpaStarterWebsocketDispatcherConfig.java
View File

@@ -1,34 +0,0 @@
package ca.uhn.fhir.jpa.starter;
import org.eclipse.jetty.webapp.WebAppContext;
import org.eclipse.jetty.websocket.server.config.JettyWebSocketServletContainerInitializer;
import org.springframework.boot.web.embedded.jetty.JettyServletWebServerFactory;
import org.springframework.boot.web.server.WebServerFactoryCustomizer;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
/**
* This class ensures that websockets work with
* Spring + Spring Boot + Jetty
*/
@Configuration
public class JpaStarterWebsocketDispatcherConfig {
@Bean
public Jetty10WebSocketServletWebServerCustomizer jetty10WebSocketServletWebServerCustomizer() {
return new Jetty10WebSocketServletWebServerCustomizer();
}
static class Jetty10WebSocketServletWebServerCustomizer implements WebServerFactoryCustomizer<JettyServletWebServerFactory> {
@Override
public void customize(JettyServletWebServerFactory factory) {
factory.addServerCustomizers(server -> {
WebAppContext ctx = (WebAppContext) server.getHandler();
JettyWebSocketServletContainerInitializer.configure(ctx, null);
});
}
}
}

4
src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java
View File

@@ -12,13 +12,13 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
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 static org.junit.jupiter.api.Assertions.assertEquals;
@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:dbr4-mt",
"hapi.fhir.fhir_version=r4",

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

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

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

@@ -1,7 +1,7 @@
spring:
main:
allow-circular-references: true
#allow-bean-definition-overriding: true
allow-bean-definition-overriding: true
flyway:
enabled: false
check-location: false
@@ -20,11 +20,20 @@ spring:
properties:
hibernate.format_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.hbm2ddl.auto: update
# hibernate.jdbc.batch_size: 20
# hibernate.cache.use_query_cache: false