Personal-Twin/hapi-fhir-jpaserver-starter
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Merge branch 'origin-master' into spring-pr

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# Conflicts:
#	pom.xml
#	src/main/java/ca/uhn/fhir/jpa/empi/EmpiConfig.java
This commit is contained in:
jkv
2020-09-04 23:50:06 +02:00
parent 5f237256ca c9c944d236
commit 6eb46d2b39
10 changed files with 152 additions and 144 deletions
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4
pom.xml
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@@ -1,5 +1,6 @@
<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">
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>
<!-- mvn clean package spring-boot:repackage && java -jar target/hapi-fhir-jpaserver.war -->
@@ -380,6 +381,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>3.0.0-M5</version>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</configuration>

9
src/main/java/ca/uhn/fhir/jpa/starter/EmpiConfig.java → src/main/java/ca/uhn/fhir/jpa/empi/EmpiConfig.java
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@@ -1,20 +1,23 @@
package ca.uhn.fhir.jpa.starter;
package ca.uhn.fhir.jpa.empi;
import ca.uhn.fhir.empi.api.IEmpiSettings;
import ca.uhn.fhir.empi.rules.config.EmpiRuleValidator;
import ca.uhn.fhir.empi.rules.config.EmpiSettings;
import ca.uhn.fhir.jpa.starter.HapiProperties;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Profile;
import org.springframework.core.io.DefaultResourceLoader;
import org.springframework.core.io.Resource;
import java.io.IOException;
/**
* TODO: Move this to package "ca.uhn.fhir.jpa.starter" in HAPI FHIR 5.2.0+. The lousy component scan
* in 5.1.0 picks this up even if EMPI is disabled currently.
*/
@Configuration
@Profile("empi")
public class EmpiConfig {
@Bean

14
src/main/java/ca/uhn/fhir/jpa/starter/Application.java
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@@ -20,20 +20,20 @@ public class Application {
SpringApplication.run(Application.class, args);
//Server is now accessible at eg. http://localhost:8080/fhir/metadata
//UI is now accessible at http://localhost:8080/
}
@Bean
public ServletRegistrationBean servletRegistrationBean() {
AnnotationConfigWebApplicationContext ctx = new AnnotationConfigWebApplicationContext();
AnnotationConfigWebApplicationContext annotationConfigWebApplicationContext = new AnnotationConfigWebApplicationContext();
annotationConfigWebApplicationContext.register(FhirTesterConfig.class);
DispatcherServlet dispatcherServlet = new DispatcherServlet(annotationConfigWebApplicationContext);
dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
dispatcherServlet.setContextConfigLocation(FhirTesterConfig.class.getName());
ctx.register(FhirTesterConfig.class);
DispatcherServlet api = new DispatcherServlet(ctx);
api.setContextClass(AnnotationConfigWebApplicationContext.class);
api.setContextConfigLocation(FhirTesterConfig.class.getName());
ServletRegistrationBean registrationBean = new ServletRegistrationBean();
registrationBean.setServlet(api);
registrationBean.setServlet(dispatcherServlet);
registrationBean.addUrlMappings("/*");
registrationBean.setLoadOnStartup(1);
return registrationBean;

1
src/main/java/ca/uhn/fhir/jpa/starter/ApplicationContext.java
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@@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.empi.EmpiConfig;
import ca.uhn.fhir.jpa.empi.config.EmpiConsumerConfig;
import ca.uhn.fhir.jpa.empi.config.EmpiSubmitterConfig;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;

1
src/main/resources/empi-rules.json
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@@ -1,4 +1,5 @@
{
"version": "1",
"candidateSearchParams": [
{
"resourceType": "Patient",

12
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java
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@@ -9,13 +9,13 @@ import ca.uhn.fhir.test.utilities.JettyUtil;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.webapp.WebAppContext;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import java.nio.file.Paths;
import static org.junit.Assert.assertEquals;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class ExampleServerDstu2IT {
@@ -45,12 +45,12 @@ public class ExampleServerDstu2IT {
assertEquals(methodName, pt2.getName().get(0).getFamily().get(0).getValue());
}
@AfterClass
@AfterAll
public static void afterClass() throws Exception {
ourServer.stop();
}
@BeforeClass
@BeforeAll
public static void beforeClass() throws Exception {
String path = Paths.get("").toAbsolutePath().toString();

202
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java
View File

@@ -18,9 +18,9 @@ import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Subscription;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import java.net.URI;
import java.nio.file.Paths;
@@ -28,130 +28,130 @@ import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.junit.Assert.assertEquals;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class ExampleServerDstu3IT {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu3IT.class);
private static IGenericClient ourClient;
private static FhirContext ourCtx;
private static int ourPort;
private static Server ourServer;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu3IT.class);
private static IGenericClient ourClient;
private static FhirContext ourCtx;
private static int ourPort;
private static Server ourServer;
static {
HapiProperties.forceReload();
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "DSTU3");
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr3");
HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
HapiProperties.setProperty(HapiProperties.ALLOW_EXTERNAL_REFERENCES, "true");
HapiProperties.setProperty(HapiProperties.ALLOW_PLACEHOLDER_REFERENCES, "true");
ourCtx = FhirContext.forDstu3();
}
static {
HapiProperties.forceReload();
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "DSTU3");
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr3");
HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
HapiProperties.setProperty(HapiProperties.ALLOW_EXTERNAL_REFERENCES, "true");
HapiProperties.setProperty(HapiProperties.ALLOW_PLACEHOLDER_REFERENCES, "true");
ourCtx = FhirContext.forDstu3();
}
@Test
public void testCreateAndRead() {
ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
String methodName = "testCreateResourceConditional";
@Test
public void testCreateAndRead() {
ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
String methodName = "testCreateResourceConditional";
Patient pt = new Patient();
pt.addName().setFamily(methodName);
IIdType id = ourClient.create().resource(pt).execute().getId();
Patient pt = new Patient();
pt.addName().setFamily(methodName);
IIdType id = ourClient.create().resource(pt).execute().getId();
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(methodName, pt2.getName().get(0).getFamily());
}
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(methodName, pt2.getName().get(0).getFamily());
}
@Test
public void testWebsocketSubscription() throws Exception {
/*
* Create subscription
*/
Subscription subscription = new Subscription();
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
subscription.setCriteria("Observation?status=final");
@Test
public void testWebsocketSubscription() throws Exception {
/*
* Create subscription
*/
Subscription subscription = new Subscription();
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
subscription.setStatus(Subscription.SubscriptionStatus.REQUESTED);
subscription.setCriteria("Observation?status=final");
Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET);
channel.setPayload("application/json");
subscription.setChannel(channel);
Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent();
channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET);
channel.setPayload("application/json");
subscription.setChannel(channel);
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
IIdType mySubscriptionId = methodOutcome.getId();
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
IIdType mySubscriptionId = methodOutcome.getId();
// Wait for the subscription to be activated
waitForSize(1, () -> ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size());
// Wait for the subscription to be activated
waitForSize(1, () -> ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size());
/*
* Attach websocket
*/
/*
* Attach websocket
*/
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
myWebSocketClient.start();
URI echoUri = new URI("ws://localhost:" + ourPort + "/hapi-fhir-jpaserver/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);
myWebSocketClient.start();
URI echoUri = new URI("ws://localhost:" + ourPort + "/hapi-fhir-jpaserver/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);
ourLog.info("Connected to WS: {}", session.isOpen());
ourLog.info("Connected to WS: {}", session.isOpen());
/*
* Create a matching resource
*/
Observation obs = new Observation();
obs.setStatus(Observation.ObservationStatus.FINAL);
ourClient.create().resource(obs).execute();
/*
* Create a matching resource
*/
Observation obs = new Observation();
obs.setStatus(Observation.ObservationStatus.FINAL);
ourClient.create().resource(obs).execute();
// Give some time for the subscription to deliver
Thread.sleep(2000);
// Give some time for the subscription to deliver
Thread.sleep(2000);
/*
* Ensure that we receive a ping on the websocket
*/
waitForSize(1, () -> mySocketImplementation.myPingCount);
/*
* Ensure that we receive a ping on the websocket
*/
waitForSize(1, () -> mySocketImplementation.myPingCount);
/*
* Clean up
*/
ourClient.delete().resourceById(mySubscriptionId).execute();
}
/*
* Clean up
*/
ourClient.delete().resourceById(mySubscriptionId).execute();
}
@AfterClass
public static void afterClass() throws Exception {
ourServer.stop();
}
@AfterAll
public static void afterClass() throws Exception {
ourServer.stop();
}
@BeforeClass
public static void beforeClass() throws Exception {
String path = Paths.get("").toAbsolutePath().toString();
@BeforeAll
public static void beforeClass() throws Exception {
String path = Paths.get("").toAbsolutePath().toString();
ourLog.info("Project base path is: {}", path);
ourLog.info("Project base path is: {}", path);
ourServer = new Server(0);
ourServer = new Server(0);
WebAppContext webAppContext = new WebAppContext();
webAppContext.setContextPath("/hapi-fhir-jpaserver");
webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
webAppContext.setParentLoaderPriority(true);
WebAppContext webAppContext = new WebAppContext();
webAppContext.setContextPath("/hapi-fhir-jpaserver");
webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
webAppContext.setParentLoaderPriority(true);
ourServer.setHandler(webAppContext);
ourServer.start();
ourServer.setHandler(webAppContext);
ourServer.start();
ourPort = JettyUtil.getPortForStartedServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
String ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
String ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
public static void main(String[] theArgs) throws Exception {
ourPort = 8080;
beforeClass();
}
public static void main(String[] theArgs) throws Exception {
ourPort = 8080;
beforeClass();
}
}

17
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
View File

@@ -21,9 +21,9 @@ import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Person;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Subscription;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import java.net.URI;
import java.nio.file.Paths;
@@ -35,8 +35,8 @@ import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.awaitility.Awaitility.await;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class ExampleServerR4IT {
@@ -61,6 +61,9 @@ public class ExampleServerR4IT {
String methodName = "testCreateResourceConditional";
Patient pt = new Patient();
pt.setActive(true);
pt.getBirthDateElement().setValueAsString("2020-01-01");
pt.addIdentifier().setSystem("http://foo").setValue("12345");
pt.addName().setFamily(methodName);
IIdType id = ourClient.create().resource(pt).execute().getId();
@@ -151,12 +154,12 @@ public class ExampleServerR4IT {
return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
}
@AfterClass
@AfterAll
public static void afterClass() throws Exception {
ourServer.stop();
}
@BeforeClass
@BeforeAll
public static void beforeClass() throws Exception {
String path = Paths.get("").toAbsolutePath().toString();

24
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java
View File

@@ -20,9 +20,9 @@ import org.hl7.fhir.r5.model.Observation;
import org.hl7.fhir.r5.model.Patient;
import org.hl7.fhir.r5.model.Subscription;
import org.hl7.fhir.r5.model.SubscriptionTopic;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import java.net.URI;
import java.nio.file.Paths;
@@ -30,7 +30,8 @@ import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.junit.Assert.assertEquals;
import static org.awaitility.Awaitility.await;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class ExampleServerR5IT {
@@ -77,9 +78,9 @@ public class ExampleServerR5IT {
subscription.getTopic().setResource(topic);
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
subscription.setStatus(Enumerations.SubscriptionState.REQUESTED);
subscription.getChannelType()
.setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
.setCode("websocket");
subscription.getChannelType()
.setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
.setCode("websocket");
subscription.setContentType("application/json");
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
@@ -111,13 +112,10 @@ public class ExampleServerR5IT {
obs.setStatus(Enumerations.ObservationStatus.FINAL);
ourClient.create().resource(obs).execute();
// Give some time for the subscription to deliver
Thread.sleep(2000);
/*
* Ensure that we receive a ping on the websocket
*/
waitForSize(1, () -> mySocketImplementation.myPingCount);
await().until(()->mySocketImplementation.myPingCount > 0);
/*
* Clean up
@@ -125,12 +123,12 @@ public class ExampleServerR5IT {
ourClient.delete().resourceById(mySubscriptionId).execute();
}
@AfterClass
@AfterAll
public static void afterClass() throws Exception {
ourServer.stop();
}
@BeforeClass
@BeforeAll
public static void beforeClass() throws Exception {
String path = Paths.get("").toAbsolutePath().toString();

12
src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java
View File

@@ -15,13 +15,13 @@ import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import java.nio.file.Paths;
import static org.junit.Assert.assertEquals;
import static org.junit.jupiter.api.Assertions.assertEquals;
public class MultitenantServerR4IT {
@@ -94,12 +94,12 @@ public class MultitenantServerR4IT {
assertEquals("Family B", pt2.getName().get(0).getFamily());
}
@AfterClass
@AfterAll
public static void afterClass() throws Exception {
ourServer.stop();
}
@BeforeClass
@BeforeAll
public static void beforeClass() throws Exception {
String path = Paths.get("").toAbsolutePath().toString();