Personal-Twin/hapi-fhir-jpaserver-starter
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' into more_properties

Browse Source
This commit is contained in:
James Agnew
2019-03-15 11:30:37 -04:00
committed by GitHub
parent b13bf8cf10 d1a0949d42
commit 0f88181943
13 changed files with 332 additions and 111 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
README.md
View File

@@ -12,7 +12,7 @@ In order to use this sample, you should have:
# Running Locally
The easiest way to run this server is to run it directly in Maven using a built-in Jetty server. To do this, execute the following command:
The easiest way to run this server is to run it directly in Maven using a built-in Jetty server. To do this, change `src/main/resources/hapi.properties` `server_address` and `server.base` with the values commented out as *For Jetty, use this* and then execute the following command:
```
mvn jetty:run

26
src/main/java/ca/uhn/fhir/jpa/starter/ApplicationContext.java Normal file
View File

@@ -0,0 +1,26 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirVersionEnum;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
public class ApplicationContext extends AnnotationConfigWebApplicationContext {
public ApplicationContext() {
FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
if (fhirVersion == FhirVersionEnum.DSTU2) {
register(FhirServerConfigDstu2.class, FhirServerConfigCommon.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
register(FhirServerConfigDstu3.class, FhirServerConfigCommon.class);
} else if (fhirVersion == FhirVersionEnum.R4) {
register(FhirServerConfigR4.class, FhirServerConfigCommon.class);
} else {
throw new IllegalStateException();
}
if (HapiProperties.getSubscriptionWebsocketEnabled()) {
register(ca.uhn.fhir.jpa.config.WebsocketDispatcherConfig.class);
}
}
}

13
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
View File

@@ -90,14 +90,19 @@ public class FhirServerConfigCommon {
retVal.setFetchSizeDefaultMaximum(maxFetchSize);
ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE? "'unlimited'": maxFetchSize));
// You can enable these if you want to support Subscriptions from your server
if (this.subscriptionRestHookEnabled) {
// Subscriptions are enabled by channel type
if (HapiProperties.getSubscriptionRestHookEnabled()) {
ourLog.info("Enabling REST-hook subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.RESTHOOK);
}
if (this.subscriptionEmailEnabled) {
if (HapiProperties.getSubscriptionEmailEnabled()) {
ourLog.info("Enabling email subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.EMAIL);
}
if (HapiProperties.getSubscriptionWebsocketEnabled()) {
ourLog.info("Enabling websocket subscriptions");
retVal.addSupportedSubscriptionType(Subscription.SubscriptionChannelType.WEBSOCKET);
}
return retVal;
}

1
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java
View File

@@ -18,6 +18,7 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
@Autowired
private DataSource myDataSource;
/**
* We override the paging provider definition so that we can customize
* the default/max page sizes for search results. You can set these however

13
src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java
View File

@@ -38,6 +38,7 @@ public class HapiProperties {
static final String SERVER_NAME = "server.name";
static final String SUBSCRIPTION_EMAIL_ENABLED = "subscription.email.enabled";
static final String SUBSCRIPTION_RESTHOOK_ENABLED = "subscription.resthook.enabled";
static final String SUBSCRIPTION_WEBSOCKET_ENABLED = "subscription.websocket.enabled";
static final String TEST_PORT = "test.port";
static final String ALLOW_CONTAINS_SEARCHES = "allow_contains_searches";
static final String ALLOW_OVERRIDE_DEFAULT_SEARCH_PARAMS = "allow_override_default_search_params";
@@ -237,11 +238,11 @@ public class HapiProperties {
}
public static Boolean getAllowMultipleDelete() {
return HapiProperties.getBooleanProperty(ALLOW_MULTIPLE_DELETE, true);
return HapiProperties.getBooleanProperty(ALLOW_MULTIPLE_DELETE, false);
}
public static Boolean getAllowExternalReferences() {
return HapiProperties.getBooleanProperty(ALLOW_EXTERNAL_REFERENCES, true);
return HapiProperties.getBooleanProperty(ALLOW_EXTERNAL_REFERENCES, false);
}
public static Boolean getExpungeEnabled() {
@@ -269,11 +270,15 @@ public class HapiProperties {
}
public static Boolean getSubscriptionEmailEnabled() {
return HapiProperties.getBooleanProperty(SUBSCRIPTION_EMAIL_ENABLED, true);
return HapiProperties.getBooleanProperty(SUBSCRIPTION_EMAIL_ENABLED, false);
}
public static Boolean getSubscriptionRestHookEnabled() {
return HapiProperties.getBooleanProperty(SUBSCRIPTION_RESTHOOK_ENABLED, true);
return HapiProperties.getBooleanProperty(SUBSCRIPTION_RESTHOOK_ENABLED, false);
}
public static Boolean getSubscriptionWebsocketEnabled() {
return HapiProperties.getBooleanProperty(SUBSCRIPTION_WEBSOCKET_ENABLED, false);
}
public static Boolean getAllowContainsSearches() {

45
src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
View File

@@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.model.interceptor.api.IInterceptorRegistry;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
@@ -14,6 +15,8 @@ import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
import ca.uhn.fhir.jpa.provider.r4.TerminologyUploaderProviderR4;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.subscription.SubscriptionActivatingInterceptor;
import ca.uhn.fhir.jpa.subscription.SubscriptionMatcherInterceptor;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
@@ -22,7 +25,7 @@ import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Meta;
import org.springframework.context.annotation.AnnotationConfigApplicationContext;
import org.springframework.context.ApplicationContext;
import javax.servlet.ServletException;
import java.util.List;
@@ -30,12 +33,6 @@ import java.util.List;
public class JpaRestfulServer extends RestfulServer {
private static final long serialVersionUID = 1L;
private AnnotationConfigApplicationContext appCtx;
@Override
public void destroy() {
appCtx.close();
}
@SuppressWarnings("unchecked")
@Override
@@ -46,34 +43,33 @@ public class JpaRestfulServer extends RestfulServer {
* Create a FhirContext object that uses the version of FHIR
* specified in the properties file.
*/
FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
setFhirContext(new FhirContext(fhirVersion));
ApplicationContext appCtx = (ApplicationContext) getServletContext().getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
appCtx = new AnnotationConfigApplicationContext();
// if (HapiProperties.getSubscriptionWebsocketEnabled()) {
// appCtx.register(WebsocketDispatcherConfig.class);
// }
/*
* ResourceProviders are fetched from the Spring context
*/
FhirVersionEnum fhirVersion = HapiProperties.getFhirVersion();
List<IResourceProvider> resourceProviders;
Object systemProvider;
if (fhirVersion == FhirVersionEnum.DSTU2) {
appCtx.register(FhirServerConfigDstu2.class, FhirServerConfigCommon.class);
appCtx.refresh();
resourceProviders = appCtx.getBean("myResourceProvidersDstu2", List.class);
systemProvider = appCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
appCtx.register(FhirServerConfigDstu3.class, FhirServerConfigCommon.class);
appCtx.refresh();
resourceProviders = appCtx.getBean("myResourceProvidersDstu3", List.class);
systemProvider = appCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
} else if (fhirVersion == FhirVersionEnum.R4) {
appCtx.register(FhirServerConfigR4.class, FhirServerConfigCommon.class);
appCtx.refresh();
resourceProviders = appCtx.getBean("myResourceProvidersR4", List.class);
systemProvider = appCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class);
} else {
throw new IllegalStateException();
}
setFhirContext(appCtx.getBean(FhirContext.class));
registerProviders(resourceProviders);
registerProvider(systemProvider);
@@ -173,6 +169,23 @@ public class JpaRestfulServer extends RestfulServer {
SubscriptionTriggeringProvider retriggeringProvider = appCtx.getBean(SubscriptionTriggeringProvider.class);
registerProvider(retriggeringProvider);
}
// If subscriptions are enabled, we want to register the interceptor that
// will activate them and match results against them
if (HapiProperties.getSubscriptionWebsocketEnabled() ||
HapiProperties.getSubscriptionEmailEnabled() ||
HapiProperties.getSubscriptionRestHookEnabled()) {
IInterceptorRegistry interceptorRegistry = appCtx.getBean(IInterceptorRegistry.class);
SubscriptionActivatingInterceptor subscriptionActivatingInterceptor = appCtx.getBean(SubscriptionActivatingInterceptor.class);
interceptorRegistry.registerInterceptor(subscriptionActivatingInterceptor);
SubscriptionMatcherInterceptor subscriptionMatcherInterceptor = appCtx.getBean(SubscriptionMatcherInterceptor.class);
subscriptionMatcherInterceptor.start();
interceptorRegistry.registerInterceptor(subscriptionMatcherInterceptor);
}
}
}

33
src/main/resources/hapi.properties
View File

@@ -8,10 +8,16 @@ fhir_version=DSTU3
# server, put the DNS name of that server here.
server_address=http://localhost/fhir/
# For Jetty, use this:
# server_address=http://localhost:8080/hapi-fhir-jpaserver/fhir/
# This is the context path for the FHIR endpoint. If this is changed, the
# setting above should also be changed.
server.base=/fhir
# For Jetty, use this:
# server.base=/hapi-fhir-jpaserver/fhir
default_encoding=JSON
etag_support=ENABLED
default_page_size=20
@@ -34,14 +40,6 @@ datasource.password=
server.name=Local Tester
server.id=home
test.port=
subscription.email.enabled=true
email.enabled=false
email.from=some@test.com
email.host=
email.port=0
email.username=
email.password=
subscription.resthook.enabled=true
hibernate.dialect=ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect
hibernate.search.model_mapping=ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory
hibernate.format_sql=false
@@ -55,3 +53,22 @@ hibernate.cache.use_minimal_puts=false
hibernate.search.default.directory_provider=filesystem
hibernate.search.default.indexBase=target/lucenefiles
hibernate.search.lucene_version=LUCENE_CURRENT
##################################################
# Subscriptions
##################################################
# Enable REST Hook Subscription Channel
subscription.resthook.enabled=false
# Enable Email Subscription Channel
subscription.email.enabled=false
email.enabled=false
email.from=some@test.com
email.host=
email.port=0
email.username=
email.password=
# Enable Websocket Subscription Channel
subscription.websocket.enabled=false

11
src/main/webapp/WEB-INF/templates/tmpl-footer.html
View File

@@ -1,16 +1,5 @@
<!DOCTYPE html>
<html lang="en">
<div th:fragment="footer">
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-1395874-6', 'auto');
ga('require', 'displayfeatures');
ga('require', 'linkid', 'linkid.js');
ga('send', 'pageview');
</script>
</div>
</html>

9
src/main/webapp/WEB-INF/web.xml
View File

@@ -5,23 +5,20 @@
metadata-complete="false"
version="3.1">
<!--
<listener>
<listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
</listener>
<context-param>
<param-name>contextClass</param-name>
<param-value>
org.springframework.web.context.support.AnnotationConfigWebApplicationContext
ca.uhn.fhir.jpa.starter.ApplicationContext
</param-value>
</context-param>
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>
ca.uhn.fhir.jpa.starter.FhirServerConfig
</param-value>
</context-param>
-->
<!-- Servlets -->
<servlet>
@@ -33,7 +30,9 @@
</init-param>
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value>ca.uhn.fhir.jpa.starter.FhirTesterConfig</param-value>
<param-value>
ca.uhn.fhir.jpa.starter.FhirTesterConfig,
</param-value>
</init-param>
<load-on-startup>2</load-on-startup>
</servlet>

1
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java
View File

@@ -31,6 +31,7 @@ public class ExampleServerDstu2IT {
static {
HapiProperties.forceReload();
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "DSTU2");
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:derby:memory:dbr2;create=true");
HapiProperties.setProperty(HapiProperties.TEST_PORT, Integer.toString(PortUtil.findFreePort()));
ourCtx = FhirContext.forDstu2();
ourPort = HapiProperties.getTestPort();

1
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java
View File

@@ -30,6 +30,7 @@ public class ExampleServerDstu3IT {
static {
HapiProperties.forceReload();
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "DSTU3");
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:derby:memory:dbr3;create=true");
HapiProperties.setProperty(HapiProperties.TEST_PORT, Integer.toString(PortUtil.findFreePort()));
ourCtx = FhirContext.forDstu3();
ourPort = HapiProperties.getTestPort();

78
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
View File

@@ -1,21 +1,34 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
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 ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.util.PortUtil;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.webapp.WebAppContext;
import org.hl7.fhir.r4.model.Patient;
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.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Subscription;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.junit.Assert.assertEquals;
public class ExampleServerR4IT {
@@ -30,8 +43,10 @@ public class ExampleServerR4IT {
static {
HapiProperties.forceReload();
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:derby:memory:dbr4;create=true");
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R4");
HapiProperties.setProperty(HapiProperties.TEST_PORT, Integer.toString(PortUtil.findFreePort()));
HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
ourCtx = FhirContext.forR4();
ourPort = HapiProperties.getTestPort();
}
@@ -49,6 +64,66 @@ public class ExampleServerR4IT {
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");
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();
// 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
*/
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
myWebSocketClient.start();
URI echoUri = new URI("ws://localhost:" + ourPort + "/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());
/*
* 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);
/*
* Ensure that we receive a ping on the websocket
*/
waitForSize(1, () -> mySocketImplementation.myPingCount);
/*
* Clean up
*/
ourClient.delete().resourceById(mySubscriptionId).execute();
}
@AfterClass
public static void afterClass() throws Exception {
ourServer.stop();
@@ -73,6 +148,7 @@ public class ExampleServerR4IT {
WebAppContext webAppContext = new WebAppContext();
webAppContext.setContextPath("/");
webAppContext.setDisplayName("HAPI FHIR");
webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
webAppContext.setParentLoaderPriority(true);

88
src/test/java/ca/uhn/fhir/jpa/starter/SocketImplementation.java Normal file
View File

@@ -0,0 +1,88 @@
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 org.slf4j.Logger;
import java.util.ArrayList;
import java.util.List;
@WebSocket
public class SocketImplementation {
private static final Logger ourLog = org.slf4j.LoggerFactory.getLogger(SocketImplementation.class);
private String myCriteria;
protected String myError;
protected boolean myGotBound;
private List<String> myMessages = new ArrayList<String>();
protected int myPingCount;
protected String mySubsId;
private Session session;
public SocketImplementation(String theCriteria, EncodingEnum theEncoding) {
myCriteria = theCriteria;
}
public List<String> getMessages() {
return myMessages;
}
public void keepAlive() {
if (this.session != null) {
try {
session.getRemote().sendString("keep alive");
} catch (Throwable t) {
ourLog.error("Failure", t);
}
}
}
/**
* This method is executed when the client is connecting to the server.
* In this case, we are sending a message to create the subscription dynamiclly
*
* @param session
*/
@OnWebSocketConnect
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);
ourLog.info("Connection: DONE");
} catch (Throwable t) {
t.printStackTrace();
ourLog.error("Failure", t);
}
}
/**
* This is the message handler for the client
*
* @param theMsg
*/
@OnWebSocketMessage
public void onMessage(String theMsg) {
ourLog.info("Got msg: " + theMsg);
myMessages.add(theMsg);
if (theMsg.startsWith("bound ")) {
myGotBound = true;
mySubsId = (theMsg.substring("bound ".length()));
} else if (myGotBound && theMsg.startsWith("add " + mySubsId + "\n")) {
String text = theMsg.substring(("add " + mySubsId + "\n").length());
ourLog.info("text: " + text);
} else if (theMsg.startsWith("ping ")) {
myPingCount++;
} else {
myError = "Unexpected message: " + theMsg;
}
}
}