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Merge pull request #12 from jjcosare/master

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Docs of hapi-fhir-testpage-overlay not loading properly due to local conformance statement issue
This commit is contained in:
James Agnew
2019-03-19 10:35:32 -04:00
committed by GitHub
parent fc39fc9252 95ac3dcb4a
commit 17bce10699
15 changed files with 198 additions and 136 deletions
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19
README.md
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@@ -20,7 +20,7 @@ mvn jetty:run
Then, browse to the following link to use the server:
[http://localhost:8080/hapi-fhir-jpaserver/](http://localhost:8080/hapi-fhir-jpaserver/)
[http://localhost:8080/](http://localhost:8080/)
# Deploying to a Container
@@ -40,7 +40,7 @@ This will create a file called `hapi-fhir-jpaserver.war` in your `target` direct
Again, browse to the following link to use the server (note that the port 8080 may not be correct depending on how your server is configured).
[http://localhost:8080/hapi-fhir-jpaserver/](http://localhost:8080/hapi-fhir-jpaserver/)
[http://localhost:8080/](http://localhost:8080/)
# Customizing The Web Testpage UI
@@ -56,10 +56,21 @@ Much of this HAPI starter project can be configured using the properties file in
## MySql
To configure the starter app to use MySQL, instead of the default Derby, update the hapi.properties file to have the following:
To configure the starter app to use MySQL, instead of the default Derby:
* datasource.driver=com.mysql.jdbc.Driver
> Add user and database on your mysql server via mysql cli
```
CREATE USER 'hapiDbUser'@'localhost' IDENTIFIED BY 'hapiDbPass';
CREATE DATABASE hapi_dstu3;
GRANT ALL PRIVILEGES ON hapi_dstu3.* to 'hapiDbUser'@'localhost';
FLUSH PRIVILEGES;
```
> Update hapi.properties file to have the following
* datasource.driver=com.mysql.cj.jdbc.Driver
* datasource.url=jdbc:mysql://localhost:3306/hapi_dstu3
* datasource.username=hapiDbUser
* datasource.password=hapiDbPass
* hibernate.dialect=org.hibernate.dialect.MySQL5Dialect
It is important to use MySQL5Dialect when using MySQL version 5+.

43
pom.xml
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@@ -24,7 +24,7 @@
<repository>
<id>oss-snapshots</id>
<snapshots>
<enabled>true</enabled>
<enabled>false</enabled>
</snapshots>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository>
@@ -111,17 +111,6 @@
</dependency>
<!-- Used for CORS support -->
<dependency>
<groupId>org.ebaysf.web</groupId>
<artifactId>cors-filter</artifactId>
<exclusions>
<exclusion>
<artifactId>servlet-api</artifactId>
<groupId>javax.servlet</groupId>
</exclusion>
</exclusions>
</dependency>
<!-- Spring Web is used to deploy the server to a web container. -->
<dependency>
<groupId>org.springframework</groupId>
@@ -207,24 +196,20 @@
<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver.war -->
<finalName>hapi-fhir-jpaserver</finalName>
<!-- The following is not required for the application to build, but allows you to test it by issuing "mvn jetty:run" from the command line. -->
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<version>9.4.8.v20180619</version>
<configuration>
<webApp>
<contextPath>/hapi-fhir-jpaserver</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<!-- The following is not required for the application to build, but allows you to test it by issuing "mvn jetty:run" from the command line. -->
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<version>9.4.8.v20180619</version>
<configuration>
<webApp>
<contextPath>/</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
<!-- Tell Maven which Java source version you want to use -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>

1
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java
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@@ -18,7 +18,6 @@ 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

1
src/main/java/ca/uhn/fhir/jpa/starter/FhirTesterConfig.java
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@@ -43,6 +43,7 @@ public class FhirTesterConfig {
.withFhirVersion(HapiProperties.getFhirVersion())
.withBaseUrl(HapiProperties.getServerAddress())
.withName(HapiProperties.getServerName());
retVal.setRefuseToFetchThirdPartyUrls(HapiProperties.getTesterConfigRefustToFetchThirdPartyUrls());
return retVal;
}

15
src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java
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@@ -40,6 +40,9 @@ public class HapiProperties {
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 TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS = "tester.config.refuse_to_fetch_third_party_urls";
static final String CORS_ENABLED = "cors.enabled";
static final String CORS_ALLOWED_ORIGIN = "cors.allowed_origin";
static final String ALLOW_CONTAINS_SEARCHES = "allow_contains_searches";
static final String ALLOW_OVERRIDE_DEFAULT_SEARCH_PARAMS = "allow_override_default_search_params";
static final String EMAIL_FROM = "email.from";
@@ -253,6 +256,18 @@ public class HapiProperties {
return HapiProperties.getIntegerProperty(TEST_PORT, 0);
}
public static Boolean getTesterConfigRefustToFetchThirdPartyUrls() {
return HapiProperties.getBooleanProperty(TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS, false);
}
public static Boolean getCorsEnabled() {
return HapiProperties.getBooleanProperty(CORS_ENABLED, true);
}
public static String getCorsAllowedOrigin() {
return HapiProperties.getProperty(CORS_ALLOWED_ORIGIN, "*");
}
public static String getServerBase() {
return HapiProperties.getProperty(SERVER_BASE, "/fhir");
}

50
src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java
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@@ -4,7 +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.model.interceptor.executor.InterceptorService;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
@@ -15,19 +15,22 @@ 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.jpa.subscription.SubscriptionInterceptorLoader;
import ca.uhn.fhir.jpa.subscription.module.interceptor.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
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.web.cors.CorsConfiguration;
import org.springframework.context.ApplicationContext;
import javax.servlet.ServletException;
import java.util.Arrays;
import java.util.List;
public class JpaRestfulServer extends RestfulServer {
@@ -45,10 +48,6 @@ public class JpaRestfulServer extends RestfulServer {
*/
ApplicationContext appCtx = (ApplicationContext) getServletContext().getAttribute("org.springframework.web.context.WebApplicationContext.ROOT");
// if (HapiProperties.getSubscriptionWebsocketEnabled()) {
// appCtx.register(WebsocketDispatcherConfig.class);
// }
/*
* ResourceProviders are fetched from the Spring context
*/
@@ -170,22 +169,43 @@ public class JpaRestfulServer extends RestfulServer {
registerProvider(retriggeringProvider);
}
// Define your CORS configuration. This is an example
// showing a typical setup. You should customize this
// to your specific needs
if(HapiProperties.getCorsEnabled()) {
CorsConfiguration config = new CorsConfiguration();
config.addAllowedHeader("x-fhir-starter");
config.addAllowedHeader("Origin");
config.addAllowedHeader("Accept");
config.addAllowedHeader("X-Requested-With");
config.addAllowedHeader("Content-Type");
config.addAllowedOrigin(HapiProperties.getCorsAllowedOrigin());
config.addExposedHeader("Location");
config.addExposedHeader("Content-Location");
config.setAllowedMethods(Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS", "PATCH"));
// Create the interceptor and register it
CorsInterceptor interceptor = new CorsInterceptor(config);
registerInterceptor(interceptor);
}
// 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);
// Loads subscription interceptors (SubscriptionActivatingInterceptor, SubscriptionMatcherInterceptor)
// with activation of scheduled subscription
SubscriptionInterceptorLoader subscriptionInterceptorLoader = appCtx.getBean(SubscriptionInterceptorLoader.class);
subscriptionInterceptorLoader.registerInterceptors();
SubscriptionActivatingInterceptor subscriptionActivatingInterceptor = appCtx.getBean(SubscriptionActivatingInterceptor.class);
interceptorRegistry.registerInterceptor(subscriptionActivatingInterceptor);
SubscriptionMatcherInterceptor subscriptionMatcherInterceptor = appCtx.getBean(SubscriptionMatcherInterceptor.class);
subscriptionMatcherInterceptor.start();
interceptorRegistry.registerInterceptor(subscriptionMatcherInterceptor);
// Subscription debug logging
InterceptorService interceptorService = (InterceptorService) appCtx.getBean("interceptorService");
interceptorService.registerInterceptor(new SubscriptionDebugLogInterceptor());
}
}
}

11
src/main/resources/hapi.properties
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@@ -6,18 +6,12 @@ fhir_version=DSTU3
# This is the address that the FHIR server will report as its own address.
# If this server will be deployed (for example) to an internet accessible
# 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/
server_address=http://localhost:8080/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
@@ -53,6 +47,9 @@ hibernate.cache.use_minimal_puts=false
hibernate.search.default.directory_provider=filesystem
hibernate.search.default.indexBase=target/lucenefiles
hibernate.search.lucene_version=LUCENE_CURRENT
tester.config.refuse_to_fetch_third_party_urls=false
cors.enabled=true
cors.allowed_origin=*
##################################################
# Subscriptions

30
src/main/webapp/WEB-INF/templates/tmpl-head.html Normal file
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@@ -0,0 +1,30 @@
<!DOCTYPE html>
<html lang="en">
<head th:fragment="head">
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="description" content="" />
<meta name="author" content="" />
<link rel="icon" type="image/x-icon" href="img/favicon.ico">
<script src="js/jquery-2.1.0.min.js"></script>
<script src="js/bootstrap.min.js"></script>
<link href="css/bootstrap.min.css" rel="stylesheet" />
<link href="css/tester.css" rel="stylesheet" />
<script type="text/javascript" th:utext="'var conformance = ' + ${jsonEncodedConf} + ';'">
</script>
<script type="text/javascript" th:utext="'var resourceName = \'' + ${resourceName} + '\';'">
</script>
<link href="fa/css/font-awesome.min.css" rel="stylesheet" />
<link href="css/hapi-narrative.css" rel="stylesheet" />
<script type="text/javascript" src="js/moment-with-locales.min.js"></script>
<link href="css/bootstrap-datetimepicker.min.css" rel="stylesheet" />
<script src="js/bootstrap-datetimepicker.min.js"></script>
<link href="css/select2.css" rel="stylesheet"/>
<script src="js/select2.min.js"></script>
<script src="js/RestfulTester.js" type="text/javascript" ></script>
</head>
</html>

60
src/main/webapp/WEB-INF/web.xml
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@@ -31,74 +31,24 @@
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value>
ca.uhn.fhir.jpa.starter.FhirTesterConfig,
ca.uhn.fhir.jpa.starter.FhirTesterConfig
</param-value>
</init-param>
<load-on-startup>2</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>spring</servlet-name>
<url-pattern>/</url-pattern>
</servlet-mapping>
<servlet>
<servlet-name>fhirServlet</servlet-name>
<servlet-class>ca.uhn.fhir.jpa.starter.JpaRestfulServer</servlet-class>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>fhirServlet</servlet-name>
<url-pattern>/fhir/*</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>spring</servlet-name>
<url-pattern>/</url-pattern>
</servlet-mapping>
<!-- This filters provide support for Cross Origin Resource Sharing (CORS) -->
<filter>
<filter-name>CORS Filter</filter-name>
<filter-class>org.ebaysf.web.cors.CORSFilter</filter-class>
<init-param>
<description>A comma separated list of allowed origins. Note: An '*' cannot be used for an allowed origin when using credentials.</description>
<param-name>cors.allowed.origins</param-name>
<param-value>*</param-value>
</init-param>
<init-param>
<description>A comma separated list of HTTP verbs, using which a CORS request can be made.</description>
<param-name>cors.allowed.methods</param-name>
<param-value>GET,POST,PUT,DELETE,OPTIONS</param-value>
</init-param>
<init-param>
<description>A comma separated list of allowed headers when making a non simple CORS request.</description>
<param-name>cors.allowed.headers</param-name>
<param-value>Accept,Access-Control-Request-Headers,Access-Control-Request-Method,Cache-Control,Content-Type,Origin,Prefer,X-FHIR-Starter,X-Requested-With</param-value>
</init-param>
<init-param>
<description>A comma separated list non-standard response headers that will be exposed to XHR2 object.</description>
<param-name>cors.exposed.headers</param-name>
<param-value>Location,Content-Location</param-value>
</init-param>
<init-param>
<description>A flag that suggests if CORS is supported with cookies</description>
<param-name>cors.support.credentials</param-name>
<param-value>true</param-value>
</init-param>
<init-param>
<description>A flag to control logging</description>
<param-name>cors.logging.enabled</param-name>
<param-value>true</param-value>
</init-param>
<init-param>
<description>Indicates how long (in seconds) the results of a preflight request can be cached in a preflight result cache.</description>
<param-name>cors.preflight.maxage</param-name>
<param-value>300</param-value>
</init-param>
</filter>
<filter-mapping>
<filter-name>CORS Filter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
</web-app>

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9
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java
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@@ -15,6 +15,7 @@ import org.junit.Test;
import java.io.File;
import java.io.IOException;
import java.nio.file.Paths;
import static org.junit.Assert.assertEquals;
@@ -57,13 +58,7 @@ public class ExampleServerDstu2IT {
@BeforeClass
public static void beforeClass() throws Exception {
/*
* This runs under maven, and I'm not sure how else to figure out the target directory from code..
*/
String path = ExampleServerDstu2IT.class.getClassLoader().getResource(".keep_hapi-fhir-jpaserver-starter").getPath();
path = new File(path).getParent();
path = new File(path).getParent();
path = new File(path).getParent();
String path = Paths.get("").toAbsolutePath().toString();
ourLog.info("Project base path is: {}", path);

82
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java
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@@ -1,14 +1,27 @@
package ca.uhn.fhir.jpa.starter;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.junit.Assert.assertEquals;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.nio.file.Paths;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
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.util.PortUtil;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.webapp.WebAppContext;
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.Bundle;
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.*;
@@ -32,6 +45,7 @@ public class ExampleServerDstu3IT {
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()));
HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
ourCtx = FhirContext.forDstu3();
ourPort = HapiProperties.getTestPort();
}
@@ -49,6 +63,64 @@ public class ExampleServerDstu3IT {
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();
@@ -56,13 +128,7 @@ public class ExampleServerDstu3IT {
@BeforeClass
public static void beforeClass() throws Exception {
/*
* This runs under maven, and I'm not sure how else to figure out the target directory from code..
*/
String path = ExampleServerDstu3IT.class.getClassLoader().getResource(".keep_hapi-fhir-jpaserver-starter").getPath();
path = new File(path).getParent();
path = new File(path).getParent();
path = new File(path).getParent();
String path = Paths.get("").toAbsolutePath().toString();
ourLog.info("Project base path is: {}", path);

12
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
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@@ -22,9 +22,9 @@ 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.nio.file.Paths;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
@@ -64,7 +64,6 @@ public class ExampleServerR4IT {
assertEquals(methodName, pt2.getName().get(0).getFamily());
}
@Test
public void testWebsocketSubscription() throws Exception {
/*
@@ -123,7 +122,6 @@ public class ExampleServerR4IT {
ourClient.delete().resourceById(mySubscriptionId).execute();
}
@AfterClass
public static void afterClass() throws Exception {
ourServer.stop();
@@ -131,13 +129,7 @@ public class ExampleServerR4IT {
@BeforeClass
public static void beforeClass() throws Exception {
/*
* This runs under maven, and I'm not sure how else to figure out the target directory from code..
*/
String path = ExampleServerR4IT.class.getClassLoader().getResource(".keep_hapi-fhir-jpaserver-starter").getPath();
path = new File(path).getParent();
path = new File(path).getParent();
path = new File(path).getParent();
String path = Paths.get("").toAbsolutePath().toString();
ourLog.info("Project base path is: {}", path);

0
src/test/resources/.keep_hapi-fhir-jpaserver-starter
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