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hapi-fhir
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Merge branch 'master' into issue-2904-Swagger-ui-Doesn't-Work-with-Partitions

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katie_smilecdr 2021-08-23 15:33:09 -04:00
parent 712fdbd802 75ff7557fc
commit 789695621a
222 changed files with 1272 additions and 84783 deletions
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11
example-projects/README.md
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# Unsupported
Most of the projects in this module are no longer supported.
The test in hapi-fhir-jpaserver-cds-example is @Disabledd until Chris Schuler is able to make a change to the pom
this module depends on.
## Supported JPA Example:
The supported HAPI-FHIR JPA example is available in the [hapi-fhir-jpaserver-starter](https://github.com/hapifhir/hapi-fhir-jpaserver-starter)
project within the [hapifhir](https://github.com/hapifhir) GitHub Organization.

82
example-projects/hapi-fhir-base-example-embedded-ws/pom.xml
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<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">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>4.0.0-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>
<packaging>jar</packaging>
<artifactId>hapi-fhir-base-example-embedded-ws</artifactId>
<dependencies>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>com.google.inject</groupId>
<artifactId>guice</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>com.google.inject.extensions</groupId>
<artifactId>guice-servlet</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>com.sun.jersey.contribs</groupId>
<artifactId>jersey-guice</artifactId>
<version>1.19.1</version>
</dependency>
<dependency>
<groupId>org.ebaysf.web</groupId>
<artifactId>cors-filter</artifactId>
<version>1.0.1</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>1.7.21</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jul-to-slf4j</artifactId>
<version>1.7.21</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</build>
</project>

27
example-projects/hapi-fhir-base-example-embedded-ws/src/main/java/embedded/ContextListener.java
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package embedded;
import javax.inject.Singleton;
import org.ebaysf.web.cors.CORSFilter;
import com.google.inject.Guice;
import com.google.inject.Injector;
import com.google.inject.servlet.GuiceServletContextListener;
import com.sun.jersey.guice.JerseyServletModule;
public class ContextListener extends GuiceServletContextListener {
@Override
protected Injector getInjector() {
return Guice.createInjector(new JerseyServletModule() {
@Override
protected void configureServlets() {
bind(CORSFilter.class).in(Singleton.class);
filter("/*").through(CORSFilter.class);
serve("/model/*").with(FhirRestfulServlet.class);
}
});
}
}

38
example-projects/hapi-fhir-base-example-embedded-ws/src/main/java/embedded/FhirRestfulServlet.java
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package embedded;
import java.util.ArrayList;
import java.util.List;
import javax.inject.Singleton;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
@Singleton
public class FhirRestfulServlet extends RestfulServer {
/**
*
*/
private static final long serialVersionUID = -3931111342737918913L;
public FhirRestfulServlet() {
super(FhirContext.forDstu2()); // Support DSTU2
}
/**
* This method is called automatically when the servlet is initializing.
*/
@Override
public void initialize() {
final List<IResourceProvider> providers = new ArrayList<IResourceProvider>();
providers.add(new SomeResourceProvider());
setResourceProviders(providers);
registerInterceptor(new ResponseHighlighterInterceptor());
}
}

32
example-projects/hapi-fhir-base-example-embedded-ws/src/main/java/embedded/ServerStartup.java
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package embedded;
import java.util.EnumSet;
import javax.servlet.DispatcherType;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.DefaultServlet;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.slf4j.bridge.SLF4JBridgeHandler;
import com.google.inject.servlet.GuiceFilter;
public class ServerStartup {
public static void main(final String[] args) throws Exception {
SLF4JBridgeHandler.removeHandlersForRootLogger();
SLF4JBridgeHandler.install();
final Server server = new Server(9090);
final ServletContextHandler sch = new ServletContextHandler(server, "/");
sch.addEventListener(new ContextListener());
sch.addFilter(GuiceFilter.class, "/*", EnumSet.of(DispatcherType.REQUEST));
sch.addServlet(DefaultServlet.class, "/");
server.start();
// Service is now accessible through
// http://localhost:9090/model/Practitioner
}
}

31
example-projects/hapi-fhir-base-example-embedded-ws/src/main/java/embedded/SomeResourceProvider.java
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package embedded;
import java.util.List;
import org.hl7.fhir.instance.model.api.IBaseResource;
import com.google.common.collect.Lists;
import ca.uhn.fhir.model.dstu2.resource.Practitioner;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
public class SomeResourceProvider implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
return Practitioner.class;
}
@Search()
public List<Practitioner> findPractitionersByName(
@RequiredParam(name = Practitioner.SP_NAME) final StringDt theName) {
// throw new UnprocessableEntityException(
// "Please provide more than 4 characters for the name");
return Lists.newArrayList();
}
}

5
example-projects/hapi-fhir-jaxrs-sse/README.md
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This example sets up a FHIR server that can ship out Server-sent events using standard Jersey 2.x components. Start up the server and eg. issue the following curl request 'curl -v -X GET http://localhost:8080/Patient/listen'. The will block curl and once any events are shipped to the server, they will automatically be sent to the curl client.
Changes can be sent to the server on localhost:8080/Patient which accepts any kind of patients that has at least one identifier.
Voila

91
example-projects/hapi-fhir-jaxrs-sse/pom.xml
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<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">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>2.5-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-jaxrs-sse</artifactId>
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
</dependency>
<dependency>
<groupId>org.ebaysf.web</groupId>
<artifactId>cors-filter</artifactId>
<version>1.0.1</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.media</groupId>
<artifactId>jersey-media-sse</artifactId>
<version>${jersey_version}</version>
</dependency>
<dependency>
<groupId>org.glassfish.jersey.containers</groupId>
<artifactId>jersey-container-servlet</artifactId>
<version>${jersey_version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jaxrsserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>1.7.21</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jul-to-slf4j</artifactId>
<version>1.7.21</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.21</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.glassfish.hk2/hk2-locator -->
<dependency>
<groupId>org.glassfish.hk2</groupId>
<artifactId>hk2-locator</artifactId>
<version>2.4.0-b34</version>
</dependency>
<dependency>
<groupId>org.glassfish.hk2</groupId>
<artifactId>guice-bridge</artifactId>
<version>2.4.0-b34</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>30.1.1-jre</version>
</dependency>
<dependency>
<groupId>com.google.inject.extensions</groupId>
<artifactId>guice-servlet</artifactId>
<version>4.1.0</version>
</dependency>
</dependencies>
</project>

129
example-projects/hapi-fhir-jaxrs-sse/src/main/java/embedded/example/JaxRsPatientProvider.java
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package embedded.example;
import java.io.IOException;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import javax.inject.Inject;
import javax.inject.Singleton;
import javax.ws.rs.GET;
import javax.ws.rs.Path;
import javax.ws.rs.Produces;
import javax.ws.rs.core.MediaType;
import org.glassfish.jersey.media.sse.EventOutput;
import org.glassfish.jersey.media.sse.OutboundEvent;
import org.glassfish.jersey.media.sse.SseBroadcaster;
import org.glassfish.jersey.media.sse.SseFeature;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Patient;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jaxrs.server.AbstractJaxRsResourceProvider;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import jersey.repackaged.com.google.common.collect.Maps;
@Singleton
@Path("Patient")
@Produces({ MediaType.APPLICATION_JSON, Constants.CT_FHIR_JSON, Constants.CT_FHIR_XML })
public class JaxRsPatientProvider extends AbstractJaxRsResourceProvider<Patient> {
private final Map<String, Patient> patients = Maps.newConcurrentMap();
private final SseBroadcaster broadcaster = new SseBroadcaster();
@Inject
public JaxRsPatientProvider() {
super(FhirContext.forDstu3(), JaxRsPatientProvider.class);
}
@Search
public List<Patient> search(@RequiredParam(name = Patient.SP_NAME) final StringParam name) {
final List<Patient> result = new LinkedList<Patient>();
for (final Patient patient : patients.values()) {
Patient single = null;
if (name == null
|| patient.getName().get(0).getFamilyElement().getValueNotNull().equals(name.getValueNotNull())) {
single = patient;
}
if (single != null) {
result.add(single);
}
}
return result;
}
@Create
public MethodOutcome create(@ResourceParam final Patient patient, @ConditionalUrlParam final String theConditional)
throws Exception {
storePatient(patient);
final MethodOutcome result = new MethodOutcome().setCreated(true);
result.setResource(patient);
result.setId(new IdType(patient.getId()));
return result;
}
// Conceptual wrapper for storing in a db
private void storePatient(final Patient patient) {
try {
patients.put(patient.getIdentifierFirstRep().getValue(), patient);
// if storing is successful the notify the listeners that listens on
// any patient => patient/*
final String bundleToString = currentPatientsAsJsonString();
broadcaster
.broadcast(new OutboundEvent.Builder().name("patients").data(String.class, bundleToString).build());
} catch (final Exception e) {
e.printStackTrace();
}
}
private String currentPatientsAsJsonString() {
final IParser jsonParser = this.getFhirContext().newJsonParser().setPrettyPrint(true);
final org.hl7.fhir.dstu3.model.Bundle bundle = new org.hl7.fhir.dstu3.model.Bundle();
for (final Patient p : patients.values())
bundle.addEntry(new BundleEntryComponent().setResource(p));
final String bundleToString = jsonParser.encodeResourceToString(bundle);
return bundleToString;
}
@Override
public ETagSupportEnum getETagSupport() {
return ETagSupportEnum.DISABLED;
}
@Override
public Class<Patient> getResourceType() {
return Patient.class;
}
@GET
@Path("listen")
@Produces(SseFeature.SERVER_SENT_EVENTS)
public EventOutput listenToBroadcast() throws IOException {
final EventOutput eventOutput = new EventOutput();
final String bundleToString = currentPatientsAsJsonString();
eventOutput.write(
new OutboundEvent.Builder().name("patients").data(String.class, bundleToString).build());
this.broadcaster.add(eventOutput);
return eventOutput;
}
}

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example-projects/hapi-fhir-jaxrs-sse/src/main/java/embedded/example/jerseyguice/GuiceHk2Helper.java
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package embedded.example.jerseyguice;
import java.net.URL;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.glassfish.hk2.api.ServiceLocator;
import org.glassfish.jersey.server.ResourceConfig;
import org.glassfish.jersey.server.spi.Container;
import org.glassfish.jersey.server.spi.ContainerLifecycleListener;
import org.glassfish.jersey.servlet.ServletContainer;
import org.jvnet.hk2.guice.bridge.api.GuiceBridge;
import org.jvnet.hk2.guice.bridge.api.GuiceIntoHK2Bridge;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.base.Function;
import com.google.common.collect.FluentIterable;
import com.google.inject.Injector;
import com.google.inject.Scopes;
import com.google.inject.servlet.ServletModule;
public abstract class GuiceHk2Helper extends ServletModule {
private static final Logger log = LoggerFactory.getLogger(GuiceHk2Helper.class);
@Override
abstract protected void configureServlets();
public interface RestKeyBindingBuilder {
void packages(String... packages);
void packages(Package... packages);
void packages(Class<?>... clazz);
}
protected RestKeyBindingBuilder rest(final String... urlPatterns) {
return new RestKeyBindingBuilderImpl(Arrays.asList(urlPatterns));
}
private class RestKeyBindingBuilderImpl implements RestKeyBindingBuilder {
List<String> paths;
public RestKeyBindingBuilderImpl(final List<String> paths) {
this.paths = paths;
}
private boolean checkIfPackageExistsAndLog(final String packge) {
boolean exists = false;
final String resourcePath = packge.replace(".", "/");
final URL resource = getClass().getClassLoader().getResource(resourcePath);
if (resource != null) {
exists = true;
log.info("rest(" + paths + ").packages(" + packge + ")");
} else {
log.info("No Beans in '" + packge + "' found. Requests " + paths + " will fail.");
}
return exists;
}
@Override
public void packages(final String... packages) {
final StringBuilder sb = new StringBuilder();
for (final String pkg : packages) {
if (sb.length() > 0) {
sb.append(',');
}
checkIfPackageExistsAndLog(pkg);
sb.append(pkg);
}
final Map<String, String> params = new HashMap<>();
params.put("javax.ws.rs.Application", GuiceResourceConfig.class.getCanonicalName());
if (sb.length() > 0) {
params.put("jersey.config.server.provider.packages", sb.toString());
}
bind(ServletContainer.class).in(Scopes.SINGLETON);
for (final String path : paths) {
serve(path).with(ServletContainer.class, params);
}
}
@Override
public void packages(final Package... packages) {
packages(FluentIterable.from(packages).transform(new Function<Package, String>() {
@Override
public String apply(final Package arg0) {
return arg0.getName();
}
}).toArray(String.class));
}
@Override
public void packages(final Class<?>... clazz) {
packages(FluentIterable.from(clazz).transform(new Function<Class<?>, String>() {
@Override
public String apply(final Class<?> arg0) {
return arg0.getPackage().getName();
}
}).toArray(String.class));
}
}
}
class GuiceResourceConfig extends ResourceConfig {
public GuiceResourceConfig() {
register(new ContainerLifecycleListener() {
@Override
public void onStartup(final Container container) {
final ServletContainer servletContainer = (ServletContainer) container;
final ServiceLocator serviceLocator = container.getApplicationHandler().getServiceLocator();
GuiceBridge.getGuiceBridge().initializeGuiceBridge(serviceLocator);
final GuiceIntoHK2Bridge guiceBridge = serviceLocator.getService(GuiceIntoHK2Bridge.class);
final Injector injector = (Injector) servletContainer.getServletContext()
.getAttribute(Injector.class.getName());
guiceBridge.bridgeGuiceInjector(injector);
}
@Override
public void onReload(final Container container) {
}
@Override
public void onShutdown(final Container container) {
}
});
}
}

73
example-projects/hapi-fhir-jaxrs-sse/src/main/java/embedded/example/jerseyguice/GuiceJersey2ServletContextListener.java
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/*
* Copyright (c) 2016 Aberger Software GmbH. All Rights Reserved.
* http://www.aberger.at
*
* Licensed under the Apache License, Version 2.0 (the "License"); you
* may not use this file except in compliance with the License. You may
* obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
* implied. See the License for the specific language governing
* permissions and limitations under the License.
*/
package embedded.example.jerseyguice;
import java.awt.Desktop;
import java.net.URI;
import java.util.EnumSet;
import java.util.List;
import javax.servlet.DispatcherType;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletContextHandler;
import org.slf4j.bridge.SLF4JBridgeHandler;
import com.google.common.collect.Lists;
import com.google.inject.Guice;
import com.google.inject.Injector;
import com.google.inject.Module;
import com.google.inject.Stage;
import com.google.inject.servlet.GuiceFilter;
import com.google.inject.servlet.GuiceServletContextListener;
import embedded.example.JaxRsPatientProvider;
public class GuiceJersey2ServletContextListener extends GuiceServletContextListener {
@Override
protected Injector getInjector() {
final List<Module> modules = Lists.newArrayList();
modules.add(new GuiceHk2Helper() {
@Override
protected void configureServlets() {
// bind(JaxRsPatientProvider.class).in(Scopes.SINGLETON);
rest("/*").packages(JaxRsPatientProvider.class);
}
});
return Guice.createInjector(Stage.PRODUCTION, modules);
}
public static void main(final String[] args) throws Exception {
SLF4JBridgeHandler.removeHandlersForRootLogger();
SLF4JBridgeHandler.install();
final Server server = new Server(8080);
final ServletContextHandler sch = new ServletContextHandler(server, "/");
sch.addEventListener(new GuiceJersey2ServletContextListener());
sch.addFilter(GuiceFilter.class, "/*", EnumSet.of(DispatcherType.REQUEST));
server.start();
Desktop.getDesktop().browse(new URI("http://localhost:8080/Patient"));
}
}

22
example-projects/hapi-fhir-jaxrs-sse/src/main/webapp/WEB-INF/web.xml
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<?xml version="1.0"?>
<web-app>
<filter>
<filter-name>Guice Filter</filter-name>
<filter-class>com.google.inject.servlet.GuiceFilter</filter-class>
</filter>
<filter-mapping>
<filter-name>Guice Filter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
<listener>
<listener-class>embedded.example.ContextListener</listener-class>
</listener>
<!-- <context-param> <param-name>username</param-name> <param-value>username</param-value>
</context-param> <context-param> <param-name>password</param-name> <param-value>password</param-value>
</context-param> -->
<context-param>
<param-name>serverAddress</param-name>
<param-value>http://fhirtest.uhn.ca/baseDstu2</param-value>
</context-param>
</web-app>

14
example-projects/hapi-fhir-jaxrs-sse/src/test/java/test/WarTester.java
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package test;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.webapp.WebAppContext;
public class WarTester {
public static void main(String[] args) throws Exception {
final Server server = new Server(8080);
server.setHandler(new WebAppContext("target/fhirtester.war", "/"));
server.start();
}
}

128
example-projects/hapi-fhir-jpaserver-cds-example/.gitignore vendored
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/target
/jpaserver_derby_files
*.log
ca.uhn.fhir.jpa.entity.ResourceTable/
# Created by https://www.gitignore.io
### Java ###
*.class
# Mobile Tools for Java (J2ME)
.mtj.tmp/
# Package Files #
*.jar
*.war
*.ear
# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*
### Maven ###
target/
pom.xml.tag
pom.xml.releaseBackup
pom.xml.versionsBackup
pom.xml.next
release.properties
dependency-reduced-pom.xml
buildNumber.properties
### Vim ###
[._]*.s[a-w][a-z]
[._]s[a-w][a-z]
*.un~
Session.vim
.netrwhist
*~
### Intellij ###
# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm
*.iml
## Directory-based project format:
.idea/
# if you remove the above rule, at least ignore the following:
# User-specific stuff:
# .idea/workspace.xml
# .idea/tasks.xml
# .idea/dictionaries
# Sensitive or high-churn files:
# .idea/dataSources.ids
# .idea/dataSources.xml
# .idea/sqlDataSources.xml
# .idea/dynamic.xml
# .idea/uiDesigner.xml
# Gradle:
# .idea/gradle.xml
# .idea/libraries
# Mongo Explorer plugin:
# .idea/mongoSettings.xml
## File-based project format:
*.ipr
*.iws
## Plugin-specific files:
# IntelliJ
/out/
# mpeltonen/sbt-idea plugin
.idea_modules/
# JIRA plugin
atlassian-ide-plugin.xml
# Crashlytics plugin (for Android Studio and IntelliJ)
com_crashlytics_export_strings.xml
crashlytics.properties
crashlytics-build.properties
### Eclipse ###
*.pydevproject
.metadata
.gradle
bin/
tmp/
*.tmp
*.bak
*.swp
*~.nib
local.properties
.loadpath
# Eclipse Core
.project
# External tool builders
.externalToolBuilders/
# Locally stored "Eclipse launch configurations"
*.launch
# CDT-specific
.cproject
# JDT-specific (Eclipse Java Development Tools)
# PDT-specific
.buildpath
# sbteclipse plugin
.target
# TeXlipse plugin
.texlipse

304
example-projects/hapi-fhir-jpaserver-cds-example/pom.xml
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@ -1,304 +0,0 @@
<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">
<modelVersion>4.0.0</modelVersion>
<!--
Note: HAPI projects use the "hapi-fhir" POM as their base to provide easy management.
You do not need to use this in your own projects, so the "parent" tag and it's
contents below may be removed
if you are using this file as a basis for your own project.
-->
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>4.0.0-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-jpaserver-cds-example</artifactId>
<packaging>war</packaging>
<name>HAPI FHIR JPA Clinical Decision Support Server - Example</name>
<repositories>
<repository>
<id>oss-snapshots</id>
<snapshots>
<enabled>true</enabled>
</snapshots>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-api</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-client</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<version>8.0.16</version>
</dependency>
<!-- This dependency includes the core HAPI-FHIR classes -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
</dependency>
<!-- At least one "structures" JAR must also be included -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency includes the JPA server itself, which is packaged separately from the rest of HAPI FHIR -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency is used for the "FHIR Tester" web app overlay -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<type>war</type>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<classifier>classes</classifier>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.opencds.cqf</groupId>
<artifactId>cqf-ruler</artifactId>
<version>0.1.2-SNAPSHOT</version>
</dependency>
<!-- HAPI-FHIR uses Logback for logging support. The logback library is included automatically by Maven as a part of the hapi-fhir-base dependency, but you also need to include a logging library. Logback
is used here, but log4j would also be fine. -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<!-- Needed for JEE/Servlet support -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
<!-- If you are using HAPI narrative generation, you will need to include Thymeleaf as well. Otherwise the following can be omitted. -->
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
</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>
<artifactId>spring-web</artifactId>
</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>
<artifactId>commons-dbcp2</artifactId>
</dependency>
<!-- This example uses Derby embedded database. If you are using another database such as Mysql or Oracle, you may omit the following dependencies and replace them with an appropriate database client
dependency for your database platform. -->
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbynet</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
</dependency>
<!--<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyshared</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbytools</artifactId>
</dependency>-->
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
<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-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>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<exclusions>
<exclusion>
<artifactId>Saxon-HE</artifactId>
<groupId>net.sf.saxon</groupId>
</exclusion>
</exclusions>
</dependency>
<!--
For some reason JavaDoc crashed during site generation unless we have this dependency
-->
<dependency>
<groupId>javax.interceptor</groupId>
<artifactId>javax.interceptor-api</artifactId>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver-example.war -->
<finalName>hapi-fhir-jpaserver-cds</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>
<configuration>
<webApp>
<contextPath>/hapi-fhir-jpaserver-cds</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<!--
The CQF-Ruler project has some OWASP dependency security failures which we don't want
to cause the whole build to fail. TODO: investigate these
-->
<plugin>
<groupId>org.owasp</groupId>
<artifactId>dependency-check-maven</artifactId>
<configuration>
<failBuildOnCVSS>99</failBuildOnCVSS>
<failOnError>false</failOnError>
</configuration>
</plugin>
<!-- The configuration here tells the WAR plugin to include the FHIR Tester overlay. You can omit it if you are not using that feature. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<archive>
<manifestEntries>
<Build-Time>${maven.build.timestamp}</Build-Time>
</manifestEntries>
</archive>
<overlays>
<overlay>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
</overlay>
</overlays>
<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
</configuration>
</plugin>
<!-- This plugin is just a part of the HAPI internal build process, you do not need to incude it in your own projects -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<!-- This is to run the integration tests -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</configuration>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

16
example-projects/hapi-fhir-jpaserver-cds-example/src/main/java/ca/uhn/fhir/jpa/cds/example/CdsHooksServerExample.java
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@ -1,16 +0,0 @@
package ca.uhn.fhir.jpa.cds.example;
import org.opencds.cqf.servlet.CdsServicesServlet;
public class CdsHooksServerExample extends CdsServicesServlet {
// @Override
// protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
// // Change how requests are handled
// }
// @Override
// protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
// // Change discovery response
// }
}

19
example-projects/hapi-fhir-jpaserver-cds-example/src/main/java/ca/uhn/fhir/jpa/cds/example/CdsServerExample.java
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@ -1,19 +0,0 @@
package ca.uhn.fhir.jpa.cds.example;
import org.opencds.cqf.servlet.BaseServlet;
import javax.servlet.ServletException;
public class CdsServerExample extends BaseServlet {
// Default setup - STU3 support only
// Source project location: https://github.com/DBCG/cqf-ruler
@SuppressWarnings("unchecked")
@Override
protected void initialize() throws ServletException {
super.initialize();
// Add additional config and/or resource providers
}
}

67
example-projects/hapi-fhir-jpaserver-cds-example/src/main/webapp/WEB-INF/templates/about.html
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@ -1,67 +0,0 @@
<!DOCTYPE html>
<html lang="en">
<head th:include="tmpl-head :: head">
<title>About This Server</title>
</head>
<body>
<form action="" method="get" id="outerForm">
<div th:replace="tmpl-navbar-top :: top" ></div>
<div class="container-fluid">
<div class="row">
<div th:replace="tmpl-navbar-left :: left" ></div>
<div class="col-sm-9 col-sm-offset-3 col-md-9 col-md-offset-3 main">
<div th:replace="tmpl-banner :: banner"></div>
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">About This Server</h3>
</div>
<div class="panel-body">
<div class="pull-right">
<object data="img/fhirtest-architecture.svg" width="383" height="369" type="image/svg+xml"></object>
</div>
<p>
This server provides a nearly complete implementation of the FHIR Specification
using a 100% open source software stack. It is hosted by University Health Network.
</p>
<p>
The architecture in use here is shown in the image on the right. This server is built
from a number of modules of the
<a href="https://github.com/hapifhir/hapi-fhir/">HAPI FHIR</a>
project, which is a 100% open-source (Apache 2.0 Licensed) Java based
implementation of the FHIR specification.
</p>
<p>
</p>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">Data On This Server</h3>
</div>
<div class="panel-body">
<p>
This server is regularly loaded with a standard set of test data sourced
from UHN's own testing environment. Do not use this server to store any data
that you will need later, as we will be regularly resetting it.
</p>
<p>
This is not a production server and it provides no privacy. Do not store any
confidential data here.
</p>
</div>
</div>
</div>
</div>
</div>
<div th:replace="tmpl-footer :: footer" ></div>
</form>
</body>
</html>

16
example-projects/hapi-fhir-jpaserver-cds-example/src/main/webapp/WEB-INF/templates/tmpl-footer.html
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@ -1,16 +0,0 @@
<!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>

50
example-projects/hapi-fhir-jpaserver-cds-example/src/main/webapp/WEB-INF/templates/tmpl-home-welcome.html
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@ -1,50 +0,0 @@
<!DOCTYPE html>
<html lang="en">
<div th:fragment="banner" class="well">
<th:block th:if="${serverId} == 'home'">
<p>
This is the home for the FHIR test server operated by
<a href="http://uhn.ca">University Health Network</a>. This server
(and the testing application you are currently using to access it)
is entirely built using
<a href="https://github.com/hapifhir/hapi-fhir">HAPI-FHIR</a>,
a 100% open-source Java implementation of the
<a href="http://hl7.org/implement/standards/fhir/">FHIR specification</a>.
</p>
<p>
Here are some things you might wish to try:
</p>
<ul>
<li>
View a
<a href="http://fhirtest.uhn.ca/search?serverId=home&amp;encoding=json&amp;pretty=true&amp;resource=Patient&amp;param.0.type=string&amp;param.0.name=_id&amp;param.0.0=&amp;resource-search-limit=">list of patients</a>
on this server.
</li>
<li>
Construct a
<a href="http://fhirtest.uhn.ca/resource?serverId=home&amp;encoding=json&amp;pretty=true&amp;resource=Patient">search query</a>
on this server.
</li>
<li>
Access a
<a href="http://fhirtest.uhn.ca/home?serverId=furore">different server</a>
(use the <b>Server</b> menu at the top of the page to see a list of public FHIR servers)
</li>
</ul>
</th:block>
<th:block th:if="${serverId} != 'home'">
<p>
You are accessing the public FHIR server
<b th:text="${baseName}"/>. This server is hosted elsewhere on the internet
but is being accessed using the HAPI client implementation.
</p>
</th:block>
<p>
<b class="text-danger"><span class="glyphicon glyphicon-warning-sign"/></b>
<b><span class="text-danger">This is not a production server!</span></b>
Do not store any information here that contains personal health information
or any other confidential information. This server will be regularly purged
and reloaded with fixed test data.
</p>
</div>
</html>

121
example-projects/hapi-fhir-jpaserver-cds-example/src/main/webapp/WEB-INF/web.xml
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@ -1,121 +0,0 @@
<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="3.0"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./xsd/web-app_3_0.xsd" metadata-complete="true">
<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
</param-value>
</context-param>
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>
org.opencds.cqf.config.FhirServerConfigDstu3
</param-value>
</context-param>
<!-- Servlets -->
<servlet>
<servlet-name>cdsServicesServlet</servlet-name>
<servlet-class>ca.uhn.fhir.jpa.cds.example.CdsHooksServerExample</servlet-class>
<load-on-startup>3</load-on-startup>
</servlet>
<servlet>
<servlet-name>spring</servlet-name>
<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
<init-param>
<param-name>contextClass</param-name>
<param-value>org.springframework.web.context.support.AnnotationConfigWebApplicationContext</param-value>
</init-param>
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value>org.opencds.cqf.config.FhirTesterConfigDstu3</param-value>
</init-param>
<load-on-startup>2</load-on-startup>
</servlet>
<servlet>
<servlet-name>cdsServerExample</servlet-name>
<servlet-class>ca.uhn.fhir.jpa.cds.example.CdsServerExample</servlet-class>
<init-param>
<param-name>ImplementationDescription</param-name>
<param-value>FHIR CQF Ruler-of-All-Knowledge JPA Server</param-value>
</init-param>
<init-param>
<param-name>FhirVersion</param-name>
<param-value>DSTU3</param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>cdsServerExample</servlet-name>
<url-pattern>/baseDstu3/*</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>spring</servlet-name>
<url-pattern>/tester/*</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>cdsServicesServlet</servlet-name>
<url-pattern>/cds-services</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>cdsServicesServlet</servlet-name>
<url-pattern>/cds-services/*</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>X-FHIR-Starter,Origin,Accept,Authorization,X-Requested-With,Content-Type,Access-Control-Request-Method,Access-Control-Request-Headers</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>

2419
example-projects/hapi-fhir-jpaserver-cds-example/src/main/webapp/WEB-INF/xsd/javaee_6.xsd
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example-projects/hapi-fhir-jpaserver-cds-example/src/main/webapp/WEB-INF/xsd/jsp_2_2.xsd
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<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema xmlns="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://java.sun.com/xml/ns/javaee"
xmlns:javaee="http://java.sun.com/xml/ns/javaee"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified"
attributeFormDefault="unqualified"
version="2.2">
<xsd:annotation>
<xsd:documentation>
DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
Copyright 2003-2009 Sun Microsystems, Inc. All rights reserved.
The contents of this file are subject to the terms of either the
GNU General Public License Version 2 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with
the License. You can obtain a copy of the License at
https://glassfish.dev.java.net/public/CDDL+GPL.html or
glassfish/bootstrap/legal/LICENSE.txt. See the License for the
specific language governing permissions and limitations under the
License.
When distributing the software, include this License Header
Notice in each file and include the License file at
glassfish/bootstrap/legal/LICENSE.txt. Sun designates this
particular file as subject to the "Classpath" exception as
provided by Sun in the GPL Version 2 section of the License file
that accompanied this code. If applicable, add the following
below the License Header, with the fields enclosed by brackets []
replaced by your own identifying information:
"Portions Copyrighted [year] [name of copyright owner]"
Contributor(s):
If you wish your version of this file to be governed by only the
CDDL or only the GPL Version 2, indicate your decision by adding
"[Contributor] elects to include this software in this
distribution under the [CDDL or GPL Version 2] license." If you
don't indicate a single choice of license, a recipient has the
option to distribute your version of this file under either the
CDDL, the GPL Version 2 or to extend the choice of license to its
licensees as provided above. However, if you add GPL Version 2
code and therefore, elected the GPL Version 2 license, then the
option applies only if the new code is made subject to such
option by the copyright holder.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
This is the XML Schema for the JSP 2.2 deployment descriptor
types. The JSP 2.2 schema contains all the special
structures and datatypes that are necessary to use JSP files
from a web application.
The contents of this schema is used by the web-common_3_0.xsd
file to define JSP specific content.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
The following conventions apply to all Java EE
deployment descriptor elements unless indicated otherwise.
- In elements that specify a pathname to a file within the
same JAR file, relative filenames (i.e., those not
starting with "/") are considered relative to the root of
the JAR file's namespace. Absolute filenames (i.e., those
starting with "/") also specify names in the root of the
JAR file's namespace. In general, relative names are
preferred. The exception is .war files where absolute
names are preferred for consistency with the Servlet API.
</xsd:documentation>
</xsd:annotation>
<xsd:include schemaLocation="javaee_6.xsd"/>
<!-- **************************************************** -->
<xsd:complexType name="jsp-configType">
<xsd:annotation>
<xsd:documentation>
The jsp-configType is used to provide global configuration
information for the JSP files in a web application. It has
two subelements, taglib and jsp-property-group.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="taglib"
type="javaee:taglibType"
minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element name="jsp-property-group"
type="javaee:jsp-property-groupType"
minOccurs="0"
maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="jsp-fileType">
<xsd:annotation>
<xsd:documentation>
The jsp-file element contains the full path to a JSP file
within the web application beginning with a `/'.
</xsd:documentation>
</xsd:annotation>
<xsd:simpleContent>
<xsd:restriction base="javaee:pathType"/>
</xsd:simpleContent>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="jsp-property-groupType">
<xsd:annotation>
<xsd:documentation>
The jsp-property-groupType is used to group a number of
files so they can be given global property information.
All files so described are deemed to be JSP files. The
following additional properties can be described:
- Control whether EL is ignored.
- Control whether scripting elements are invalid.
- Indicate pageEncoding information.
- Indicate that a resource is a JSP document (XML).
- Prelude and Coda automatic includes.
- Control whether the character sequence #{ is allowed
when used as a String literal.
- Control whether template text containing only
whitespaces must be removed from the response output.
- Indicate the default contentType information.
- Indicate the default buffering model for JspWriter
- Control whether error should be raised for the use of
undeclared namespaces in a JSP page.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:group ref="javaee:descriptionGroup"/>
<xsd:element name="url-pattern"
type="javaee:url-patternType"
maxOccurs="unbounded"/>
<xsd:element name="el-ignored"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Can be used to easily set the isELIgnored
property of a group of JSP pages. By default, the
EL evaluation is enabled for Web Applications using
a Servlet 2.4 or greater web.xml, and disabled
otherwise.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="page-encoding"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of page-encoding are those of the
pageEncoding page directive. It is a
translation-time error to name different encodings
in the pageEncoding attribute of the page directive
of a JSP page and in a JSP configuration element
matching the page. It is also a translation-time
error to name different encodings in the prolog
or text declaration of a document in XML syntax and
in a JSP configuration element matching the document.
It is legal to name the same encoding through
mulitple mechanisms.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="scripting-invalid"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Can be used to easily disable scripting in a
group of JSP pages. By default, scripting is
enabled.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="is-xml"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
If true, denotes that the group of resources
that match the URL pattern are JSP documents,
and thus must be interpreted as XML documents.
If false, the resources are assumed to not
be JSP documents, unless there is another
property group that indicates otherwise.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="include-prelude"
type="javaee:pathType"
minOccurs="0"
maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>
The include-prelude element is a context-relative
path that must correspond to an element in the
Web Application. When the element is present,
the given path will be automatically included (as
in an include directive) at the beginning of each
JSP page in this jsp-property-group.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="include-coda"
type="javaee:pathType"
minOccurs="0"
maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>
The include-coda element is a context-relative
path that must correspond to an element in the
Web Application. When the element is present,
the given path will be automatically included (as
in an include directive) at the end of each
JSP page in this jsp-property-group.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="deferred-syntax-allowed-as-literal"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The character sequence #{ is reserved for EL expressions.
Consequently, a translation error occurs if the #{
character sequence is used as a String literal, unless
this element is enabled (true). Disabled (false) by
default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="trim-directive-whitespaces"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Indicates that template text containing only whitespaces
must be removed from the response output. It has no
effect on JSP documents (XML syntax). Disabled (false)
by default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="default-content-type"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of default-content-type are those of the
contentType page directive. It specifies the default
response contentType if the page directive does not include
a contentType attribute.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="buffer"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of buffer are those of the
buffer page directive. It specifies if buffering should be
used for the output to response, and if so, the size of the
buffer to use.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="error-on-undeclared-namespace"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The default behavior when a tag with unknown namespace is used
in a JSP page (regular syntax) is to silently ignore it. If
set to true, then an error must be raised during the translation
time when an undeclared tag is used in a JSP page. Disabled
(false) by default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="taglibType">
<xsd:annotation>
<xsd:documentation>
The taglibType defines the syntax for declaring in
the deployment descriptor that a tag library is
available to the application. This can be done
to override implicit map entries from TLD files and
from the container.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="taglib-uri"
type="javaee:string">
<xsd:annotation>
<xsd:documentation>
A taglib-uri element describes a URI identifying a
tag library used in the web application. The body
of the taglib-uri element may be either an
absolute URI specification, or a relative URI.
There should be no entries in web.xml with the
same taglib-uri value.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="taglib-location"
type="javaee:pathType">
<xsd:annotation>
<xsd:documentation>
the taglib-location element contains the location
(as a resource relative to the root of the web
application) where to find the Tag Library
Description file for the tag library.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
</xsd:schema>

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<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema xmlns="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://java.sun.com/xml/ns/javaee"
xmlns:javaee="http://java.sun.com/xml/ns/javaee"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified"
attributeFormDefault="unqualified"
version="3.0">
<xsd:annotation>
<xsd:documentation>
DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
Copyright 2003-2009 Sun Microsystems, Inc. All rights reserved.
The contents of this file are subject to the terms of either the
GNU General Public License Version 2 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with
the License. You can obtain a copy of the License at
https://glassfish.dev.java.net/public/CDDL+GPL.html or
glassfish/bootstrap/legal/LICENSE.txt. See the License for the
specific language governing permissions and limitations under the
License.
When distributing the software, include this License Header
Notice in each file and include the License file at
glassfish/bootstrap/legal/LICENSE.txt. Sun designates this
particular file as subject to the "Classpath" exception as
provided by Sun in the GPL Version 2 section of the License file
that accompanied this code. If applicable, add the following
below the License Header, with the fields enclosed by brackets []
replaced by your own identifying information:
"Portions Copyrighted [year] [name of copyright owner]"
Contributor(s):
If you wish your version of this file to be governed by only the
CDDL or only the GPL Version 2, indicate your decision by adding
"[Contributor] elects to include this software in this
distribution under the [CDDL or GPL Version 2] license." If you
don't indicate a single choice of license, a recipient has the
option to distribute your version of this file under either the
CDDL, the GPL Version 2 or to extend the choice of license to its
licensees as provided above. However, if you add GPL Version 2
code and therefore, elected the GPL Version 2 license, then the
option applies only if the new code is made subject to such
option by the copyright holder.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
<![CDATA[[
This is the XML Schema for the Servlet 3.0 deployment descriptor.
The deployment descriptor must be named "WEB-INF/web.xml" in the
web application's war file. All Servlet deployment descriptors
must indicate the web application schema by using the Java EE
namespace:
http://java.sun.com/xml/ns/javaee
and by indicating the version of the schema by
using the version element as shown below:
<web-app xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="..."
version="3.0">
...
</web-app>
The instance documents may indicate the published version of
the schema using the xsi:schemaLocation attribute for Java EE
namespace with the following location:
http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd
]]>
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
The following conventions apply to all Java EE
deployment descriptor elements unless indicated otherwise.
- In elements that specify a pathname to a file within the
same JAR file, relative filenames (i.e., those not
starting with "/") are considered relative to the root of
the JAR file's namespace. Absolute filenames (i.e., those
starting with "/") also specify names in the root of the
JAR file's namespace. In general, relative names are
preferred. The exception is .war files where absolute
names are preferred for consistency with the Servlet API.
</xsd:documentation>
</xsd:annotation>
<xsd:include schemaLocation="web-common_3_0.xsd"/>
<!-- **************************************************** -->
<xsd:element name="web-app"
type="javaee:web-appType">
<xsd:annotation>
<xsd:documentation>
The web-app element is the root of the deployment
descriptor for a web application. Note that the sub-elements
of this element can be in the arbitrary order. Because of
that, the multiplicity of the elements of distributable,
session-config, welcome-file-list, jsp-config, login-config,
and locale-encoding-mapping-list was changed from "?" to "*"
in this schema. However, the deployment descriptor instance
file must not contain multiple elements of session-config,
jsp-config, and login-config. When there are multiple elements of
welcome-file-list or locale-encoding-mapping-list, the container
must concatenate the element contents. The multiple occurence
of the element distributable is redundant and the container
treats that case exactly in the same way when there is only
one distributable.
</xsd:documentation>
</xsd:annotation>
<xsd:unique name="web-common-servlet-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The servlet element contains the name of a servlet.
The name must be unique within the web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:servlet"/>
<xsd:field xpath="javaee:servlet-name"/>
</xsd:unique>
<xsd:unique name="web-common-filter-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The filter element contains the name of a filter.
The name must be unique within the web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:filter"/>
<xsd:field xpath="javaee:filter-name"/>
</xsd:unique>
<xsd:unique name="web-common-ejb-local-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The ejb-local-ref-name element contains the name of an EJB
reference. The EJB reference is an entry in the web
application's environment and is relative to the
java:comp/env context. The name must be unique within
the web application.
It is recommended that name is prefixed with "ejb/".
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:ejb-local-ref"/>
<xsd:field xpath="javaee:ejb-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-ejb-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The ejb-ref-name element contains the name of an EJB
reference. The EJB reference is an entry in the web
application's environment and is relative to the
java:comp/env context. The name must be unique within
the web application.
It is recommended that name is prefixed with "ejb/".
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:ejb-ref"/>
<xsd:field xpath="javaee:ejb-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-resource-env-ref-uniqueness">
<xsd:annotation>
<xsd:documentation>
The resource-env-ref-name element specifies the name of
a resource environment reference; its value is the
environment entry name used in the web application code.
The name is a JNDI name relative to the java:comp/env
context and must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:resource-env-ref"/>
<xsd:field xpath="javaee:resource-env-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-message-destination-ref-uniqueness">
<xsd:annotation>
<xsd:documentation>
The message-destination-ref-name element specifies the name of
a message destination reference; its value is the
environment entry name used in the web application code.
The name is a JNDI name relative to the java:comp/env
context and must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:message-destination-ref"/>
<xsd:field xpath="javaee:message-destination-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-res-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The res-ref-name element specifies the name of a
resource manager connection factory reference. The name
is a JNDI name relative to the java:comp/env context.
The name must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:resource-ref"/>
<xsd:field xpath="javaee:res-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-env-entry-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The env-entry-name element contains the name of a web
application's environment entry. The name is a JNDI
name relative to the java:comp/env context. The name
must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:env-entry"/>
<xsd:field xpath="javaee:env-entry-name"/>
</xsd:unique>
<xsd:key name="web-common-role-name-key">
<xsd:annotation>
<xsd:documentation>
A role-name-key is specified to allow the references
from the security-role-refs.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:security-role"/>
<xsd:field xpath="javaee:role-name"/>
</xsd:key>
<xsd:keyref name="web-common-role-name-references"
refer="javaee:web-common-role-name-key">
<xsd:annotation>
<xsd:documentation>
The keyref indicates the references from
security-role-ref to a specified role-name.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:servlet/javaee:security-role-ref"/>
<xsd:field xpath="javaee:role-link"/>
</xsd:keyref>
</xsd:element>
</xsd:schema>

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<?xml version='1.0'?>
<?xml-stylesheet href="../2008/09/xsd.xsl" type="text/xsl"?>
<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns ="http://www.w3.org/1999/xhtml"
xml:lang="en">
<xs:annotation>
<xs:documentation>
<div>
<h1>About the XML namespace</h1>
<div class="bodytext">
<p>
This schema document describes the XML namespace, in a form
suitable for import by other schema documents.
</p>
<p>
See <a href="http://www.w3.org/XML/1998/namespace.html">
http://www.w3.org/XML/1998/namespace.html</a> and
<a href="http://www.w3.org/TR/REC-xml">
http://www.w3.org/TR/REC-xml</a> for information
about this namespace.
</p>
<p>
Note that local names in this namespace are intended to be
defined only by the World Wide Web Consortium or its subgroups.
The names currently defined in this namespace are listed below.
They should not be used with conflicting semantics by any Working
Group, specification, or document instance.
</p>
<p>
See further below in this document for more information about <a
href="#usage">how to refer to this schema document from your own
XSD schema documents</a> and about <a href="#nsversioning">the
namespace-versioning policy governing this schema document</a>.
</p>
</div>
</div>
</xs:documentation>
</xs:annotation>
<xs:attribute name="lang">
<xs:annotation>
<xs:documentation>
<div>
<h3>lang (as an attribute name)</h3>
<p>
denotes an attribute whose value
is a language code for the natural language of the content of
any element; its value is inherited. This name is reserved
by virtue of its definition in the XML specification.</p>
</div>
<div>
<h4>Notes</h4>
<p>
Attempting to install the relevant ISO 2- and 3-letter
codes as the enumerated possible values is probably never
going to be a realistic possibility.
</p>
<p>
See BCP 47 at <a href="http://www.rfc-editor.org/rfc/bcp/bcp47.txt">
http://www.rfc-editor.org/rfc/bcp/bcp47.txt</a>
and the IANA language subtag registry at
<a href="http://www.iana.org/assignments/language-subtag-registry">
http://www.iana.org/assignments/language-subtag-registry</a>
for further information.
</p>
<p>
The union allows for the 'un-declaration' of xml:lang with
the empty string.
</p>
</div>
</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:union memberTypes="xs:language">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value=""/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="space">
<xs:annotation>
<xs:documentation>
<div>
<h3>space (as an attribute name)</h3>
<p>
denotes an attribute whose
value is a keyword indicating what whitespace processing
discipline is intended for the content of the element; its
value is inherited. This name is reserved by virtue of its
definition in the XML specification.</p>
</div>
</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:NCName">
<xs:enumeration value="default"/>
<xs:enumeration value="preserve"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="base" type="xs:anyURI"> <xs:annotation>
<xs:documentation>
<div>
<h3>base (as an attribute name)</h3>
<p>
denotes an attribute whose value
provides a URI to be used as the base for interpreting any
relative URIs in the scope of the element on which it
appears; its value is inherited. This name is reserved
by virtue of its definition in the XML Base specification.</p>
<p>
See <a
href="http://www.w3.org/TR/xmlbase/">http://www.w3.org/TR/xmlbase/</a>
for information about this attribute.
</p>
</div>
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="id" type="xs:ID">
<xs:annotation>
<xs:documentation>
<div>
<h3>id (as an attribute name)</h3>
<p>
denotes an attribute whose value
should be interpreted as if declared to be of type ID.
This name is reserved by virtue of its definition in the
xml:id specification.</p>
<p>
See <a
href="http://www.w3.org/TR/xml-id/">http://www.w3.org/TR/xml-id/</a>
for information about this attribute.
</p>
</div>
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attributeGroup name="specialAttrs">
<xs:attribute ref="xml:base"/>
<xs:attribute ref="xml:lang"/>
<xs:attribute ref="xml:space"/>
<xs:attribute ref="xml:id"/>
</xs:attributeGroup>
<xs:annotation>
<xs:documentation>
<div>
<h3>Father (in any context at all)</h3>
<div class="bodytext">
<p>
denotes Jon Bosak, the chair of
the original XML Working Group. This name is reserved by
the following decision of the W3C XML Plenary and
XML Coordination groups:
</p>
<blockquote>
<p>
In appreciation for his vision, leadership and
dedication the W3C XML Plenary on this 10th day of
February, 2000, reserves for Jon Bosak in perpetuity
the XML name "xml:Father".
</p>
</blockquote>
</div>
</div>
</xs:documentation>
</xs:annotation>
<xs:annotation>
<xs:documentation>
<div xml:id="usage" id="usage">
<h2><a name="usage">About this schema document</a></h2>
<div class="bodytext">
<p>
This schema defines attributes and an attribute group suitable
for use by schemas wishing to allow <code>xml:base</code>,
<code>xml:lang</code>, <code>xml:space</code> or
<code>xml:id</code> attributes on elements they define.
</p>
<p>
To enable this, such a schema must import this schema for
the XML namespace, e.g. as follows:
</p>
<pre>
&lt;schema . . .>
. . .
&lt;import namespace="http://www.w3.org/XML/1998/namespace"
schemaLocation="http://www.w3.org/2001/xml.xsd"/>
</pre>
<p>
or
</p>
<pre>
&lt;import namespace="http://www.w3.org/XML/1998/namespace"
schemaLocation="http://www.w3.org/2009/01/xml.xsd"/>
</pre>
<p>
Subsequently, qualified reference to any of the attributes or the
group defined below will have the desired effect, e.g.
</p>
<pre>
&lt;type . . .>
. . .
&lt;attributeGroup ref="xml:specialAttrs"/>
</pre>
<p>
will define a type which will schema-validate an instance element
with any of those attributes.
</p>
</div>
</div>
</xs:documentation>
</xs:annotation>
<xs:annotation>
<xs:documentation>
<div id="nsversioning" xml:id="nsversioning">
<h2><a name="nsversioning">Versioning policy for this schema document</a></h2>
<div class="bodytext">
<p>
In keeping with the XML Schema WG's standard versioning
policy, this schema document will persist at
<a href="http://www.w3.org/2009/01/xml.xsd">
http://www.w3.org/2009/01/xml.xsd</a>.
</p>
<p>
At the date of issue it can also be found at
<a href="http://www.w3.org/2001/xml.xsd">
http://www.w3.org/2001/xml.xsd</a>.
</p>
<p>
The schema document at that URI may however change in the future,
in order to remain compatible with the latest version of XML
Schema itself, or with the XML namespace itself. In other words,
if the XML Schema or XML namespaces change, the version of this
document at <a href="http://www.w3.org/2001/xml.xsd">
http://www.w3.org/2001/xml.xsd
</a>
will change accordingly; the version at
<a href="http://www.w3.org/2009/01/xml.xsd">
http://www.w3.org/2009/01/xml.xsd
</a>
will not change.
</p>
<p>
Previous dated (and unchanging) versions of this schema
document are at:
</p>
<ul>
<li><a href="http://www.w3.org/2009/01/xml.xsd">
http://www.w3.org/2009/01/xml.xsd</a></li>
<li><a href="http://www.w3.org/2007/08/xml.xsd">
http://www.w3.org/2007/08/xml.xsd</a></li>
<li><a href="http://www.w3.org/2004/10/xml.xsd">
http://www.w3.org/2004/10/xml.xsd</a></li>
<li><a href="http://www.w3.org/2001/03/xml.xsd">
http://www.w3.org/2001/03/xml.xsd</a></li>
</ul>
</div>
</div>
</xs:documentation>
</xs:annotation>
</xs:schema>

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package ca.uhn.fhir.jpa.cds.example;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.primitive.IdDt;
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.rest.server.IResourceProvider;
import ca.uhn.fhir.test.utilities.JettyUtil;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.webapp.WebAppContext;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.jupiter.api.*; import static org.hamcrest.MatcherAssert.assertThat;
import java.io.*;
import java.net.HttpURLConnection;
import java.net.URL;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.List;
import java.util.Scanner;
// TODO Remove @Disabled once Chris Schuler has fixed the external jar this project depends on
@Disabled
public class CdsExampleTests {
private static IGenericClient ourClient;
private static FhirContext ourCtx = FhirContext.forDstu3();
protected static int ourPort;
private static Server ourServer;
private static String ourServerBase;
private static Collection<IResourceProvider> providers;
@BeforeAll
public static void beforeClass() throws Exception {
// Configure and spin up server
String path = Paths.get("").toAbsolutePath().toString();
ourServer = new Server(0);
WebAppContext webAppContext = new WebAppContext();
webAppContext.setContextPath("/hapi-fhir-jpaserver-cds");
webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-cds");
webAppContext.setParentLoaderPriority(true);
ourServer.setHandler(webAppContext);
JettyUtil.startServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver-cds/baseDstu3";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
// Load terminology for measure tests (HEDIS measures)
putResource("measure-terminology-bundle.json", "");
// load test data and conversion library for $apply operation tests
putResource("general-practitioner.json", "Practitioner-12208");
putResource("general-patient.json", "Patient-12214");
putResource("general-fhirhelpers-3.json", "FHIRHelpers");
}
@AfterAll
public static void afterClass() throws Exception {
JettyUtil.closeServer(ourServer);
}
private static void putResource(String resourceFileName, String id) {
InputStream is = CdsExampleTests.class.getResourceAsStream(resourceFileName);
Scanner scanner = new Scanner(is).useDelimiter("\\A");
String json = scanner.hasNext() ? scanner.next() : "";
boolean isJson = resourceFileName.endsWith("json");
IBaseResource resource = isJson ? ourCtx.newJsonParser().parseResource(json) : ourCtx.newXmlParser().parseResource(json);
if (resource instanceof Bundle) {
ourClient.transaction().withBundle((Bundle) resource).execute();
}
else {
ourClient.update().resource(resource).withId(id).execute();
}
}
/*
*
* Testing Individual Measure
* This test patient satisfies all the group population criteria for this measure.
*
* */
@Test
public void PatientMeasureTest() {
// load measure specific test data
putResource("patient-measure-test-bundle.json", "");
Parameters inParams = new Parameters();
inParams.addParameter().setName("patient").setValue(new StringType("Patient/Patient-6529"));
inParams.addParameter().setName("periodStart").setValue(new DateType("2003-01-01"));
inParams.addParameter().setName("periodEnd").setValue(new DateType("2003-12-31"));
Parameters outParams = ourClient
.operation()
.onInstance(new IdDt("Measure", "measure-asf"))
.named("$evaluate-measure")
.withParameters(inParams)
.useHttpGet()
.execute();
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
Assert.assertTrue(!response.isEmpty());
Parameters.ParametersParameterComponent component = response.get(0);
Assert.assertTrue(component.getResource() instanceof MeasureReport);
MeasureReport report = (MeasureReport) component.getResource();
for (MeasureReport.MeasureReportGroupComponent group : report.getGroup()) {
for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
Assert.assertTrue(population.getCount() > 0);
}
}
}
/*
*
* Testing Patient List Measure
* This test is only testing for valid initial population membership.
* There are 2 patients that reference Practitioner-2520 as their general practitioner.
* However, only one meets the initial population criteria for the measure.
*
* */
@Test
public void PatientListMeasureTest() {
// load measure specific test data
putResource("patient-list-measure-test-bundle.json", "");
Parameters inParams = new Parameters();
inParams.addParameter().setName("reportType").setValue(new StringType("patient-list"));
inParams.addParameter().setName("practitioner").setValue(new StringType("Practitioner/Practitioner-2520"));
inParams.addParameter().setName("periodStart").setValue(new DateType("1997-01-01"));
inParams.addParameter().setName("periodEnd").setValue(new DateType("1997-12-31"));
Parameters outParams = ourClient
.operation()
.onInstance(new IdDt("Measure", "measure-ccs"))
.named("$evaluate-measure")
.withParameters(inParams)
.useHttpGet()
.execute();
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
Assert.assertTrue(!response.isEmpty());
Parameters.ParametersParameterComponent component = response.get(0);
Assert.assertTrue(component.getResource() instanceof MeasureReport);
MeasureReport report = (MeasureReport) component.getResource();
for (MeasureReport.MeasureReportGroupComponent group : report.getGroup()) {
for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
if (population.getCode().getCodingFirstRep().getCode().equals("initial-population")) {
Assert.assertTrue(population.getCount() == 1);
}
}
}
}
/*
*
* Testing Population (or Summary) Measure
* This tests a population of 100 patients. 10 patients satisfy the initial population criteria.
* However, only 2 meet the numerator criteria.
*
* */
@Test
public void PopulationMeasureTest() {
// load measure specific test data
putResource("population-measure-network-bundle.json", "");
putResource("population-measure-patients-bundle.json", "");
putResource("population-measure-test-bundle.json", "");
Parameters inParams = new Parameters();
inParams.addParameter().setName("reportType").setValue(new StringType("population"));
inParams.addParameter().setName("periodStart").setValue(new DateType("1997-01-01"));
inParams.addParameter().setName("periodEnd").setValue(new DateType("1997-12-31"));
Parameters outParams = ourClient
.operation()
.onInstance(new IdDt("Measure", "measure-bcs"))
.named("$evaluate-measure")
.withParameters(inParams)
.useHttpGet()
.execute();
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
Assert.assertTrue(!response.isEmpty());
Parameters.ParametersParameterComponent component = response.get(0);
Assert.assertTrue(component.getResource() instanceof MeasureReport);
MeasureReport report = (MeasureReport) component.getResource();
Assert.assertTrue(report.getEvaluatedResources() != null);
for (MeasureReport.MeasureReportGroupComponent group : report.getGroup()) {
for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
Assert.assertTrue(population.getCount() > 0);
}
}
}
/*
*
* Testing Patient View CDS Hook
* This tests whether a patient has had appropriate labs/orders for Breast Cancer detection.
* If not, a suggestion will be returned.
*
* */
@Test
public void PatientViewCdsHooksTest() throws IOException {
// load terminology and test data specific to hook
putResource("cds-codesystems.json", "");
putResource("cds-valuesets.json", "");
putResource("cds-bcs-bundle.json", "");
// Get the CDS Hooks request
InputStream is = this.getClass().getResourceAsStream("cds-bcs-request.json");
Scanner scanner = new Scanner(is).useDelimiter("\\A");
String cdsHooksRequest = scanner.hasNext() ? scanner.next() : "";
cdsHooksRequest = cdsHooksRequest.replace("XXXXX", ourServerBase);
byte[] data = cdsHooksRequest.getBytes("UTF-8");
URL url = new URL("http://localhost:" + ourPort + "/hapi-fhir-jpaserver-cds/cds-services/bcs-decision-support");
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestMethod("POST");
conn.setRequestProperty("Content-Type", "application/json");
conn.setRequestProperty("Content-Length", String.valueOf(data.length));
conn.setDoOutput(true);
conn.getOutputStream().write(data);
StringBuilder response = new StringBuilder();
try(Reader in = new BufferedReader(new InputStreamReader(conn.getInputStream(), "UTF-8")))
{
for (int i; (i = in.read()) >= 0;) {
response.append((char) i);
}
}
String expected = "{\n" +
" \"cards\": [\n" +
" {\n" +
" \"summary\": \"A Mammogram procedure for the patient is recommended\",\n" +
" \"indicator\": \"warning\",\n" +
" \"detail\": \"The patient has not had a Mammogram procedure in the last 39 months\",\n" +
" \"source\": {},\n" +
" \"suggestions\": [\n" +
" {\n" +
" \"label\": \"Mammogram request\",\n" +
" \"actions\": [\n" +
" {\n" +
" \"type\": \"create\",\n" +
" \"description\": \"The patient has not had a Mammogram procedure in the last 39 months\",\n" +
" \"resource\": {\n" +
" \"resourceType\": \"ProcedureRequest\",\n" +
" \"status\": \"draft\",\n" +
" \"intent\": \"order\",\n" +
" \"code\": {\n" +
" \"coding\": [\n" +
" {\n" +
" \"system\": \"http://www.ama-assn.org/go/cpt\",\n" +
" \"code\": \"77056\",\n" +
" \"display\": \"Mammography; bilateral\"\n" +
" }\n" +
" ]\n" +
" },\n" +
" \"subject\": {\n" +
" \"reference\": \"Patient/Patient-6535\"\n" +
" }\n" +
" }\n" +
" }\n" +
" ]\n" +
" }\n" +
" ]\n" +
" }\n" +
" ]\n" +
"}\n";
String withoutID = response.toString().replaceAll("\"id\":.*\\s", "");
Assert.assertTrue(
withoutID.replaceAll("\\s+", "")
.equals(expected.replaceAll("\\s+", ""))
);
}
/*
*
* Testing $apply operation for a PlanDefinition resource
* This test applies a PlanDefinition and returns a CarePlan with a dynamic property populated.
*
* */
@Test
public void PlanDefinitionApplyTest() throws ClassNotFoundException {
putResource("plandefinition-apply-library.json", "plandefinitionApplyTest");
putResource("plandefinition-apply.json", "apply-example");
Parameters inParams = new Parameters();
inParams.addParameter().setName("patient").setValue(new StringType("Patient-12214"));
Parameters outParams = ourClient
.operation()
.onInstance(new IdDt("PlanDefinition", "apply-example"))
.named("$apply")
.withParameters(inParams)
.useHttpGet()
.execute();
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
Assert.assertTrue(!response.isEmpty());
Resource resource = response.get(0).getResource();
Assert.assertTrue(resource instanceof CarePlan);
CarePlan carePlan = (CarePlan) resource;
Assert.assertTrue(carePlan.getTitle().equals("This is a dynamic definition!"));
}
/*
*
* Testing $apply operation for an ActivityDefinition resource
* This test applies an ActivityDefinition and returns a ProcedureRequest with a dynamic property populated.
*
* */
@Test
public void ActivityDefinitionApplyTest() {
putResource("activitydefinition-apply-library.json", "activityDefinitionApplyTest");
putResource("activitydefinition-apply.json", "ad-apply-example");
Parameters inParams = new Parameters();
inParams.addParameter().setName("patient").setValue(new StringType("Patient-12214"));
Parameters outParams = ourClient
.operation()
.onInstance(new IdDt("ActivityDefinition", "ad-apply-example"))
.named("$apply")
.withParameters(inParams)
.useHttpGet()
.execute();
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
Assert.assertTrue(!response.isEmpty());
Resource resource = response.get(0).getResource();
Assert.assertTrue(resource instanceof ProcedureRequest);
ProcedureRequest procedureRequest = (ProcedureRequest) resource;
Assert.assertTrue(procedureRequest.getDoNotPerform());
}
}

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{
"resourceType": "Library",
"id": "activityDefinitionApplyTest",
"version": "1.0",
"status": "draft",
"type": {
"coding": [
{
"code": "logic-library"
}
]
},
"content": [
{
"contentType": "text/cql",
"data": "bGlicmFyeSBhY3Rpdml0eURlZmluaXRpb25BcHBseVRlc3QgdmVyc2lvbiAnMS4wJw0KDQpkZWZpbmUgIkR5bmFtaWMgZG9Ob3RQZXJmb3JtIFNldHRpbmciOg0KICAgIHRydWU="
}
]
}

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{
"resourceType": "ActivityDefinition",
"id": "ad-apply-example",
"status": "draft",
"description": "This is a test.",
"library": [
{
"reference": "Library/activityDefinitionApplyTest"
}
],
"kind": "ProcedureRequest",
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "303653007",
"display": "Computed tomography of head"
}
]
},
"dynamicValue": [
{
"description": "Set ProcedureRequest doNotPerform property",
"path": "doNotPerform",
"expression": "activityDefinitionApplyTest.\"Dynamic doNotPerform Setting\""
}
]
}

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{
"hookInstance": "d1577c69-dfbe-44ad-ba6d-3e05e953b2ea",
"fhirServer": "XXXXX",
"hook": "patient-view",
"user": "Practitioner/example",
"context": {
"patientId": "Patient/Patient-6535"
}
}

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{
"resourceType": "Patient",
"id": "Patient-12214",
"active": false,
"name": [
{
"family": "N Geriatric",
"given": [
"2"
],
"suffix": [
"Jr"
]
}
],
"telecom": [
{
"system": "phone",
"value": "586-555-7576",
"use": "home"
},
{
"system": "phone",
"value": "586-555-0297",
"use": "work"
}
],
"gender": "male",
"birthDate": "1946-05-07",
"address": [
{
"line": [
"202 Burlington Rd."
],
"city": "Bedford",
"state": "MA",
"postalCode": "01730"
}
]
}

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{
"resourceType": "Practitioner",
"id": "Practitioner-12208",
"identifier": [
{
"use": "official",
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/identifier-type",
"code": "SB",
"display": "Social Beneficiary Identifier"
}
],
"text": "US Social Security Number"
},
"system": "http://hl7.org/fhir/sid/us-ssn",
"value": "000012208"
},
{
"use": "official",
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/v2/0203",
"code": "PRN",
"display": "Provider number"
}
],
"text": "US National Provider Identifier"
},
"system": "http://hl7.org/fhir/sid/us-npi",
"value": "9999912208"
},
{
"use": "official",
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/identifier-type",
"code": "SB",
"display": "Social Beneficiary Identifier"
}
],
"text": "Michigan Common Key Service Identifier"
},
"system": "http://mihin.org/fhir/cks",
"value": "c6cc1bbaf5ea41c5a0d267e3a655def1"
}
],
"name": [
{
"family": "Sawyer",
"given": [
"Jay",
"McCann"
],
"suffix": [
"MD"
]
}
],
"telecom": [
{
"system": "phone",
"value": "989-555-8443",
"use": "home"
},
{
"system": "phone",
"value": "989-555-5764",
"use": "work"
}
],
"address": [
{
"line": [
"77 S Pine Place"
],
"city": "Beaverton",
"state": "MI",
"postalCode": "48612"
}
],
"gender": "male",
"birthDate": "1970-08-07",
"qualification": [
{
"identifier": [
{
"use": "official",
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/v2/0203",
"code": "MD",
"display": "Medical License number"
}
],
"text": "Michigan Medical License"
},
"system": "http://michigan.gov/fhir/medical-license",
"value": "LARA-12208",
"assigner": {
"display": "State of Michigan"
}
}
],
"code": {
"coding": [
{
"system": "http://michigan.gov/lara/license-type",
"code": "4305",
"display": "Medical Doctor"
}
]
}
}
]
}

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{
"resourceType": "Library",
"id": "plandefinitionApplyTest",
"version": "1.0",
"status": "draft",
"type": {
"coding": [
{
"code": "logic-library"
}
]
},
"content": [
{
"contentType": "text/cql",
"data": "bGlicmFyeSBwbGFuZGVmaW5pdGlvbkFwcGx5VGVzdCB2ZXJzaW9uICcxLjAnDQoNCmRlZmluZSBSZXN1bHRzOg0KICAgIHRydWUNCg0KZGVmaW5lICJEeW5hbWljIERldGFpbCBEZWZpbml0aW9uIjoNCiAgICAnVGhpcyBpcyBhIGR5bmFtaWMgZGVmaW5pdGlvbiEn"
}
]
}

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{
"resourceType": "PlanDefinition",
"id": "apply-example",
"identifier": [
{
"use": "official",
"value": "apply-example"
}
],
"version": "1.0",
"name": "Example",
"title": "Example for PlanDefinition $apply operation",
"type": {
"coding": [
{
"system": "http://hl7.org/fhir/plan-definition-type",
"code": "eca-rule",
"display": "ECA Rule"
}
]
},
"status": "draft",
"date": "2017-09-18",
"purpose": "Testing",
"usage": "This resource is to be used only for testing",
"topic": [
{
"text": "Testing $apply operation"
}
],
"library": [
{
"reference": "Library/plandefinitionApplyTest"
}
],
"action": [
{
"condition": [
{
"kind": "applicability",
"description": "Simple test",
"language": "text/cql",
"expression": "plandefinitionApplyTest.Results"
}
],
"dynamicValue": [
{
"description": "Set CarePlan detail definition",
"path": "title",
"expression": "plandefinitionApplyTest.\"Dynamic Detail Definition\""
}
]
}
]
}

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<h2> <a id="description" class="anchor" href="#description" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Description</h2>
<p>This project has been built with hapi-fhir-jpaserver-example as a base. It has been made more dynamic by replacing <code>web.xml</code> with <code>ca.uhn.fhir.jpa.demo.WebInitializer</code> class which extends Spring <code>org.springframework.web.WebApplicationInitializer</code> class and loads application contexts in a dynamic manner, so that based on environment and/or property variables it can be started either as dstu2 or dstu3 version of HAPI-FHIR JPA Server. Some of the classes have been also refactored to make them more generic.</p>
<h4> <a id="environment-variables" class="anchor" href="#environment-variables" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Environment variables</h4>
<p>There are number of environment variables that will control the behavior of the application at run time (such as start as dstu2 or dstu3 version, whether database schema gets recreated or no, database url, etc..). They can also be defined in Property files, see section below. These are environment variables that can be set before application starts:</p>
<ul>
<li> <p><code>DB_URL</code> - database url in a standard jdbc url format, specific to a database of your choosing. For example for Postgres it will be: <code>jdbc:postgresql://localhost:5432/&lt;databaseName&gt;?user=&lt;username&gt;&amp;password=&lt;password&gt;</code>. So far support has been added for MySQL, derby and Postgres databases.</p> </li>
<li> <p><code>DATABASE_URL</code> - if you deploy your server to HEROKU and create a Postgres database, its URL will be exposed through <code>DATABASE_URL</code> environment variable set by HEROKU. If <code>DATABASE_URL</code> is present it will overwrite <code>DB_URL</code> and its value will be used as jdbc url. This implementations assumes that Heroku will be setup with Postgres database, so current implementation handles postgres <code>DATABASE_URL</code> that gets set in this format: <code>postgres://&lt;username&gt;:&lt;password&gt;@&lt;hostname&gt;:5432/&lt;databaseName&gt;</code>. We convert it into standard jdbc format: <code>jdbc:postgresql://localhost:5432/&lt;databaseName&gt;?user=&lt;username&gt;&amp;password=&lt;password&gt;</code></p> </li>
<li> <p><code>SCHEMA_NAME</code> - used only if <code>DATABASE_URL</code> is set, which is expected to be Postgres database url set by HEROKU. If it's set <code>currentSchema</code> parameter will be added to the jdbc url, e.g.:<br /> <code>jdbc:postgresql://localhost:5432/&lt;databaseName&gt;?user=&lt;username&gt;&amp;password=&lt;password&gt;&amp;currentScema=&lt;schemaName&gt;</code>. Note that schema has to be created beforehand and user should have the right permissions to create tables.</p> </li>
<li> <p><code>STU_VERSION</code> - can be set to <code>dstu2</code> or <code>dstu3</code>. If not set by default <code>dstu3</code> will be used. Corresponding classes will get dynamically loaded at a server startup.</p> </li>
<li> <p><code>ENV</code> - environment this server will run in, and based on which corresponding property files will be loaded.</p> <p>It can be one of those values: <code>local, dev, stg, prod</code>. Based on the value one of the property files will be loaded: <code>resources/config/&lt;STU_VERSION&gt;/app_&lt;ENV&gt;.properties</code>.</p> <p>So for example if <code>ENV=local</code> and <code>STU_VERSION=dstu3</code> this file will be loaded:</p> <p><code>resources/config/dstu3/app_local.properties</code></p> </li>
<li> <p><code>HIBERNATE_CREATE</code> - can be set to <code>true</code> or <code>false</code>. If set to <code>true</code> database schema will be dropped and recreated again upon application startup. If set to <code>false</code> hibernate will run with <code>validate</code> as a schema setting.</p> </li>
</ul>
<h4> <a id="property-files" class="anchor" href="#property-files" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Property files</h4>
<p>There are number of property files created for different environments: <code>local, dev, stg, prod</code>. So if <code>ENV</code> environment variable is set to one of those values corresponding property file will be loaded at a run time, by default <code>local</code> files will be loaded. Property files are located at: <code>src/main/resources/config/dstu2</code> and <code>src/main/resources/config/dstu3s</code> directories. These are the files:</p>
<pre><code> app_local.properties
app_dev.properties
app_stg.properties
app_prod.properties
immutable.properties - DO NOT modify any of the properties defined in that file.
</code></pre>
<p>Any of the Environment variables can be defined in one of the <code>app_&lt;ENV&gt;.properties</code> property files. If a property is also defined as Environment variable it will overwrite value defined in property file. Properties defined in <code>immutable.properties</code> should not be changed, those are servlet/Spring mappings and names of classes that will be loaded at a run time and are specific to dstu version being used.</p>
<h2> <a id="running-hapi-fhir-jpaserver-dynamic-with-a-webapp-runner" class="anchor" href="#running-hapi-fhir-jpaserver-dynamic-with-a-webapp-runner" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Running hapi-fhir-jpaserver-dynamic with a webapp-runner</h2>
<p>You can run the web application with webapp-runner and pass environment variables to it.</p>
<p>Here is a sample command to run the webapp runner which will start dynamic HAPI-FHIR server with version dstu3, postgres database and hibernate schema being dropped and re-created.</p>
<p>Note optional command to unset DATABASE_URL, so that only DB_URL is used locally. Also make sure to replace placeholder parameters <code>&lt;databasename&gt;</code>, <code>&lt;username&gt;</code> and <code>&lt;password&gt;</code> with actual values.</p>
<pre><code>mvn clean install
unset DATABASE_URL
java $JAVA_OPTS -DSTU_VERSION=dstu3 -DHIBERNATE_CREATE=true -DDB_URL='jdbc:postgresql://localhost:5432/&lt;databaseName&gt;?user=&lt;username&gt;&amp;password=&lt;password&gt;' -DENV=local -jar target/dependency/webapp-runner.jar target/*.war
</code></pre>
<p>You should be able to access HAPI_FHIR server at: <a href="http://localhost:8080/" rel="nofollow">http://localhost:8080/</a> .</p>
<p>If you'd like to open a debugging port run this command and attach remote debugger in IDE of your choice to port 5000. Again make sure to replace placeholder parameters with actual values before you run the command.</p>
<pre><code>java $JAVA_OPTS -Xdebug -Xrunjdwp:transport=dt_socket,server=y,address=5000,suspend=n -DSTU_VERSION=dstu3 -DHIBERNATE_CREATE=false -DDB_URL='jdbc:postgresql://localhost:5432/&lt;databaseName&gt;?user=&lt;username&gt;&amp;password=&lt;password&gt;' -DENV=local -jar target/dependency/webapp-runner.jar target/*.war
</code></pre>
<h2> <a id="running-hapi-fhir-jpaserver-dynamic-in-tomcat-from-intellij" class="anchor" href="#running-hapi-fhir-jpaserver-dynamic-in-tomcat-from-intellij" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Running hapi-fhir-jpaserver-dynamic in Tomcat from IntelliJ</h2>
<p>Install Tomcat.</p>
<p>Make sure you have Tomcat set up in IntelliJ.</p>
<ul>
<li>File-&gt;Settings-&gt;Build, Execution, Deployment-&gt;Application Servers</li>
<li>Click +</li>
<li>Select &quot;Tomcat Server&quot;</li>
<li>Enter the path to your tomcat deployment for both Tomcat Home (IntelliJ will fill in base directory for you)</li>
</ul>
<p>Add a Run Configuration for running hapi-fhir-jpaserver-dynamic under Tomcat</p>
<ul>
<li>Run-&gt;Edit Configurations</li>
<li>Click the green +</li>
<li>Select Tomcat Server, Local</li>
<li>Change the name to whatever you wish</li>
<li>Uncheck the &quot;After launch&quot; checkbox</li>
<li>On the &quot;Deployment&quot; tab, click the green +</li>
<li>Select &quot;Artifact&quot;</li>
<li>Select &quot;hapi-fhir-jpaserver-dynamic:war&quot;</li>
<li>In &quot;Application context&quot; type /hapi</li>
</ul>
<p>Run the configuration.</p>
<ul>
<li>You should now have an &quot;Application Servers&quot; in the list of windows at the bottom.</li>
<li>Click it.</li>
<li>Select your server, and click the green triangle (or the bug if you want to debug)</li>
<li>Wait for the console output to stop</li>
</ul>
<p>Point your browser (or fiddler, or what have you) to <code>http://localhost:8080/fhir/base/Patient</code></p>
<p>You should get an empty bundle back.</p>
<h2> <a id="running-hapi-fhir-jpaserver-dynamic-in-a-docker-container" class="anchor" href="#running-hapi-fhir-jpaserver-dynamic-in-a-docker-container" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Running hapi-fhir-jpaserver-dynamic in a Docker container</h2>
<p>Execute the <code>build-docker-image.sh</code> script to build the docker image.</p>
<p>Use this command to start the container: <code>docker run -d --name hapi-fhir-jpaserver-dynamic -p 8080:8080 hapi-fhir/hapi-fhir-jpaserver-dynamic</code></p>
<p>Note: with this command data is persisted across container restarts, but not after removal of the container. Use a docker volume mapping on /var/lib/jetty/target to achieve this.</p>
<p>There is also Dockerfile.tomcat which contains docker commands to run hapi-fhir-jpaserver-dynamic within tomcat. Rename Dockerfile.tomcat to Dockerfile if you would rather use tomcat as your application container.</p>
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/target
/jpaserver_derby_files
*.log
ca.uhn.fhir.jpa.entity.ResourceTable/
# Created by https://www.gitignore.io
### Java ###
*.class
# Mobile Tools for Java (J2ME)
.mtj.tmp/
# Package Files #
*.jar
*.war
*.ear
overlays/
# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*
### Maven ###
target/
pom.xml.tag
pom.xml.releaseBackup
pom.xml.versionsBackup
pom.xml.next
release.properties
dependency-reduced-pom.xml
buildNumber.properties
### Vim ###
[._]*.s[a-w][a-z]
[._]s[a-w][a-z]
*.un~
Session.vim
.netrwhist
*~
### Intellij ###
# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm
*.iml
## Directory-based project format:
.idea/
# if you remove the above rule, at least ignore the following:
# User-specific stuff:
# .idea/workspace.xml
# .idea/tasks.xml
# .idea/dictionaries
# Sensitive or high-churn files:
# .idea/dataSources.ids
# .idea/dataSources.xml
# .idea/sqlDataSources.xml
# .idea/dynamic.xml
# .idea/uiDesigner.xml
# Gradle:
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# .idea/mongoSettings.xml
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*.ipr
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# IntelliJ
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### Eclipse ###
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*~.nib
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# Eclipse Core
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.externalToolBuilders/
# Locally stored "Eclipse launch configurations"
*.launch
# CDT-specific
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# JDT-specific (Eclipse Java Development Tools)
# PDT-specific
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# TeXlipse plugin
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FROM jetty:9-jre8-alpine
USER jetty:jetty
ADD ./target/hapi-fhir-jpaserver-dynamic.war /var/lib/jetty/webapps/root.war
EXPOSE 8080

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FROM tomcat:8
COPY ["./hapi-fhir-jpaserver-dynamic.war","/usr/local/tomcat/webapps/"]
CMD ["catalina.sh","run"]
EXPOSE 8080

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## Description
This project has been built with hapi-fhir-jpaserver-example as a base. It has been made more dynamic by replacing `web.xml` with `ca.uhn.fhir.jpa.demo.WebInitializer` class which extends
Spring `org.springframework.web.WebApplicationInitializer` class and loads application contexts in a dynamic manner, so that based on environment and/or property variables it can be started either as dstu2 or dstu3 version of HAPI-FHIR JPA Server. Some of the classes have been also refactored to make them more generic.
#### Environment variables
There are number of environment variables that will control the behavior of the application at run time (such as start as dstu2 or dstu3 version, whether
database schema gets recreated or no, database url, etc..). They can also be defined in Property files, see section below. These are environment variables that can be set before application starts:
* `DB_URL` - database url in a standard jdbc url format, specific to a database of your choosing. For example for Postgres it will be: `jdbc:postgresql://localhost:5432/<databaseName>?user=<username>&password=<password>`. So far support has been added for MySQL, derby and Postgres databases.
* `DATABASE_URL` - if you deploy your server to HEROKU and create a Postgres database, its URL will be exposed through `DATABASE_URL` environment variable set by HEROKU.
If `DATABASE_URL` is present it will overwrite `DB_URL` and its value will be used as jdbc url. This implementations assumes that Heroku will be setup with Postgres database, so current implementation handles postgres `DATABASE_URL` that gets set in this format: `postgres://<username>:<password>@<hostname>:5432/<databaseName>`. We convert it into standard jdbc format: `jdbc:postgresql://localhost:5432/<databaseName>?user=<username>&password=<password>`
* `SCHEMA_NAME` - used only if `DATABASE_URL` is set, which is expected to be Postgres database url set by HEROKU. If it's set
`currentSchema` parameter will be added to the jdbc url, e.g.:
```jdbc:postgresql://localhost:5432/<databaseName>?user=<username>&password=<password>&currentScema=<schemaName>```.
Note that schema has to be created beforehand and user should have the right permissions to create tables.
* `STU_VERSION` - can be set to `dstu2` or `dstu3`. If not set by default `dstu3` will be used. Corresponding classes will get dynamically loaded at a server startup.
* `ENV` - environment this server will run in, and based on which corresponding property files will be loaded.
It can be one of those values: `local, dev, stg, prod`. Based on the value one of the property files will be loaded:
```resources/config/<STU_VERSION>/app_<ENV>.properties```.
So for example if `ENV=local` and `STU_VERSION=dstu3` this file will be loaded:
```resources/config/dstu3/app_local.properties```
* `HIBERNATE_CREATE` - can be set to `true` or `false`. If set to `true` database schema will be dropped and recreated again upon application startup. If set
to `false` hibernate will run with `validate` as a schema setting.
#### Property files
There are number of property files created for different environments: `local, dev, stg, prod`. So if `ENV` environment variable is set
to one of those values corresponding property file will be loaded at a run time, by default `local` files will be loaded. Property files are located at:
`src/main/resources/config/dstu2` and `src/main/resources/config/dstu3s` directories. These are the files:
```
app_local.properties
app_dev.properties
app_stg.properties
app_prod.properties
immutable.properties - DO NOT modify any of the properties defined in that file.
```
Any of the Environment variables can be defined in one of the `app_<ENV>.properties` property files. If a property is also defined as Environment variable it will overwrite value defined in property file. Properties defined in `immutable.properties` should not be changed, those are servlet/Spring mappings and names of classes that will be loaded at a run time and are specific to dstu version being used.
## Running hapi-fhir-jpaserver-dynamic with a webapp-runner
You can run the web application with webapp-runner and pass environment variables to it.
Here is a sample command to run the webapp runner which will start
dynamic HAPI-FHIR server with version dstu3, postgres database and hibernate schema being dropped and re-created.
Note optional command to unset DATABASE_URL, so that only DB_URL is used locally. Also make sure to replace placeholder parameters `<databasename>`, `<username>` and `<password>` with actual values.
```
mvn clean install
unset DATABASE_URL
java $JAVA_OPTS -DSTU_VERSION=dstu3 -DHIBERNATE_CREATE=true -DDB_URL='jdbc:postgresql://localhost:5432/<databaseName>?user=<username>&password=<password>' -DENV=local -jar target/dependency/webapp-runner.jar target/*.war
```
You should be able to access HAPI_FHIR server at: http://localhost:8080/ .
If you'd like to open a debugging port run this command and attach remote debugger in IDE of your choice to port 5000. Again make sure to replace placeholder parameters with actual values before you run the command.
```
java $JAVA_OPTS -Xdebug -Xrunjdwp:transport=dt_socket,server=y,address=5000,suspend=n -DSTU_VERSION=dstu3 -DHIBERNATE_CREATE=false -DDB_URL='jdbc:postgresql://localhost:5432/<databaseName>?user=<username>&password=<password>' -DENV=local -jar target/dependency/webapp-runner.jar target/*.war
```
## Running hapi-fhir-jpaserver-dynamic in Tomcat from IntelliJ
Install Tomcat.
Make sure you have Tomcat set up in IntelliJ.
- File->Settings->Build, Execution, Deployment->Application Servers
- Click +
- Select "Tomcat Server"
- Enter the path to your tomcat deployment for both Tomcat Home (IntelliJ will fill in base directory for you)
Add a Run Configuration for running hapi-fhir-jpaserver-dynamic under Tomcat
- Run->Edit Configurations
- Click the green +
- Select Tomcat Server, Local
- Change the name to whatever you wish
- Uncheck the "After launch" checkbox
- On the "Deployment" tab, click the green +
- Select "Artifact"
- Select "hapi-fhir-jpaserver-dynamic:war"
- In "Application context" type /hapi
Run the configuration.
- You should now have an "Application Servers" in the list of windows at the bottom.
- Click it.
- Select your server, and click the green triangle (or the bug if you want to debug)
- Wait for the console output to stop
Point your browser (or fiddler, or what have you) to `http://localhost:8080/fhir/base/Patient`
You should get an empty bundle back.
## Running hapi-fhir-jpaserver-dynamic in a Docker container
Execute the `build-docker-image.sh` script to build the docker image.
Use this command to start the container:
`docker run -d --name hapi-fhir-jpaserver-dynamic -p 8080:8080 hapi-fhir/hapi-fhir-jpaserver-dynamic`
Note: with this command data is persisted across container restarts, but not after removal of the container. Use a docker volume mapping on /var/lib/jetty/target to achieve this.
There is also Dockerfile.tomcat which contains docker commands to run hapi-fhir-jpaserver-dynamic within tomcat. Rename Dockerfile.tomcat to Dockerfile if you would rather use tomcat as your application container.

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example-projects/hapi-fhir-jpaserver-dynamic/build-docker-image.sh
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@ -1,5 +0,0 @@
#!/bin/sh
mvn package && \
docker build -t hapi-fhir/hapi-fhir-jpaserver-dynamic .

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example-projects/hapi-fhir-jpaserver-dynamic/pom.xml
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@ -1,352 +0,0 @@
<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">
<modelVersion>4.0.0</modelVersion>
<!--
Note: HAPI projects use the "hapi-fhir" POM as their base to provide easy management.
You do not need to use this in your own projects, so the "parent" tag and it's
contents below may be removed
if you are using this file as a basis for your own project.
-->
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>4.0.0-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-jpaserver-dynamic</artifactId>
<packaging>war</packaging>
<name>HAPI FHIR JPA Server - Example for CHIP</name>
<repositories>
<repository>
<id>oss-snapshots</id>
<snapshots>
<enabled>true</enabled>
</snapshots>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository>
<!-- <repository>
<id>jpa_base_lib</id>
<url>file://${basedir}/lib</url>
</repository> -->
</repositories>
<dependencies>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-api</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-client</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
<!-- <version>6.0.5</version>-->
<version>8.0.16</version>
</dependency>
<!--
<dependency>
<groupId>org.aspectj</groupId>
<artifactId>aspectjweaver</artifactId>
<version>1.8.9</version>
</dependency>
-->
<!-- This dependency includes the core HAPI-FHIR classes -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
</dependency>
<!-- At least one "structures" JAR must also be included -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency includes the JPA server itself, which is packaged separately from the rest of HAPI FHIR -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- This dependency is used for the "FHIR Tester" web app overlay -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<type>war</type>
<scope>runtime</scope>
<exclusions>
<exclusion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<classifier>classes</classifier>
<scope>compile</scope>
</dependency>
<!-- HAPI-FHIR uses Logback for logging support. The logback library is included automatically by Maven as a part of the hapi-fhir-base dependency, but you also need to include a logging library. Logback
is used here, but log4j would also be fine. -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<!-- Needed for JEE/Servlet support -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
<!-- If you are using HAPI narrative generation, you will need to include Thymeleaf as well. Otherwise the following can be omitted. -->
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
</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>
<artifactId>spring-web</artifactId>
</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>
<artifactId>commons-dbcp2</artifactId>
</dependency>
<!-- This example uses Derby embedded database. If you are using another database such as Mysql or Oracle, you may omit the following dependencies and replace them with an appropriate database client
dependency for your database platform. -->
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbynet</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
</dependency>
<!-- <dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyshared</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbytools</artifactId>
</dependency> -->
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
<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-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>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-test-utilities</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<exclusions>
<exclusion>
<artifactId>Saxon-HE</artifactId>
<groupId>net.sf.saxon</groupId>
</exclusion>
</exclusions>
</dependency>
<!--
For some reason JavaDoc crashed during site generation unless we have this dependency
-->
<dependency>
<groupId>javax.interceptor</groupId>
<artifactId>javax.interceptor-api</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>42.1.4</version>
</dependency>
</dependencies>
<build>
<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver-dynamic.war -->
<finalName>hapi-fhir-jpaserver-dynamic</finalName>
<!-- The following is not required for the application to build, but allows you to test it by issuing "mvn jetty:run" from the command line. -->
<!-- <pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<configuration>
<webApp>
<contextPath>/hapi-fhir-jpaserver-dynamic</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
</plugins>
</pluginManagement> -->
<plugins>
<!-- Tell Maven which Java source version you want to use -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<!-- The configuration here tells the WAR plugin to include the FHIR Tester overlay. You can omit it if you are not using that feature. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<archive>
<manifestEntries>
<Build-Time>${maven.build.timestamp}</Build-Time>
</manifestEntries>
</archive>
<overlays>
<overlay>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
</overlay>
</overlays>
<failOnMissingWebXml>false</failOnMissingWebXml>
<!-- <webXml>src/main/webapp/WEB-INF/web.xml</webXml> -->
</configuration>
</plugin>
<!-- This plugin is just a part of the HAPI internal build process, you do not need to incude it in your own projects -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<!-- This is to run the integration tests -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</configuration>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- for Heroku deployment -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals><goal>copy</goal></goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>com.github.jsimone</groupId>
<artifactId>webapp-runner-main</artifactId>
<version>8.5.23.1</version>
<destFileName>webapp-runner.jar</destFileName>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
<!--<plugin>
<groupId>com.heroku.sdk</groupId>
<artifactId>heroku-maven-plugin</artifactId>
<version>2.0.0</version>
</plugin>-->
</plugins>
</build>
</project>

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@ -1,111 +0,0 @@
package ca.uhn.fhir.jpa.demo;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.PropertySource;
import org.springframework.context.annotation.PropertySources;
import org.springframework.core.env.Environment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
/**
* This is the primary configuration file for the dynamic jpa server running with dstu3 version.
* It will load 2 property files: <br>
* <i>config/dstu3/immutable.properties</i> and <i>config/dstu3/app_${ENV}.properties</i> <br>
* where <b>${ENV}</b> is an environment variable named <b>ENV</b> which should be set to one of the strings:
* <i>local, dev, stg or prod</i>.
*
* By default it will be set to <i>local</i>, so <b>config/dstu3/app_local.properties</b> file will be loaded.
* It expects properties to be exposed either as as environment variables or through property files. Note that environment variable take precedence over
* property files.
* <ul>
* <li><b>ENV</b> - default value set to <i>"local"</i>. Can be set to <i>"local"</i>, <i>"dev"</i>, <i>"stg"</i> or <i>"prod"</i>.</li>
* <li><b>DB_URL</b> - database url, can be exposed either as environment variable or in environment specific property file, e.g. app_local.properties</li>
* <li><b>DATABASE_URL</b> - this url will be set by Heroku as a db url, if it's set, it'll overwrite db settings set with
* <b>DB_URL</b></li>
* <li><b>HIBERNATE_CREATE</b> - if set to <b>true</b>, hibernate will drop and recreate schema, if set to <b>false</b>,
* will validate the schema
* <li><b>SCHEMA_NAME</b> - if set, schema name will be used in the database url, used only when <b>DATABASE_URL</b> is set.
* </ul>
*
*/
@Configuration
@EnableTransactionManagement()
@PropertySources({
@PropertySource("classpath:config/dstu3/immutable.properties"),
@PropertySource("classpath:config/dstu3/app_${ENV:local}.properties") })
public class FhirServerConfig extends BaseJavaConfigDstu3 {
private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(FhirServerConfig.class);
@Autowired
private Environment env;
/**
* Configure FHIR properties around the the JPA server via this bean
*/
@Bean
public DaoConfig daoConfig() {
return FhirServerConfigCommon.getDaoConfig();
}
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
* directory called "jpaserver_derby_files".
*
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
@Bean(destroyMethod = "close")
public DataSource dataSource() {
return FhirServerConfigCommon.getDataSource(env);
}
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
return FhirServerConfigCommon.getEntityManagerFactory(env, dataSource(), fhirContextDstu3());
}
/**
* Do some fancy logging to create a nice access log that has details about each incoming request.
* @return
*/
public LoggingInterceptor loggingInterceptor() {
return FhirServerConfigCommon.loggingInterceptor();
}
/**
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
* @return
*/
@Bean(autowire = Autowire.BY_TYPE)
public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
return FhirServerConfigCommon.getResponseHighlighterInterceptor();
}
@Bean(autowire = Autowire.BY_TYPE)
public IServerInterceptor subscriptionSecurityInterceptor() {
String stuVersion = (env.getProperty(Utils.STU_VERSION) == null)?Utils.DSTU3:env.getProperty(Utils.STU_VERSION) ;
logger.info("-------STU_VERSION: " + stuVersion);
SubscriptionsRequireManualActivationInterceptorDstu3 interceptor = new SubscriptionsRequireManualActivationInterceptorDstu3();
return interceptor;
}
@Bean
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
return FhirServerConfigCommon.getTransactionManager(entityManagerFactory);
}
}

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@ -1,172 +0,0 @@
package ca.uhn.fhir.jpa.demo;
import java.sql.SQLException;
import java.util.Properties;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.util.DerbyTenSevenHapiFhirDialect;
import org.apache.commons.dbcp2.BasicDataSource;
import org.apache.commons.lang3.time.DateUtils;
import org.springframework.core.env.Environment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
/**
* Common code for dstu2 and dstu3 classes moved into static methods so that they can be called from version specific class.
*
* @author anoushmouradian
*
*/
public class FhirServerConfigCommon {
private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
/**
* Configure FHIR properties around the the JPA server via this bean
*/
@SuppressWarnings("deprecation")
public static DaoConfig getDaoConfig() {
DaoConfig daoConfig = new DaoConfig();
daoConfig.setSubscriptionEnabled(true);
daoConfig.setSubscriptionPollDelay(5000);
daoConfig.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);
daoConfig.setAllowMultipleDelete(true);
return daoConfig;
}
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
* directory called "jpaserver_derby_files".
*
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
public static DataSource getDataSource(Environment env) {
String dbUrl = (env.getProperty(Utils.DB_URL) != null)?env.getProperty(Utils.DB_URL).toLowerCase():"";
String herokuDbUrl = env.getProperty(Utils.HEROKU_DATABASE_URL);
if(herokuDbUrl != null) {
// url will come as: postgres://user:pass@host:5432/dbname
String fromUserName = herokuDbUrl.substring(herokuDbUrl.indexOf("//") + 2);
String userName = fromUserName.substring(0, fromUserName.indexOf(":"));
String pass = fromUserName.substring(fromUserName.indexOf(":") +1, fromUserName.indexOf("@"));
String fromHost = fromUserName.substring(fromUserName.indexOf("@")+1);
String schemaName = env.getProperty(Utils.SCHEMA_NAME);
//build this url: jdbc:postgresql://host:5432/dbName?user=username&password=pass&currentSchema='
dbUrl = "jdbc:postgresql://" + fromHost + "?user=" + userName + "&password=" + pass + "&sslmode=require";
if(schemaName != null) {
dbUrl += "&currentSchema=" + schemaName;
}
logger.info("------DB Url: " + dbUrl);
}
BasicDataSource dataSource = new BasicDataSource();
try {
if(dbUrl.indexOf("mysql") > -1 ) {
dataSource.setDriver(new com.mysql.jdbc.Driver());
} else if(dbUrl.indexOf("postgres") > -1) {
dataSource.setDriver(new org.postgresql.Driver());
} else if(dbUrl.indexOf("derby") > -1) {
dataSource.setDriver(new org.apache.derby.jdbc.EmbeddedDriver());
}
} catch (SQLException e) {
logger.error("----FhiServerConfigCommon: getDataSource: setting driver error: " + e.getMessage());
}
dataSource.setUrl(dbUrl);
// A check for WS-2020-0287
assert dataSource.getJmxName() == null;
return dataSource;
}
public static LocalContainerEntityManagerFactoryBean getEntityManagerFactory(Environment env, DataSource dataSource, FhirContext theCtx) {
LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
BaseConfig.configureEntityManagerFactory(retVal, theCtx);
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(dataSource);
retVal.setJpaProperties(jpaProperties(env));
return retVal;
}
/**
* Do some fancy logging to create a nice access log that has details about each incoming request.
* @return
*/
public static LoggingInterceptor loggingInterceptor() {
LoggingInterceptor retVal = new LoggingInterceptor();
retVal.setLoggerName("fhirtest.access");
retVal.setMessageFormat(
"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
retVal.setLogExceptions(true);
retVal.setErrorMessageFormat("ERROR - ${requestVerb} ${requestUrl}");
return retVal;
}
/**
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
* @return
*/
public static ResponseHighlighterInterceptor getResponseHighlighterInterceptor() {
ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
return retVal;
}
public static JpaTransactionManager getTransactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
private static Properties jpaProperties(Environment env) {
Properties extraProperties = new Properties();
String dbUrl = (env.getProperty(Utils.HEROKU_DATABASE_URL) == null)?env.getProperty(Utils.DB_URL):env.getProperty(Utils.HEROKU_DATABASE_URL);
if(dbUrl != null && dbUrl.indexOf("mysql") > -1) {
extraProperties.put("hibernate.dialect", org.hibernate.dialect.MySQL5Dialect.class.getName());
extraProperties.put("hibernate.dialect.storage_engine","innodb");
}
else if(dbUrl != null && dbUrl.indexOf("postgres") > -1) {
extraProperties.put("hibernate.dialect", org.hibernate.dialect.PostgreSQL9Dialect.class.getName());
}
else if(dbUrl != null && dbUrl.indexOf("derby") > -1) {
extraProperties.put("hibernate.dialect", DerbyTenSevenHapiFhirDialect.class.getName());
}
boolean hibernateCreate = new Boolean(env.getProperty(Utils.HIBERNATE_CREATE));
logger.info("------DB hibernateCreate: " + hibernateCreate);
if(hibernateCreate){
extraProperties.put("hibernate.hbm2ddl.auto", "create");
} else {
extraProperties.put("hibernate.hbm2ddl.auto", "validate");
}
extraProperties.put("hibernate.format_sql", "true");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.jdbc.batch_size", "20");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");
extraProperties.put("hibernate.cache.use_structured_entries", "false");
extraProperties.put("hibernate.cache.use_minimal_puts", "false");
extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
extraProperties.put("hibernate.search.autoregister_listeners", "false");
extraProperties.put("hibernate.search.default.indexBase", "./target/lucenefiles");
extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
extraProperties.put("hibernate.search.indexing_strategy", "manual");
extraProperties.put("hibernate.search.default.worker.execution", "async");
return extraProperties;
}
}

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package ca.uhn.fhir.jpa.demo;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.PropertySource;
import org.springframework.context.annotation.PropertySources;
import org.springframework.core.env.Environment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
/**
* This is the primary configuration file for the dynamic jpa server running with dstu2 version.
* It will load 2 property files: <br>
* <i>config/dstu2/immutable.properties</i> and <i>config/dstu2/app_${ENV}.properties</i> <br>
* where <b>${ENV}</b> is an environment variable named <b>ENV</b> which should be set to one of the strings:
* <i>local, dev, stg or prod</i>.
*
* By default it will be set to <i>local</i>, so <b>config/dstu2/app_local.properties</b> file will be loaded.
* It expects properties to be exposed either as as environment variables or through property files. Note that environment variable take precedence over
* property files.
* <ul>
* <li><b>ENV</b> - default value set to <i>"local"</i>. Can be set to <i>"local"</i>, <i>"dev"</i>, <i>"stg"</i> or <i>"prod"</i>.</li>
* <li><b>DB_URL</b> - database url, can be exposed either as environment variable or in environment specific property file, e.g. app_local.properties</li>
* <li><b>DATABASE_URL</b> - this url will be set by Heroku as a db url, if it's set, it'll overwrite db settings set with
* <b>DB_URL</b></li>
* <li><b>HIBERNATE_CREATE</b> - if set to <b>true</b>, hibernate will drop and recreate schema, if set to <b>false</b>,
* will validate the schema
* <li><b>SCHEMA_NAME</b> - if set, schema name will be used in the database url, used only when <b>DATABASE_URL</b> is set.
* </ul>
*
*/
@Configuration
@EnableTransactionManagement()
@PropertySources({
@PropertySource("classpath:config/dstu2/immutable.properties"),
@PropertySource("classpath:config/dstu2/app_${ENV:local}.properties") })
public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(FhirServerConfigDstu2.class);
@Autowired
private Environment env;
/**
* Configure FHIR properties around the the JPA server via this bean
*/
@SuppressWarnings("deprecation")
@Bean
public DaoConfig daoConfig() {
return FhirServerConfigCommon.getDaoConfig();
}
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
* directory called "jpaserver_derby_files".
*
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
@Bean(destroyMethod = "close")
public DataSource dataSource() {
return FhirServerConfigCommon.getDataSource(env);
}
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
return FhirServerConfigCommon.getEntityManagerFactory(env, dataSource(), fhirContextDstu2());
}
/**
* Do some fancy logging to create a nice access log that has details about each incoming request.
* @return
*/
public LoggingInterceptor loggingInterceptor() {
return FhirServerConfigCommon.loggingInterceptor();
}
/**
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
* @return
*/
@Bean(autowire = Autowire.BY_TYPE)
public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
return FhirServerConfigCommon.getResponseHighlighterInterceptor();
}
@Bean(autowire = Autowire.BY_TYPE)
public IServerInterceptor subscriptionSecurityInterceptor() {
String stuVersion = (env.getProperty(Utils.STU_VERSION) == null)?Utils.DSTU2:env.getProperty(Utils.STU_VERSION) ;
logger.info("-------STU_VERSION: " + stuVersion);
SubscriptionsRequireManualActivationInterceptorDstu2 interceptor = new SubscriptionsRequireManualActivationInterceptorDstu2();
return interceptor;
}
@Bean
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
return FhirServerConfigCommon.getTransactionManager(entityManagerFactory);
}
}

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package ca.uhn.fhir.jpa.demo;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.PropertySource;
import org.springframework.context.annotation.PropertySources;
import org.springframework.core.env.Environment;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.to.FhirTesterMvcConfig;
import ca.uhn.fhir.to.TesterConfig;
//@formatter:off
/**
* This spring config file configures the web testing module. It serves two
* purposes:
* 1. It imports FhirTesterMvcConfig, which is the spring config for the
* tester itself
* 2. It tells the tester which server(s) to talk to, via the testerConfig()
* method below.<br>
* It will also load properties defined in <b>config/dstu3/immutable.properties</b> file.
*/
@Configuration
@PropertySources({
@PropertySource("classpath:config/dstu3/immutable.properties") })
@Import(FhirTesterMvcConfig.class)
public class FhirTesterConfig {
@Autowired
private Environment env;
/**
* This bean tells the testing webpage which servers it should configure itself
* to communicate with. In this example we configure it to talk to the local
* server, as well as one public server. If you are creating a project to
* deploy somewhere else, you might choose to only put your own server's
* address here.
*
* Note the use of the ${serverBase} variable below. This will be replaced with
* the base URL as reported by the server itself. Often for a simple Tomcat
* (or other container) installation, this will end up being something
* like "http://localhost:8080/hapi-fhir-jpaserver-example". If you are
* deploying your server to a place with a fully qualified domain name,
* you might want to use that instead of using the variable.
*/
@Bean
public TesterConfig testerConfig() {
TesterConfig retVal = new TesterConfig();
String baseFhirMapping = env.getProperty(Utils.BASE_FHIR_MAPPING);
baseFhirMapping = (baseFhirMapping == null)?"fhir":baseFhirMapping;
retVal
.addServer()
.withId("home")
.withFhirVersion(FhirVersionEnum.DSTU3)
.withBaseUrl("${serverBase}/" + baseFhirMapping)
.withName("Local Tester")
.addServer()
.withId("hapi")
.withFhirVersion(FhirVersionEnum.DSTU3)
.withBaseUrl("http://fhirtest.uhn.ca/" + baseFhirMapping)
.withName("Public HAPI Test Server");
return retVal;
}
}
//@formatter:on

71
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package ca.uhn.fhir.jpa.demo;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.to.FhirTesterMvcConfig;
import ca.uhn.fhir.to.TesterConfig;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.PropertySource;
import org.springframework.context.annotation.PropertySources;
import org.springframework.core.env.Environment;
//@formatter:off
/**
* This spring config file configures the web testing module. It serves two
* purposes:
* 1. It imports FhirTesterMvcConfig, which is the spring config for the
* tester itself
* 2. It tells the tester which server(s) to talk to, via the testerConfig()
* method below<br>
* It will also load properties defined in <b>config/dstu2/immutable.properties</b> file.
*/
@Configuration
@PropertySources({
@PropertySource("classpath:config/dstu2/immutable.properties") })
@Import(FhirTesterMvcConfig.class)
public class FhirTesterConfigDstu2 {
private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(FhirTesterConfigDstu2.class);
@Autowired
private Environment env;
/**
* This bean tells the testing webpage which servers it should configure itself
* to communicate with. In this example we configure it to talk to the local
* server, as well as one public server. If you are creating a project to
* deploy somewhere else, you might choose to only put your own server's
* address here.
*
* Note the use of the ${serverBase} variable below. This will be replaced with
* the base URL as reported by the server itself. Often for a simple Tomcat
* (or other container) installation, this will end up being something
* like "http://localhost:8080/hapi-fhir-jpaserver-example". If you are
* deploying your server to a place with a fully qualified domain name,
* you might want to use that instead of using the variable.
*/
@Bean
public TesterConfig testerConfig() {
logger.info("-------FhirTesterConfigDstu2:" + "testerConfig");
TesterConfig retVal = new TesterConfig();
String baseFhirMapping = env.getProperty(Utils.BASE_FHIR_MAPPING);
baseFhirMapping = (baseFhirMapping == null)?"fhir":baseFhirMapping;
retVal
.addServer()
.withId("home")
.withFhirVersion(FhirVersionEnum.DSTU2)
.withBaseUrl("${serverBase}/" + baseFhirMapping)
.withName("Local Tester")
.addServer()
.withId("hapi")
.withFhirVersion(FhirVersionEnum.DSTU2)
.withBaseUrl("http://fhirtest.uhn.ca/" + baseFhirMapping)
.withName("Public HAPI Test Server");
return retVal;
}
}
//@formatter:on

64
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package ca.uhn.fhir.jpa.demo;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.PropertySource;
/**
* Load immutable properties from /resources/config/<STU_VERSION>/immutable.properties file. STU_VERSION environment variable can be set to dstu2 or dstu3, which will translate to the
* file path, e.g.: /resources/config/immutable/dstu3/immutable.properties
* By default it'll set path to dstu3.
*
* @author anoushmouradian
*
*/
@Configuration
@PropertySource("classpath:config/${STU_VERSION:dstu3}/immutable.properties")
public class ImmutablePropertiesConfig {
@Value("${FHIR_VERSION}")
private String fhirVersion;
@Value("${fhirServerConfigClass}")
private String fhirServerConfigClass;
@Value("${fhirTesterConfigClass}")
private String fhirTesterConfigClass;
@Value("${jpaDemoClass}")
private String jpaDemoClass;
@Value("${jpaDemoMapping}")
private String jpaDemoMapping;
public String getFhirVersion() {
return fhirVersion;
}
public void setFhirVersion(String fhirVersion) {
this.fhirVersion = fhirVersion;
}
public String getFhirServerConfigClass() {
return fhirServerConfigClass;
}
public void setFhirServerConfigClass(String fhirServerConfigClass) {
this.fhirServerConfigClass = fhirServerConfigClass;
}
public String getFhirTesterConfigClass() {
return fhirTesterConfigClass;
}
public void setFhirTesterConfigClass(String fhirTesterConfigClass) {
this.fhirTesterConfigClass = fhirTesterConfigClass;
}
public String getJpaDemoClass() {
return jpaDemoClass;
}
public void setJpaDemoClass(String jpaDemoClass) {
this.jpaDemoClass = jpaDemoClass;
}
public String getJpaDemoMapping() {
return jpaDemoMapping;
}
public void setJpaDemoMapping(String jpaDemoMapping) {
this.jpaDemoMapping = jpaDemoMapping;
}
}

155
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package ca.uhn.fhir.jpa.demo;
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.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.subscription.SubscriptionInterceptorLoader;
import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Meta;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
import javax.servlet.ServletException;
import java.util.List;
public class JpaServerDemo extends RestfulServer {
private static final long serialVersionUID = 1L;
private WebApplicationContext myAppCtx;
@SuppressWarnings("unchecked")
@Override
protected void initialize() throws ServletException {
super.initialize();
/*
* We want to support FHIR DSTU2 format. This means that the server
* will use the DSTU2 bundle format and other DSTU2 encoding changes.
*
* If you want to use DSTU1 instead, change the following line, and change the 2 occurrences of dstu2 in web.xml to dstu1
*/
FhirVersionEnum fhirVersion = FhirVersionEnum.DSTU3;
setFhirContext(new FhirContext(fhirVersion));
// Get the spring context from the web container (it's declared in web.xml)
myAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
/*
* The BaseJavaConfigDstu2.java class is a spring configuration
* file which is automatically generated as a part of hapi-fhir-jpaserver-base and
* contains bean definitions for a resource provider for each resource type
*/
String resourceProviderBeanName;
if (fhirVersion == FhirVersionEnum.DSTU2) {
resourceProviderBeanName = "myResourceProvidersDstu2";
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
resourceProviderBeanName = "myResourceProvidersDstu3";
} else {
throw new IllegalStateException();
}
ResourceProviderFactory beans = myAppCtx.getBean(resourceProviderBeanName, ResourceProviderFactory.class);
registerProviders(beans.createProviders());
/*
* The system provider implements non-resource-type methods, such as
* transaction, and global history.
*/
Object systemProvider;
if (fhirVersion == FhirVersionEnum.DSTU2) {
systemProvider = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
systemProvider = myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
} else {
throw new IllegalStateException();
}
registerProviders(systemProvider);
/*
* The conformance provider exports the supported resources, search parameters, etc for
* this server. The JPA version adds resource counts to the exported statement, so it
* is a nice addition.
*/
if (fhirVersion == FhirVersionEnum.DSTU2) {
IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = myAppCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao,
myAppCtx.getBean(DaoConfig.class));
confProvider.setImplementationDescription("Example Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
IFhirSystemDao<Bundle, Meta> systemDao = myAppCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
myAppCtx.getBean(DaoConfig.class));
confProvider.setImplementationDescription("Example Server");
setServerConformanceProvider(confProvider);
} else {
throw new IllegalStateException();
}
/*
* Enable ETag Support (this is already the default)
*/
setETagSupport(ETagSupportEnum.ENABLED);
/*
* This server tries to dynamically generate narratives
*/
FhirContext ctx = getFhirContext();
ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
/*
* Default to JSON and pretty printing
*/
setDefaultPrettyPrint(true);
setDefaultResponseEncoding(EncodingEnum.JSON);
/*
* -- New in HAPI FHIR 1.5 --
* This configures the server to page search results to and from
* the database, instead of only paging them to memory. This may mean
* a performance hit when performing searches that return lots of results,
* but makes the server much more scalable.
*/
setPagingProvider(myAppCtx.getBean(DatabaseBackedPagingProvider.class));
/*
* Register interceptors for the server based on DaoConfig.getSupportedSubscriptionTypes()
*/
SubscriptionInterceptorLoader subscriptionInterceptorLoader = myAppCtx.getBean(SubscriptionInterceptorLoader.class);
subscriptionInterceptorLoader.registerInterceptors();
/*
* If you are hosting this server at a specific DNS name, the server will try to
* figure out the FHIR base URL based on what the web container tells it, but
* this doesn't always work. If you are setting links in your search bundles that
* just refer to "localhost", you might want to use a server address strategy:
*/
//setServerAddressStrategy(new HardcodedServerAddressStrategy("http://mydomain.com/fhir/baseDstu2"));
/*
* If you are using DSTU3+, you may want to add a terminology uploader, which allows
* uploading of external terminologies such as Snomed CT. Note that this uploader
* does not have any security attached (any anonymous user may use it by default)
* so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
* with this feature.
*/
//if (fhirVersion == FhirVersionEnum.DSTU3) {
// registerProvider(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
//}
}
}

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package ca.uhn.fhir.jpa.demo;
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.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.subscription.SubscriptionInterceptorLoader;
import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Meta;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
import javax.servlet.ServletException;
import java.util.List;
public class JpaServerDemoDstu2 extends RestfulServer {
private static final long serialVersionUID = 1L;
private WebApplicationContext myAppCtx;
@SuppressWarnings("unchecked")
@Override
protected void initialize() throws ServletException {
super.initialize();
/*
* We want to support FHIR DSTU2 format. This means that the server
* will use the DSTU2 bundle format and other DSTU2 encoding changes.
*
* If you want to use DSTU1 instead, change the following line, and change the 2 occurrences of dstu2 in web.xml to dstu1
*/
FhirVersionEnum fhirVersion = FhirVersionEnum.DSTU2;
setFhirContext(new FhirContext(fhirVersion));
// Get the spring context from the web container (it's declared in web.xml)
myAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
/*
* The BaseJavaConfigDstu2.java class is a spring configuration
* file which is automatically generated as a part of hapi-fhir-jpaserver-base and
* contains bean definitions for a resource provider for each resource type
*/
String resourceProviderBeanName;
if (fhirVersion == FhirVersionEnum.DSTU2) {
resourceProviderBeanName = "myResourceProvidersDstu2";
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
resourceProviderBeanName = "myResourceProvidersDstu3";
} else {
throw new IllegalStateException();
}
ResourceProviderFactory beans = myAppCtx.getBean(resourceProviderBeanName, ResourceProviderFactory.class);
registerProviders(beans.createProviders());
/*
* The system provider implements non-resource-type methods, such as
* transaction, and global history.
*/
Object systemProvider;
if (fhirVersion == FhirVersionEnum.DSTU2) {
systemProvider = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
systemProvider = myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
} else {
throw new IllegalStateException();
}
registerProvider(systemProvider);
/*
* The conformance provider exports the supported resources, search parameters, etc for
* this server. The JPA version adds resource counts to the exported statement, so it
* is a nice addition.
*/
if (fhirVersion == FhirVersionEnum.DSTU2) {
IFhirSystemDao<ca.uhn.fhir.model.dstu2.resource.Bundle, MetaDt> systemDao = myAppCtx.getBean("mySystemDaoDstu2", IFhirSystemDao.class);
JpaConformanceProviderDstu2 confProvider = new JpaConformanceProviderDstu2(this, systemDao,
myAppCtx.getBean(DaoConfig.class));
confProvider.setImplementationDescription("Example Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.DSTU3) {
IFhirSystemDao<Bundle, Meta> systemDao = myAppCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao,
myAppCtx.getBean(DaoConfig.class));
confProvider.setImplementationDescription("Example Server");
setServerConformanceProvider(confProvider);
} else {
throw new IllegalStateException();
}
/*
* Enable ETag Support (this is already the default)
*/
setETagSupport(ETagSupportEnum.ENABLED);
/*
* This server tries to dynamically generate narratives
*/
FhirContext ctx = getFhirContext();
ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
/*
* Default to JSON and pretty printing
*/
setDefaultPrettyPrint(true);
setDefaultResponseEncoding(EncodingEnum.JSON);
/*
* -- New in HAPI FHIR 1.5 --
* This configures the server to page search results to and from
* the database, instead of only paging them to memory. This may mean
* a performance hit when performing searches that return lots of results,
* but makes the server much more scalable.
*/
setPagingProvider(myAppCtx.getBean(DatabaseBackedPagingProvider.class));
/*
* Register interceptors for the server based on DaoConfig.getSupportedSubscriptionTypes()
*/
SubscriptionInterceptorLoader subscriptionInterceptorLoader = myAppCtx.getBean(SubscriptionInterceptorLoader.class);
subscriptionInterceptorLoader.registerInterceptors();
/*
* If you are hosting this server at a specific DNS name, the server will try to
* figure out the FHIR base URL based on what the web container tells it, but
* this doesn't always work. If you are setting links in your search bundles that
* just refer to "localhost", you might want to use a server address strategy:
*/
//setServerAddressStrategy(new HardcodedServerAddressStrategy("http://mydomain.com/fhir/baseDstu2"));
/*
* If you are using DSTU3+, you may want to add a terminology uploader, which allows
* uploading of external terminologies such as Snomed CT. Note that this uploader
* does not have any security attached (any anonymous user may use it by default)
* so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
* with this feature.
*/
//if (fhirVersion == FhirVersionEnum.DSTU3) {
// registerProvider(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
//}
}
}

18
example-projects/hapi-fhir-jpaserver-dynamic/src/main/java/ca/uhn/fhir/jpa/demo/Utils.java
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@ -1,18 +0,0 @@
package ca.uhn.fhir.jpa.demo;
/**
* @author anoushmouradian
*
*/
public class Utils {
public static final String HEROKU_DATABASE_URL = "DATABASE_URL";
public static final String DB_URL = "DB_URL";
public static final String HIBERNATE_CREATE = "HIBERNATE_CREATE";
public static final String STU_VERSION = "STU_VERSION";
public static final String DSTU2 = "dstu2";
public static final String DSTU3 = "dstu3";
public static final String SCHEMA_NAME= "SCHEMA_NAME";
public static final String BASE_FHIR_MAPPING = "baseFhirMapping";
}

74
example-projects/hapi-fhir-jpaserver-dynamic/src/main/java/ca/uhn/fhir/jpa/demo/WebInitializer.java
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@ -1,74 +0,0 @@
package ca.uhn.fhir.jpa.demo;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
import javax.servlet.FilterRegistration;
import javax.servlet.ServletContext;
import javax.servlet.ServletException;
import javax.servlet.ServletRegistration;
import org.springframework.context.ConfigurableApplicationContext;
import org.springframework.context.annotation.AnnotationConfigApplicationContext;
import org.springframework.web.WebApplicationInitializer;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
import org.springframework.web.servlet.DispatcherServlet;
/**
* replace web.xml with Spring web initializer, so that various version specific
* classes can be loaded on startup dynamically
*
* @author anoushmouradian
*
*/
public class WebInitializer implements WebApplicationInitializer {
private static final org.slf4j.Logger logger = org.slf4j.LoggerFactory.getLogger(WebInitializer.class);
@Override
public void onStartup(ServletContext container) throws ServletException {
ConfigurableApplicationContext propContext = new AnnotationConfigApplicationContext(ImmutablePropertiesConfig.class);
ImmutablePropertiesConfig props = propContext.getBean(ImmutablePropertiesConfig.class);
logger.info("This is FHIR_VERSION: " + props.getFhirVersion());
propContext.close();
AnnotationConfigWebApplicationContext context = new AnnotationConfigWebApplicationContext();
context.setConfigLocation(props.getFhirServerConfigClass());
container.addListener(new ContextLoaderListener(context));
context.close();
AnnotationConfigWebApplicationContext dispatcherContext = new AnnotationConfigWebApplicationContext();
dispatcherContext.setConfigLocation(props.getFhirTesterConfigClass());
ServletRegistration.Dynamic springDispatcher = container.addServlet("spring", new DispatcherServlet(dispatcherContext));
springDispatcher.setLoadOnStartup(2);
springDispatcher.addMapping("/");
dispatcherContext.close();
ServletRegistration.Dynamic fhirServlet = container.addServlet("fhirServlet", props.getJpaDemoClass());
fhirServlet.setInitParameter("ImplementationDescription", "FHIR JPA Server");
fhirServlet.setInitParameter("FhirVersion", props.getFhirVersion());
fhirServlet.setLoadOnStartup(1);
fhirServlet.addMapping(props.getJpaDemoMapping());
FilterRegistration.Dynamic corsFilter = container.addFilter("CORS Filter", "org.ebaysf.web.cors.CORSFilter");
corsFilter.addMappingForUrlPatterns(null, false, "/*");
Map<String, String> corsMap = Collections.unmodifiableMap(new HashMap<String, String>() {
{
put("cors.allowed.origins", "*");
put("cors.allowed.methods", "GET,POST,PUT,DELETE,OPTIONS");
put("cors.allowed.headers",
"X-FHIR-Starter,Origin,Accept,X-Requested-With,Content-Type,Access-Control-Request-Method,Access-Control-Request-Headers");
put("cors.exposed.headers", "Location,Content-Location");
put("cors.support.credentials", "true");
put("cors.logging.enabled", "true");
put("cors.preflight.maxage", "300");
}
});
corsFilter.setInitParameters(corsMap);
}
}

2
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/config/dstu2/app_dev.properties
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@ -1,2 +0,0 @@
#DB_URL=jdbc:postgresql://<host>:5432/<dbName>?user=<username>&password=<password>&sslmode=require
HIBERNATE_CREATE=false

2
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/config/dstu2/app_local.properties
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@ -1,2 +0,0 @@
#DB_URL=jdbc:postgresql://localhost:5432/<dbName>?user=<username>&password=<password>
HIBERNATE_CREATE=false

2
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/config/dstu2/app_prod.properties
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@ -1,2 +0,0 @@
#DB_URL=jdbc:postgresql://<host>:5432/<dbName>?user=<username>&password=<password>&sslmode=require
HIBERNATE_CREATE=false

2
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/config/dstu2/app_stg.properties
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@ -1,2 +0,0 @@
#DB_URL=jdbc:postgresql://<host>:5432/<dbName>?user=<username>&password=<password>&sslmode=require
HIBERNATE_CREATE=false

6
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/config/dstu2/immutable.properties
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@ -1,6 +0,0 @@
FHIR_VERSION=DSTU2
fhirServerConfigClass=ca.uhn.fhir.jpa.demo.FhirServerConfigDstu2
fhirTesterConfigClass=ca.uhn.fhir.jpa.demo.FhirTesterConfigDstu2
jpaDemoClass=ca.uhn.fhir.jpa.demo.JpaServerDemoDstu2
jpaDemoMapping=/fhir/*
baseFhirMapping=fhir

2
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/config/dstu3/app_dev.properties
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@ -1,2 +0,0 @@
#DB_URL=jdbc:postgresql://<host>:5432/<dbName>?user=<username>&password=<password>&sslmode=require
HIBERNATE_CREATE=false

2
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/config/dstu3/app_local.properties
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@ -1,2 +0,0 @@
#DB_URL=jdbc:postgresql://localhost:5432/<dbName>?user=<username>&password=<password>
HIBERNATE_CREATE=false

2
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/config/dstu3/app_prod.properties
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@ -1,2 +0,0 @@
#DB_URL=jdbc:postgresql://<host>:5432/<dbName>?user=<username>&password=<password>&sslmode=require
HIBERNATE_CREATE=false

2
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/config/dstu3/app_stg.properties
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@ -1,2 +0,0 @@
#DB_URL=jdbc:postgresql://<host>:5432/<dbName>?user=<username>&password=<password>&sslmode=require
HIBERNATE_CREATE=false

6
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/config/dstu3/immutable.properties
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@ -1,6 +0,0 @@
FHIR_VERSION=DSTU3
fhirServerConfigClass=ca.uhn.fhir.jpa.demo.FhirServerConfig
fhirTesterConfigClass=ca.uhn.fhir.jpa.demo.FhirTesterConfig
jpaDemoClass=ca.uhn.fhir.jpa.demo.JpaServerDemo
jpaDemoMapping=/fhir/*
baseFhirMapping=fhir

16
example-projects/hapi-fhir-jpaserver-dynamic/src/main/resources/logback.xml
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@ -1,16 +0,0 @@
<configuration scan="true" scanPeriod="30 seconds">
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
<level>ERROR</level>
</filter>
<encoder>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
</encoder>
</appender>
<root level="ERROR">
<appender-ref ref="STDOUT" />
</root>
</configuration>

67
example-projects/hapi-fhir-jpaserver-dynamic/src/main/webapp/WEB-INF/templates/about.html
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@ -1,67 +0,0 @@
<!DOCTYPE html>
<html lang="en">
<head th:include="tmpl-head :: head">
<title>About This Server</title>
</head>
<body>
<form action="" method="get" id="outerForm">
<div th:replace="tmpl-navbar-top :: top" ></div>
<div class="container-fluid">
<div class="row">
<div th:replace="tmpl-navbar-left :: left" ></div>
<div class="col-sm-9 col-sm-offset-3 col-md-9 col-md-offset-3 main">
<div th:replace="tmpl-banner :: banner"></div>
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">About This Server</h3>
</div>
<div class="panel-body">
<div class="pull-right">
<object data="img/fhirtest-architecture.svg" width="383" height="369" type="image/svg+xml"></object>
</div>
<p>
This server provides a nearly complete implementation of the FHIR Specification
using a 100% open source software stack. It is hosted by University Health Network.
</p>
<p>
The architecture in use here is shown in the image on the right. This server is built
from a number of modules of the
<a href="https://github.com/hapifhir/hapi-fhir/">HAPI FHIR</a>
project, which is a 100% open-source (Apache 2.0 Licensed) Java based
implementation of the FHIR specification.
</p>
<p>
</p>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">Data On This Server</h3>
</div>
<div class="panel-body">
<p>
This server is regularly loaded with a standard set of test data sourced
from UHN's own testing environment. Do not use this server to store any data
that you will need later, as we will be regularly resetting it.
</p>
<p>
This is not a production server and it provides no privacy. Do not store any
confidential data here.
</p>
</div>
</div>
</div>
</div>
</div>
<div th:replace="tmpl-footer :: footer" ></div>
</form>
</body>
</html>

16
example-projects/hapi-fhir-jpaserver-dynamic/src/main/webapp/WEB-INF/templates/tmpl-footer.html
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@ -1,16 +0,0 @@
<!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>

50
example-projects/hapi-fhir-jpaserver-dynamic/src/main/webapp/WEB-INF/templates/tmpl-home-welcome.html
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@ -1,50 +0,0 @@
<!DOCTYPE html>
<html lang="en">
<div th:fragment="banner" class="well">
<th:block th:if="${serverId} == 'home'">
<p>
This is the home for the FHIR test server operated by
<a href="http://uhn.ca">University Health Network</a>. This server
(and the testing application you are currently using to access it)
is entirely built using
<a href="https://github.com/hapifhir/hapi-fhir">HAPI-FHIR</a>,
a 100% open-source Java implementation of the
<a href="http://hl7.org/implement/standards/fhir/">FHIR specification</a>.
</p>
<p>
Here are some things you might wish to try:
</p>
<ul>
<li>
View a
<a href="http://fhirtest.uhn.ca/search?serverId=home&amp;encoding=json&amp;pretty=true&amp;resource=Patient&amp;param.0.type=string&amp;param.0.name=_id&amp;param.0.0=&amp;resource-search-limit=">list of patients</a>
on this server.
</li>
<li>
Construct a
<a href="http://fhirtest.uhn.ca/resource?serverId=home&amp;encoding=json&amp;pretty=true&amp;resource=Patient">search query</a>
on this server.
</li>
<li>
Access a
<a href="http://fhirtest.uhn.ca/home?serverId=furore">different server</a>
(use the <b>Server</b> menu at the top of the page to see a list of public FHIR servers)
</li>
</ul>
</th:block>
<th:block th:if="${serverId} != 'home'">
<p>
You are accessing the public FHIR server
<b th:text="${baseName}"/>. This server is hosted elsewhere on the internet
but is being accessed using the HAPI client implementation.
</p>
</th:block>
<p>
<b class="text-danger"><span class="glyphicon glyphicon-warning-sign"/></b>
<b><span class="text-danger">This is not a production server!</span></b>
Do not store any information here that contains personal health information
or any other confidential information. This server will be regularly purged
and reloaded with fixed test data.
</p>
</div>
</html>

106
example-projects/hapi-fhir-jpaserver-dynamic/src/main/webapp/WEB-INF/web-dstu2.xml
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@ -1,106 +0,0 @@
<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="3.0"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./xsd/web-app_3_0.xsd">
<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
</param-value>
</context-param>
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>
ca.uhn.fhir.jpa.demo.FhirServerConfigDstu2
</param-value>
</context-param>
<!-- Servlets -->
<servlet>
<servlet-name>spring</servlet-name>
<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
<init-param>
<param-name>contextClass</param-name>
<param-value>org.springframework.web.context.support.AnnotationConfigWebApplicationContext</param-value>
</init-param>
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value>ca.uhn.fhir.jpa.demo.FhirTesterConfigDstu2</param-value>
</init-param>
<load-on-startup>2</load-on-startup>
</servlet>
<servlet>
<servlet-name>fhirServlet</servlet-name>
<servlet-class>ca.uhn.fhir.jpa.demo.JpaServerDemoDstu2</servlet-class>
<init-param>
<param-name>ImplementationDescription</param-name>
<param-value>FHIR JPA Server</param-value>
</init-param>
<init-param>
<param-name>FhirVersion</param-name>
<param-value>DSTU2</param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>fhirServlet</servlet-name>
<url-pattern>/baseDstu2/*</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>X-FHIR-Starter,Origin,Accept,X-Requested-With,Content-Type,Access-Control-Request-Method,Access-Control-Request-Headers</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>

108
example-projects/hapi-fhir-jpaserver-dynamic/src/main/webapp/WEB-INF/web-dstu3.xml
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@ -1,108 +0,0 @@
<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="3.0"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./xsd/web-app_3_0.xsd">
<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
</param-value>
</context-param>
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>
ca.uhn.fhir.jpa.demo.FhirServerConfig
</param-value>
</context-param>
<!-- Servlets -->
<servlet>
<servlet-name>spring</servlet-name>
<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
<init-param>
<param-name>contextClass</param-name>
<param-value>org.springframework.web.context.support.AnnotationConfigWebApplicationContext</param-value>
</init-param>
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value>ca.uhn.fhir.jpa.demo.FhirTesterConfig</param-value>
</init-param>
<load-on-startup>2</load-on-startup>
</servlet>
<servlet>
<servlet-name>fhirServlet</servlet-name>
<servlet-class>ca.uhn.fhir.jpa.demo.JpaServerDemo</servlet-class>
<init-param>
<param-name>ImplementationDescription</param-name>
<param-value>FHIR JPA Server</param-value>
</init-param>
<init-param>
<param-name>FhirVersion</param-name>
<param-value>DSTU3</param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>fhirServlet</servlet-name>
<url-pattern>/baseDstu3/*</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>X-FHIR-Starter,Origin,Accept,X-Requested-With,Content-Type,Access-Control-Request-Method,Access-Control-Request-Headers</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>

106
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<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="3.0"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./xsd/web-app_3_0.xsd">
<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
</param-value>
</context-param>
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>
ca.uhn.fhir.jpa.demo.FhirServerConfigDstu2
</param-value>
</context-param>
<!-- Servlets -->
<servlet>
<servlet-name>spring</servlet-name>
<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
<init-param>
<param-name>contextClass</param-name>
<param-value>org.springframework.web.context.support.AnnotationConfigWebApplicationContext</param-value>
</init-param>
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value>ca.uhn.fhir.jpa.demo.FhirTesterConfigDstu2</param-value>
</init-param>
<load-on-startup>2</load-on-startup>
</servlet>
<servlet>
<servlet-name>fhirServlet</servlet-name>
<servlet-class>ca.uhn.fhir.jpa.demo.JpaServerDemoDstu2</servlet-class>
<init-param>
<param-name>ImplementationDescription</param-name>
<param-value>FHIR JPA Server</param-value>
</init-param>
<init-param>
<param-name>FhirVersion</param-name>
<param-value>DSTU2</param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>fhirServlet</servlet-name>
<url-pattern>/baseDstu2/*</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>X-FHIR-Starter,Origin,Accept,X-Requested-With,Content-Type,Access-Control-Request-Method,Access-Control-Request-Headers</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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<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema xmlns="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://java.sun.com/xml/ns/javaee"
xmlns:javaee="http://java.sun.com/xml/ns/javaee"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified"
attributeFormDefault="unqualified"
version="2.2">
<xsd:annotation>
<xsd:documentation>
DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
Copyright 2003-2009 Sun Microsystems, Inc. All rights reserved.
The contents of this file are subject to the terms of either the
GNU General Public License Version 2 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with
the License. You can obtain a copy of the License at
https://glassfish.dev.java.net/public/CDDL+GPL.html or
glassfish/bootstrap/legal/LICENSE.txt. See the License for the
specific language governing permissions and limitations under the
License.
When distributing the software, include this License Header
Notice in each file and include the License file at
glassfish/bootstrap/legal/LICENSE.txt. Sun designates this
particular file as subject to the "Classpath" exception as
provided by Sun in the GPL Version 2 section of the License file
that accompanied this code. If applicable, add the following
below the License Header, with the fields enclosed by brackets []
replaced by your own identifying information:
"Portions Copyrighted [year] [name of copyright owner]"
Contributor(s):
If you wish your version of this file to be governed by only the
CDDL or only the GPL Version 2, indicate your decision by adding
"[Contributor] elects to include this software in this
distribution under the [CDDL or GPL Version 2] license." If you
don't indicate a single choice of license, a recipient has the
option to distribute your version of this file under either the
CDDL, the GPL Version 2 or to extend the choice of license to its
licensees as provided above. However, if you add GPL Version 2
code and therefore, elected the GPL Version 2 license, then the
option applies only if the new code is made subject to such
option by the copyright holder.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
This is the XML Schema for the JSP 2.2 deployment descriptor
types. The JSP 2.2 schema contains all the special
structures and datatypes that are necessary to use JSP files
from a web application.
The contents of this schema is used by the web-common_3_0.xsd
file to define JSP specific content.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
The following conventions apply to all Java EE
deployment descriptor elements unless indicated otherwise.
- In elements that specify a pathname to a file within the
same JAR file, relative filenames (i.e., those not
starting with "/") are considered relative to the root of
the JAR file's namespace. Absolute filenames (i.e., those
starting with "/") also specify names in the root of the
JAR file's namespace. In general, relative names are
preferred. The exception is .war files where absolute
names are preferred for consistency with the Servlet API.
</xsd:documentation>
</xsd:annotation>
<xsd:include schemaLocation="javaee_6.xsd"/>
<!-- **************************************************** -->
<xsd:complexType name="jsp-configType">
<xsd:annotation>
<xsd:documentation>
The jsp-configType is used to provide global configuration
information for the JSP files in a web application. It has
two subelements, taglib and jsp-property-group.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="taglib"
type="javaee:taglibType"
minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element name="jsp-property-group"
type="javaee:jsp-property-groupType"
minOccurs="0"
maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="jsp-fileType">
<xsd:annotation>
<xsd:documentation>
The jsp-file element contains the full path to a JSP file
within the web application beginning with a `/'.
</xsd:documentation>
</xsd:annotation>
<xsd:simpleContent>
<xsd:restriction base="javaee:pathType"/>
</xsd:simpleContent>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="jsp-property-groupType">
<xsd:annotation>
<xsd:documentation>
The jsp-property-groupType is used to group a number of
files so they can be given global property information.
All files so described are deemed to be JSP files. The
following additional properties can be described:
- Control whether EL is ignored.
- Control whether scripting elements are invalid.
- Indicate pageEncoding information.
- Indicate that a resource is a JSP document (XML).
- Prelude and Coda automatic includes.
- Control whether the character sequence #{ is allowed
when used as a String literal.
- Control whether template text containing only
whitespaces must be removed from the response output.
- Indicate the default contentType information.
- Indicate the default buffering model for JspWriter
- Control whether error should be raised for the use of
undeclared namespaces in a JSP page.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:group ref="javaee:descriptionGroup"/>
<xsd:element name="url-pattern"
type="javaee:url-patternType"
maxOccurs="unbounded"/>
<xsd:element name="el-ignored"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Can be used to easily set the isELIgnored
property of a group of JSP pages. By default, the
EL evaluation is enabled for Web Applications using
a Servlet 2.4 or greater web.xml, and disabled
otherwise.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="page-encoding"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of page-encoding are those of the
pageEncoding page directive. It is a
translation-time error to name different encodings
in the pageEncoding attribute of the page directive
of a JSP page and in a JSP configuration element
matching the page. It is also a translation-time
error to name different encodings in the prolog
or text declaration of a document in XML syntax and
in a JSP configuration element matching the document.
It is legal to name the same encoding through
mulitple mechanisms.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="scripting-invalid"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Can be used to easily disable scripting in a
group of JSP pages. By default, scripting is
enabled.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="is-xml"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
If true, denotes that the group of resources
that match the URL pattern are JSP documents,
and thus must be interpreted as XML documents.
If false, the resources are assumed to not
be JSP documents, unless there is another
property group that indicates otherwise.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="include-prelude"
type="javaee:pathType"
minOccurs="0"
maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>
The include-prelude element is a context-relative
path that must correspond to an element in the
Web Application. When the element is present,
the given path will be automatically included (as
in an include directive) at the beginning of each
JSP page in this jsp-property-group.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="include-coda"
type="javaee:pathType"
minOccurs="0"
maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>
The include-coda element is a context-relative
path that must correspond to an element in the
Web Application. When the element is present,
the given path will be automatically included (as
in an include directive) at the end of each
JSP page in this jsp-property-group.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="deferred-syntax-allowed-as-literal"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The character sequence #{ is reserved for EL expressions.
Consequently, a translation error occurs if the #{
character sequence is used as a String literal, unless
this element is enabled (true). Disabled (false) by
default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="trim-directive-whitespaces"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Indicates that template text containing only whitespaces
must be removed from the response output. It has no
effect on JSP documents (XML syntax). Disabled (false)
by default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="default-content-type"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of default-content-type are those of the
contentType page directive. It specifies the default
response contentType if the page directive does not include
a contentType attribute.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="buffer"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of buffer are those of the
buffer page directive. It specifies if buffering should be
used for the output to response, and if so, the size of the
buffer to use.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="error-on-undeclared-namespace"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The default behavior when a tag with unknown namespace is used
in a JSP page (regular syntax) is to silently ignore it. If
set to true, then an error must be raised during the translation
time when an undeclared tag is used in a JSP page. Disabled
(false) by default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="taglibType">
<xsd:annotation>
<xsd:documentation>
The taglibType defines the syntax for declaring in
the deployment descriptor that a tag library is
available to the application. This can be done
to override implicit map entries from TLD files and
from the container.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="taglib-uri"
type="javaee:string">
<xsd:annotation>
<xsd:documentation>
A taglib-uri element describes a URI identifying a
tag library used in the web application. The body
of the taglib-uri element may be either an
absolute URI specification, or a relative URI.
There should be no entries in web.xml with the
same taglib-uri value.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="taglib-location"
type="javaee:pathType">
<xsd:annotation>
<xsd:documentation>
the taglib-location element contains the location
(as a resource relative to the root of the web
application) where to find the Tag Library
Description file for the tag library.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
</xsd:schema>

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<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema xmlns="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://java.sun.com/xml/ns/javaee"
xmlns:javaee="http://java.sun.com/xml/ns/javaee"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified"
attributeFormDefault="unqualified"
version="3.0">
<xsd:annotation>
<xsd:documentation>
DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
Copyright 2003-2009 Sun Microsystems, Inc. All rights reserved.
The contents of this file are subject to the terms of either the
GNU General Public License Version 2 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with
the License. You can obtain a copy of the License at
https://glassfish.dev.java.net/public/CDDL+GPL.html or
glassfish/bootstrap/legal/LICENSE.txt. See the License for the
specific language governing permissions and limitations under the
License.
When distributing the software, include this License Header
Notice in each file and include the License file at
glassfish/bootstrap/legal/LICENSE.txt. Sun designates this
particular file as subject to the "Classpath" exception as
provided by Sun in the GPL Version 2 section of the License file
that accompanied this code. If applicable, add the following
below the License Header, with the fields enclosed by brackets []
replaced by your own identifying information:
"Portions Copyrighted [year] [name of copyright owner]"
Contributor(s):
If you wish your version of this file to be governed by only the
CDDL or only the GPL Version 2, indicate your decision by adding
"[Contributor] elects to include this software in this
distribution under the [CDDL or GPL Version 2] license." If you
don't indicate a single choice of license, a recipient has the
option to distribute your version of this file under either the
CDDL, the GPL Version 2 or to extend the choice of license to its
licensees as provided above. However, if you add GPL Version 2
code and therefore, elected the GPL Version 2 license, then the
option applies only if the new code is made subject to such
option by the copyright holder.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
<![CDATA[[
This is the XML Schema for the Servlet 3.0 deployment descriptor.
The deployment descriptor must be named "WEB-INF/web.xml" in the
web application's war file. All Servlet deployment descriptors
must indicate the web application schema by using the Java EE
namespace:
http://java.sun.com/xml/ns/javaee
and by indicating the version of the schema by
using the version element as shown below:
<web-app xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="..."
version="3.0">
...
</web-app>
The instance documents may indicate the published version of
the schema using the xsi:schemaLocation attribute for Java EE
namespace with the following location:
http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd
]]>
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
The following conventions apply to all Java EE
deployment descriptor elements unless indicated otherwise.
- In elements that specify a pathname to a file within the
same JAR file, relative filenames (i.e., those not
starting with "/") are considered relative to the root of
the JAR file's namespace. Absolute filenames (i.e., those
starting with "/") also specify names in the root of the
JAR file's namespace. In general, relative names are
preferred. The exception is .war files where absolute
names are preferred for consistency with the Servlet API.
</xsd:documentation>
</xsd:annotation>
<xsd:include schemaLocation="web-common_3_0.xsd"/>
<!-- **************************************************** -->
<xsd:element name="web-app"
type="javaee:web-appType">
<xsd:annotation>
<xsd:documentation>
The web-app element is the root of the deployment
descriptor for a web application. Note that the sub-elements
of this element can be in the arbitrary order. Because of
that, the multiplicity of the elements of distributable,
session-config, welcome-file-list, jsp-config, login-config,
and locale-encoding-mapping-list was changed from "?" to "*"
in this schema. However, the deployment descriptor instance
file must not contain multiple elements of session-config,
jsp-config, and login-config. When there are multiple elements of
welcome-file-list or locale-encoding-mapping-list, the container
must concatenate the element contents. The multiple occurence
of the element distributable is redundant and the container
treats that case exactly in the same way when there is only
one distributable.
</xsd:documentation>
</xsd:annotation>
<xsd:unique name="web-common-servlet-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The servlet element contains the name of a servlet.
The name must be unique within the web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:servlet"/>
<xsd:field xpath="javaee:servlet-name"/>
</xsd:unique>
<xsd:unique name="web-common-filter-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The filter element contains the name of a filter.
The name must be unique within the web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:filter"/>
<xsd:field xpath="javaee:filter-name"/>
</xsd:unique>
<xsd:unique name="web-common-ejb-local-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The ejb-local-ref-name element contains the name of an EJB
reference. The EJB reference is an entry in the web
application's environment and is relative to the
java:comp/env context. The name must be unique within
the web application.
It is recommended that name is prefixed with "ejb/".
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:ejb-local-ref"/>
<xsd:field xpath="javaee:ejb-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-ejb-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The ejb-ref-name element contains the name of an EJB
reference. The EJB reference is an entry in the web
application's environment and is relative to the
java:comp/env context. The name must be unique within
the web application.
It is recommended that name is prefixed with "ejb/".
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:ejb-ref"/>
<xsd:field xpath="javaee:ejb-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-resource-env-ref-uniqueness">
<xsd:annotation>
<xsd:documentation>
The resource-env-ref-name element specifies the name of
a resource environment reference; its value is the
environment entry name used in the web application code.
The name is a JNDI name relative to the java:comp/env
context and must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:resource-env-ref"/>
<xsd:field xpath="javaee:resource-env-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-message-destination-ref-uniqueness">
<xsd:annotation>
<xsd:documentation>
The message-destination-ref-name element specifies the name of
a message destination reference; its value is the
environment entry name used in the web application code.
The name is a JNDI name relative to the java:comp/env
context and must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:message-destination-ref"/>
<xsd:field xpath="javaee:message-destination-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-res-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The res-ref-name element specifies the name of a
resource manager connection factory reference. The name
is a JNDI name relative to the java:comp/env context.
The name must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:resource-ref"/>
<xsd:field xpath="javaee:res-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-env-entry-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The env-entry-name element contains the name of a web
application's environment entry. The name is a JNDI
name relative to the java:comp/env context. The name
must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:env-entry"/>
<xsd:field xpath="javaee:env-entry-name"/>
</xsd:unique>
<xsd:key name="web-common-role-name-key">
<xsd:annotation>
<xsd:documentation>
A role-name-key is specified to allow the references
from the security-role-refs.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:security-role"/>
<xsd:field xpath="javaee:role-name"/>
</xsd:key>
<xsd:keyref name="web-common-role-name-references"
refer="javaee:web-common-role-name-key">
<xsd:annotation>
<xsd:documentation>
The keyref indicates the references from
security-role-ref to a specified role-name.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:servlet/javaee:security-role-ref"/>
<xsd:field xpath="javaee:role-link"/>
</xsd:keyref>
</xsd:element>
</xsd:schema>

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<?xml version='1.0'?>
<?xml-stylesheet href="../2008/09/xsd.xsl" type="text/xsl"?>
<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns ="http://www.w3.org/1999/xhtml"
xml:lang="en">
<xs:annotation>
<xs:documentation>
<div>
<h1>About the XML namespace</h1>
<div class="bodytext">
<p>
This schema document describes the XML namespace, in a form
suitable for import by other schema documents.
</p>
<p>
See <a href="http://www.w3.org/XML/1998/namespace.html">
http://www.w3.org/XML/1998/namespace.html</a> and
<a href="http://www.w3.org/TR/REC-xml">
http://www.w3.org/TR/REC-xml</a> for information
about this namespace.
</p>
<p>
Note that local names in this namespace are intended to be
defined only by the World Wide Web Consortium or its subgroups.
The names currently defined in this namespace are listed below.
They should not be used with conflicting semantics by any Working
Group, specification, or document instance.
</p>
<p>
See further below in this document for more information about <a
href="#usage">how to refer to this schema document from your own
XSD schema documents</a> and about <a href="#nsversioning">the
namespace-versioning policy governing this schema document</a>.
</p>
</div>
</div>
</xs:documentation>
</xs:annotation>
<xs:attribute name="lang">
<xs:annotation>
<xs:documentation>
<div>
<h3>lang (as an attribute name)</h3>
<p>
denotes an attribute whose value
is a language code for the natural language of the content of
any element; its value is inherited. This name is reserved
by virtue of its definition in the XML specification.</p>
</div>
<div>
<h4>Notes</h4>
<p>
Attempting to install the relevant ISO 2- and 3-letter
codes as the enumerated possible values is probably never
going to be a realistic possibility.
</p>
<p>
See BCP 47 at <a href="http://www.rfc-editor.org/rfc/bcp/bcp47.txt">
http://www.rfc-editor.org/rfc/bcp/bcp47.txt</a>
and the IANA language subtag registry at
<a href="http://www.iana.org/assignments/language-subtag-registry">
http://www.iana.org/assignments/language-subtag-registry</a>
for further information.
</p>
<p>
The union allows for the 'un-declaration' of xml:lang with
the empty string.
</p>
</div>
</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:union memberTypes="xs:language">
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:enumeration value=""/>
</xs:restriction>
</xs:simpleType>
</xs:union>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="space">
<xs:annotation>
<xs:documentation>
<div>
<h3>space (as an attribute name)</h3>
<p>
denotes an attribute whose
value is a keyword indicating what whitespace processing
discipline is intended for the content of the element; its
value is inherited. This name is reserved by virtue of its
definition in the XML specification.</p>
</div>
</xs:documentation>
</xs:annotation>
<xs:simpleType>
<xs:restriction base="xs:NCName">
<xs:enumeration value="default"/>
<xs:enumeration value="preserve"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="base" type="xs:anyURI"> <xs:annotation>
<xs:documentation>
<div>
<h3>base (as an attribute name)</h3>
<p>
denotes an attribute whose value
provides a URI to be used as the base for interpreting any
relative URIs in the scope of the element on which it
appears; its value is inherited. This name is reserved
by virtue of its definition in the XML Base specification.</p>
<p>
See <a
href="http://www.w3.org/TR/xmlbase/">http://www.w3.org/TR/xmlbase/</a>
for information about this attribute.
</p>
</div>
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="id" type="xs:ID">
<xs:annotation>
<xs:documentation>
<div>
<h3>id (as an attribute name)</h3>
<p>
denotes an attribute whose value
should be interpreted as if declared to be of type ID.
This name is reserved by virtue of its definition in the
xml:id specification.</p>
<p>
See <a
href="http://www.w3.org/TR/xml-id/">http://www.w3.org/TR/xml-id/</a>
for information about this attribute.
</p>
</div>
</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attributeGroup name="specialAttrs">
<xs:attribute ref="xml:base"/>
<xs:attribute ref="xml:lang"/>
<xs:attribute ref="xml:space"/>
<xs:attribute ref="xml:id"/>
</xs:attributeGroup>
<xs:annotation>
<xs:documentation>
<div>
<h3>Father (in any context at all)</h3>
<div class="bodytext">
<p>
denotes Jon Bosak, the chair of
the original XML Working Group. This name is reserved by
the following decision of the W3C XML Plenary and
XML Coordination groups:
</p>
<blockquote>
<p>
In appreciation for his vision, leadership and
dedication the W3C XML Plenary on this 10th day of
February, 2000, reserves for Jon Bosak in perpetuity
the XML name "xml:Father".
</p>
</blockquote>
</div>
</div>
</xs:documentation>
</xs:annotation>
<xs:annotation>
<xs:documentation>
<div xml:id="usage" id="usage">
<h2><a name="usage">About this schema document</a></h2>
<div class="bodytext">
<p>
This schema defines attributes and an attribute group suitable
for use by schemas wishing to allow <code>xml:base</code>,
<code>xml:lang</code>, <code>xml:space</code> or
<code>xml:id</code> attributes on elements they define.
</p>
<p>
To enable this, such a schema must import this schema for
the XML namespace, e.g. as follows:
</p>
<pre>
&lt;schema . . .>
. . .
&lt;import namespace="http://www.w3.org/XML/1998/namespace"
schemaLocation="http://www.w3.org/2001/xml.xsd"/>
</pre>
<p>
or
</p>
<pre>
&lt;import namespace="http://www.w3.org/XML/1998/namespace"
schemaLocation="http://www.w3.org/2009/01/xml.xsd"/>
</pre>
<p>
Subsequently, qualified reference to any of the attributes or the
group defined below will have the desired effect, e.g.
</p>
<pre>
&lt;type . . .>
. . .
&lt;attributeGroup ref="xml:specialAttrs"/>
</pre>
<p>
will define a type which will schema-validate an instance element
with any of those attributes.
</p>
</div>
</div>
</xs:documentation>
</xs:annotation>
<xs:annotation>
<xs:documentation>
<div id="nsversioning" xml:id="nsversioning">
<h2><a name="nsversioning">Versioning policy for this schema document</a></h2>
<div class="bodytext">
<p>
In keeping with the XML Schema WG's standard versioning
policy, this schema document will persist at
<a href="http://www.w3.org/2009/01/xml.xsd">
http://www.w3.org/2009/01/xml.xsd</a>.
</p>
<p>
At the date of issue it can also be found at
<a href="http://www.w3.org/2001/xml.xsd">
http://www.w3.org/2001/xml.xsd</a>.
</p>
<p>
The schema document at that URI may however change in the future,
in order to remain compatible with the latest version of XML
Schema itself, or with the XML namespace itself. In other words,
if the XML Schema or XML namespaces change, the version of this
document at <a href="http://www.w3.org/2001/xml.xsd">
http://www.w3.org/2001/xml.xsd
</a>
will change accordingly; the version at
<a href="http://www.w3.org/2009/01/xml.xsd">
http://www.w3.org/2009/01/xml.xsd
</a>
will not change.
</p>
<p>
Previous dated (and unchanging) versions of this schema
document are at:
</p>
<ul>
<li><a href="http://www.w3.org/2009/01/xml.xsd">
http://www.w3.org/2009/01/xml.xsd</a></li>
<li><a href="http://www.w3.org/2007/08/xml.xsd">
http://www.w3.org/2007/08/xml.xsd</a></li>
<li><a href="http://www.w3.org/2004/10/xml.xsd">
http://www.w3.org/2004/10/xml.xsd</a></li>
<li><a href="http://www.w3.org/2001/03/xml.xsd">
http://www.w3.org/2001/03/xml.xsd</a></li>
</ul>
</div>
</div>
</xs:documentation>
</xs:annotation>
</xs:schema>

90
example-projects/hapi-fhir-jpaserver-dynamic/src/test/java/ca/uhn/fhir/jpa/demo/ExampleServerIT.java
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@ -1,90 +0,0 @@
package ca.uhn.fhir.jpa.demo;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.webapp.WebAppContext;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeEachClass;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.StringDt;
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.test.utilities.JettyUtil;
public class ExampleServerIT {
private static IGenericClient ourClient;
private static FhirContext ourCtx = FhirContext.forDstu2();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerIT.class);
private static int ourPort;
private static Server ourServer;
private static String ourServerBase;
@Test
@Disabled
public void testCreateAndRead() throws IOException {
ourLog.info("Base URL is: http://localhost:" + ourPort + "/baseDstu2");
String methodName = "testCreateResourceConditional";
Patient pt = new Patient();
StringDt famName = new StringDt(methodName);
List<StringDt> famNames =Arrays.asList(famName);
pt.addName().setFamily(famNames);
IIdType id = ourClient.create().resource(pt).execute().getId();
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(famNames, pt2.getName().get(0).getFamily());
}
@AfterAll
public static void afterClass() throws Exception {
JettyUtil.closeServer(ourServer);
}
@BeforeAll
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 = ExampleServerIT.class.getClassLoader().getResource(".keep_hapi-fhir-jpaserver-example").getPath();
path = new File(path).getParent();
path = new File(path).getParent();
path = new File(path).getParent();
ourLog.info("Project base path is: {}", path);
ourServer = new Server(0);
WebAppContext webAppContext = new WebAppContext();
webAppContext.setContextPath("/");
//webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-example");
webAppContext.setParentLoaderPriority(true);
ourServer.setHandler(webAppContext);
JettyUtil.startServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
ourServerBase = "http://localhost:" + ourPort + "/baseDstu2";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
}

0
example-projects/hapi-fhir-jpaserver-dynamic/src/test/resources/.keep_hapi-fhir-jpaserver-example
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nothing

249
example-projects/hapi-fhir-jpaserver-example-postgres/pom.xml
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<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">
<modelVersion>4.0.0</modelVersion>
<!--
Note: HAPI projects use the "hapi-fhir" POM as their base to provide easy management.
You do not need to use this in your own projects, so the "parent" tag and it's
contents below may be removed
if you are using this file as a basis for your own project.
-->
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>4.0.0-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>
<groupId>ca.uhn.hapi.fhir.example</groupId>
<artifactId>hapi-fhir-jpaserver-example-postgres</artifactId>
<packaging>war</packaging>
<name>HAPI FHIR JPA Server - Example (Postgres)</name>
<dependencies>
<!-- This dependency includes the core HAPI-FHIR classes -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency includes the JPA server itself, which is packaged separately from the rest of HAPI FHIR -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency is used for the "FHIR Tester" web app overlay -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<type>war</type>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>${project.version}</version>
<classifier>classes</classifier>
<scope>provided</scope>
</dependency>
<!-- HAPI-FHIR uses Logback for logging support. The logback library is included automatically by Maven as a part of the hapi-fhir-base dependency, but you also need to include a logging library. Logback
is used here, but log4j would also be fine. -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<!-- Needed for JEE/Servlet support -->
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
<scope>provided</scope>
</dependency>
<!-- If you are using HAPI narrative generation, you will need to include Thymeleaf as well. Otherwise the following can be omitted. -->
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
</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>
<artifactId>spring-web</artifactId>
</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>
<artifactId>commons-dbcp2</artifactId>
</dependency>
<!-- This example uses Derby embedded database. If you are using another database such as Mysql or Oracle, you may omit the following dependencies and replace them with an appropriate database client
dependency for your database platform. -->
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbynet</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
</dependency>
<!--<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyshared</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbytools</artifactId>
</dependency>-->
<!-- The following dependencies are only needed for automated unit tests, you do not neccesarily need them to run the example. -->
<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</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>com.helger</groupId>
<artifactId>ph-schematron</artifactId>
<exclusions>
<exclusion>
<artifactId>Saxon-HE</artifactId>
<groupId>net.sf.saxon</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>9.4.1210.jre7</version>
</dependency>
</dependencies>
<build>
<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver-example.war -->
<finalName>hapi-fhir-jpaserver-example</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>
<configuration>
<webApp>
<contextPath>/hapi-fhir-jpaserver-example</contextPath>
<allowDuplicateFragmentNames>true</allowDuplicateFragmentNames>
</webApp>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<!-- Tell Maven which Java source version you want to use -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<!-- The configuration here tells the WAR plugin to include the FHIR Tester overlay. You can omit it if you are not using that feature. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<archive>
<manifestEntries>
<Build-Time>${maven.build.timestamp}</Build-Time>
</manifestEntries>
</archive>
<overlays>
<overlay>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
</overlay>
</overlays>
<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
</configuration>
</plugin>
<!-- This plugin is just a part of the HAPI internal build process, you do not need to incude it in your own projects -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<!-- This is to run the integration tests -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</configuration>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<description>a</description>
</project>

33
example-projects/hapi-fhir-jpaserver-example-postgres/readme.intellij.txt
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@ -1,33 +0,0 @@
Running hapi-fhir-jpaserver-example in Tomcat from IntelliJ
Install Tomcat.
Install mvn
run `mvn clean install`
Make sure you have Tomcat set up in IntelliJ.
File->Settings->Build, Execution, Deployment->Application Servers
Click +
Select "Tomcat Server"
Enter the path to your tomcat deployment for both Tomcat Home (IntelliJ will fill in base directory for you)
Add a Run Configuration for running hapi-fhir-jpaserver-example under Tomcat
Run->Edit Configurations
Click the green +
Select Tomcat Server, Local
Change the name to whatever you wish
Uncheck the "After launch" checkbox
On the "Deployment" tab, click the green +
Select "Artifact"
Select "hapi-fhir-jpaserver-example:war"
In "Application context" type /hapi
Run the configuration
You should now have an "Application Servers" in the list of windows at the bottom.
Click it.
Select your server, and click the green triangle (or the bug if you want to debug)
Wait for the console output to stop
Point your browser (or fiddler, or what have you) to
http://localhost:8080/hapi/baseDstu3/Patient
You should get an empty bundle back.

131
example-projects/hapi-fhir-jpaserver-example-postgres/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java
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@ -1,131 +0,0 @@
package ca.uhn.fhir.jpa.demo;
import java.util.Properties;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import org.apache.commons.dbcp2.BasicDataSource;
import org.apache.commons.lang3.time.DateUtils;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
/**
* This class isn't used by default by the example, but
* you can use it as a config if you want to support DSTU3
* instead of DSTU2 in your server.
*
* See https://github.com/hapifhir/hapi-fhir/issues/278
*/
@Configuration
@EnableTransactionManagement()
public class FhirServerConfig extends BaseJavaConfigDstu3 {
/**
* Configure FHIR properties around the the JPA server via this bean
*/
@Bean
public DaoConfig daoConfig() {
DaoConfig retVal = new DaoConfig();
retVal.setSubscriptionEnabled(true);
retVal.setSubscriptionPollDelay(5000);
retVal.setSubscriptionPurgeInactiveAfterMillis(DateUtils.MILLIS_PER_HOUR);
retVal.setAllowMultipleDelete(true);
return retVal;
}
/**
* The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
* directory called "jpaserver_derby_files".
*
* A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
*/
@Bean(destroyMethod = "close")
public DataSource dataSource() {
BasicDataSource retVal = new BasicDataSource();
retVal.setDriver(new org.postgresql.Driver());
retVal.setUrl("jdbc:postgresql://localhost:5432/hapi");
retVal.setUsername("hapi");
retVal.setPassword("mysecretpassword");
return retVal;
}
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());
return retVal;
}
private Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.dialect", org.hibernate.dialect.PostgreSQL94Dialect.class.getName());
extraProperties.put("hibernate.format_sql", "true");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.jdbc.batch_size", "20");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");
extraProperties.put("hibernate.cache.use_structured_entries", "false");
extraProperties.put("hibernate.cache.use_minimal_puts", "false");
extraProperties.put("hibernate.search.model_mapping", LuceneSearchMappingFactory.class.getName());
extraProperties.put("hibernate.search.default.directory_provider", "filesystem");
extraProperties.put("hibernate.search.default.indexBase", "target/lucenefiles");
extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
// extraProperties.put("hibernate.search.default.worker.execution", "async");
return extraProperties;
}
/**
* Do some fancy logging to create a nice access log that has details about each incoming request.
* @return
*/
public LoggingInterceptor loggingInterceptor() {
LoggingInterceptor retVal = new LoggingInterceptor();
retVal.setLoggerName("fhirtest.access");
retVal.setMessageFormat(
"Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
retVal.setLogExceptions(true);
retVal.setErrorMessageFormat("ERROR - ${requestVerb} ${requestUrl}");
return retVal;
}
/**
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
* @return
*/
@Bean(autowire = Autowire.BY_TYPE)
public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
public IServerInterceptor subscriptionSecurityInterceptor() {
SubscriptionsRequireManualActivationInterceptorDstu3 retVal = new SubscriptionsRequireManualActivationInterceptorDstu3();
return retVal;
}
@Bean
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;
}
}

51
example-projects/hapi-fhir-jpaserver-example-postgres/src/main/java/ca/uhn/fhir/jpa/demo/FhirTesterConfig.java
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@ -1,51 +0,0 @@
package ca.uhn.fhir.jpa.demo;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.to.FhirTesterMvcConfig;
import ca.uhn.fhir.to.TesterConfig;
//@formatter:off
/**
* This spring config file configures the web testing module. It serves two
* purposes:
* 1. It imports FhirTesterMvcConfig, which is the spring config for the
* tester itself
* 2. It tells the tester which server(s) to talk to, via the testerConfig()
* method below
*/
@Configuration
@Import(FhirTesterMvcConfig.class)
public class FhirTesterConfig {
/**
* This bean tells the testing webpage which servers it should configure itself
* to communicate with. In this example we configure it to talk to the local
* server, as well as one public server. If you are creating a project to
* deploy somewhere else, you might choose to only put your own server's
* address here.
*
* Note the use of the ${serverBase} variable below. This will be replaced with
* the base URL as reported by the server itself. Often for a simple Tomcat
* (or other container) installation, this will end up being something
* like "http://localhost:8080/hapi-fhir-jpaserver-example". If you are
* deploying your server to a place with a fully qualified domain name,
* you might want to use that instead of using the variable.
*/
@Bean
public TesterConfig testerConfig() {
TesterConfig retVal = new TesterConfig();
retVal
.addServer()
.withId("home")
.withFhirVersion(FhirVersionEnum.DSTU3)
.withBaseUrl("${serverBase}/baseDstu3")
.withName("Local Tester");
return retVal;
}
}
//@formatter:on

120
example-projects/hapi-fhir-jpaserver-example-postgres/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java
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@ -1,120 +0,0 @@
package ca.uhn.fhir.jpa.demo;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.subscription.SubscriptionInterceptorLoader;
import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import org.hl7.fhir.dstu3.model.Meta;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
import javax.servlet.ServletException;
import java.util.List;
public class JpaServerDemo extends RestfulServer {
private static final long serialVersionUID = 1L;
private WebApplicationContext myAppCtx;
@SuppressWarnings("unchecked")
@Override
protected void initialize() throws ServletException {
super.initialize();
/*
* We want to support FHIR DSTU3 format. This means that the server
* will use the DSTU3 bundle format and other DSTU3 encoding changes.
*
* If you want to use DSTU1 instead, change the following line, and change the 3 occurrences of dstu2 in web.xml to dstu1
*/
setFhirContext(FhirContext.forDstu3());
// Get the spring context from the web container (it's declared in web.xml)
myAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
/*
* The BaseJavaConfigDstu3.java class is a spring configuration
* file which is automatically generated as a part of hapi-fhir-jpaserver-base and
* contains bean definitions for a resource provider for each resource type
*/
ResourceProviderFactory beans = myAppCtx.getBean("myResourceProvidersDstu3", ResourceProviderFactory.class);
registerProviders(beans.createProviders());
/*
* The system provider implements non-resource-type methods, such as
* transaction, and global history.
*/
registerProviders(myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class));
/*
* The conformance provider exports the supported resources, search parameters, etc for
* this server. The JPA version adds resource counts to the exported statement, so it
* is a nice addition.
*/
IFhirSystemDao<org.hl7.fhir.dstu3.model.Bundle, Meta> systemDao = myAppCtx.getBean("mySystemDaoDstu3", IFhirSystemDao.class);
JpaConformanceProviderDstu3 confProvider = new JpaConformanceProviderDstu3(this, systemDao, myAppCtx.getBean(DaoConfig.class));
confProvider.setImplementationDescription("Example Server");
setServerConformanceProvider(confProvider);
/*
* Enable ETag Support (this is already the default)
*/
setETagSupport(ETagSupportEnum.ENABLED);
/*
* This server tries to dynamically generate narratives
*/
FhirContext ctx = getFhirContext();
ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
/*
* Default to JSON and pretty printing
*/
setDefaultPrettyPrint(true);
setDefaultResponseEncoding(EncodingEnum.JSON);
/*
* -- New in HAPI FHIR 1.5 --
* This configures the server to page search results to and from
* the database, instead of only paging them to memory. This may mean
* a performance hit when performing searches that return lots of results,
* but makes the server much more scalable.
*/
setPagingProvider(myAppCtx.getBean(DatabaseBackedPagingProvider.class));
/*
* Register interceptors for the server based on DaoConfig.getSupportedSubscriptionTypes()
*/
SubscriptionInterceptorLoader subscriptionInterceptorLoader = myAppCtx.getBean(SubscriptionInterceptorLoader.class);
subscriptionInterceptorLoader.registerInterceptors();
/*
* If you are hosting this server at a specific DNS name, the server will try to
* figure out the FHIR base URL based on what the web container tells it, but
* this doesn't always work. If you are setting links in your search bundles that
* just refer to "localhost", you might want to use a server address strategy:
*/
//setServerAddressStrategy(new HardcodedServerAddressStrategy("http://mydomain.com/fhir/baseDstu2"));
/*
* If you are using DSTU3+, you may want to add a terminology uploader, which allows
* uploading of external terminologies such as Snomed CT. Note that this uploader
* does not have any security attached (any anonymous user may use it by default)
* so it is a potential security vulnerability. Consider using an AuthorizationInterceptor
* with this feature.
*/
registerProvider(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
}
}

16
example-projects/hapi-fhir-jpaserver-example-postgres/src/main/resources/logback.xml
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<configuration scan="true" scanPeriod="30 seconds">
<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
<level>INFO</level>
</filter>
<encoder>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
</encoder>
</appender>
<root level="INFO">
<appender-ref ref="STDOUT" />
</root>
</configuration>

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@ -1,67 +0,0 @@
<!DOCTYPE html>
<html lang="en">
<head th:include="tmpl-head :: head">
<title>About This Server</title>
</head>
<body>
<form action="" method="get" id="outerForm">
<div th:replace="tmpl-navbar-top :: top" ></div>
<div class="container-fluid">
<div class="row">
<div th:replace="tmpl-navbar-left :: left" ></div>
<div class="col-sm-9 col-sm-offset-3 col-md-9 col-md-offset-3 main">
<div th:replace="tmpl-banner :: banner"></div>
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">About This Server</h3>
</div>
<div class="panel-body">
<div class="pull-right">
<object data="img/fhirtest-architecture.svg" width="383" height="369" type="image/svg+xml"></object>
</div>
<p>
This server provides a nearly complete implementation of the FHIR Specification
using a 100% open source software stack. It is hosted by University Health Network.
</p>
<p>
The architecture in use here is shown in the image on the right. This server is built
from a number of modules of the
<a href="https://github.com/hapifhir/hapi-fhir/">HAPI FHIR</a>
project, which is a 100% open-source (Apache 2.0 Licensed) Java based
implementation of the FHIR specification.
</p>
<p>
</p>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">Data On This Server</h3>
</div>
<div class="panel-body">
<p>
This server is regularly loaded with a standard set of test data sourced
from UHN's own testing environment. Do not use this server to store any data
that you will need later, as we will be regularly resetting it.
</p>
<p>
This is not a production server and it provides no privacy. Do not store any
confidential data here.
</p>
</div>
</div>
</div>
</div>
</div>
<div th:replace="tmpl-footer :: footer" ></div>
</form>
</body>
</html>

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@ -1,16 +0,0 @@
<!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>

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example-projects/hapi-fhir-jpaserver-example-postgres/src/main/webapp/WEB-INF/templates/tmpl-home-welcome.html
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@ -1,50 +0,0 @@
<!DOCTYPE html>
<html lang="en">
<div th:fragment="banner" class="well">
<th:block th:if="${serverId} == 'home'">
<p>
This is the home for the FHIR test server operated by
<a href="http://uhn.ca">University Health Network</a>. This server
(and the testing application you are currently using to access it)
is entirely built using
<a href="https://github.com/hapifhir/hapi-fhir">HAPI-FHIR</a>,
a 100% open-source Java implementation of the
<a href="http://hl7.org/implement/standards/fhir/">FHIR specification</a>.
</p>
<p>
Here are some things you might wish to try:
</p>
<ul>
<li>
View a
<a href="http://fhirtest.uhn.ca/search?serverId=home&amp;encoding=json&amp;pretty=true&amp;resource=Patient&amp;param.0.type=string&amp;param.0.name=_id&amp;param.0.0=&amp;resource-search-limit=">list of patients</a>
on this server.
</li>
<li>
Construct a
<a href="http://fhirtest.uhn.ca/resource?serverId=home&amp;encoding=json&amp;pretty=true&amp;resource=Patient">search query</a>
on this server.
</li>
<li>
Access a
<a href="http://fhirtest.uhn.ca/home?serverId=furore">different server</a>
(use the <b>Server</b> menu at the top of the page to see a list of public FHIR servers)
</li>
</ul>
</th:block>
<th:block th:if="${serverId} != 'home'">
<p>
You are accessing the public FHIR server
<b th:text="${baseName}"/>. This server is hosted elsewhere on the internet
but is being accessed using the HAPI client implementation.
</p>
</th:block>
<p>
<b class="text-danger"><span class="glyphicon glyphicon-warning-sign"/></b>
<b><span class="text-danger">This is not a production server!</span></b>
Do not store any information here that contains personal health information
or any other confidential information. This server will be regularly purged
and reloaded with fixed test data.
</p>
</div>
</html>

108
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<web-app xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="3.0"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee ./xsd/web-app_3_0.xsd">
<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
</param-value>
</context-param>
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>
ca.uhn.fhir.jpa.demo.FhirServerConfig
</param-value>
</context-param>
<!-- Servlets -->
<servlet>
<servlet-name>spring</servlet-name>
<servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
<init-param>
<param-name>contextClass</param-name>
<param-value>org.springframework.web.context.support.AnnotationConfigWebApplicationContext</param-value>
</init-param>
<init-param>
<param-name>contextConfigLocation</param-name>
<param-value>ca.uhn.fhir.jpa.demo.FhirTesterConfig</param-value>
</init-param>
<load-on-startup>2</load-on-startup>
</servlet>
<servlet>
<servlet-name>fhirServlet</servlet-name>
<servlet-class>ca.uhn.fhir.jpa.demo.JpaServerDemo</servlet-class>
<init-param>
<param-name>ImplementationDescription</param-name>
<param-value>FHIR JPA Server</param-value>
</init-param>
<init-param>
<param-name>FhirVersion</param-name>
<param-value>DSTU2</param-value>
</init-param>
<load-on-startup>1</load-on-startup>
</servlet>
<servlet-mapping>
<servlet-name>fhirServlet</servlet-name>
<url-pattern>/baseDstu3/*</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>X-FHIR-Starter,Origin,Accept,X-Requested-With,Content-Type,Access-Control-Request-Method,Access-Control-Request-Headers</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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example-projects/hapi-fhir-jpaserver-example-postgres/src/main/webapp/WEB-INF/xsd/jsp_2_2.xsd
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<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema xmlns="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://java.sun.com/xml/ns/javaee"
xmlns:javaee="http://java.sun.com/xml/ns/javaee"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified"
attributeFormDefault="unqualified"
version="2.2">
<xsd:annotation>
<xsd:documentation>
DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
Copyright 2003-2009 Sun Microsystems, Inc. All rights reserved.
The contents of this file are subject to the terms of either the
GNU General Public License Version 2 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with
the License. You can obtain a copy of the License at
https://glassfish.dev.java.net/public/CDDL+GPL.html or
glassfish/bootstrap/legal/LICENSE.txt. See the License for the
specific language governing permissions and limitations under the
License.
When distributing the software, include this License Header
Notice in each file and include the License file at
glassfish/bootstrap/legal/LICENSE.txt. Sun designates this
particular file as subject to the "Classpath" exception as
provided by Sun in the GPL Version 2 section of the License file
that accompanied this code. If applicable, add the following
below the License Header, with the fields enclosed by brackets []
replaced by your own identifying information:
"Portions Copyrighted [year] [name of copyright owner]"
Contributor(s):
If you wish your version of this file to be governed by only the
CDDL or only the GPL Version 2, indicate your decision by adding
"[Contributor] elects to include this software in this
distribution under the [CDDL or GPL Version 2] license." If you
don't indicate a single choice of license, a recipient has the
option to distribute your version of this file under either the
CDDL, the GPL Version 2 or to extend the choice of license to its
licensees as provided above. However, if you add GPL Version 2
code and therefore, elected the GPL Version 2 license, then the
option applies only if the new code is made subject to such
option by the copyright holder.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
This is the XML Schema for the JSP 2.2 deployment descriptor
types. The JSP 2.2 schema contains all the special
structures and datatypes that are necessary to use JSP files
from a web application.
The contents of this schema is used by the web-common_3_0.xsd
file to define JSP specific content.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
The following conventions apply to all Java EE
deployment descriptor elements unless indicated otherwise.
- In elements that specify a pathname to a file within the
same JAR file, relative filenames (i.e., those not
starting with "/") are considered relative to the root of
the JAR file's namespace. Absolute filenames (i.e., those
starting with "/") also specify names in the root of the
JAR file's namespace. In general, relative names are
preferred. The exception is .war files where absolute
names are preferred for consistency with the Servlet API.
</xsd:documentation>
</xsd:annotation>
<xsd:include schemaLocation="javaee_6.xsd"/>
<!-- **************************************************** -->
<xsd:complexType name="jsp-configType">
<xsd:annotation>
<xsd:documentation>
The jsp-configType is used to provide global configuration
information for the JSP files in a web application. It has
two subelements, taglib and jsp-property-group.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="taglib"
type="javaee:taglibType"
minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element name="jsp-property-group"
type="javaee:jsp-property-groupType"
minOccurs="0"
maxOccurs="unbounded"/>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="jsp-fileType">
<xsd:annotation>
<xsd:documentation>
The jsp-file element contains the full path to a JSP file
within the web application beginning with a `/'.
</xsd:documentation>
</xsd:annotation>
<xsd:simpleContent>
<xsd:restriction base="javaee:pathType"/>
</xsd:simpleContent>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="jsp-property-groupType">
<xsd:annotation>
<xsd:documentation>
The jsp-property-groupType is used to group a number of
files so they can be given global property information.
All files so described are deemed to be JSP files. The
following additional properties can be described:
- Control whether EL is ignored.
- Control whether scripting elements are invalid.
- Indicate pageEncoding information.
- Indicate that a resource is a JSP document (XML).
- Prelude and Coda automatic includes.
- Control whether the character sequence #{ is allowed
when used as a String literal.
- Control whether template text containing only
whitespaces must be removed from the response output.
- Indicate the default contentType information.
- Indicate the default buffering model for JspWriter
- Control whether error should be raised for the use of
undeclared namespaces in a JSP page.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:group ref="javaee:descriptionGroup"/>
<xsd:element name="url-pattern"
type="javaee:url-patternType"
maxOccurs="unbounded"/>
<xsd:element name="el-ignored"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Can be used to easily set the isELIgnored
property of a group of JSP pages. By default, the
EL evaluation is enabled for Web Applications using
a Servlet 2.4 or greater web.xml, and disabled
otherwise.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="page-encoding"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of page-encoding are those of the
pageEncoding page directive. It is a
translation-time error to name different encodings
in the pageEncoding attribute of the page directive
of a JSP page and in a JSP configuration element
matching the page. It is also a translation-time
error to name different encodings in the prolog
or text declaration of a document in XML syntax and
in a JSP configuration element matching the document.
It is legal to name the same encoding through
mulitple mechanisms.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="scripting-invalid"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Can be used to easily disable scripting in a
group of JSP pages. By default, scripting is
enabled.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="is-xml"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
If true, denotes that the group of resources
that match the URL pattern are JSP documents,
and thus must be interpreted as XML documents.
If false, the resources are assumed to not
be JSP documents, unless there is another
property group that indicates otherwise.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="include-prelude"
type="javaee:pathType"
minOccurs="0"
maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>
The include-prelude element is a context-relative
path that must correspond to an element in the
Web Application. When the element is present,
the given path will be automatically included (as
in an include directive) at the beginning of each
JSP page in this jsp-property-group.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="include-coda"
type="javaee:pathType"
minOccurs="0"
maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>
The include-coda element is a context-relative
path that must correspond to an element in the
Web Application. When the element is present,
the given path will be automatically included (as
in an include directive) at the end of each
JSP page in this jsp-property-group.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="deferred-syntax-allowed-as-literal"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The character sequence #{ is reserved for EL expressions.
Consequently, a translation error occurs if the #{
character sequence is used as a String literal, unless
this element is enabled (true). Disabled (false) by
default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="trim-directive-whitespaces"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
Indicates that template text containing only whitespaces
must be removed from the response output. It has no
effect on JSP documents (XML syntax). Disabled (false)
by default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="default-content-type"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of default-content-type are those of the
contentType page directive. It specifies the default
response contentType if the page directive does not include
a contentType attribute.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="buffer"
type="javaee:string"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The valid values of buffer are those of the
buffer page directive. It specifies if buffering should be
used for the output to response, and if so, the size of the
buffer to use.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="error-on-undeclared-namespace"
type="javaee:true-falseType"
minOccurs="0">
<xsd:annotation>
<xsd:documentation>
The default behavior when a tag with unknown namespace is used
in a JSP page (regular syntax) is to silently ignore it. If
set to true, then an error must be raised during the translation
time when an undeclared tag is used in a JSP page. Disabled
(false) by default.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
<!-- **************************************************** -->
<xsd:complexType name="taglibType">
<xsd:annotation>
<xsd:documentation>
The taglibType defines the syntax for declaring in
the deployment descriptor that a tag library is
available to the application. This can be done
to override implicit map entries from TLD files and
from the container.
</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="taglib-uri"
type="javaee:string">
<xsd:annotation>
<xsd:documentation>
A taglib-uri element describes a URI identifying a
tag library used in the web application. The body
of the taglib-uri element may be either an
absolute URI specification, or a relative URI.
There should be no entries in web.xml with the
same taglib-uri value.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="taglib-location"
type="javaee:pathType">
<xsd:annotation>
<xsd:documentation>
the taglib-location element contains the location
(as a resource relative to the root of the web
application) where to find the Tag Library
Description file for the tag library.
</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="id"
type="xsd:ID"/>
</xsd:complexType>
</xsd:schema>

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@ -1,272 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<xsd:schema xmlns="http://www.w3.org/2001/XMLSchema"
targetNamespace="http://java.sun.com/xml/ns/javaee"
xmlns:javaee="http://java.sun.com/xml/ns/javaee"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
elementFormDefault="qualified"
attributeFormDefault="unqualified"
version="3.0">
<xsd:annotation>
<xsd:documentation>
DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
Copyright 2003-2009 Sun Microsystems, Inc. All rights reserved.
The contents of this file are subject to the terms of either the
GNU General Public License Version 2 only ("GPL") or the Common
Development and Distribution License("CDDL") (collectively, the
"License"). You may not use this file except in compliance with
the License. You can obtain a copy of the License at
https://glassfish.dev.java.net/public/CDDL+GPL.html or
glassfish/bootstrap/legal/LICENSE.txt. See the License for the
specific language governing permissions and limitations under the
License.
When distributing the software, include this License Header
Notice in each file and include the License file at
glassfish/bootstrap/legal/LICENSE.txt. Sun designates this
particular file as subject to the "Classpath" exception as
provided by Sun in the GPL Version 2 section of the License file
that accompanied this code. If applicable, add the following
below the License Header, with the fields enclosed by brackets []
replaced by your own identifying information:
"Portions Copyrighted [year] [name of copyright owner]"
Contributor(s):
If you wish your version of this file to be governed by only the
CDDL or only the GPL Version 2, indicate your decision by adding
"[Contributor] elects to include this software in this
distribution under the [CDDL or GPL Version 2] license." If you
don't indicate a single choice of license, a recipient has the
option to distribute your version of this file under either the
CDDL, the GPL Version 2 or to extend the choice of license to its
licensees as provided above. However, if you add GPL Version 2
code and therefore, elected the GPL Version 2 license, then the
option applies only if the new code is made subject to such
option by the copyright holder.
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
<![CDATA[[
This is the XML Schema for the Servlet 3.0 deployment descriptor.
The deployment descriptor must be named "WEB-INF/web.xml" in the
web application's war file. All Servlet deployment descriptors
must indicate the web application schema by using the Java EE
namespace:
http://java.sun.com/xml/ns/javaee
and by indicating the version of the schema by
using the version element as shown below:
<web-app xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="..."
version="3.0">
...
</web-app>
The instance documents may indicate the published version of
the schema using the xsi:schemaLocation attribute for Java EE
namespace with the following location:
http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd
]]>
</xsd:documentation>
</xsd:annotation>
<xsd:annotation>
<xsd:documentation>
The following conventions apply to all Java EE
deployment descriptor elements unless indicated otherwise.
- In elements that specify a pathname to a file within the
same JAR file, relative filenames (i.e., those not
starting with "/") are considered relative to the root of
the JAR file's namespace. Absolute filenames (i.e., those
starting with "/") also specify names in the root of the
JAR file's namespace. In general, relative names are
preferred. The exception is .war files where absolute
names are preferred for consistency with the Servlet API.
</xsd:documentation>
</xsd:annotation>
<xsd:include schemaLocation="web-common_3_0.xsd"/>
<!-- **************************************************** -->
<xsd:element name="web-app"
type="javaee:web-appType">
<xsd:annotation>
<xsd:documentation>
The web-app element is the root of the deployment
descriptor for a web application. Note that the sub-elements
of this element can be in the arbitrary order. Because of
that, the multiplicity of the elements of distributable,
session-config, welcome-file-list, jsp-config, login-config,
and locale-encoding-mapping-list was changed from "?" to "*"
in this schema. However, the deployment descriptor instance
file must not contain multiple elements of session-config,
jsp-config, and login-config. When there are multiple elements of
welcome-file-list or locale-encoding-mapping-list, the container
must concatenate the element contents. The multiple occurence
of the element distributable is redundant and the container
treats that case exactly in the same way when there is only
one distributable.
</xsd:documentation>
</xsd:annotation>
<xsd:unique name="web-common-servlet-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The servlet element contains the name of a servlet.
The name must be unique within the web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:servlet"/>
<xsd:field xpath="javaee:servlet-name"/>
</xsd:unique>
<xsd:unique name="web-common-filter-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The filter element contains the name of a filter.
The name must be unique within the web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:filter"/>
<xsd:field xpath="javaee:filter-name"/>
</xsd:unique>
<xsd:unique name="web-common-ejb-local-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The ejb-local-ref-name element contains the name of an EJB
reference. The EJB reference is an entry in the web
application's environment and is relative to the
java:comp/env context. The name must be unique within
the web application.
It is recommended that name is prefixed with "ejb/".
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:ejb-local-ref"/>
<xsd:field xpath="javaee:ejb-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-ejb-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The ejb-ref-name element contains the name of an EJB
reference. The EJB reference is an entry in the web
application's environment and is relative to the
java:comp/env context. The name must be unique within
the web application.
It is recommended that name is prefixed with "ejb/".
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:ejb-ref"/>
<xsd:field xpath="javaee:ejb-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-resource-env-ref-uniqueness">
<xsd:annotation>
<xsd:documentation>
The resource-env-ref-name element specifies the name of
a resource environment reference; its value is the
environment entry name used in the web application code.
The name is a JNDI name relative to the java:comp/env
context and must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:resource-env-ref"/>
<xsd:field xpath="javaee:resource-env-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-message-destination-ref-uniqueness">
<xsd:annotation>
<xsd:documentation>
The message-destination-ref-name element specifies the name of
a message destination reference; its value is the
environment entry name used in the web application code.
The name is a JNDI name relative to the java:comp/env
context and must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:message-destination-ref"/>
<xsd:field xpath="javaee:message-destination-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-res-ref-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The res-ref-name element specifies the name of a
resource manager connection factory reference. The name
is a JNDI name relative to the java:comp/env context.
The name must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:resource-ref"/>
<xsd:field xpath="javaee:res-ref-name"/>
</xsd:unique>
<xsd:unique name="web-common-env-entry-name-uniqueness">
<xsd:annotation>
<xsd:documentation>
The env-entry-name element contains the name of a web
application's environment entry. The name is a JNDI
name relative to the java:comp/env context. The name
must be unique within a web application.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:env-entry"/>
<xsd:field xpath="javaee:env-entry-name"/>
</xsd:unique>
<xsd:key name="web-common-role-name-key">
<xsd:annotation>
<xsd:documentation>
A role-name-key is specified to allow the references
from the security-role-refs.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:security-role"/>
<xsd:field xpath="javaee:role-name"/>
</xsd:key>
<xsd:keyref name="web-common-role-name-references"
refer="javaee:web-common-role-name-key">
<xsd:annotation>
<xsd:documentation>
The keyref indicates the references from
security-role-ref to a specified role-name.
</xsd:documentation>
</xsd:annotation>
<xsd:selector xpath="javaee:servlet/javaee:security-role-ref"/>
<xsd:field xpath="javaee:role-link"/>
</xsd:keyref>
</xsd:element>
</xsd:schema>

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