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Merge branch 'master' into loinc_loader_update

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James Agnew 2018-03-20 07:53:41 -04:00
commit 308ac63a77
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example-projects/hapi-fhir-jpaserver-cds-example/.gitignore vendored Normal file
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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
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.target
# TeXlipse plugin
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example-projects/hapi-fhir-jpaserver-cds-example/pom.xml Normal file
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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>3.3.0-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.opencds.cqf</groupId>
<artifactId>cqf-ruler</artifactId>
<version>0.1.0-SNAPSHOT</version>
</dependency>
<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>
</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>
<!-- 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>
<!-- 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>com.phloc</groupId>
<artifactId>phloc-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>
<!-- 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>
<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>

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example-projects/hapi-fhir-jpaserver-cds-example/src/main/java/ca/uhn/fhir/jpa/cds/example/CdsHooksServerExample.java Normal file
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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
// }
}

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example-projects/hapi-fhir-jpaserver-cds-example/src/main/java/ca/uhn/fhir/jpa/cds/example/CdsServerExample.java Normal file
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package ca.uhn.fhir.jpa.cds.example;
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.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
import ca.uhn.fhir.jpa.rp.dstu3.ActivityDefinitionResourceProvider;
import ca.uhn.fhir.jpa.rp.dstu3.MeasureResourceProvider;
import ca.uhn.fhir.jpa.rp.dstu3.PlanDefinitionResourceProvider;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
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 ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Meta;
import org.opencds.cqf.providers.FHIRActivityDefinitionResourceProvider;
import org.opencds.cqf.providers.FHIRMeasureResourceProvider;
import org.opencds.cqf.providers.FHIRPlanDefinitionResourceProvider;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
import javax.servlet.ServletException;
import java.util.Collection;
import java.util.List;
public class CdsServerExample extends RestfulServer {
@SuppressWarnings("unchecked")
@Override
protected void initialize() throws ServletException {
super.initialize();
FhirVersionEnum fhirVersion = FhirVersionEnum.DSTU3;
setFhirContext(new FhirContext(fhirVersion));
// Get the spring context from the web container (it's declared in web.xml)
WebApplicationContext myAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
if (myAppCtx == null) {
throw new ServletException("Error retrieving spring context from the web container");
}
String resourceProviderBeanName = "myResourceProvidersDstu3";
List<IResourceProvider> beans = myAppCtx.getBean(resourceProviderBeanName, List.class);
setResourceProviders(beans);
Object systemProvider = myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
setPlainProviders(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.
*/
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);
/*
* 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));
/*
* Load interceptors for the server from Spring (these are defined in FhirServerConfig.java)
*/
Collection<IServerInterceptor> interceptorBeans = myAppCtx.getBeansOfType(IServerInterceptor.class).values();
for (IServerInterceptor interceptor : interceptorBeans) {
this.registerInterceptor(interceptor);
}
/*
* Adding resource providers from the cqf-ruler
*/
// Measure processing
FHIRMeasureResourceProvider measureProvider = new FHIRMeasureResourceProvider(getResourceProviders());
MeasureResourceProvider jpaMeasureProvider = (MeasureResourceProvider) getProvider("Measure");
measureProvider.setDao(jpaMeasureProvider.getDao());
measureProvider.setContext(jpaMeasureProvider.getContext());
// PlanDefinition processing
FHIRPlanDefinitionResourceProvider planDefProvider = new FHIRPlanDefinitionResourceProvider(getResourceProviders());
PlanDefinitionResourceProvider jpaPlanDefProvider =
(PlanDefinitionResourceProvider) getProvider("PlanDefinition");
planDefProvider.setDao(jpaPlanDefProvider.getDao());
planDefProvider.setContext(jpaPlanDefProvider.getContext());
// ActivityDefinition processing
FHIRActivityDefinitionResourceProvider actDefProvider = new FHIRActivityDefinitionResourceProvider(getResourceProviders());
ActivityDefinitionResourceProvider jpaActDefProvider =
(ActivityDefinitionResourceProvider) getProvider("ActivityDefinition");
actDefProvider.setDao(jpaActDefProvider.getDao());
actDefProvider.setContext(jpaActDefProvider.getContext());
try {
unregisterProvider(jpaMeasureProvider);
unregisterProvider(jpaPlanDefProvider);
unregisterProvider(jpaActDefProvider);
} catch (Exception e) {
throw new ServletException("Unable to unregister provider: " + e.getMessage());
}
registerProvider(measureProvider);
registerProvider(planDefProvider);
registerProvider(actDefProvider);
/*
* 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));
}
public IResourceProvider getProvider(String name) {
for (IResourceProvider res : getResourceProviders()) {
if (res.getResourceType().getSimpleName().equals(name)) {
return res;
}
}
throw new IllegalArgumentException("This should never happen!");
}
}

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example-projects/hapi-fhir-jpaserver-cds-example/src/main/java/ca/uhn/fhir/jpa/cds/example/FhirServerConfig.java Normal file
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package ca.uhn.fhir.jpa.cds.example;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory;
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 org.apache.commons.dbcp2.BasicDataSource;
import org.apache.commons.lang3.time.DateUtils;
import org.hibernate.jpa.HibernatePersistenceProvider;
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 javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.util.Properties;
/**
* This is the primary configuration file for the example server
*/
@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.apache.derby.jdbc.EmbeddedDriver());
retVal.setUrl("jdbc:derby:directory:target/jpaserver_derby_files;create=true");
retVal.setUsername("");
retVal.setPassword("");
return retVal;
}
@Bean()
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(dataSource());
retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
retVal.setPersistenceProvider(new HibernatePersistenceProvider());
retVal.setJpaProperties(jpaProperties());
return retVal;
}
private Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.dialect", org.hibernate.dialect.DerbyTenSevenDialect.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.
*/
public IServerInterceptor 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
*/
@Bean(autowire = Autowire.BY_TYPE)
public IServerInterceptor 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;
}
}

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example-projects/hapi-fhir-jpaserver-cds-example/src/main/java/ca/uhn/fhir/jpa/cds/example/FhirTesterConfig.java Normal file
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package ca.uhn.fhir.jpa.cds.example;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.to.FhirTesterMvcConfig;
import ca.uhn.fhir.to.TesterConfig;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
//@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")
.addServer()
.withId("hapi")
.withFhirVersion(FhirVersionEnum.DSTU3)
.withBaseUrl("http://fhirtest.uhn.ca/baseDstu3")
.withName("Public HAPI Test Server");
return retVal;
}
}
//@formatter:on

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<!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/jamesagnew/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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<!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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<!DOCTYPE html>
<html lang="en">
<div th:fragment="banner" class="well">
<th:block th:if="${serverId} == 'home'">
<p>
This is the home for the FHIR test server operated by
<a href="http://uhn.ca">University Health Network</a>. This server
(and the testing application you are currently using to access it)
is entirely built using
<a href="https://github.com/jamesagnew/hapi-fhir">HAPI-FHIR</a>,
a 100% open-source Java implementation of the
<a href="http://hl7.org/implement/standards/fhir/">FHIR specification</a>.
</p>
<p>
Here are some things you might wish to try:
</p>
<ul>
<li>
View a
<a href="http://fhirtest.uhn.ca/search?serverId=home&amp;encoding=json&amp;pretty=true&amp;resource=Patient&amp;param.0.type=string&amp;param.0.name=_id&amp;param.0.0=&amp;resource-search-limit=">list of patients</a>
on this server.
</li>
<li>
Construct a
<a href="http://fhirtest.uhn.ca/resource?serverId=home&amp;encoding=json&amp;pretty=true&amp;resource=Patient">search query</a>
on this server.
</li>
<li>
Access a
<a href="http://fhirtest.uhn.ca/home?serverId=furore">different server</a>
(use the <b>Server</b> menu at the top of the page to see a list of public FHIR servers)
</li>
</ul>
</th:block>
<th:block th:if="${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 style="color: red;">
<span class="glyphicon glyphicon-warning-sign"/>
This is not a production server!
</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>

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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.cds.example.FhirServerConfig
</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>ca.uhn.fhir.jpa.cds.example.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.cds.example.CdsServerExample</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>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>
<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,Prefer</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>

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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 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.AfterClass;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.*;
import java.net.HttpURLConnection;
import java.net.ServerSocket;
import java.net.URL;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Scanner;
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;
@BeforeClass
public static void beforeClass() throws Exception {
String path = Paths.get("").toAbsolutePath().toString();
ourPort = RandomServerPortProvider.findFreePort();
ourServer = new Server(ourPort);
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);
ourServer.start();
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 test data
// Normally, I would use a transaction bundle, but issues with the random ports prevents that...
// So, doing it the old-fashioned way =)
// General
putResource("general-practitioner.json", "Practitioner-12208");
putResource("general-patient.json", "Patient-12214");
putResource("general-fhirhelpers-3.json", "FHIRHelpers");
}
@AfterClass
public static void afterClass() throws Exception {
ourServer.stop();
}
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() : "";
IBaseResource resource = ourCtx.newJsonParser().parseResource(json);
ourClient.update(id, resource);
}
@Test
public void MeasureProcessingTest() {
putResource("measure-processing-library.json", "col-logic");
putResource("measure-processing-measure.json", "col");
putResource("measure-processing-procedure.json", "Procedure-9");
putResource("measure-processing-condition.json", "Condition-13");
putResource("measure-processing-valueset-1.json", "2.16.840.1.113883.3.464.1003.108.11.1001");
putResource("measure-processing-valueset-2.json", "2.16.840.1.113883.3.464.1003.198.12.1019");
putResource("measure-processing-valueset-3.json", "2.16.840.1.113883.3.464.1003.108.12.1020");
putResource("measure-processing-valueset-4.json", "2.16.840.1.113883.3.464.1003.198.12.1010");
putResource("measure-processing-valueset-5.json", "2.16.840.1.113883.3.464.1003.198.12.1011");
Parameters inParams = new Parameters();
inParams.addParameter().setName("patient").setValue(new StringType("Patient-12214"));
inParams.addParameter().setName("startPeriod").setValue(new DateType("2001-01-01"));
inParams.addParameter().setName("endPeriod").setValue(new DateType("2015-03-01"));
Parameters outParams = ourClient
.operation()
.onInstance(new IdDt("Measure", "col"))
.named("$evaluate")
.withParameters(inParams)
.useHttpGet()
.execute();
List<Parameters.ParametersParameterComponent> response = outParams.getParameter();
Assert.assertTrue(!response.isEmpty());
Parameters.ParametersParameterComponent component = response.get(0);
Assert.assertTrue(component.getResource() instanceof MeasureReport);
MeasureReport report = (MeasureReport) component.getResource();
Assert.assertTrue(report.getEvaluatedResources() != null);
for (MeasureReport.MeasureReportGroupComponent group : report.getGroup()) {
if (group.getIdentifier().getValue().equals("history-of-colorectal-cancer")) {
Assert.assertTrue(group.getPopulation().get(0).getCount() > 0);
}
if (group.getIdentifier().getValue().equals("history-of-total-colectomy")) {
Assert.assertTrue(group.getPopulation().get(0).getCount() > 0);
}
}
}
@Test
public void PlanDefinitionApplyTest() throws ClassNotFoundException {
putResource("plandefinition-apply-library.json", "plandefinitionApplyTest");
putResource("plandefinition-apply.json", "apply-example");
Parameters inParams = new Parameters();
inParams.addParameter().setName("patient").setValue(new StringType("Patient-12214"));
Parameters outParams = ourClient
.operation()
.onInstance(new IdDt("PlanDefinition", "apply-example"))
.named("$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!"));
}
@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());
}
//@Test
public void CdsHooksPatientViewTest() throws IOException {
putResource("cds-bcs-library.json", "patient-view");
putResource("cds-bcs-patient.json", "Patient-6532");
putResource("cds-bcs-plandefinition.json", "bcs-decision-support");
putResource("cds-bcs-activitydefinition.json", "mammogram-service-request");
// 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() : "";
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\": \"High risk for opioid overdose - taper now\",\n" +
" \"indicator\": \"warning\",\n" +
" \"detail\": \"Total morphine milligram equivalent (MME) is 20200.700mg/d. Taper to less than 50.\"\n" +
" }\n" +
" ]\n" +
"}";
Assert.assertTrue(
response.toString().replaceAll("\\s+", "")
.equals(expected.replaceAll("\\s+", ""))
);
}
}
class RandomServerPortProvider {
private static List<Integer> ourPorts = new ArrayList<>();
static int findFreePort() {
ServerSocket server;
try {
server = new ServerSocket(0);
int port = server.getLocalPort();
ourPorts.add(port);
server.close();
Thread.sleep(500);
return port;
} catch (IOException | InterruptedException e) {
throw new Error(e);
}
}
public static List<Integer> list() {
return ourPorts;
}
}

19
example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/activitydefinition-apply-library.json Normal file
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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",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">ActivityDefinition $apply operation example.</div>"
},
"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\""
}
]
}

37
example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/cds-bcs-activitydefinition.json Normal file
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{
"resourceType": "ActivityDefinition",
"id": "mammogram-service-request",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">Create ServiceRequest for Mammogrm Procedure</div>"
},
"status": "draft",
"description": "Create ServiceRequest for Mammogram Procedure",
"kind": "ProcedureRequest",
"code": {
"coding": [
{
"system": "http://www.ama-assn.org/go/cpt",
"code": "77056",
"display": "Mammography; bilateral"
}
]
},
"timingTiming": {
"_event": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/cqif-basic-cqlExpression",
"valueString": "Now()"
}
]
}
]
},
"participant": [
{
"type": "practitioner"
}
]
}

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{
"resourceType": "Patient",
"id": "Patient-6532",
"extension": [
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/v3/Race",
"code": "2106-3",
"display": "White"
}
]
}
},
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/v3/Ethnicity",
"code": "2186-5",
"display": "Not Hispanic or Latino"
}
]
}
},
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-religion",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/v3/ReligiousAffiliation",
"code": "1041",
"display": "Roman Catholic Church"
}
]
}
}
],
"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": "000006532"
}
],
"active": true,
"name": [
{
"family": "Brandt",
"given": [
"Edith",
"Elaine"
]
}
],
"telecom": [
{
"system": "phone",
"value": "616-555-1082",
"use": "home"
},
{
"system": "phone",
"value": "616-555-1211",
"use": "mobile"
}
],
"gender": "female",
"birthDate": "1987-07-16",
"address": [
{
"use": "home",
"type": "postal",
"line": [
"893 N Elm Drive"
],
"city": "Grand Rapids",
"district": "Kent County",
"state": "MI",
"postalCode": "49504"
}
]
}

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example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/cds-bcs-plandefinition.json Normal file
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{
"resourceType": "PlanDefinition",
"id": "bcs-decision-support",
"status": "draft",
"library": {
"reference": "Library/patient-view"
},
"action": [
{
"condition": [
{
"kind": "applicability",
"language": "text/cql",
"expression": "Does Patient Qualify?"
}
],
"action": [
{
"condition": [
{
"kind": "applicability",
"language": "text/cql",
"expression": "Needs Mammogram"
}
],
"definition": {
"reference": "ActivityDefinition/mammogram-service-request"
}
}
]
}
]
}

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example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/cds-bcs-request.json Normal file
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{
"hookInstance": "d1577c69-dfbe-44ad-ba6d-3e05e953b2ea",
"fhirServer": "https://sb-fhir-dstu2.smarthealthit.org/smartdstu2/open",
"hook": "patient-view",
"user": "Practitioner/example",
"context": [],
"patient": "Patient/Patient-6535",
"prefetch": {}
}

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example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/general-fhirhelpers-3.json Normal file
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{
"resourceType": "Patient",
"id": "Patient-12214",
"meta": {
"versionId": "1",
"lastUpdated": "2017-07-17T16:34:10.814+00:00"
},
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\">2 <b>N GERIATRIC </b>Jr</div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>7f3672feb3b54789953e012d8aef5246</td></tr><tr><td>Address</td><td><span>202 Burlington Rd. </span><br/><span>Bedford </span><span>MA </span></td></tr><tr><td>Date of birth</td><td><span>07 May 1946</span></td></tr></tbody></table></div>"
},
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/us-core-race",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/v3/Race",
"code": "2106-3",
"display": "White"
}
]
}
},
{
"url": "http://hl7.org/fhir/StructureDefinition/us-core-ethnicity",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/v3/Ethnicity",
"code": "2186-5",
"display": "Not Hispanic or Latino"
}
]
}
},
{
"url": "http://hl7.org/fhir/StructureDefinition/us-core-religion",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/v3/ReligiousAffiliation",
"code": "1007",
"display": "Atheism"
}
]
}
}
],
"identifier": [
{
"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": "7f3672feb3b54789953e012d8aef5246"
}
],
"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"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/us-core-direct",
"valueBoolean": true
}
],
"system": "email",
"value": "2.N.Geriatric@direct.mihintest.org",
"use": "home"
}
],
"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",
"meta": {
"versionId": "1",
"lastUpdated": "2017-07-17T16:34:10.814+00:00"
},
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/us-core-race",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/v3/Race",
"code": "2056-0",
"display": "Black"
}
]
}
},
{
"url": "http://hl7.org/fhir/StructureDefinition/us-core-ethnicity",
"valueCodeableConcept": {
"coding": [
{
"system": "http://hl7.org/fhir/v3/Ethnicity",
"code": "2186-5",
"display": "Not Hispanic or Latino"
}
]
}
},
{
"url": "http://gov.onc.fhir.extension.taxonomy",
"valueCodeableConcept": {
"coding": [
{
"system": "http://org.nucc.taxonomy",
"code": "208D00000X",
"display": "General Practice"
}
]
}
},
{
"url": "http://org.mihin.fhir.extension.electronic-service",
"valueReference": {
"reference": "ElectronicService/ElectronicService-2415",
"display": "Jay.M.Sawyer@direct.mihintest.org"
}
}
],
"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"
}
]
},
"issuer": {
"reference": "Organization/Organization-2000",
"display": "Michigan Department of Licensing and Regulatory Affairs"
}
}
]
}

319
example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/library-col.elm.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<library xmlns="urn:hl7-org:elm:r1" xmlns:t="urn:hl7-org:elm-types:r1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:fhir="http://hl7.org/fhir" xmlns:a="urn:hl7-org:cql-annotations:r1">
<identifier id="COL" version="1"/>
<schemaIdentifier id="urn:hl7-org:elm" version="r1"/>
<usings>
<def localIdentifier="System" uri="urn:hl7-org:elm-types:r1"/>
<def localIdentifier="FHIR" uri="http://hl7.org/fhir" version="1.6"/>
</usings>
<parameters>
<def name="MeasurementPeriod" accessLevel="Public">
<parameterTypeSpecifier xsi:type="IntervalTypeSpecifier">
<pointType name="t:DateTime" xsi:type="NamedTypeSpecifier"/>
</parameterTypeSpecifier>
</def>
</parameters>
<codeSystems>
<def name="CPT" id="urn:oid:2.16.840.1.113883.6.12" accessLevel="Public"/>
<def name="SNOMED-CT" id="urn:oid:2.16.840.1.113883.6.96" accessLevel="Public"/>
<def name="LOINC" id="http://loinc.org" accessLevel="Public"/>
</codeSystems>
<valueSets>
<def name="Malignant Neoplasm of Colon" id="2.16.840.1.113883.3.464.1003.108.11.1001" accessLevel="Public"/>
<def name="Total Colectomy" id="2.16.840.1.113883.3.464.1003.198.12.1019" accessLevel="Public"/>
<def name="Colonoscopy" id="2.16.840.1.113883.3.464.1003.108.12.1020" accessLevel="Public"/>
<def name="Flexible Sigmoidoscopy" id="2.16.840.1.113883.3.464.1003.198.12.1010" accessLevel="Public"/>
<def name="Fecal Occult Blood Test (FOBT)" id="2.16.840.1.113883.3.464.1003.198.12.1011" accessLevel="Public"/>
</valueSets>
<statements>
<def name="Patient" context="Patient">
<expression xsi:type="SingletonFrom">
<operand dataType="fhir:Patient" xsi:type="Retrieve"/>
</expression>
</def>
<def name="Lookback Interval One Year" context="Patient" accessLevel="Public">
<expression lowClosed="true" highClosed="true" xsi:type="Interval">
<low xsi:type="Subtract">
<operand xsi:type="Start">
<operand name="MeasurementPeriod" xsi:type="ParameterRef"/>
</operand>
<operand value="1" unit="years" xsi:type="Quantity"/>
</low>
<high xsi:type="End">
<operand name="MeasurementPeriod" xsi:type="ParameterRef"/>
</high>
</expression>
</def>
<def name="Lookback Interval Five Years" context="Patient" accessLevel="Public">
<expression lowClosed="true" highClosed="true" xsi:type="Interval">
<low xsi:type="Subtract">
<operand xsi:type="Start">
<operand name="MeasurementPeriod" xsi:type="ParameterRef"/>
</operand>
<operand value="5" unit="years" xsi:type="Quantity"/>
</low>
<high xsi:type="End">
<operand name="MeasurementPeriod" xsi:type="ParameterRef"/>
</high>
</expression>
</def>
<def name="Lookback Interval Ten Years" context="Patient" accessLevel="Public">
<expression lowClosed="true" highClosed="true" xsi:type="Interval">
<low xsi:type="Subtract">
<operand xsi:type="Start">
<operand name="MeasurementPeriod" xsi:type="ParameterRef"/>
</operand>
<operand value="10" unit="years" xsi:type="Quantity"/>
</low>
<high xsi:type="End">
<operand name="MeasurementPeriod" xsi:type="ParameterRef"/>
</high>
</expression>
</def>
<def name="In Demographic" context="Patient" accessLevel="Public">
<expression xsi:type="GreaterOrEqual">
<operand precision="Year" xsi:type="CalculateAgeAt">
<operand path="birthDate.value" xsi:type="Property">
<source name="Patient" xsi:type="ExpressionRef"/>
</operand>
<operand xsi:type="Start">
<operand name="MeasurementPeriod" xsi:type="ParameterRef"/>
</operand>
</operand>
<operand valueType="t:Integer" value="50" xsi:type="Literal"/>
</expression>
</def>
<def name="Hx Colorectal Cancer" context="Patient" accessLevel="Public">
<expression xsi:type="Query">
<source alias="C">
<expression dataType="fhir:Condition" codeProperty="code" xsi:type="Retrieve">
<codes name="Malignant Neoplasm of Colon" xsi:type="ValueSetRef"/>
</expression>
</source>
<where xsi:type="And">
<operand xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="clinicalStatus" scope="C" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="active" xsi:type="Literal"/>
</operand>
<operand xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="verificationStatus" scope="C" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="confirmed" xsi:type="Literal"/>
</operand>
</where>
</expression>
</def>
<def name="Hx Total Colectomy" context="Patient" accessLevel="Public">
<expression xsi:type="Query">
<source alias="T">
<expression dataType="fhir:Procedure" codeProperty="code" xsi:type="Retrieve">
<codes name="Total Colectomy" xsi:type="ValueSetRef"/>
</expression>
</source>
<where xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="status" scope="T" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="completed" xsi:type="Literal"/>
</where>
</expression>
</def>
<def name="Colonoscopy Performed" context="Patient" accessLevel="Public">
<expression xsi:type="Query">
<source alias="C">
<expression dataType="fhir:Procedure" codeProperty="code" xsi:type="Retrieve">
<codes name="Colonoscopy" xsi:type="ValueSetRef"/>
</expression>
</source>
<where xsi:type="And">
<operand xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="status" scope="C" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="completed" xsi:type="Literal"/>
</operand>
<operand xsi:type="In">
<operand path="value" xsi:type="Property">
<source path="end" xsi:type="Property">
<source path="performedPeriod" scope="C" xsi:type="Property"/>
</source>
</operand>
<operand name="Lookback Interval Ten Years" xsi:type="ExpressionRef"/>
</operand>
</where>
</expression>
</def>
<def name="Colonoscopy Results" context="Patient" accessLevel="Public">
<expression xsi:type="Query">
<source alias="C">
<expression dataType="fhir:Observation" codeProperty="code" xsi:type="Retrieve">
<codes name="Colonoscopy" xsi:type="ValueSetRef"/>
</expression>
</source>
<where xsi:type="And">
<operand xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="status" scope="C" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="final" xsi:type="Literal"/>
</operand>
<operand xsi:type="In">
<operand path="value" xsi:type="Property">
<source path="effectiveDateTime" scope="C" xsi:type="Property"/>
</operand>
<operand name="Lookback Interval Ten Years" xsi:type="ExpressionRef"/>
</operand>
</where>
</expression>
</def>
<def name="Sigmoidoscopy Procedure" context="Patient" accessLevel="Public">
<expression xsi:type="Query">
<source alias="S">
<expression dataType="fhir:Procedure" codeProperty="code" xsi:type="Retrieve">
<codes name="Flexible Sigmoidoscopy" xsi:type="ValueSetRef"/>
</expression>
</source>
<where xsi:type="And">
<operand xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="status" scope="S" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="completed" xsi:type="Literal"/>
</operand>
<operand xsi:type="In">
<operand path="value" xsi:type="Property">
<source path="end" xsi:type="Property">
<source path="performedPeriod" scope="S" xsi:type="Property"/>
</source>
</operand>
<operand name="Lookback Interval Five Years" xsi:type="ExpressionRef"/>
</operand>
</where>
</expression>
</def>
<def name="Sigmoidoscopy Observation" context="Patient" accessLevel="Public">
<expression xsi:type="Query">
<source alias="O">
<expression dataType="fhir:Observation" codeProperty="code" xsi:type="Retrieve">
<codes name="Flexible Sigmoidoscopy" xsi:type="ValueSetRef"/>
</expression>
</source>
<where xsi:type="And">
<operand xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="status" scope="O" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="final" xsi:type="Literal"/>
</operand>
<operand xsi:type="In">
<operand path="value" xsi:type="Property">
<source path="effectiveDateTime" scope="O" xsi:type="Property"/>
</operand>
<operand name="Lookback Interval Five Years" xsi:type="ExpressionRef"/>
</operand>
</where>
</expression>
</def>
<def name="FOBT Procedure" context="Patient" accessLevel="Public">
<expression xsi:type="Query">
<source alias="F">
<expression dataType="fhir:Procedure" codeProperty="code" xsi:type="Retrieve">
<codes name="Fecal Occult Blood Test (FOBT)" xsi:type="ValueSetRef"/>
</expression>
</source>
<where xsi:type="And">
<operand xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="status" scope="F" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="completed" xsi:type="Literal"/>
</operand>
<operand xsi:type="In">
<operand path="value" xsi:type="Property">
<source path="end" xsi:type="Property">
<source path="performedPeriod" scope="F" xsi:type="Property"/>
</source>
</operand>
<operand name="Lookback Interval One Year" xsi:type="ExpressionRef"/>
</operand>
</where>
</expression>
</def>
<def name="FOBT Observation" context="Patient" accessLevel="Public">
<expression xsi:type="Query">
<source alias="O">
<expression dataType="fhir:Observation" codeProperty="code" xsi:type="Retrieve">
<codes name="Fecal Occult Blood Test (FOBT)" xsi:type="ValueSetRef"/>
</expression>
</source>
<where xsi:type="And">
<operand xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="status" scope="O" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="final" xsi:type="Literal"/>
</operand>
<operand xsi:type="In">
<operand path="value" xsi:type="Property">
<source path="effectiveDateTime" scope="O" xsi:type="Property"/>
</operand>
<operand name="Lookback Interval One Year" xsi:type="ExpressionRef"/>
</operand>
</where>
</expression>
</def>
<def name="Colonoscopy Procedure" context="Patient" accessLevel="Public">
<expression xsi:type="Query">
<source alias="C">
<expression dataType="fhir:Procedure" codeProperty="code" xsi:type="Retrieve">
<codes name="Colonoscopy" xsi:type="ValueSetRef"/>
</expression>
</source>
<where xsi:type="And">
<operand xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="status" scope="C" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="completed" xsi:type="Literal"/>
</operand>
<operand xsi:type="In">
<operand path="value" xsi:type="Property">
<source path="end" xsi:type="Property">
<source path="performedPeriod" scope="C" xsi:type="Property"/>
</source>
</operand>
<operand name="Lookback Interval Ten Years" xsi:type="ExpressionRef"/>
</operand>
</where>
</expression>
</def>
<def name="Colonoscopy Observation" context="Patient" accessLevel="Public">
<expression xsi:type="Query">
<source alias="O">
<expression dataType="fhir:Observation" codeProperty="code" xsi:type="Retrieve">
<codes name="Colonoscopy" xsi:type="ValueSetRef"/>
</expression>
</source>
<where xsi:type="And">
<operand xsi:type="Equal">
<operand path="value" xsi:type="Property">
<source path="status" scope="O" xsi:type="Property"/>
</operand>
<operand valueType="t:String" value="final" xsi:type="Literal"/>
</operand>
<operand xsi:type="In">
<operand path="value" xsi:type="Property">
<source path="effectiveDateTime" scope="O" xsi:type="Property"/>
</operand>
<operand name="Lookback Interval Ten Years" xsi:type="ExpressionRef"/>
</operand>
</where>
</expression>
</def>
</statements>
</library>

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<?xml version="1.0" encoding="UTF-8"?>
<Measure xmlns="http://hl7.org/fhir" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://hl7.org/fhir ../../schema/measure.xsd">
<id value="col"/>
<text>
<status value="additional"/>
<div xmlns="http://www.w3.org/1999/xhtml">
Cohort definition for Colorectal Cancer Screening.
</div>
</text>
<identifier>
<use value="official"/>
<system value="http://hl7.org/fhir/cqi/ecqm/Measure/Identifier/payer-extract"/>
<value value="COL"/>
</identifier>
<version value="1.0.0"/>
<title value="Colorectal Cancer Screening. Cohort Definition"/>
<status value="active"/>
<experimental value="true"/>
<description value="Colorectal Cancer Screening. Cohort Definition"/>
<topic>
<coding>
<system value="http://hl7.org/fhir/c80-doc-typecodes"/>
<code value="57024-2"/>
</coding>
</topic>
<library>
<reference value="Library/col-logic"/>
</library>
<scoring value="cohort"/>
<group>
<identifier>
<value value="in-demographic"/>
</identifier>
<population>
<type value="initial-population"/>
<identifier>
<value value="in-demographic"/>
</identifier>
<criteria value="In Demographic"/>
</population>
</group>
<group>
<identifier>
<value value="history-of-colorectal-cancer"/>
</identifier>
<population>
<type value="initial-population"/>
<identifier>
<value value="history-of-colorectal-cancer"/>
</identifier>
<criteria value="Hx Colorectal Cancer"/>
</population>
</group>
<group>
<identifier>
<value value="history-of-total-colectomy"/>
</identifier>
<population>
<type value="initial-population"/>
<identifier>
<value value="history-of-total-colectomy"/>
</identifier>
<criteria value="Hx Total Colectomy"/>
</population>
</group>
<group>
<identifier>
<value value="colonoscopy-performed"/>
</identifier>
<population>
<type value="initial-population"/>
<identifier>
<value value="colonoscopy-performed"/>
</identifier>
<criteria value="Colonoscopy Performed"/>
</population>
</group>
<group>
<identifier>
<value value="colonoscopy-results"/>
</identifier>
<population>
<type value="initial-population"/>
<identifier>
<value value="colonoscopy-results"/>
</identifier>
<criteria value="Colonoscopy Results"/>
</population>
</group>
<group>
<identifier>
<value value="sigmoidoscopy-procedure"/>
</identifier>
<population>
<type value="initial-population"/>
<identifier>
<value value="sigmoidoscopy-procedure"/>
</identifier>
<criteria value="Sigmoidoscopy Procedure"/>
</population>
</group>
<group>
<identifier>
<value value="sigmoidoscopy-observation"/>
</identifier>
<population>
<type value="initial-population"/>
<identifier>
<value value="sigmoidoscopy-observation"/>
</identifier>
<criteria value="Sigmoidoscopy Observation"/>
</population>
</group>
<group>
<identifier>
<value value="fobt-procedure"/>
</identifier>
<population>
<type value="initial-population"/>
<identifier>
<value value="fobt-procedure"/>
</identifier>
<criteria value="FOBT Procedure"/>
</population>
</group>
<group>
<identifier>
<value value="fobt-observation"/>
</identifier>
<population>
<type value="initial-population"/>
<identifier>
<value value="fobt-observation"/>
</identifier>
<criteria value="FOBT Observation"/>
</population>
</group>
</Measure>

49
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{
"resourceType": "Condition",
"id": "Condition-13",
"meta": {
"versionId": "1",
"lastUpdated": "2017-09-09T21:52:17.035-06:00"
},
"extension": [
{
"url": "http://mihin.org/fhir/templateId",
"valueString": "2.16.840.1.113883.10.20.22.4.3"
},
{
"url": "http://mihin.org/fhir/templateId",
"valueString": "2.16.840.1.113883.10.20.24.3.137"
}
],
"clinicalStatus": "active",
"verificationStatus": "confirmed",
"category": [
{
"coding": [
{
"system": "http://hl7.org/fhir/condition-category",
"code": "diagnosis",
"display": "Diagnosis"
}
],
"text": "This is a judgment made by a healthcare provider that the patient has a particular disease or condition"
}
],
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "363414004"
}
],
"text": "Diagnosis: Malignant Neoplasm Of Colon"
},
"subject": {
"reference": "Patient/Patient-12214",
"display": "2 N Geriatric Jr"
},
"asserter": {
"reference": "Practitioner/Practitioner-12208",
"display": "Jay McCann Sawyer MD"
}
}

22
example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/measure-processing-library.json Normal file
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158
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{
"resourceType": "Measure",
"id": "col",
"meta": {
"versionId": "1",
"lastUpdated": "2017-09-09T21:26:03.890-06:00"
},
"text": {
"status": "additional",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n Cohort definition for Colorectal Cancer Screening.\n </div>"
},
"identifier": [
{
"use": "official",
"system": "http://hl7.org/fhir/cqi/ecqm/Measure/Identifier/payer-extract",
"value": "COL"
}
],
"version": "1.0.0",
"title": "Colorectal Cancer Screening. Cohort Definition",
"status": "active",
"experimental": true,
"description": "Colorectal Cancer Screening. Cohort Definition",
"topic": [
{
"coding": [
{
"system": "http://hl7.org/fhir/c80-doc-typecodes",
"code": "57024-2"
}
]
}
],
"library": [
{
"reference": "Library/col-logic"
}
],
"group": [
{
"identifier": {
"value": "in-demographic"
},
"population": [
{
"identifier": {
"value": "in-demographic"
},
"criteria": "In Demographic"
}
]
},
{
"identifier": {
"value": "history-of-colorectal-cancer"
},
"population": [
{
"identifier": {
"value": "history-of-colorectal-cancer"
},
"criteria": "Hx Colorectal Cancer"
}
]
},
{
"identifier": {
"value": "history-of-total-colectomy"
},
"population": [
{
"identifier": {
"value": "history-of-total-colectomy"
},
"criteria": "Hx Total Colectomy"
}
]
},
{
"identifier": {
"value": "colonoscopy-performed"
},
"population": [
{
"identifier": {
"value": "colonoscopy-performed"
},
"criteria": "Colonoscopy Performed"
}
]
},
{
"identifier": {
"value": "colonoscopy-results"
},
"population": [
{
"identifier": {
"value": "colonoscopy-results"
},
"criteria": "Colonoscopy Results"
}
]
},
{
"identifier": {
"value": "sigmoidoscopy-procedure"
},
"population": [
{
"identifier": {
"value": "sigmoidoscopy-procedure"
},
"criteria": "Sigmoidoscopy Procedure"
}
]
},
{
"identifier": {
"value": "sigmoidoscopy-observation"
},
"population": [
{
"identifier": {
"value": "sigmoidoscopy-observation"
},
"criteria": "Sigmoidoscopy Observation"
}
]
},
{
"identifier": {
"value": "fobt-procedure"
},
"population": [
{
"identifier": {
"value": "fobt-procedure"
},
"criteria": "FOBT Procedure"
}
]
},
{
"identifier": {
"value": "fobt-observation"
},
"population": [
{
"identifier": {
"value": "fobt-observation"
},
"criteria": "FOBT Observation"
}
]
}
]
}

68
example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/measure-processing-procedure.json Normal file
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{
"resourceType": "Procedure",
"id": "Procedure-9",
"meta": {
"versionId": "1",
"lastUpdated": "2017-09-09T21:52:35.933-06:00"
},
"extension": [
{
"url": "http://mihin.org/fhir/templateId",
"valueString": "2.16.840.1.113883.10.20.24.3.64"
},
{
"url": "http://mihin.org/fhir/templateId",
"valueString": "2.16.840.1.113883.10.20.22.4.14"
}
],
"identifier": [
{
"system": "http://hl7.org/fhir/identifier",
"value": "1.3.6.1.4.1.115:579f4eb5aeac500a550c5c7b"
}
],
"status": "completed",
"category": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "387713003",
"display": "Surgical Procedure"
}
]
},
"code": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "36192008"
}
],
"text": "Procedure, Performed: Total Colectomy"
},
"subject": {
"reference": "Patient/Patient-12214",
"display": "2 N Geriatric Jr"
},
"performedPeriod": {
"start": "2010-10-12T06:00:00-04:00",
"end": "2010-10-12T08:15:00-04:00"
},
"performer": [
{
"role": {
"coding": [
{
"system": "http://hl7.org/fhir/ValueSet/performer-role",
"code": "112247003",
"display": "Medical doctor (occupation)"
}
]
},
"actor": {
"reference": "Practitioner/Practitioner-12208",
"display": "Jay McCann Sawyer MD"
}
}
]
}

416
example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/measure-processing-valueset-1.json Normal file
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{
"resourceType": "ValueSet",
"id": "2.16.840.1.113883.3.464.1003.108.11.1001",
"meta": {
"versionId": "3",
"lastUpdated": "2017-07-25T09:54:33.579+00:00"
},
"url": "http://measure.eval.kanvix.com/cqf-ruler/baseDstu3/Valueset/2.16.840.1.113883.3.464.1003.108.11.1001",
"name": "Malignant Neoplasm of Colon (SNOMED CT) eCQM",
"status": "active",
"compose": {
"include": [
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"concept": [
{
"code": "187758006"
},
{
"code": "109838007"
},
{
"code": "1701000119104"
},
{
"code": "187757001"
},
{
"code": "269533000"
},
{
"code": "269544008"
},
{
"code": "285312008"
},
{
"code": "285611007"
},
{
"code": "301756000"
},
{
"code": "312111009"
},
{
"code": "312112002"
},
{
"code": "312113007"
},
{
"code": "312114001"
},
{
"code": "312115000"
},
{
"code": "314965007"
},
{
"code": "315058005"
},
{
"code": "363406005"
},
{
"code": "363407001"
},
{
"code": "363408006"
},
{
"code": "363409003"
},
{
"code": "363410008"
},
{
"code": "363412000"
},
{
"code": "363413005"
},
{
"code": "363414004"
},
{
"code": "363510005"
},
{
"code": "425178004"
},
{
"code": "449218003"
},
{
"code": "93683002"
},
{
"code": "93761005"
},
{
"code": "93771007"
},
{
"code": "93826009"
},
{
"code": "93980002"
},
{
"code": "94006002"
},
{
"code": "94072004"
},
{
"code": "94105000"
},
{
"code": "94179005"
},
{
"code": "94260004"
},
{
"code": "94271003"
},
{
"code": "94328005"
},
{
"code": "94509004"
},
{
"code": "94538001"
},
{
"code": "94604000"
},
{
"code": "94643001"
}
]
}
]
},
"expansion": {
"identifier": "http://open-api2.hspconsortium.org/payerextract/data/ValueSet/2.16.840.1.113883.3.464.1003.108.11.1001",
"timestamp": "2016-09-19T14:05:21.939-04:00",
"total": 43,
"offset": 0,
"contains": [
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "425178004",
"display": "Adenocarcinoma of rectosigmoid junction"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "301756000",
"display": "Adenocarcinoma of sigmoid colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "312111009",
"display": "Carcinoma of ascending colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "269533000",
"display": "Carcinoma of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "312113007",
"display": "Carcinoma of descending colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "312114001",
"display": "Carcinoma of hepatic flexure"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "285312008",
"display": "Carcinoma of sigmoid colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "312115000",
"display": "Carcinoma of splenic flexure"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "269544008",
"display": "Carcinoma of the rectosigmoid junction"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "312112002",
"display": "Carcinoma of transverse colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "315058005",
"display": "Lynch syndrome"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "314965007",
"display": "Local recurrence of malignant tumor of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "449218003",
"display": "Lymphoma of sigmoid colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "187758006",
"display": "Malignant neoplasm of other specified sites of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "187757001",
"display": "Malignant neoplasm, overlapping lesion of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "363412000",
"display": "Malignant tumor of ascending colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "363406005",
"display": "Malignant tumor of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "363409003",
"display": "Malignant tumor of descending colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "363407001",
"display": "Malignant tumor of hepatic flexure"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "363510005",
"display": "Malignant tumor of large intestine"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "363414004",
"display": "Malignant tumor of rectosigmoid junction"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "363410008",
"display": "Malignant tumor of sigmoid colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "363413005",
"display": "Malignant tumor of splenic flexure"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "363408006",
"display": "Malignant tumor of transverse colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "285611007",
"display": "Metastasis to colon of unknown primary"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "109838007",
"display": "Overlapping malignant neoplasm of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "1701000119104",
"display": "Primary adenocarcinoma of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "93683002",
"display": "Primary malignant neoplasm of ascending colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "93761005",
"display": "Primary malignant neoplasm of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "93771007",
"display": "Primary malignant neoplasm of descending colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "93826009",
"display": "Primary malignant neoplasm of hepatic flexure of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "93980002",
"display": "Primary malignant neoplasm of rectosigmoid junction"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94006002",
"display": "Primary malignant neoplasm of sigmoid colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94072004",
"display": "Primary malignant neoplasm of splenic flexure of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94105000",
"display": "Primary malignant neoplasm of transverse colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94179005",
"display": "Secondary malignant neoplasm of ascending colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94260004",
"display": "Secondary malignant neoplasm of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94271003",
"display": "Secondary malignant neoplasm of descending colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94328005",
"display": "Secondary malignant neoplasm of hepatic flexure of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94509004",
"display": "Secondary malignant neoplasm of rectosigmoid junction"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94538001",
"display": "Secondary malignant neoplasm of sigmoid colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94604000",
"display": "Secondary malignant neoplasm of splenic flexure of colon"
},
{
"system": "http://snomed.info/sct",
"version": "2015.03.14AB",
"code": "94643001",
"display": "Secondary malignant neoplasm of transverse colon"
}
]
}
}

181
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{
"resourceType": "ValueSet",
"id": "2.16.840.1.113883.3.464.1003.198.12.1019",
"meta": {
"versionId": "3",
"lastUpdated": "2017-07-25T09:54:33.579+00:00"
},
"url": "http://measure.eval.kanvix.com/cql-measure-processor/baseDstu3/Valueset/2.16.840.1.113883.3.464.1003.198.12.1019 ",
"name": "Total Colectomy eMeasure",
"compose": {
"include": [
{
"system": "http://www.ama-assn.org/go/cpt",
"version": "2016.1.15AA",
"concept": [
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421
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208
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"system": "http://www.ama-assn.org/go/cpt",
"code": "45342",
"display": "Sigmoidoscopy, flexible; with transendoscopic ultrasound guided intramural or transmural fine needle aspiration/biopsy(s)"
}
]
}
}

147
example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/measure-processing-valueset-5.json Normal file
View File

@ -0,0 +1,147 @@
{
"resourceType": "ValueSet",
"id": "2.16.840.1.113883.3.464.1003.198.12.1011",
"meta": {
"versionId": "3",
"lastUpdated": "2017-07-25T09:54:33.579+00:00"
},
"url": "http://measure.eval.kanvix.com/cql-measure-processor/baseDstu3/Valueset/2.16.840.1.113883.3.464.1003.198.12.1011",
"name": "Fecal Occult Blood Test (FOBT) eMeasure",
"compose": {
"include": [
{
"system": "http://loinc.org",
"version": "2.44.13AA",
"concept": [
{
"code": "27396-1"
},
{
"code": "58453-2"
},
{
"code": "2335-8"
},
{
"code": "14563-1"
},
{
"code": "14564-9"
},
{
"code": "14565-6"
},
{
"code": "12503-9"
},
{
"code": "12504-7"
},
{
"code": "27401-9"
},
{
"code": "27925-7"
},
{
"code": "27926-5"
},
{
"code": "29771-3"
},
{
"code": "57905-2"
},
{
"code": "56490-6"
},
{
"code": "56491-4"
}
]
}
]
},
"expansion": {
"timestamp": "2016-09-20T13:32:34.390-04:00",
"total": 15,
"offset": 0,
"contains": [
{
"system": "http://loinc.org",
"code": "27396-1",
"display": "Hemoglobin.gastrointestinal [Mass/mass] in Stool"
},
{
"system": "http://loinc.org",
"code": "58453-2",
"display": "Hemoglobin.gastrointestinal [Mass/volume] in Stool by Immunologic method"
},
{
"system": "http://loinc.org",
"code": "2335-8",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool"
},
{
"system": "http://loinc.org",
"code": "14563-1",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool --1st specimen"
},
{
"system": "http://loinc.org",
"code": "14564-9",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool --2nd specimen"
},
{
"system": "http://loinc.org",
"code": "14565-6",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool --3rd specimen"
},
{
"system": "http://loinc.org",
"code": "12503-9",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool --4th specimen"
},
{
"system": "http://loinc.org",
"code": "12504-7",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool --5th specimen"
},
{
"system": "http://loinc.org",
"code": "27401-9",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool --6th specimen"
},
{
"system": "http://loinc.org",
"code": "27925-7",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool --7th specimen"
},
{
"system": "http://loinc.org",
"code": "27926-5",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool --8th specimen"
},
{
"system": "http://loinc.org",
"code": "29771-3",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool by Immunologic method"
},
{
"system": "http://loinc.org",
"code": "57905-2",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool by Immunologic method --1st specimen"
},
{
"system": "http://loinc.org",
"code": "56490-6",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool by Immunologic method --2nd specimen"
},
{
"system": "http://loinc.org",
"code": "56491-4",
"display": "Hemoglobin.gastrointestinal [Presence] in Stool by Immunologic method --3rd specimen"
}
]
}
}

19
example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/plandefinition-apply-library.json Normal file
View File

@ -0,0 +1,19 @@
{
"resourceType": "Library",
"id": "plandefinitionApplyTest",
"version": "1.0",
"status": "draft",
"type": {
"coding": [
{
"code": "logic-library"
}
]
},
"content": [
{
"contentType": "text/cql",
"data": "bGlicmFyeSBwbGFuZGVmaW5pdGlvbkFwcGx5VGVzdCB2ZXJzaW9uICcxLjAnDQoNCmRlZmluZSBSZXN1bHRzOg0KICAgIHRydWUNCg0KZGVmaW5lICJEeW5hbWljIERldGFpbCBEZWZpbml0aW9uIjoNCiAgICAnVGhpcyBpcyBhIGR5bmFtaWMgZGVmaW5pdGlvbiEn"
}
]
}

59
example-projects/hapi-fhir-jpaserver-cds-example/src/test/resources/ca/uhn/fhir/jpa/cds/example/plandefinition-apply.json Normal file
View File

@ -0,0 +1,59 @@
{
"resourceType": "PlanDefinition",
"id": "apply-example",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">General PlanDefinition $apply example resource</div>"
},
"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\""
}
]
}
]
}

2
hapi-fhir-base/pom.xml
View File

@ -133,7 +133,7 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<!--

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
View File

@ -149,8 +149,12 @@ public class FhirContext {
myVersion = FhirVersionEnum.DSTU2.getVersionImplementation();
} else if (FhirVersionEnum.DSTU2_HL7ORG.isPresentOnClasspath()) {
myVersion = FhirVersionEnum.DSTU2_HL7ORG.getVersionImplementation();
} else if (FhirVersionEnum.DSTU2_1.isPresentOnClasspath()) {
myVersion = FhirVersionEnum.DSTU2_1.getVersionImplementation();
} else if (FhirVersionEnum.DSTU3.isPresentOnClasspath()) {
myVersion = FhirVersionEnum.DSTU3.getVersionImplementation();
} else if (FhirVersionEnum.R4.isPresentOnClasspath()) {
myVersion = FhirVersionEnum.R4.getVersionImplementation();
} else {
throw new IllegalStateException(getLocalizer().getMessage(FhirContext.class, "noStructures"));
}

25
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnum.java
View File

@ -605,4 +605,29 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
}
public static final class ExtensionResourceMetadataKey extends ResourceMetadataKeyEnum<ExtensionDt> {
public ExtensionResourceMetadataKey(String url) {
super(url);
}
@Override
public ExtensionDt get(IResource theResource) {
Object retValObj = theResource.getResourceMetadata().get(this);
if (retValObj == null) {
return null;
} else if (retValObj instanceof ExtensionDt) {
return (ExtensionDt) retValObj;
}
throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName()
+ "' in resource metadata for key " + this.name() + " - Expected "
+ ExtensionDt.class.getCanonicalName());
}
@Override
public void put(IResource theResource, ExtensionDt theObject) {
theResource.getResourceMetadata().put(this, theObject);
}
}
}

12
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -918,6 +918,18 @@ public abstract class BaseParser implements IParser {
throw new DataFormatException(nextChild + " has no child of type " + theType);
}
protected List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> getExtensionMetadataKeys(IResource resource) {
List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> extensionMetadataKeys = new ArrayList<Map.Entry<ResourceMetadataKeyEnum<?>, Object>>();
for (Map.Entry<ResourceMetadataKeyEnum<?>, Object> entry : resource.getResourceMetadata().entrySet()) {
if (entry.getKey() instanceof ResourceMetadataKeyEnum.ExtensionResourceMetadataKey) {
extensionMetadataKeys.add(entry);
}
}
return extensionMetadataKeys;
}
protected static <T> List<T> extractMetadataListNotNull(IResource resource, ResourceMetadataKeyEnum<List<T>> key) {
List<? extends T> securityLabels = key.get(resource);
if (securityLabels == null) {

27
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -45,10 +45,7 @@ import java.io.IOException;
import java.io.Reader;
import java.io.Writer;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import java.util.*;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.ID_DATATYPE;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_DATATYPE;
@ -654,8 +651,9 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
if (isBlank(versionIdPart)) {
versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
}
List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> extensionMetadataKeys = getExtensionMetadataKeys(resource);
if (super.shouldEncodeResourceMeta(resource) && ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) {
if (super.shouldEncodeResourceMeta(resource) && (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, tags, profiles) == false) || !extensionMetadataKeys.isEmpty()) {
beginObject(theEventWriter, "meta");
writeOptionalTagWithTextNode(theEventWriter, "versionId", versionIdPart);
writeOptionalTagWithTextNode(theEventWriter, "lastUpdated", updated);
@ -695,6 +693,8 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
theEventWriter.endArray();
}
addExtensionMetadata(theResDef, theResource, theContainedResource, theSubResource, extensionMetadataKeys, resDef, theEventWriter);
theEventWriter.endObject(); // end meta
}
}
@ -704,6 +704,23 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
theEventWriter.endObject();
}
private void addExtensionMetadata(RuntimeResourceDefinition theResDef, IBaseResource theResource,
boolean theContainedResource, boolean theSubResource,
List<Map.Entry<ResourceMetadataKeyEnum<?>, Object>> extensionMetadataKeys,
RuntimeResourceDefinition resDef,
JsonLikeWriter theEventWriter) throws IOException {
if (extensionMetadataKeys.isEmpty()) {
return;
}
ExtensionDt metaResource = new ExtensionDt();
for (Map.Entry<ResourceMetadataKeyEnum<?>, Object> entry : extensionMetadataKeys) {
metaResource.addUndeclaredExtension((ExtensionDt) entry.getValue());
}
encodeCompositeElementToStreamWriter(theResDef, theResource, metaResource, theEventWriter, theContainedResource, theSubResource, new CompositeChildElement(resDef, theSubResource));
}
/**
* This is useful only for the two cases where extensions are encoded as direct children (e.g. not in some object
* called _name): resource extensions, and extension extensions

19
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java
View File

@ -841,6 +841,25 @@ class ParserState<T> {
}
}
@Override
public void enteringNewElementExtension(StartElement theElem, String theUrlAttr, boolean theIsModifier, final String baseServerUrl) {
ResourceMetadataKeyEnum.ExtensionResourceMetadataKey resourceMetadataKeyEnum = new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(theUrlAttr);
Object metadataValue = myMap.get(resourceMetadataKeyEnum);
ExtensionDt newExtension;
if (metadataValue == null) {
newExtension = new ExtensionDt(theIsModifier);
} else if (metadataValue instanceof ExtensionDt) {
newExtension = (ExtensionDt) metadataValue;
} else {
throw new IllegalStateException("Expected ExtensionDt as custom resource metadata type, got: " + metadataValue.getClass().getSimpleName());
}
newExtension.setUrl(theUrlAttr);
myMap.put(resourceMetadataKeyEnum, newExtension);
ExtensionState newState = new ExtensionState(getPreResourceState(), newExtension);
push(newState);
}
}
private class MetaVersionElementState extends BaseState {

15
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ReferenceParam.java
View File

@ -104,24 +104,33 @@ public class ReferenceParam extends BaseParam /*implements IQueryParameterType*/
void doSetValueAsQueryToken(FhirContext theContext, String theParamName, String theQualifier, String theValue) {
String q = theQualifier;
String resourceType = null;
boolean skipSetValue = false;
if (isNotBlank(q)) {
if (q.startsWith(":")) {
int nextIdx = q.indexOf('.');
if (nextIdx != -1) {
resourceType = q.substring(1, nextIdx);
myChain = q.substring(nextIdx + 1);
// type is explicitly defined so use it
myId.setParts(null, resourceType, theValue, null);
skipSetValue = true;
} else {
resourceType = q.substring(1);
}
} else if (q.startsWith(".")) {
myChain = q.substring(1);
// type not defined but this is a chain, so treat value as opaque
myId.setParts(null, null, theValue, null);
skipSetValue = true;
}
}
setValue(theValue);
if (!skipSetValue) {
setValue(theValue);
if (isNotBlank(resourceType) && isBlank(getResourceType())) {
setValue(resourceType + '/' + theValue);
if (isNotBlank(resourceType) && isBlank(getResourceType())) {
setValue(resourceType + '/' + theValue);
}
}
}

106
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/StopWatch.java
View File

@ -6,8 +6,11 @@ import org.apache.commons.lang3.time.DateUtils;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.Date;
import java.util.LinkedHashMap;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
* #%L
* HAPI FHIR - Core Library
@ -17,9 +20,9 @@ import java.util.concurrent.TimeUnit;
* 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.
@ -29,6 +32,14 @@ import java.util.concurrent.TimeUnit;
*/
/**
* A multipurpose stopwatch which can be used to time tasks and produce
* human readable output about task duration, throughput, estimated task completion,
* etc.
* <p>
* <p>
* <b>Thread Safety Note: </b> StopWatch is not intended to be thread safe.
* </p>
*
* @since HAPI FHIR 3.3.0
*/
public class StopWatch {
@ -37,6 +48,9 @@ public class StopWatch {
private static final NumberFormat TEN_DAY_FORMAT = new DecimalFormat("0");
private static Long ourNowForUnitTest;
private long myStarted = now();
private long myCurrentTaskStarted = -1L;
private LinkedHashMap<String, Long> myTaskTotals;
private String myCurrentTaskName;
/**
* Constructor
@ -54,6 +68,66 @@ public class StopWatch {
myStarted = theStart.getTime();
}
private void ensureTaskTotalsMapExists() {
if (myTaskTotals == null) {
myTaskTotals = new LinkedHashMap<>();
}
}
/**
* Finish the counter on the current task (which was started by calling
* {@link #startTask(String)}. This method has no effect if no task
* is currently started so it's ok to call it more than once.
*/
public void endCurrentTask() {
if (isNotBlank(myCurrentTaskName)) {
ensureTaskTotalsMapExists();
Long existingTotal = myTaskTotals.get(myCurrentTaskName);
long taskTimeElapsed = now() - myCurrentTaskStarted;
Long newTotal = existingTotal != null ? existingTotal + taskTimeElapsed : taskTimeElapsed;
myTaskTotals.put(myCurrentTaskName, newTotal);
}
myCurrentTaskName = null;
}
/**
* Returns a string providing the durations of all tasks collected by {@link #startTask(String)}
*/
public String formatTaskDurations() {
// Flush the current task if it's ongoing
String continueTask = myCurrentTaskName;
if (isNotBlank(myCurrentTaskName)) {
endCurrentTask();
startTask(continueTask);
}
ensureTaskTotalsMapExists();
StringBuilder b = new StringBuilder();
for (String nextTask : myTaskTotals.keySet()) {
if (b.length() > 0) {
b.append("\n");
}
b.append(nextTask);
b.append(": ");
b.append(formatMillis(myTaskTotals.get(nextTask)));
}
return b.toString();
}
/**
* Determine the current throughput per unit of time (specified in theUnit)
* assuming that theNumOperations operations have happened.
* <p>
* For example, if this stopwatch has 2 seconds elapsed, and this method is
* called for theNumOperations=30 and TimeUnit=SECONDS,
* this method will return 15
* </p>
*
* @see #getThroughput(int, TimeUnit)
*/
public String formatThroughput(int theNumOperations, TimeUnit theUnit) {
double throughput = getThroughput(theNumOperations, theUnit);
return new DecimalFormat("0.0").format(throughput);
@ -99,6 +173,17 @@ public class StopWatch {
return new Date(myStarted);
}
/**
* Determine the current throughput per unit of time (specified in theUnit)
* assuming that theNumOperations operations have happened.
* <p>
* For example, if this stopwatch has 2 seconds elapsed, and this method is
* called for theNumOperations=30 and TimeUnit=SECONDS,
* this method will return 15
* </p>
*
* @see #formatThroughput(int, TimeUnit)
*/
public double getThroughput(int theNumOperations, TimeUnit theUnit) {
if (theNumOperations <= 0) {
return 0.0f;
@ -117,6 +202,23 @@ public class StopWatch {
myStarted = now();
}
/**
* Starts a counter for a sub-task
* <p>
* <b>Thread Safety Note: </b> This method is not threadsafe! Do not use subtasks in a
* multithreaded environment.
* </p>
*
* @param theTaskName Note that if theTaskName is blank or empty, no task is started
*/
public void startTask(String theTaskName) {
endCurrentTask();
if (isNotBlank(theTaskName)) {
myCurrentTaskStarted = now();
}
myCurrentTaskName = theTaskName;
}
/**
* Formats value in an appropriate format. See {@link #formatMillis(long)}}
* for a description of the format

25
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/StopWatchTest.java
View File

@ -103,17 +103,32 @@ public class StopWatchTest {
assertEquals("00:01:00.000", StopWatch.formatMillis(DateUtils.MILLIS_PER_MINUTE));
assertEquals("00:01:01", StopWatch.formatMillis(DateUtils.MILLIS_PER_MINUTE + DateUtils.MILLIS_PER_SECOND));
assertEquals("01:00:00", StopWatch.formatMillis(DateUtils.MILLIS_PER_HOUR));
assertEquals("1.0 day", StopWatch.formatMillis(DateUtils.MILLIS_PER_DAY));
assertEquals("2.0 days", StopWatch.formatMillis(DateUtils.MILLIS_PER_DAY * 2));
assertEquals("2.0 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 2) + 1));
assertEquals("2.4 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 2) + (10 * DateUtils.MILLIS_PER_HOUR)));
assertEquals("1.0 day", StopWatch.formatMillis(DateUtils.MILLIS_PER_DAY).replace(',', '.'));
assertEquals("2.0 days", StopWatch.formatMillis(DateUtils.MILLIS_PER_DAY * 2).replace(',', '.'));
assertEquals("2.0 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 2) + 1).replace(',', '.'));
assertEquals("2.4 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 2) + (10 * DateUtils.MILLIS_PER_HOUR)).replace(',', '.'));
assertEquals("11 days", StopWatch.formatMillis((DateUtils.MILLIS_PER_DAY * 11) + (10 * DateUtils.MILLIS_PER_HOUR)));
}
@Test
public void testFormatTaskDurations() {
StopWatch sw = new StopWatch();
StopWatch.setNowForUnitTestForUnitTest(1000L);
sw.startTask("TASK1");
StopWatch.setNowForUnitTestForUnitTest(1500L);
sw.startTask("TASK2");
StopWatch.setNowForUnitTestForUnitTest(1600L);
String taskDurations = sw.formatTaskDurations();
assertEquals("TASK1: 500ms\nTASK2: 100ms", taskDurations);
}
@Test
public void testFormatThroughput60Ops4Min() {
StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -4));
String throughput = sw.formatThroughput(60, TimeUnit.MINUTES);
String throughput = sw.formatThroughput(60, TimeUnit.MINUTES).replace(',', '.');
ourLog.info("{} operations in {}ms = {} ops / second", 60, sw.getMillis(), throughput);
assertThat(throughput, oneOf("14.9", "15.0", "15.1", "14,9", "15,0", "15,1"));
}

2
hapi-fhir-client/pom.xml
View File

@ -66,7 +66,7 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
</plugins>

4
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/impl/GenericClient.java
View File

@ -2105,14 +2105,14 @@ public class GenericClient extends BaseClient implements IGenericClient {
@Override
public IUpdateTyped resource(IBaseResource theResource) {
Validate.notNull(theResource, "Resource can not be null");
//Validate.notNull(theResource, "Resource can not be null");
myResource = theResource;
return this;
}
@Override
public IUpdateTyped resource(String theResourceBody) {
Validate.notBlank(theResourceBody, "Body can not be null or blank");
//Validate.notBlank(theResourceBody, "Body can not be null or blank");
myResourceBody = theResourceBody;
return this;
}

114
hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/AbstractJaxRsConformanceProvider.java
View File

@ -34,8 +34,6 @@ import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.hapi.rest.server.ServerCapabilityStatementProvider;
import org.hl7.fhir.dstu3.model.CapabilityStatement;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.LoggerFactory;
@ -67,10 +65,10 @@ public abstract class AbstractJaxRsConformanceProvider extends AbstractJaxRsProv
/** the conformance. It is created once during startup */
private org.hl7.fhir.r4.model.CapabilityStatement myR4CapabilityStatement;
private CapabilityStatement myDstu3CapabilityStatement;
private org.hl7.fhir.dstu3.model.CapabilityStatement myDstu3CapabilityStatement;
private org.hl7.fhir.dstu2016may.model.Conformance myDstu2_1Conformance;
private ca.uhn.fhir.model.dstu2.resource.Conformance myDstu2Conformance;
private org.hl7.fhir.instance.model.Conformance myDstu2Hl7OrgConformance;
private ca.uhn.fhir.model.dstu2.resource.Conformance myDstu2Conformance;
/**
* Constructor allowing the description, servername and server to be set
@ -127,26 +125,35 @@ public abstract class AbstractJaxRsConformanceProvider extends AbstractJaxRsProv
HardcodedServerAddressStrategy hardcodedServerAddressStrategy = new HardcodedServerAddressStrategy();
hardcodedServerAddressStrategy.setValue(getBaseForServer());
serverConfiguration.setServerAddressStrategy(hardcodedServerAddressStrategy);
if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.R4)) {
org.hl7.fhir.r4.hapi.rest.server.ServerCapabilityStatementProvider serverCapabilityStatementProvider = new org.hl7.fhir.r4.hapi.rest.server.ServerCapabilityStatementProvider(serverConfiguration);
serverCapabilityStatementProvider.initializeOperations();
myR4CapabilityStatement = serverCapabilityStatementProvider.getServerConformance(null);
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU3)) {
ServerCapabilityStatementProvider serverCapabilityStatementProvider = new ServerCapabilityStatementProvider(serverConfiguration);
serverCapabilityStatementProvider.initializeOperations();
myDstu3CapabilityStatement = serverCapabilityStatementProvider.getServerConformance(null);
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU2_1)) {
org.hl7.fhir.dstu2016may.hapi.rest.server.ServerConformanceProvider serverCapabilityStatementProvider = new org.hl7.fhir.dstu2016may.hapi.rest.server.ServerConformanceProvider(serverConfiguration);
serverCapabilityStatementProvider.initializeOperations();
myDstu2_1Conformance = serverCapabilityStatementProvider.getServerConformance(null);
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU2)) {
ca.uhn.fhir.rest.server.provider.dstu2.ServerConformanceProvider serverCapabilityStatementProvider = new ca.uhn.fhir.rest.server.provider.dstu2.ServerConformanceProvider(serverConfiguration);
serverCapabilityStatementProvider.initializeOperations();
myDstu2Conformance = serverCapabilityStatementProvider.getServerConformance(null);
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU2_HL7ORG)) {
org.hl7.fhir.instance.conf.ServerConformanceProvider serverCapabilityStatementProvider = new org.hl7.fhir.instance.conf.ServerConformanceProvider(serverConfiguration);
serverCapabilityStatementProvider.initializeOperations();
myDstu2Hl7OrgConformance = serverCapabilityStatementProvider.getServerConformance(null);
FhirVersionEnum fhirContextVersion = super.getFhirContext().getVersion().getVersion();
switch (fhirContextVersion) {
case R4:
org.hl7.fhir.r4.hapi.rest.server.ServerCapabilityStatementProvider r4ServerCapabilityStatementProvider = new org.hl7.fhir.r4.hapi.rest.server.ServerCapabilityStatementProvider(serverConfiguration);
r4ServerCapabilityStatementProvider.initializeOperations();
myR4CapabilityStatement = r4ServerCapabilityStatementProvider.getServerConformance(null);
break;
case DSTU3:
org.hl7.fhir.dstu3.hapi.rest.server.ServerCapabilityStatementProvider dstu3ServerCapabilityStatementProvider = new org.hl7.fhir.dstu3.hapi.rest.server.ServerCapabilityStatementProvider(serverConfiguration);
dstu3ServerCapabilityStatementProvider.initializeOperations();
myDstu3CapabilityStatement = dstu3ServerCapabilityStatementProvider.getServerConformance(null);
break;
case DSTU2_1:
org.hl7.fhir.dstu2016may.hapi.rest.server.ServerConformanceProvider dstu2_1ServerConformanceProvider = new org.hl7.fhir.dstu2016may.hapi.rest.server.ServerConformanceProvider(serverConfiguration);
dstu2_1ServerConformanceProvider.initializeOperations();
myDstu2_1Conformance = dstu2_1ServerConformanceProvider.getServerConformance(null);
break;
case DSTU2_HL7ORG:
org.hl7.fhir.instance.conf.ServerConformanceProvider dstu2Hl7OrgServerConformanceProvider = new org.hl7.fhir.instance.conf.ServerConformanceProvider(serverConfiguration);
dstu2Hl7OrgServerConformanceProvider.initializeOperations();
myDstu2Hl7OrgConformance = dstu2Hl7OrgServerConformanceProvider.getServerConformance(null);
break;
case DSTU2:
ca.uhn.fhir.rest.server.provider.dstu2.ServerConformanceProvider dstu2ServerConformanceProvider = new ca.uhn.fhir.rest.server.provider.dstu2.ServerConformanceProvider(serverConfiguration);
dstu2ServerConformanceProvider.initializeOperations();
myDstu2Conformance = dstu2ServerConformanceProvider.getServerConformance(null);
break;
default:
throw new ConfigurationException("Unsupported Fhir version: " + fhirContextVersion);
}
}
@ -181,20 +188,26 @@ public abstract class AbstractJaxRsConformanceProvider extends AbstractJaxRsProv
IRestfulResponse response = request.build().getResponse();
response.addHeader(Constants.HEADER_CORS_ALLOW_ORIGIN, "*");
IBaseResource conformance = null;
if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.R4)) {
conformance = myR4CapabilityStatement;
// return (Response) response.returnResponse(ParseAction.create(myDstu3CapabilityStatement), Constants.STATUS_HTTP_200_OK, true, null, getResourceType().getSimpleName());
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU3)) {
conformance = myDstu3CapabilityStatement;
// return (Response) response.returnResponse(ParseAction.create(myDstu3CapabilityStatement), Constants.STATUS_HTTP_200_OK, true, null, getResourceType().getSimpleName());
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU2_1)) {
conformance = myDstu2_1Conformance;
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU2)) {
conformance = myDstu2Conformance;
// return (Response) response.returnResponse(ParseAction.create(myDstu2CapabilityStatement), Constants.STATUS_HTTP_200_OK, true, null, getResourceType().getSimpleName());
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU2_HL7ORG)) {
conformance = myDstu2Hl7OrgConformance;
IBaseResource conformance;
FhirVersionEnum fhirContextVersion = super.getFhirContext().getVersion().getVersion();
switch (fhirContextVersion) {
case R4:
conformance = myR4CapabilityStatement;
break;
case DSTU3:
conformance = myDstu3CapabilityStatement;
break;
case DSTU2_1:
conformance = myDstu2_1Conformance;
break;
case DSTU2_HL7ORG:
conformance = myDstu2Hl7OrgConformance;
break;
case DSTU2:
conformance = myDstu2Conformance;
break;
default:
throw new ConfigurationException("Unsupported Fhir version: " + fhirContextVersion);
}
if (conformance != null) {
@ -279,18 +292,21 @@ public abstract class AbstractJaxRsConformanceProvider extends AbstractJaxRsProv
@SuppressWarnings("unchecked")
@Override
public Class<IBaseResource> getResourceType() {
if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.R4)) {
return Class.class.cast(org.hl7.fhir.r4.model.CapabilityStatement.class);
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU3)) {
return Class.class.cast(CapabilityStatement.class);
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU2_1)) {
return Class.class.cast(org.hl7.fhir.dstu2016may.model.Conformance.class);
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU2)) {
return Class.class.cast(ca.uhn.fhir.model.dstu2.resource.Conformance.class);
} else if (super.getFhirContext().getVersion().getVersion().equals(FhirVersionEnum.DSTU2_HL7ORG)) {
return Class.class.cast(org.hl7.fhir.instance.model.Conformance.class);
FhirVersionEnum fhirContextVersion = super.getFhirContext().getVersion().getVersion();
switch (fhirContextVersion) {
case R4:
return Class.class.cast(org.hl7.fhir.r4.model.CapabilityStatement.class);
case DSTU3:
return Class.class.cast(org.hl7.fhir.dstu3.model.CapabilityStatement.class);
case DSTU2_1:
return Class.class.cast(org.hl7.fhir.dstu2016may.model.Conformance.class);
case DSTU2_HL7ORG:
return Class.class.cast(org.hl7.fhir.instance.model.Conformance.class);
case DSTU2:
return Class.class.cast(ca.uhn.fhir.model.dstu2.resource.Conformance.class);
default:
throw new ConfigurationException("Unsupported Fhir version: " + fhirContextVersion);
}
return null;
}
}

75
hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/server/util/JaxRsRequest.java
View File

@ -28,12 +28,11 @@ import javax.ws.rs.core.HttpHeaders;
import javax.ws.rs.core.MediaType;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.model.IdType;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jaxrs.server.AbstractJaxRsProvider;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.IRestfulResponse;
import ca.uhn.fhir.rest.api.server.RequestDetails;
@ -93,28 +92,68 @@ public class JaxRsRequest extends RequestDetails {
FhirVersionEnum fhirContextVersion = myServer.getFhirContext().getVersion().getVersion();
if (StringUtils.isNotBlank(myVersion)) {
if (FhirVersionEnum.DSTU3.equals(fhirContextVersion) || FhirVersionEnum.DSTU2_HL7ORG.equals(fhirContextVersion)) {
result.setId(
new IdType(myServer.getBaseForRequest(), UrlUtil.unescape(myId), UrlUtil.unescape(myVersion)));
} else if (FhirVersionEnum.DSTU2.equals(fhirContextVersion)) {
result.setId(
new IdDt(myServer.getBaseForRequest(), UrlUtil.unescape(myId), UrlUtil.unescape(myVersion)));
}
switch (fhirContextVersion) {
case R4:
result.setId(new org.hl7.fhir.r4.model.IdType(myServer.getBaseForRequest(), UrlUtil.unescape(myId), UrlUtil.unescape(myVersion)));
break;
case DSTU3:
result.setId(new org.hl7.fhir.dstu3.model.IdType(myServer.getBaseForRequest(), UrlUtil.unescape(myId), UrlUtil.unescape(myVersion)));
break;
case DSTU2_1:
result.setId(new org.hl7.fhir.dstu2016may.model.IdType(myServer.getBaseForRequest(), UrlUtil.unescape(myId), UrlUtil.unescape(myVersion)));
break;
case DSTU2_HL7ORG:
result.setId(new org.hl7.fhir.instance.model.IdType(myServer.getBaseForRequest(), UrlUtil.unescape(myId), UrlUtil.unescape(myVersion)));
break;
case DSTU2:
result.setId(new ca.uhn.fhir.model.primitive.IdDt(myServer.getBaseForRequest(), UrlUtil.unescape(myId), UrlUtil.unescape(myVersion)));
break;
default:
throw new ConfigurationException("Unsupported Fhir version: " + fhirContextVersion);
}
} else if (StringUtils.isNotBlank(myId)) {
if (FhirVersionEnum.DSTU3.equals(fhirContextVersion) || FhirVersionEnum.DSTU2_HL7ORG.equals(fhirContextVersion)) {
result.setId(new IdType(myServer.getBaseForRequest(), UrlUtil.unescape(myId)));
} else if (FhirVersionEnum.DSTU2.equals(fhirContextVersion)) {
result.setId(new IdDt(myServer.getBaseForRequest(), UrlUtil.unescape(myId)));
}
switch (fhirContextVersion) {
case R4:
result.setId(new org.hl7.fhir.r4.model.IdType(myServer.getBaseForRequest(), UrlUtil.unescape(myId)));
break;
case DSTU3:
result.setId(new org.hl7.fhir.dstu3.model.IdType(myServer.getBaseForRequest(), UrlUtil.unescape(myId)));
break;
case DSTU2_1:
result.setId(new org.hl7.fhir.dstu2016may.model.IdType(myServer.getBaseForRequest(), UrlUtil.unescape(myId)));
break;
case DSTU2_HL7ORG:
result.setId(new org.hl7.fhir.instance.model.IdType(myServer.getBaseForRequest(), UrlUtil.unescape(myId)));
break;
case DSTU2:
result.setId(new ca.uhn.fhir.model.primitive.IdDt(myServer.getBaseForRequest(), UrlUtil.unescape(myId)));
break;
default:
throw new ConfigurationException("Unsupported Fhir version: " + fhirContextVersion);
}
}
if (myRestOperation == RestOperationTypeEnum.UPDATE) {
String contentLocation = result.getHeader(Constants.HEADER_CONTENT_LOCATION);
if (contentLocation != null) {
if (FhirVersionEnum.DSTU3.equals(fhirContextVersion) || FhirVersionEnum.DSTU2_HL7ORG.equals(fhirContextVersion)) {
result.setId(new IdType(contentLocation));
} else if (FhirVersionEnum.DSTU2.equals(fhirContextVersion)) {
result.setId(new IdDt(contentLocation));
switch (fhirContextVersion) {
case R4:
result.setId(new org.hl7.fhir.r4.model.IdType(contentLocation));
break;
case DSTU3:
result.setId(new org.hl7.fhir.dstu3.model.IdType(contentLocation));
break;
case DSTU2_1:
result.setId(new org.hl7.fhir.dstu2016may.model.IdType(contentLocation));
break;
case DSTU2_HL7ORG:
result.setId(new org.hl7.fhir.instance.model.IdType(contentLocation));
break;
case DSTU2:
result.setId(new ca.uhn.fhir.model.primitive.IdDt(contentLocation));
break;
default:
throw new ConfigurationException("Unsupported Fhir version: " + fhirContextVersion);
}
}
}

2
hapi-fhir-jpaserver-base/pom.xml
View File

@ -600,7 +600,7 @@
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<runOrder>alphabetical</runOrder>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx1024m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx1024m</argLine>
<forkCount>0.6C</forkCount>
</configuration>
</plugin>

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSubscriptionDstu3.java
View File

@ -99,11 +99,7 @@ public class FhirResourceDaoSubscriptionDstu3 extends FhirResourceDaoDstu3<Subsc
}
protected void validateChannelPayload(Subscription theResource) {
if (isBlank(theResource.getChannel().getPayload())) {
throw new UnprocessableEntityException("Subscription.channel.payload must be populated for rest-hook subscriptions");
}
if (EncodingEnum.forContentType(theResource.getChannel().getPayload()) == null) {
if (!isBlank(theResource.getChannel().getPayload()) && EncodingEnum.forContentType(theResource.getChannel().getPayload()) == null) {
throw new UnprocessableEntityException("Invalid value for Subscription.channel.payload: " + theResource.getChannel().getPayload());
}
}

42
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3.java
View File

@ -32,8 +32,6 @@ import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.rest.param.ParameterUtil;
import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
import org.hibernate.Session;
import org.hibernate.internal.SessionImpl;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.*;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
@ -150,7 +148,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
if (transactionType == null) {
String message = "Transactiion Bundle did not specify valid Bundle.type, assuming " + BundleType.TRANSACTION.toCode();
String message = "Transaction Bundle did not specify valid Bundle.type, assuming " + BundleType.TRANSACTION.toCode();
ourLog.warn(message);
transactionType = BundleType.TRANSACTION;
}
@ -158,9 +156,10 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
throw new InvalidRequestException("Unable to process transaction where incoming Bundle.type = " + transactionType.toCode());
}
ourLog.info("Beginning {} with {} resources", theActionName, theRequest.getEntry().size());
ourLog.debug("Beginning {} with {} resources", theActionName, theRequest.getEntry().size());
long start = System.currentTimeMillis();
// long start = System.currentTimeMillis();
final StopWatch transactionSw = new StopWatch();
final Date updateTime = new Date();
final Set<IdType> allIds = new LinkedHashSet<IdType>();
@ -202,7 +201,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
* Basically if the resource has a match URL that references a placeholder,
* we try to handle the resource with the placeholder first.
*/
Set<String> placeholderIds = new HashSet<String>();
Set<String> placeholderIds = new HashSet<>();
final List<BundleEntryComponent> entries = theRequest.getEntry();
for (BundleEntryComponent nextEntry : entries) {
if (isNotBlank(nextEntry.getFullUrl()) && nextEntry.getFullUrl().startsWith(IdType.URN_PREFIX)) {
@ -224,7 +223,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
Map<BundleEntryComponent, ResourceTable> entriesToProcess = txManager.execute(new TransactionCallback<Map<BundleEntryComponent, ResourceTable>>() {
@Override
public Map<BundleEntryComponent, ResourceTable> doInTransaction(TransactionStatus status) {
return doTransactionWriteOperations(theRequestDetails, theRequest, theActionName, updateTime, allIds, idSubstitutions, idToPersistedOutcome, response, originalRequestOrder, entries);
return doTransactionWriteOperations(theRequestDetails, theRequest, theActionName, updateTime, allIds, idSubstitutions, idToPersistedOutcome, response, originalRequestOrder, entries, transactionSw);
}
});
for (Entry<BundleEntryComponent, ResourceTable> nextEntry : entriesToProcess.entrySet()) {
@ -237,8 +236,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
/*
* Loop through the request and process any entries of type GET
*/
for (int i = 0; i < getEntries.size(); i++) {
BundleEntryComponent nextReqEntry = getEntries.get(i);
for (BundleEntryComponent nextReqEntry : getEntries) {
Integer originalOrder = originalRequestOrder.get(nextReqEntry);
BundleEntryComponent nextRespEntry = response.getEntry().get(originalOrder);
@ -258,7 +256,7 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
for (NameValuePair next : parameters) {
paramValues.put(next.getName(), next.getValue());
}
for (java.util.Map.Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
for (Entry<String, Collection<String>> nextParamEntry : paramValues.asMap().entrySet()) {
String[] nextValue = nextParamEntry.getValue().toArray(new String[nextParamEntry.getValue().size()]);
requestDetails.addParameter(nextParamEntry.getKey(), nextValue);
}
@ -302,8 +300,8 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
long delay = System.currentTimeMillis() - start;
ourLog.info(theActionName + " completed in {}ms", new Object[] { delay });
ourLog.info(theActionName + " completed in {}", transactionSw.toString());
ourLog.info(theActionName + " details:\n{}", transactionSw.formatTaskDurations());
response.setType(BundleType.TRANSACTIONRESPONSE);
return response;
@ -311,12 +309,12 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
@SuppressWarnings("unchecked")
private Map<BundleEntryComponent, ResourceTable> doTransactionWriteOperations(ServletRequestDetails theRequestDetails, Bundle theRequest, String theActionName, Date updateTime, Set<IdType> allIds,
Map<IdType, IdType> theIdSubstitutions, Map<IdType, DaoMethodOutcome> idToPersistedOutcome, Bundle response, IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder, List<BundleEntryComponent> theEntries) {
Set<String> deletedResources = new HashSet<String>();
List<DeleteConflict> deleteConflicts = new ArrayList<DeleteConflict>();
Map<BundleEntryComponent, ResourceTable> entriesToProcess = new IdentityHashMap<BundleEntryComponent, ResourceTable>();
Set<ResourceTable> nonUpdatedEntities = new HashSet<ResourceTable>();
Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<String, Class<? extends IBaseResource>>();
Map<IdType, IdType> theIdSubstitutions, Map<IdType, DaoMethodOutcome> idToPersistedOutcome, Bundle response, IdentityHashMap<BundleEntryComponent, Integer> originalRequestOrder, List<BundleEntryComponent> theEntries, StopWatch theStopWatch) {
Set<String> deletedResources = new HashSet<>();
List<DeleteConflict> deleteConflicts = new ArrayList<>();
Map<BundleEntryComponent, ResourceTable> entriesToProcess = new IdentityHashMap<>();
Set<ResourceTable> nonUpdatedEntities = new HashSet<>();
Map<String, Class<? extends IBaseResource>> conditionalRequestUrls = new HashMap<>();
/*
* Loop through the request and process any entries of type
@ -371,6 +369,8 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
String resourceType = res != null ? getContext().getResourceDefinition(res).getName() : null;
BundleEntryComponent nextRespEntry = response.getEntry().get(originalRequestOrder.get(nextReqEntry));
theStopWatch.startTask("Process entry " + i + ": " + verb + " " + defaultString(resourceType));
switch (verb) {
case POST: {
// CREATE
@ -470,6 +470,8 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
}
theStopWatch.endCurrentTask();
/*
* Make sure that there are no conflicts from deletions. E.g. we can't delete something
* if something else has a reference to it.. Unless the thing that has a reference to it
@ -538,8 +540,12 @@ public class FhirSystemDaoDstu3 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
}
theStopWatch.startTask("Flush Session");
flushJpaSession();
theStopWatch.endCurrentTask();
/*
* Double check we didn't allow any duplicates we shouldn't have
*/

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoSubscriptionR4.java
View File

@ -96,11 +96,7 @@ public class FhirResourceDaoSubscriptionR4 extends FhirResourceDaoR4<Subscriptio
}
protected void validateChannelPayload(Subscription theResource) {
if (isBlank(theResource.getChannel().getPayload())) {
throw new UnprocessableEntityException("Subscription.channel.payload must be populated for rest-hook subscriptions");
}
if (EncodingEnum.forContentType(theResource.getChannel().getPayload()) == null) {
if (!isBlank(theResource.getChannel().getPayload()) && EncodingEnum.forContentType(theResource.getChannel().getPayload()) == null) {
throw new UnprocessableEntityException("Invalid value for Subscription.channel.payload: " + theResource.getChannel().getPayload());
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirSystemDaoR4.java
View File

@ -157,7 +157,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
}
if (transactionType == null) {
String message = "Transactiion Bundle did not specify valid Bundle.type, assuming " + BundleType.TRANSACTION.toCode();
String message = "Transaction Bundle did not specify valid Bundle.type, assuming " + BundleType.TRANSACTION.toCode();
ourLog.warn(message);
transactionType = BundleType.TRANSACTION;
}
@ -165,7 +165,7 @@ public class FhirSystemDaoR4 extends BaseHapiFhirSystemDao<Bundle, Meta> {
throw new InvalidRequestException("Unable to process transaction where incoming Bundle.type = " + transactionType.toCode());
}
ourLog.info("Beginning {} with {} resources", theActionName, theRequest.getEntry().size());
ourLog.debug("Beginning {} with {} resources", theActionName, theRequest.getEntry().size());
long start = System.currentTimeMillis();
final Date updateTime = new Date();

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/BaseSubscriptionDeliverySubscriber.java
View File

@ -49,7 +49,7 @@ public abstract class BaseSubscriptionDeliverySubscriber extends BaseSubscriptio
try {
ResourceDeliveryMessage msg = (ResourceDeliveryMessage) theMessage.getPayload();
subscriptionId = msg.getPayload(getContext()).getIdElement().getValue();
subscriptionId = msg.getSubscription().getIdElement(getContext()).getValue();
if (!subscriptionTypeApplies(getContext(), msg.getSubscription().getBackingSubscription(getContext()))) {
return;

90
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/subscription/resthook/SubscriptionDeliveringRestHookSubscriber.java
View File

@ -20,24 +20,26 @@ package ca.uhn.fhir.jpa.subscription.resthook;
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.subscription.*;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.client.api.*;
import ca.uhn.fhir.rest.client.interceptor.SimpleRequestHeaderInterceptor;
import ca.uhn.fhir.rest.gclient.IClientExecutable;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.StringUtils;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Subscription;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.messaging.Message;
import org.springframework.messaging.MessagingException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -54,10 +56,38 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDe
IClientExecutable<?, ?> operation;
switch (theMsg.getOperationType()) {
case CREATE:
operation = theClient.update().resource(payloadResource);
if (payloadResource == null || payloadResource.isEmpty()) {
if (thePayloadType != null ) {
operation = theClient.create().resource(payloadResource);
} else {
sendNotification(theMsg);
return;
}
} else {
if (thePayloadType != null ) {
operation = theClient.update().resource(payloadResource);
} else {
sendNotification(theMsg);
return;
}
}
break;
case UPDATE:
operation = theClient.update().resource(payloadResource);
if (payloadResource == null || payloadResource.isEmpty()) {
if (thePayloadType != null ) {
operation = theClient.create().resource(payloadResource);
} else {
sendNotification(theMsg);
return;
}
} else {
if (thePayloadType != null ) {
operation = theClient.update().resource(payloadResource);
} else {
sendNotification(theMsg);
return;
}
}
break;
case DELETE:
operation = theClient.delete().resourceById(theMsg.getPayloadId(getContext()));
@ -67,11 +97,19 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDe
return;
}
operation.encoded(thePayloadType);
if (thePayloadType != null) {
operation.encoded(thePayloadType);
}
ourLog.info("Delivering {} rest-hook payload {} for {}", theMsg.getOperationType(), payloadResource.getIdElement().toUnqualified().getValue(), theSubscription.getIdElement(getContext()).toUnqualifiedVersionless().getValue());
operation.execute();
try {
operation.execute();
} catch (ResourceNotFoundException e) {
ourLog.error("Cannot reach "+ theMsg.getSubscription().getEndpointUrl());
e.printStackTrace();
throw e;
}
}
@Override
@ -83,13 +121,14 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDe
// Grab the payload type (encoding mimetype) from the subscription
String payloadString = subscription.getPayloadString();
payloadString = StringUtils.defaultString(payloadString, Constants.CT_FHIR_XML_NEW);
if (payloadString.contains(";")) {
payloadString = payloadString.substring(0, payloadString.indexOf(';'));
EncodingEnum payloadType = null;
if(payloadString != null) {
if (payloadString.contains(";")) {
payloadString = payloadString.substring(0, payloadString.indexOf(';'));
}
payloadString = payloadString.trim();
payloadType = EncodingEnum.forContentType(payloadString);
}
payloadString = payloadString.trim();
EncodingEnum payloadType = EncodingEnum.forContentType(payloadString);
payloadType = ObjectUtils.defaultIfNull(payloadType, EncodingEnum.XML);
// Create the client request
getContext().getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
@ -109,4 +148,23 @@ public class SubscriptionDeliveringRestHookSubscriber extends BaseSubscriptionDe
deliverPayload(theMessage, subscription, payloadType, client);
}
/**
* Sends a POST notification without a payload
* @param theMsg
*/
protected void sendNotification(ResourceDeliveryMessage theMsg) {
FhirContext context= getContext();
Map<String, List<String>> params = new HashMap();
List<Header> headers = new ArrayList<>();
StringBuilder url = new StringBuilder(theMsg.getSubscription().getEndpointUrl());
IHttpClient client = context.getRestfulClientFactory().getHttpClient(url, params, "", RequestTypeEnum.POST, headers);
IHttpRequest request = client.createParamRequest(context, params, null);
try {
IHttpResponse response = request.execute();
} catch (IOException e) {
ourLog.error("Error trying to reach "+ theMsg.getSubscription().getEndpointUrl());
e.printStackTrace();
throw new ResourceNotFoundException(e.getMessage());
}
}
}

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java
View File

@ -19,6 +19,7 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.orm.jpa.JpaSystemException;
import org.springframework.test.context.TestPropertySource;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
@ -33,6 +34,11 @@ import static org.hamcrest.Matchers.empty;
import static org.junit.Assert.*;
@SuppressWarnings({"unchecked", "deprecation"})
@TestPropertySource(properties = {
// Since scheduled tasks can cause searches, which messes up the
// value returned by SearchBuilder.getLastHandlerMechanismForUnitTest()
"scheduling_disabled=true"
})
public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4UniqueSearchParamTest.class);

60
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/AuthorizationInterceptorResourceProviderDstu3Test.java
View File

@ -20,6 +20,7 @@ import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Practitioner;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
@ -27,6 +28,7 @@ import org.junit.Test;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import static org.hamcrest.Matchers.startsWith;
@ -41,6 +43,64 @@ public class AuthorizationInterceptorResourceProviderDstu3Test extends BaseResou
unregisterInterceptors();
}
/**
* See #778
*/
@Test
public void testReadingObservationAccessRight() throws IOException {
Practitioner practitioner1 = new Practitioner();
final IIdType practitionerId1 = ourClient.create().resource(practitioner1).execute().getId().toUnqualifiedVersionless();
Practitioner practitioner2 = new Practitioner();
final IIdType practitionerId2 = ourClient.create().resource(practitioner2).execute().getId().toUnqualifiedVersionless();
Patient patient = new Patient();
patient.setActive(true);
final IIdType patientId = ourClient.create().resource(patient).execute().getId().toUnqualifiedVersionless();
ourRestServer.registerInterceptor(new AuthorizationInterceptor(PolicyEnum.DENY) {
@Override
public List<IAuthRule> buildRuleList(RequestDetails theRequestDetails) {
// allow write all Observation resource
// allow read only Observation resource in which it has a practitioner1 or practitioner2 compartment
return new RuleBuilder().allow()
.write()
.resourcesOfType(Observation.class)
.withAnyId()
.andThen()
.allow()
.read()
.resourcesOfType(Observation.class)
.inCompartment("Practitioner", Arrays.asList(practitionerId1, practitionerId2))
.andThen()
.denyAll()
.build();
}
});
Observation obs1 = new Observation();
obs1.setStatus(ObservationStatus.FINAL);
obs1.setPerformer(
Arrays.asList(new Reference(practitionerId1), new Reference(practitionerId2)));
IIdType oid1 = ourClient.create().resource(obs1).execute().getId().toUnqualified();
// Observation with practitioner1 and practitioner1 as the Performer -> should have the read access
ourClient.read().resource(Observation.class).withId(oid1).execute();
Observation obs2 = new Observation();
obs2.setStatus(ObservationStatus.FINAL);
obs2.setSubject(new Reference(patientId));
IIdType oid2 = ourClient.create().resource(obs2).execute().getId().toUnqualified();
// Observation with patient as the subject -> read access should be blocked
try {
ourClient.read().resource(Observation.class).withId(oid2).execute();
fail();
} catch (ForbiddenOperationException e) {
// good
}
}
/**
* See #667
*/

59
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/AuthorizationInterceptorResourceProviderR4Test.java
View File

@ -25,6 +25,7 @@ import org.junit.Test;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import static org.hamcrest.Matchers.startsWith;
@ -39,6 +40,64 @@ public class AuthorizationInterceptorResourceProviderR4Test extends BaseResource
unregisterInterceptors();
}
/**
* See #778
*/
@Test
public void testReadingObservationAccessRight() throws IOException {
Practitioner practitioner1 = new Practitioner();
final IIdType practitionerId1 = myClient.create().resource(practitioner1).execute().getId().toUnqualifiedVersionless();
Practitioner practitioner2 = new Practitioner();
final IIdType practitionerId2 = myClient.create().resource(practitioner2).execute().getId().toUnqualifiedVersionless();
Patient patient = new Patient();
patient.setActive(true);
final IIdType patientId = myClient.create().resource(patient).execute().getId().toUnqualifiedVersionless();
ourRestServer.registerInterceptor(new AuthorizationInterceptor(PolicyEnum.DENY) {
@Override
public List<IAuthRule> buildRuleList(RequestDetails theRequestDetails) {
// allow write all Observation resource
// allow read only Observation resource in which it has a practitioner1 or practitioner2 compartment
return new RuleBuilder().allow()
.write()
.resourcesOfType(Observation.class)
.withAnyId()
.andThen()
.allow()
.read()
.resourcesOfType(Observation.class)
.inCompartment("Practitioner", Arrays.asList(practitionerId1, practitionerId2))
.andThen()
.denyAll()
.build();
}
});
Observation obs1 = new Observation();
obs1.setStatus(ObservationStatus.FINAL);
obs1.setPerformer(
Arrays.asList(new Reference(practitionerId1), new Reference(practitionerId2)));
IIdType oid1 = myClient.create().resource(obs1).execute().getId().toUnqualified();
// Observation with practitioner1 and practitioner1 as the Performer -> should have the read access
myClient.read().resource(Observation.class).withId(oid1).execute();
Observation obs2 = new Observation();
obs2.setStatus(ObservationStatus.FINAL);
obs2.setSubject(new Reference(patientId));
IIdType oid2 = myClient.create().resource(obs2).execute().getId().toUnqualified();
// Observation with patient as the subject -> read access should be blocked
try {
myClient.read().resource(Observation.class).withId(oid2).execute();
fail();
} catch (ForbiddenOperationException e) {
// good
}
}
/**
* See #667
*/

21
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/subscription/RestHookTestDstu3Test.java
View File

@ -34,7 +34,7 @@ import static org.junit.Assert.fail;
*/
public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestHookTestDstu2Test.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(RestHookTestDstu3Test.class);
private static List<Observation> ourCreatedObservations = Lists.newArrayList();
private static int ourListenerPort;
private static RestfulServer ourListenerRestServer;
@ -311,6 +311,25 @@ public class RestHookTestDstu3Test extends BaseResourceProviderDstu3Test {
assertEquals(Constants.CT_FHIR_XML_NEW, ourContentTypes.get(0));
}
@Test
public void testRestHookSubscriptionWithoutPayload() throws Exception {
String payload = "";
String code = "1000000050";
String criteria1 = "Observation?code=SNOMED-CT|" + code;
String criteria2 = "Observation?code=SNOMED-CT|" + code + "111";
Subscription subscription1 = createSubscription(criteria1, payload, ourListenerServerBase);
Subscription subscription2 = createSubscription(criteria2, payload, ourListenerServerBase);
Observation observation1 = sendObservation(code, "SNOMED-CT");
// Should see 1 subscription notification, but no payload
waitForQueueToDrain();
waitForSize(0, ourCreatedObservations);
waitForSize(0, ourUpdatedObservations);
}
// TODO: Reenable this
@Test
@Ignore

23
hapi-fhir-jpaserver-elasticsearch/pom.xml Normal file
View File

@ -0,0 +1,23 @@
<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-deployable-pom</artifactId>
<version>3.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-jpaserver-elasticsearch</artifactId>
<packaging>jar</packaging>
<name>HAPI FHIR JPA Server - ElasticSearch Integration</name>
<dependencies>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-search-elasticsearch</artifactId>
</dependency>
</dependencies>
</project>

41
hapi-fhir-jpaserver-elasticsearch/src/main/java/ca/uhn/fhir/jpa/search/ElasticsearchMappingProvider.java Normal file
View File

@ -0,0 +1,41 @@
package ca.uhn.fhir.jpa.search;
import org.hibernate.search.elasticsearch.analyzer.definition.ElasticsearchAnalysisDefinitionRegistryBuilder;
import org.hibernate.search.elasticsearch.analyzer.definition.spi.ElasticsearchAnalysisDefinitionProvider;
public class ElasticsearchMappingProvider implements ElasticsearchAnalysisDefinitionProvider {
@Override
public void register(ElasticsearchAnalysisDefinitionRegistryBuilder builder) {
builder.analyzer("autocompleteEdgeAnalyzer")
.withTokenizer("pattern_all")
.withTokenFilters("lowercase", "stop", "edgengram_3_50");
builder.tokenizer("pattern_all").type("pattern").param("pattern", "(.*)").param("group", "1");
builder.tokenFilter("edgengram_3_50")
.type("edgeNGram")
.param("min_gram", "3")
.param("max_gram", "50");
builder.analyzer("autocompletePhoneticAnalyzer")
.withTokenizer("standard")
.withTokenFilters("standard", "stop", "snowball_english", "phonetic_doublemetaphone");
builder.tokenFilter("phonetic_doublemetaphone")
.type("phonetic")
.param("encoder", "double_metaphone");
builder.tokenFilter("snowball_english").type("snowball").param("language", "English");
builder.analyzer("autocompleteNGramAnalyzer")
.withTokenizer("standard")
.withTokenFilters("word_delimiter", "lowercase", "ngram_3_20");
builder.tokenFilter("ngram_3_20")
.type("nGram")
.param("min_gram", "3")
.param("max_gram", "20");
builder.analyzer("standardAnalyzer").withTokenizer("standard").withTokenFilters("lowercase");
builder.analyzer("exactAnalyzer").withTokenizer("standard");
builder.analyzer("conceptParentPidsAnalyzer").withTokenizer("whitespace");
}
}

14
hapi-fhir-jpaserver-example/README.md
View File

@ -41,3 +41,17 @@ Use this command to start the container:
`docker run -d --name hapi-fhir-jpaserver-example -p 8080:8080 hapi-fhir/hapi-fhir-jpaserver-example`
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.
#### Using ElasticSearch as the search engine instead of the default Apache Lucene
1. Install ElasticSearch server and the phonetic plugin
* Download ElasticSearch from https://www.elastic.co/downloads/elasticsearch
* ```cd {your elasticsearch directory}```
* ```bin/plugin install analysis-phonetic```
* start ElasticSearch server: ```./bin/elasticsearch```
2. Replace configuration in web.xml
* replace the configuration class ```ca.uhn.fhir.jpa.demo.FhirServerConfig``` in web.xml by ```ca.uhn.fhir.jpa.demo.elasticsearch.FhirServerConfig```
3. Start server by runing: ```mvn jetty:run```
4. Limitations:
* Hibernate search are not compatible with all ElasticSearch version. If you are using Hibernate search: 5.6 or 5.7, the compatible ElasticSearch version is 2.0 - 2.4. If you are using Hibernate search: 5.8 or 5.9, the compatible ElasticSearch version is
2.0 - 5.6.
* Please check all the limitations in the reference documentation: https://docs.jboss.org/hibernate/search/5.7/reference/en-US/html_single/#elasticsearch-limitations before use the integration.

6
hapi-fhir-jpaserver-example/pom.xml
View File

@ -74,6 +74,12 @@
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-elasticsearch</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency is used for the "FHIR Tester" web app overlay -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>

111
hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/elasticsearch/FhirServerConfig.java Normal file
View File

@ -0,0 +1,111 @@
package ca.uhn.fhir.jpa.demo.elasticsearch;
import java.util.Properties;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.search.ElasticsearchMappingProvider;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hibernate.search.elasticsearch.cfg.ElasticsearchEnvironment;
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;
/**
* This is the configuration file for the example server integrating the ElasticSearch engine.
*/
@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.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.apache.derby.jdbc.EmbeddedDriver());
retVal.setUrl("jdbc:derby:directory:target/jpaserver_derby_files;create=true");
retVal.setUsername("");
retVal.setPassword("");
return retVal;
}
@Bean()
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = new LocalContainerEntityManagerFactoryBean();
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(dataSource());
retVal.setPackagesToScan("ca.uhn.fhir.jpa.entity");
retVal.setPersistenceProvider(new HibernatePersistenceProvider());
retVal.setJpaProperties(jpaProperties());
return retVal;
}
private Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.dialect", org.hibernate.dialect.DerbyTenSevenDialect.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");
// the belowing properties are used for ElasticSearch integration
extraProperties.put(ElasticsearchEnvironment.ANALYZER_DEFINITION_PROVIDER, ElasticsearchMappingProvider.class.getName());
extraProperties.put("hibernate.search.default.indexmanager", "elasticsearch");
extraProperties.put("hibernate.search.default.elasticsearch.host", "http://127.0.0.1:9200");
extraProperties.put("hibernate.search.default.elasticsearch.index_schema_management_strategy", "CREATE");
extraProperties.put("hibernate.search.default.elasticsearch.index_management_wait_timeout", "10000");
extraProperties.put("hibernate.search.default.elasticsearch.required_index_status", "yellow");
return extraProperties;
}
/**
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
*/
@Bean(autowire = Autowire.BY_TYPE)
public IServerInterceptor 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;
}
}

2
hapi-fhir-server/pom.xml
View File

@ -91,7 +91,7 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
</plugins>

2
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleBuilder.java
View File

@ -362,6 +362,8 @@ public class RuleBuilder implements IAuthRuleBuilder {
for (IIdType next : theOwners) {
validateOwner(next);
}
myInCompartmentName = theCompartmentName;
myInCompartmentOwners = theOwners;
myClassifierType = ClassifierTypeEnum.IN_COMPARTMENT;
return finished();
}

2
hapi-fhir-structures-dstu/pom.xml
View File

@ -186,7 +186,7 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>

2
hapi-fhir-structures-dstu2.1/pom.xml
View File

@ -255,7 +255,7 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>

173
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java
View File

@ -31,12 +31,13 @@ import org.mockito.Mockito;
import org.mockito.internal.stubbing.answers.ThrowsException;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.io.StringReader;
import java.util.*;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.*;
import static org.hamcrest.core.IsInstanceOf.instanceOf;
import static org.junit.Assert.*;
import static org.mockito.Mockito.*;
@ -44,6 +45,33 @@ public class JsonParserDstu2Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu2Test.class);
private static FhirContext ourCtx = FhirContext.forDstu2();
private void assertExtensionMetadata(
BaseResource resource,
String url,
boolean isModifier,
Class<?> expectedType,
String expectedValue) {
ExtensionDt extension = (ExtensionDt) resource.getResourceMetadata().get(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(url));
assertThat(extension.getValue(), instanceOf(expectedType));
assertThat(extension.isModifier(), equalTo(isModifier));
assertThat(extension.getValueAsPrimitive().getValueAsString(), equalTo(expectedValue));
}
private void assertParsedResourcesExtensionMetadata(ProcedureRequest resource) {
ExtensionDt payment = (ExtensionDt) resource.getResourceMetadata().get(
new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://fhir.sjanic.com/procedureRequest/requiresPatientPayment"));
assertThat(payment.isModifier(), equalTo(true));
assertThat(((BooleanDt) payment.getValue()).getValue(), equalTo(true));
TimestampFields timestampFields = new TimestampFields(resource);
assertThat(timestampFields.user.getReference().getIdPart(), equalTo("sjanic"));
assertThat(timestampFields.instance.getValue(), equalTo(new InstantDt("2012-01-01T13:00:00Z").getValue()));
assertThat(timestampFields.organization.getReference().getIdPart(), equalTo("sjanic_org"));
assertThat(timestampFields.role.getCodingFirstRep().getSystem(), equalTo("sjanic"));
assertThat(timestampFields.role.getCodingFirstRep().getCode(), equalTo("Doctor"));
}
@Test
public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
String refVal = "http://my.org/FooBar";
@ -68,7 +96,7 @@ public class JsonParserDstu2Test {
* See #544
*/
@Test
public void testBundleStitchReferencesByUuid() throws Exception {
public void testBundleStitchReferencesByUuid() {
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
DocumentManifest dm = new DocumentManifest();
@ -145,6 +173,7 @@ public class JsonParserDstu2Test {
assertEquals("myName", ((StringDt) newPatient.getUndeclaredExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
}
@Test
public void testCustomUrlExtensioninBundle() {
final String expected = "{\"resourceType\":\"Bundle\",\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}}]}";
@ -217,7 +246,7 @@ public class JsonParserDstu2Test {
}
@Test
public void testEncodeAndParseExtensions() throws Exception {
public void testEncodeAndParseExtensions() {
Patient patient = new Patient();
patient.addIdentifier().setUse(IdentifierUseEnum.OFFICIAL).setSystem("urn:example").setValue("7000135");
@ -363,9 +392,9 @@ public class JsonParserDstu2Test {
assertEquals(2, gotLabels.size());
IdDt label = (IdDt) gotLabels.get(0);
IdDt label = gotLabels.get(0);
assertEquals("http://foo/Profile1", label.getValue());
label = (IdDt) gotLabels.get(1);
label = gotLabels.get(1);
assertEquals("http://foo/Profile2", label.getValue());
tagList = ResourceMetadataKeyEnum.TAG_LIST.get(parsed);
@ -386,7 +415,7 @@ public class JsonParserDstu2Test {
HumanNameDt name = p.addName();
name.addFamily().setValue(null).addUndeclaredExtension(new ExtensionDt(false, "http://foo", new StringDt("FOOEXT0")));
name.getFamily().get(0).setElementSpecificId("f0");
name.addFamily().setValue("V1").addUndeclaredExtension((ExtensionDt) new ExtensionDt(false, "http://foo", new StringDt("FOOEXT1")));
name.addFamily().setValue("V1").addUndeclaredExtension(new ExtensionDt(false, "http://foo", new StringDt("FOOEXT1")));
name.getFamily().get(1).setElementSpecificId("f1");
name.getFamily().get(1).getUndeclaredExtensions().get(0).setElementSpecificId("ext1id");
name.addFamily(); // this one shouldn't get encoded
@ -513,7 +542,6 @@ public class JsonParserDstu2Test {
ca.uhn.fhir.model.dstu2.resource.Bundle b = new ca.uhn.fhir.model.dstu2.resource.Bundle();
b.getText().setDiv("");
b.getText().getStatus().setValueAsString("");
;
Entry e = b.addEntry();
e.setResource(new Patient());
@ -616,7 +644,6 @@ public class JsonParserDstu2Test {
c = new Conformance();
c.getAcceptUnknownElement().setValueAsEnum(UnknownContentCodeEnum.UNKNOWN_ELEMENTS);
;
c.getAcceptUnknownElement().addUndeclaredExtension(false, "http://foo", new StringDt("AAA"));
encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(c);
@ -770,7 +797,7 @@ public class JsonParserDstu2Test {
}
@Test
public void testEncodeNarrativeSuppressed() throws Exception {
public void testEncodeNarrativeSuppressed() {
Patient patient = new Patient();
patient.setId("Patient/1/_history/1");
patient.getText().setDiv("<div>THE DIV</div>");
@ -788,6 +815,7 @@ public class JsonParserDstu2Test {
assertThat(encoded, containsString("maritalStatus"));
}
/**
* See #537
*/
@ -815,6 +843,69 @@ public class JsonParserDstu2Test {
assertThat(encoded, stringContainsInOrder("LEVEL02", "LEVEL03", "LEVEL04", "LEVEL01"));
}
@Test
public void testEncodeResourceWithExtensionMetadata() {
ProcedureRequest procedureRequest = new ProcedureRequest();
procedureRequest.setStatus(ProcedureRequestStatusEnum.ACCEPTED);
ExtensionDt timestamp = new ExtensionDt(false, "http://fhir.sjanic.com/timestamp");
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/user", new ResourceReferenceDt("sjanic"));
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/instance", new InstantDt("2012-01-01T13:00:00Z"));
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/organization", new ResourceReferenceDt("sjanic_org"));
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/role", new CodeableConceptDt().addCoding(new CodingDt("sjanic", "Doctor").setDisplay("Doctorin")));
ExtensionDt payment = new ExtensionDt(true, "http://fhir.sjanic.com/procedureRequest/requiresPatientPayment", new BooleanDt(true));
procedureRequest.getResourceMetadata().put(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(timestamp.getUrl()), timestamp);
procedureRequest.getResourceMetadata().put(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(payment.getUrl()), payment);
String json = ourCtx.newJsonParser().encodeResourceToString(procedureRequest);
// @formatter:off
assertThat(json, stringContainsInOrder(
"\"meta\":{" +
"\"extension\":[" +
"{" +
"\"url\":\"http://fhir.sjanic.com/timestamp\"," +
"\"extension\":[" +
"{" +
"\"url\":\"http://fhir.sjanic.com/timestamp/user\"," +
"\"valueReference\":{" +
"\"reference\":\"sjanic\"" +
"}" +
"}," +
"{" +
"\"url\":\"http://fhir.sjanic.com/timestamp/instance\"," +
"\"valueInstant\":\"2012-01-01T13:00:00Z\"" +
"}," +
"{" +
"\"url\":\"http://fhir.sjanic.com/timestamp/organization\"," +
"\"valueReference\":{" +
"\"reference\":\"sjanic_org\"" +
"}" +
"}," +
"{" +
"\"url\":\"http://fhir.sjanic.com/timestamp/role\"," +
"\"valueCodeableConcept\":{" +
"\"coding\":[" +
"{" +
"\"system\":\"sjanic\"," +
"\"code\":\"Doctor\"," +
"\"display\":\"Doctorin\"" +
"}" +
"]" +
"}" +
"}" +
"]" +
"}" +
"]," +
"\"modifierExtension\":[" +
"{" +
"\"url\":\"http://fhir.sjanic.com/procedureRequest/requiresPatientPayment\"," +
"\"valueBoolean\":true" +
"}" +
"]" +
"},"));
// @formatter:on
}
@Test
public void testEncodeSummary() {
Patient patient = new Patient();
@ -881,7 +972,7 @@ public class JsonParserDstu2Test {
// see #241
@Test
public void testEncodeThenParseShouldNotAddSpuriousId() throws Exception {
public void testEncodeThenParseShouldNotAddSpuriousId() {
Condition condition = new Condition().setVerificationStatus(ConditionVerificationStatusEnum.CONFIRMED);
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
ca.uhn.fhir.model.dstu2.resource.Bundle.Entry entry = new ca.uhn.fhir.model.dstu2.resource.Bundle.Entry();
@ -896,7 +987,7 @@ public class JsonParserDstu2Test {
}
@Test
public void testEncodeWithDontEncodeElements() throws Exception {
public void testEncodeWithDontEncodeElements() {
Patient patient = new Patient();
patient.setId("123");
@ -1037,6 +1128,7 @@ public class JsonParserDstu2Test {
assertEquals("2011-01-01", condition.getDateRecordedElement().getValueAsString());
}
/**
* #65
*/
@ -1054,7 +1146,7 @@ public class JsonParserDstu2Test {
}
@Test
public void testNamespacePreservationEncode() throws Exception {
public void testNamespacePreservationEncode() {
//@formatter:off
String input = "<Patient xmlns=\"http://hl7.org/fhir\" xmlns:xhtml=\"http://www.w3.org/1999/xhtml\">" +
"<text>" +
@ -1076,7 +1168,7 @@ public class JsonParserDstu2Test {
}
@Test
public void testNamespacePreservationParse() throws Exception {
public void testNamespacePreservationParse() {
String input = "{\"resourceType\":\"Patient\",\"text\":{\"div\":\"<xhtml:div xmlns:xhtml=\\\"http://www.w3.org/1999/xhtml\\\"><xhtml:img src=\\\"foo\\\"/>@fhirabend</xhtml:div>\"}}";
Patient parsed = ourCtx.newJsonParser().parseResource(Patient.class, input);
@ -1393,7 +1485,7 @@ public class JsonParserDstu2Test {
}
@Test
public void testParseAndEncodeComments() throws IOException {
public void testParseAndEncodeComments() {
//@formatter:off
String input = "{\n" +
" \"resourceType\": \"Patient\",\n" +
@ -1626,7 +1718,7 @@ public class JsonParserDstu2Test {
}
@Test
public void testParseMetadata() throws Exception {
public void testParseMetadata() {
//@formatter:off
String bundle = "{\n" +
" \"resourceType\" : \"Bundle\",\n" +
@ -1839,6 +1931,20 @@ public class JsonParserDstu2Test {
assertEquals("Patient", reincarnatedPatient.getId().getResourceType());
}
@Test
public void testParseResourceWithExtensionMetadata() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/procedure-request.json"));
IParser parser = ourCtx.newJsonParser();
IParserErrorHandler peh = mock(IParserErrorHandler.class);
parser.setParserErrorHandler(peh);
ProcedureRequest p = parser.parseResource(ProcedureRequest.class, input);
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
verify(peh, Mockito.never()).unknownElement(Mockito.isNull(IParseLocation.class), capt.capture());
assertParsedResourcesExtensionMetadata(p);
}
/**
* See #207
*/
@ -1873,19 +1979,13 @@ public class JsonParserDstu2Test {
Patient p = parser.parseResource(Patient.class, input);
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
verify(peh, times(4)).unknownElement(Mockito.isNull(IParseLocation.class), capt.capture());
//@formatter:off
List<String> strings = capt.getAllValues();
assertThat(strings, contains(
"extension",
"extension",
"modifierExtension",
"modifierExtension"
));
//@formatter:off
verify(peh, times(0)).unknownElement(Mockito.isNull(IParseLocation.class), capt.capture());
assertEquals("Smith", p.getName().get(0).getGiven().get(0).getValue());
assertExtensionMetadata(p, "fhir-request-method", false, StringDt.class, "POST");
assertExtensionMetadata(p, "fhir-request-uri", false, UriDt.class, "Patient");
assertExtensionMetadata(p, "modified-fhir-request-method", true, StringDt.class, "POST");
assertExtensionMetadata(p, "modified-fhir-request-uri", true, UriDt.class, "Patient");
}
@Test
@ -1989,4 +2089,25 @@ public class JsonParserDstu2Test {
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
private static final class TimestampFields {
ResourceReferenceDt user;
InstantDt instance;
ResourceReferenceDt organization;
CodeableConceptDt role;
TimestampFields(BaseResource resource) {
ExtensionDt timestamp = (ExtensionDt) resource.getResourceMetadata().get(
new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://fhir.sjanic.com/timestamp"));
Map<String, ExtensionDt> timestampFields = new HashMap<>(timestamp.getExtension().size());
for (ExtensionDt extensionDt : timestamp.getExtension()) {
timestampFields.put(extensionDt.getUrl(), extensionDt);
}
user = ((ResourceReferenceDt) timestampFields.get("http://fhir.sjanic.com/timestamp/user").getValue());
instance = (InstantDt) timestampFields.get("http://fhir.sjanic.com/timestamp/instance").getValue();
organization = (ResourceReferenceDt) timestampFields.get("http://fhir.sjanic.com/timestamp/organization").getValue();
role = (CodeableConceptDt) timestampFields.get("http://fhir.sjanic.com/timestamp/role").getValue();
}
}
}

70
hapi-fhir-structures-dstu2/src/test/resources/patient1.json
View File

@ -1,35 +1,35 @@
{
"id": "73b551fb-46f5-4fb8-b735-2399344e9717",
"meta": {
"extension": [
{
"url": "fhir-request-method",
"valueString": "POST"
},
{
"url": "fhir-request-uri",
"valueUri": "Patient"
}
],
"modifierExtension": [
{
"url": "fhir-request-method",
"valueString": "POST"
},
{
"url": "fhir-request-uri",
"valueUri": "Patient"
}
],
"versionId": "01e5253d-d258-494c-8d8e-f22ad6d8f19b",
"lastUpdated": "2016-02-20T11:01:56.155Z"
},
"name": [
{
"given": [
"Smith"
]
}
],
"resourceType": "Patient"
}
{
"id": "73b551fb-46f5-4fb8-b735-2399344e9717",
"meta": {
"extension": [
{
"url": "fhir-request-method",
"valueString": "POST"
},
{
"url": "fhir-request-uri",
"valueUri": "Patient"
}
],
"modifierExtension": [
{
"url": "modified-fhir-request-method",
"valueString": "POST"
},
{
"url": "modified-fhir-request-uri",
"valueUri": "Patient"
}
],
"versionId": "01e5253d-d258-494c-8d8e-f22ad6d8f19b",
"lastUpdated": "2016-02-20T11:01:56.155Z"
},
"name": [
{
"given": [
"Smith"
]
}
],
"resourceType": "Patient"
}

47
hapi-fhir-structures-dstu2/src/test/resources/procedure-request.json Normal file
View File

@ -0,0 +1,47 @@
{
"resourceType": "ProcedureRequest",
"meta": {
"extension": [
{
"url": "http://fhir.sjanic.com/timestamp",
"extension": [
{
"url": "http://fhir.sjanic.com/timestamp/user",
"valueReference": {
"reference": "sjanic"
}
},
{
"url": "http://fhir.sjanic.com/timestamp/instance",
"valueInstant": "2012-01-01T13:00:00Z"
},
{
"url": "http://fhir.sjanic.com/timestamp/organization",
"valueReference": {
"reference": "sjanic_org"
}
},
{
"url": "http://fhir.sjanic.com/timestamp/role",
"valueCodeableConcept": {
"coding": [
{
"system": "sjanic",
"code": "Doctor",
"display": "Doctorin"
}
]
}
}
]
}
],
"modifierExtension": [
{
"url": "http://fhir.sjanic.com/procedureRequest/requiresPatientPayment",
"valueBoolean": true
}
]
},
"status": "accepted"
}

2
hapi-fhir-structures-dstu3/pom.xml
View File

@ -59,7 +59,7 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>

230
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/codesystems/DeviceStatus.java
View File

@ -1,105 +1,125 @@
package org.hl7.fhir.dstu3.model.codesystems;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
// Generated on Sat, Mar 25, 2017 21:03-0400 for FHIR v3.0.0
import org.hl7.fhir.exceptions.FHIRException;
public enum DeviceStatus {
/**
* The Device is available for use. Note: This means for *implanted devices* the device is implanted in the patient.
*/
ACTIVE,
/**
* The Device is no longer available for use (e.g. lost, expired, damaged). Note: This means for *implanted devices* the device has been removed from the patient.
*/
INACTIVE,
/**
* The Device was entered in error and voided.
*/
ENTEREDINERROR,
/**
* The status of the device has not been determined.
*/
UNKNOWN,
/**
* added to help the parsers
*/
NULL;
public static DeviceStatus fromCode(String codeString) throws FHIRException {
if (codeString == null || "".equals(codeString))
return null;
if ("active".equals(codeString))
return ACTIVE;
if ("inactive".equals(codeString))
return INACTIVE;
if ("entered-in-error".equals(codeString))
return ENTEREDINERROR;
if ("unknown".equals(codeString))
return UNKNOWN;
throw new FHIRException("Unknown DeviceStatus code '"+codeString+"'");
}
public String toCode() {
switch (this) {
case ACTIVE: return "active";
case INACTIVE: return "inactive";
case ENTEREDINERROR: return "entered-in-error";
case UNKNOWN: return "unknown";
default: return "?";
}
}
public String getSystem() {
return "http://hl7.org/fhir/device-status";
}
public String getDefinition() {
switch (this) {
case ACTIVE: return "The Device is available for use. Note: This means for *implanted devices* the device is implanted in the patient.";
case INACTIVE: return "The Device is no longer available for use (e.g. lost, expired, damaged). Note: This means for *implanted devices* the device has been removed from the patient.";
case ENTEREDINERROR: return "The Device was entered in error and voided.";
case UNKNOWN: return "The status of the device has not been determined.";
default: return "?";
}
}
public String getDisplay() {
switch (this) {
case ACTIVE: return "Active";
case INACTIVE: return "Inactive";
case ENTEREDINERROR: return "Entered in Error";
case UNKNOWN: return "Unknown";
default: return "?";
}
}
}
package org.hl7.fhir.dstu3.model.codesystems;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
// Generated on Sat, Mar 25, 2017 21:03-0400 for FHIR v3.0.0
import org.hl7.fhir.exceptions.FHIRException;
public enum DeviceStatus {
/**
* The Device is available for use. Note: This means for *implanted devices* the device is implanted in the patient.
*/
ACTIVE,
/**
* The Device is no longer available for use (e.g. lost, expired, damaged). Note: This means for *implanted devices* the device has been removed from the patient.
*/
INACTIVE,
/**
* The Device was entered in error and voided.
*/
ENTEREDINERROR,
/**
* The status of the device has not been determined.
*/
UNKNOWN,
/**
* added to help the parsers
*/
NULL;
public String getDefinition() {
switch (this) {
case ACTIVE:
return "The Device is available for use. Note: This means for *implanted devices* the device is implanted in the patient.";
case INACTIVE:
return "The Device is no longer available for use (e.g. lost, expired, damaged). Note: This means for *implanted devices* the device has been removed from the patient.";
case ENTEREDINERROR:
return "The Device was entered in error and voided.";
case UNKNOWN:
return "The status of the device has not been determined.";
default:
return "?";
}
}
public String getDisplay() {
switch (this) {
case ACTIVE:
return "Active";
case INACTIVE:
return "Inactive";
case ENTEREDINERROR:
return "Entered in Error";
case UNKNOWN:
return "Unknown";
default:
return "?";
}
}
public String getSystem() {
return "http://hl7.org/fhir/device-status";
}
public String toCode() {
switch (this) {
case ACTIVE:
return "active";
case INACTIVE:
return "inactive";
case ENTEREDINERROR:
return "entered-in-error";
case UNKNOWN:
return "unknown";
default:
return "?";
}
}
public static DeviceStatus fromCode(String codeString) throws FHIRException {
if (codeString == null || "".equals(codeString))
return null;
if ("active".equals(codeString))
return ACTIVE;
if ("inactive".equals(codeString))
return INACTIVE;
if ("entered-in-error".equals(codeString))
return ENTEREDINERROR;
if ("unknown".equals(codeString))
return UNKNOWN;
throw new FHIRException("Unknown DeviceStatus code '" + codeString + "'");
}
}

140
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/codesystems/DeviceStatusEnumFactory.java
View File

@ -1,70 +1,70 @@
package org.hl7.fhir.dstu3.model.codesystems;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
// Generated on Sat, Mar 25, 2017 21:03-0400 for FHIR v3.0.0
import org.hl7.fhir.dstu3.model.EnumFactory;
public class DeviceStatusEnumFactory implements EnumFactory<DeviceStatus> {
public DeviceStatus fromCode(String codeString) throws IllegalArgumentException {
if (codeString == null || "".equals(codeString))
return null;
if ("active".equals(codeString))
return DeviceStatus.ACTIVE;
if ("inactive".equals(codeString))
return DeviceStatus.INACTIVE;
if ("entered-in-error".equals(codeString))
return DeviceStatus.ENTEREDINERROR;
if ("unknown".equals(codeString))
return DeviceStatus.UNKNOWN;
throw new IllegalArgumentException("Unknown DeviceStatus code '"+codeString+"'");
}
public String toCode(DeviceStatus code) {
if (code == DeviceStatus.ACTIVE)
return "active";
if (code == DeviceStatus.INACTIVE)
return "inactive";
if (code == DeviceStatus.ENTEREDINERROR)
return "entered-in-error";
if (code == DeviceStatus.UNKNOWN)
return "unknown";
return "?";
}
public String toSystem(DeviceStatus code) {
return code.getSystem();
}
}
package org.hl7.fhir.dstu3.model.codesystems;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
// Generated on Sat, Mar 25, 2017 21:03-0400 for FHIR v3.0.0
import org.hl7.fhir.dstu3.model.EnumFactory;
public class DeviceStatusEnumFactory implements EnumFactory<DeviceStatus> {
public DeviceStatus fromCode(String codeString) throws IllegalArgumentException {
if (codeString == null || "".equals(codeString))
return null;
if ("active".equals(codeString))
return DeviceStatus.ACTIVE;
if ("inactive".equals(codeString))
return DeviceStatus.INACTIVE;
if ("entered-in-error".equals(codeString))
return DeviceStatus.ENTEREDINERROR;
if ("unknown".equals(codeString))
return DeviceStatus.UNKNOWN;
throw new IllegalArgumentException("Unknown DeviceStatus code '" + codeString + "'");
}
public String toCode(DeviceStatus code) {
if (code == DeviceStatus.ACTIVE)
return "active";
if (code == DeviceStatus.INACTIVE)
return "inactive";
if (code == DeviceStatus.ENTEREDINERROR)
return "entered-in-error";
if (code == DeviceStatus.UNKNOWN)
return "unknown";
return "?";
}
public String toSystem(DeviceStatus code) {
return code.getSystem();
}
}

120
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/param/ReferenceParamTest.java
View File

@ -19,9 +19,61 @@ public class ReferenceParamTest {
rp.setValueAsQueryToken(ourCtx, null, null, "Location/123");
assertEquals("Location", rp.getResourceType());
assertEquals("123", rp.getIdPart());
assertEquals("Location/123", rp.getValue());
assertEquals(null, rp.getQueryParameterQualifier());
}
@Test
public void testWithResourceType_AbsoluteUrl() {
ReferenceParam rp = new ReferenceParam();
rp.setValueAsQueryToken(ourCtx, null, null, "http://a.b/c/d/e");
assertEquals("d", rp.getResourceType());
assertEquals("e", rp.getIdPart());
assertEquals("http://a.b/c/d/e", rp.getValue());
assertEquals(null, rp.getQueryParameterQualifier());
}
@Test
public void testWithNoResourceTypeAsQualifierAndChain() {
ReferenceParam rp = new ReferenceParam();
rp.setValueAsQueryToken(ourCtx, null, ".name", "FOO");
assertEquals(null, rp.getResourceType());
assertEquals("FOO", rp.getIdPart());
assertEquals("FOO", rp.getValue());
assertEquals(".name", rp.getQueryParameterQualifier());
assertEquals("name", rp.getChain());
}
@Test
public void testWithNoResourceTypeAsQualifierAndChain_RelativeUrl() {
ReferenceParam rp = new ReferenceParam();
rp.setValueAsQueryToken(ourCtx, null, ".name", "Patient/1233");
assertEquals(null, rp.getResourceType());
assertEquals("Patient/1233", rp.getIdPart());
assertEquals("Patient/1233", rp.getValue());
assertEquals(".name", rp.getQueryParameterQualifier());
assertEquals("name", rp.getChain());
}
@Test
public void testWithNoResourceTypeAsQualifierAndChain_AbsoluteUrl() {
ReferenceParam rp = new ReferenceParam();
rp.setValueAsQueryToken(ourCtx, null, ".name", "http://something.strange/a/b/c");
assertEquals(null, rp.getResourceType());
assertEquals("http://something.strange/a/b/c", rp.getIdPart());
assertEquals("http://something.strange/a/b/c", rp.getValue());
assertEquals(".name", rp.getQueryParameterQualifier());
assertEquals("name", rp.getChain());
}
@Test
public void testWithResourceTypeAsQualifier() {
@ -30,6 +82,34 @@ public class ReferenceParamTest {
rp.setValueAsQueryToken(ourCtx, null, ":Location", "123");
assertEquals("Location", rp.getResourceType());
assertEquals("123", rp.getIdPart());
assertEquals("Location/123", rp.getValue());
assertEquals(null, rp.getQueryParameterQualifier());
}
// TODO: verify this behavior is correct. If type is explicitly specified (i.e. :Location), should it be
// an error if it gets overriden by the resourceType in the url?
@Test
public void testWithResourceTypeAsQualifier_RelativeUrl() {
ReferenceParam rp = new ReferenceParam();
rp.setValueAsQueryToken(ourCtx, null, ":Location", "Patient/123");
assertEquals("Patient", rp.getResourceType());
assertEquals("123", rp.getIdPart());
assertEquals("Patient/123", rp.getValue());
assertEquals(null, rp.getQueryParameterQualifier());
}
// TODO: verify this behavior is correct. Same case as testWithResourceTypeAsQualifier_RelativeUrl()
@Test
public void testWithResourceTypeAsQualifier_AbsoluteUrl() {
ReferenceParam rp = new ReferenceParam();
rp.setValueAsQueryToken(ourCtx, null, ":Location", "http://a.b/c/d/e");
assertEquals("d", rp.getResourceType());
assertEquals("e", rp.getIdPart());
assertEquals("http://a.b/c/d/e", rp.getValue());
assertEquals(null, rp.getQueryParameterQualifier());
}
@ -42,11 +122,51 @@ public class ReferenceParamTest {
rp.setValueAsQueryToken(ourCtx, null, ":Location.name", "FOO");
assertEquals("Location", rp.getResourceType());
assertEquals("FOO", rp.getIdPart());
assertEquals("Location/FOO", rp.getValue());
assertEquals(":Location.name", rp.getQueryParameterQualifier());
assertEquals("name", rp.getChain());
}
@Test
public void testWithResourceTypeAsQualifierAndChain_IdentifierUrlAndValue() {
ReferenceParam rp = new ReferenceParam();
rp.setValueAsQueryToken(ourCtx, null, ":Patient.identifier", "http://hey.there/a/b|123");
assertEquals("Patient", rp.getResourceType());
assertEquals("http://hey.there/a/b|123", rp.getIdPart());
assertEquals("Patient/http://hey.there/a/b|123", rp.getValue());
assertEquals(":Patient.identifier", rp.getQueryParameterQualifier());
assertEquals("identifier", rp.getChain());
}
@Test
public void testWithResourceTypeAsQualifierAndChain_IdentifierUrlOnly() {
ReferenceParam rp = new ReferenceParam();
rp.setValueAsQueryToken(ourCtx, null, ":Patient.identifier", "http://hey.there/a/b|");
assertEquals("Patient", rp.getResourceType());
assertEquals("http://hey.there/a/b|", rp.getIdPart());
assertEquals("Patient/http://hey.there/a/b|", rp.getValue());
assertEquals(":Patient.identifier", rp.getQueryParameterQualifier());
assertEquals("identifier", rp.getChain());
}
@Test
public void testWithResourceTypeAsQualifierAndChain_ValueOnlyNoUrl() {
ReferenceParam rp = new ReferenceParam();
rp.setValueAsQueryToken(ourCtx, null, ":Patient.identifier", "|abc");
assertEquals("Patient", rp.getResourceType());
assertEquals("|abc", rp.getIdPart());
assertEquals("Patient/|abc", rp.getValue());
assertEquals(":Patient.identifier", rp.getQueryParameterQualifier());
assertEquals("identifier", rp.getChain());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

2
hapi-fhir-structures-hl7org-dstu2/pom.xml
View File

@ -254,7 +254,7 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>

2
hapi-fhir-structures-r4/pom.xml
View File

@ -244,7 +244,7 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>

2
hapi-fhir-utilities/pom.xml
View File

@ -104,7 +104,7 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>

2
hapi-fhir-validation/pom.xml
View File

@ -228,7 +228,7 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<argLine>${argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
<argLine>@{argLine} -Dfile.encoding=UTF-8 -Xmx712m</argLine>
</configuration>
</plugin>
<plugin>

20
pom.xml
View File

@ -390,7 +390,18 @@
<id>Tastelezz</id>
<name>Gaetano Gallo</name>
</developer>
<developer>
<id>sjanic</id>
<name>sjanic</name>
</developer>
<developer>
<id>c-schuler</id>
<name>Chris Schuler</name>
</developer>
<developer>
<id>javajeff</id>
<name>Jeff Chung</name>
</developer>
</developers>
<licenses>
@ -950,6 +961,11 @@
<artifactId>hibernate-search-orm</artifactId>
<version>${hibernate_search_version}</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-search-elasticsearch</artifactId>
<version>${hibernate_search_version}</version>
</dependency>
<dependency>
<groupId>org.javassist</groupId>
<artifactId>javassist</artifactId>
@ -1942,6 +1958,7 @@
<module>hapi-fhir-jaxrsserver-base</module>
<module>hapi-fhir-jaxrsserver-example</module>
<module>hapi-fhir-jpaserver-base</module>
<module>hapi-fhir-jpaserver-elasticsearch</module>
<module>hapi-fhir-jpaserver-example</module>
<module>restful-server-example</module>
<module>restful-server-example-test</module>
@ -1955,6 +1972,7 @@
<module>examples</module>
<module>example-projects/hapi-fhir-base-example-embedded-ws</module>
<module>example-projects/hapi-fhir-standalone-overlay-example</module>
<module>example-projects/hapi-fhir-jpaserver-cds-example</module>
<module>hapi-fhir-jacoco</module>
<module>hapi-fhir-igpacks</module>
<module>hapi-fhir-spring-boot</module>

40
src/changes/changes.xml
View File

@ -200,6 +200,46 @@
The client LoggingInterceptor now includes the number of
milliseconds spent performing each call that is logged.
</action>
<action type="add" issue="786">
ReferenceParam has been enhanced to properly return the resource type to
user code in a server via the ReferenceType#getResourceType() method
if the client has specified a reference parameter with
a resource type. Thanks to @CarthageKing for the pull request!
</action>
<action type="add" issue="776">
An entry has been added to ResourceMetadataKeyEnum which allows extensions
to be placed in the resource metadata section in DSTU2 resource (this is
possible already in DSTU3+ resources as Meta is a normal model type, but
the older structures worked a bit differently. Thanks to GitHub user
sjanic for the contribution!
</action>
<action type="add" issue="791">
An example project has een contributed which shows how to use the CQL
framework in a server with HAPI FHIR JPA. Thanks to Chris Schuler
for the pull request!
</action>
<action type="add" issue="798">
A new module has been contributed called hapi-fhir-jpaserver-elasticsearch
which adds support for Elasticsearch instead of raw Lucene for fulltext
indexing. Testing help on this would be appreciated! Thanks to
Jiajing Liang for the pull request!
</action>
<action type="fix" issue="800">
JAX-RS server now supports R4 and DSTU2_1 FHIR versions, which were
previously missing. Thanks to Clayton Bodendein for the pull
request!
</action>
<action type="fix" issue="806">
AuthorizationInterceptor did not correctly handle authorization against
against a compartment where the compartment owner was specified
as a list of IDs. Thanks to Jiajing Liang for the pull request!
</action>
<action type="add" issue="812">
REST HOOK subscriptions in the JPA server now support having
an empty/missing Subscription.channel.payload value, which
is supported according to the FHIR specification. Thanks
to Jeff Chung for the pull request!
</action>
</release>
<release version="3.2.0" date="2018-01-13">
<action type="add">

2
src/site/xdoc/download.xml.vm
View File

@ -273,7 +273,7 @@
</tr>
<tr><td style="text-align: center; font-size: 1.2em; background: #DDE; padding: 3px;" colspan="2">Validation</td></tr>
<tr>
<td style="font-weight: bold; white-space: nowrap;">hapi-fhir-validator</td>
<td style="font-weight: bold; white-space: nowrap;">hapi-fhir-validation</td>
<td>
This module contains the FHIR Profile Validator, which is used to
validate resource instances against FHIR Profiles (StructureDefinitions,