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Merge pull request #102 from hapifhir/rel_5_1_0

Browse Source 
Start Release branch for 5.1.0
This commit is contained in:
James Agnew
2020-08-13 16:17:28 -04:00
committed by GitHub
parent a70fe5bfa0 dafdf5b437
commit 555c6697e0
17 changed files with 346 additions and 148 deletions
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4
README.md
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@@ -209,6 +209,10 @@ The server may be configured with subscription support by enabling properties in
- `subscription.websocket.enabled` - Enables websocket subscriptions. With this enabled, your server will accept incoming websocket connections on the following URL (this example uses the default context path and port, you may need to tweak depending on your deployment environment): [ws://localhost:8080/hapi-fhir-jpaserver/websocket](ws://localhost:8080/hapi-fhir-jpaserver/websocket)
## Enabling EMPI
Set `empi.enabled=true` in the [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties) file to enable EMPI on this server. The EMPI matching rules are configured in [empi-rules.json](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/empi-rules.json). The rules in this example file should be replaced with actual matching rules appropriate to your data. Note that EMPI relies on subscriptions, so for EMPI to work, subscriptions must be enabled.
## Using Elasticsearch
By default, the server will use embedded lucene indexes for terminology and fulltext indexing purposes. You can switch this to using lucene by editing the properties in [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties)

54
pom.xml
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@@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.0.2</version>
<version>5.1.0</version>
</parent>
<artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -20,6 +20,20 @@
<maven>3.5.0</maven>
</prerequisites>
<packaging>war</packaging>
<name>HAPI FHIR JPA Server - Starter Project</name>
<repositories>
<repository>
<id>oss-snapshots</id>
<snapshots>
<enabled>true</enabled>
</snapshots>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
@@ -84,7 +98,12 @@
</exclusion>
</exclusions>
</dependency>
<!-- This dependency includes the JPA EMPI Server -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-empi</artifactId>
<version>${project.version}</version>
</dependency>
<!-- This dependency is used for the "FHIR Tester" web app overlay -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
@@ -249,23 +268,23 @@
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<version>4.0.0-rc1</version>
<scope>test</scope>
</dependency>
<!-- TODO: remove this and migrate to JU5 -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
</dependencies>
<packaging>war</packaging>
<name>HAPI FHIR JPA Server - Starter Project</name>
<repositories>
<repository>
<id>oss-snapshots</id>
<snapshots>
<enabled>false</enabled>
</snapshots>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository>
</repositories>
<build>
<!-- Tells Maven to name the generated WAR file as hapi-fhir-jpaserver.war -->
@@ -276,7 +295,7 @@
<plugin>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-maven-plugin</artifactId>
<version>${jetty_version}</version>
<version>${jetty_version}</version>
<configuration>
<webApp>
<contextPath>/hapi-fhir-jpaserver</contextPath>
@@ -421,6 +440,7 @@
<ignoredResourcePatterns>
<ignoredResourcePattern>.*\.txt$</ignoredResourcePattern>
<ignoredResourcePattern>.*\.html$</ignoredResourcePattern>
<ignoredResourcePattern>config/favicon.ico</ignoredResourcePattern>
</ignoredResourcePatterns>
</configuration>
</plugin>

12
src/main/java/ca/uhn/fhir/jpa/starter/ApplicationContext.java
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@@ -1,6 +1,8 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.empi.config.EmpiConsumerConfig;
import ca.uhn.fhir.jpa.empi.config.EmpiSubmitterConfig;
import ca.uhn.fhir.jpa.subscription.channel.config.SubscriptionChannelConfig;
import ca.uhn.fhir.jpa.subscription.match.config.SubscriptionProcessorConfig;
import ca.uhn.fhir.jpa.subscription.match.config.WebsocketDispatcherConfig;
@@ -28,13 +30,19 @@ public class ApplicationContext extends AnnotationConfigWebApplicationContext {
}
if (HapiProperties.getSubscriptionEmailEnabled()
|| HapiProperties.getSubscriptionRestHookEnabled()
|| HapiProperties.getSubscriptionWebsocketEnabled()) {
|| HapiProperties.getSubscriptionRestHookEnabled()
|| HapiProperties.getSubscriptionWebsocketEnabled()) {
register(SubscriptionSubmitterConfig.class);
register(SubscriptionProcessorConfig.class);
register(SubscriptionChannelConfig.class);
}
if (HapiProperties.getEmpiEnabled()) {
register(EmpiSubmitterConfig.class);
register(EmpiConsumerConfig.class);
register(EmpiConfig.class);
}
}
}

4
src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
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@@ -7,9 +7,8 @@ import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.rp.ResourceProviderFactory;
import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider;
import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
@@ -37,6 +36,7 @@ import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.rest.server.tenant.UrlBaseTenantIdentificationStrategy;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;

31
src/main/java/ca/uhn/fhir/jpa/starter/EmpiConfig.java Normal file
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@@ -0,0 +1,31 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.empi.api.IEmpiSettings;
import ca.uhn.fhir.empi.rules.config.EmpiRuleValidator;
import ca.uhn.fhir.empi.rules.config.EmpiSettings;
import ca.uhn.fhir.jpa.empi.svc.EmpiSearchParamSvc;
import ca.uhn.fhir.jpa.subscription.channel.subscription.IChannelNamer;
import ca.uhn.fhir.rest.server.util.ISearchParamRetriever;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.io.DefaultResourceLoader;
import org.springframework.core.io.Resource;
import java.io.IOException;
@Configuration
public class EmpiConfig {
@Bean
IEmpiSettings empiSettings(EmpiRuleValidator theEmpiRuleValidator) throws IOException {
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
Resource resource = resourceLoader.getResource("empi-rules.json");
String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
return new EmpiSettings(theEmpiRuleValidator).setEnabled(HapiProperties.getEmpiEnabled()).setScriptText(json);
}
}

12
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -10,7 +10,6 @@ import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hl7.fhir.dstu2.model.Subscription;
import org.springframework.beans.factory.BeanFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@@ -25,7 +24,7 @@ import java.sql.Driver;
* This is the primary configuration file for the example server
*/
@Configuration
@EnableTransactionManagement()
@EnableTransactionManagement
public class FhirServerConfigCommon {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirServerConfigCommon.class);
@@ -205,11 +204,10 @@ public class FhirServerConfigCommon {
retVal.setSmtpServerPort(this.emailPort);
retVal.setSmtpServerUsername(this.emailUsername);
retVal.setSmtpServerPassword(this.emailPassword);
// TODO KHS add these when HAPI 4.2.0 is released
// retVal.setAuth(this.emailAuth);
// retVal.setStartTlsEnable(this.emailStartTlsEnable);
// retVal.setStartTlsRequired(this.emailStartTlsRequired);
// retVal.setQuitWait(this.emailQuitWait);
retVal.setAuth(this.emailAuth);
retVal.setStartTlsEnable(this.emailStartTlsEnable);
retVal.setStartTlsRequired(this.emailStartTlsRequired);
retVal.setQuitWait(this.emailQuitWait);
SubscriptionDeliveryHandlerFactory subscriptionDeliveryHandlerFactory = myAppCtx.getBean(SubscriptionDeliveryHandlerFactory.class);
Validate.notNull(subscriptionDeliveryHandlerFactory, "No subscription delivery handler");

6
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java
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@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Primary;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -47,8 +48,9 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
return retVal;
}
@Bean()
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
@Bean
@Primary
public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;

8
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java
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@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Primary;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -32,7 +33,7 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
}
@Override
@Bean()
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory();
retVal.setPersistenceUnitName("HAPI_PU");
@@ -47,8 +48,9 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
return retVal;
}
@Bean()
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
@Bean
@Primary
public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;

6
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java
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@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Primary;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -47,8 +48,9 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
return retVal;
}
@Bean()
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
@Bean
@Primary
public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;

6
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java
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@@ -6,6 +6,7 @@ import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Primary;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
@@ -47,8 +48,9 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
return retVal;
}
@Bean()
public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
@Bean
@Primary
public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {
JpaTransactionManager retVal = new JpaTransactionManager();
retVal.setEntityManagerFactory(entityManagerFactory);
return retVal;

33
src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java
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@@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.StringUtils;
import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus;
import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy;
import org.jetbrains.annotations.NotNull;
@@ -59,6 +60,9 @@ public class HapiProperties {
static final String SUBSCRIPTION_EMAIL_ENABLED = "subscription.email.enabled";
static final String SUBSCRIPTION_RESTHOOK_ENABLED = "subscription.resthook.enabled";
static final String SUBSCRIPTION_WEBSOCKET_ENABLED = "subscription.websocket.enabled";
static final String EMPI_ENABLED = "empi.enabled";
static final String PARTITIONING_ENABLED = "partitioning.enabled";
static final String PARTITIONING_CROSS_PARTITION_REFERENCE_MODE = "partitioning.cross_partition_reference_mode";
static final String ALLOWED_BUNDLE_TYPES = "allowed_bundle_types";
static final String TEST_PORT = "test.port";
static final String TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS = "tester.config.refuse_to_fetch_third_party_urls";
@@ -76,8 +80,8 @@ public class HapiProperties {
static final String EXPIRE_SEARCH_RESULTS_AFTER_MINS = "retain_cached_searches_mins";
static final String MAX_BINARY_SIZE = "max_binary_size";
static final String PARTITIONING_MULTITENANCY_ENABLED = "partitioning.multitenancy.enabled";
private static final String PARTITIONING_INCLUDE_PARTITION_IN_SEARCH_HASHES = "partitioning.partitioning_include_in_search_hashes";
static final String CLIENT_ID_STRATEGY = "daoconfig.client_id_strategy";
private static Properties ourProperties;
public static boolean isElasticSearchEnabled() {
@@ -339,10 +343,6 @@ public class HapiProperties {
return HapiProperties.getBooleanProperty("expunge_enabled", true);
}
public static Integer getTestPort() {
return HapiProperties.getIntegerProperty(TEST_PORT, 0);
}
public static Boolean getTesterConfigRefustToFetchThirdPartyUrls() {
return HapiProperties.getBooleanProperty(TESTER_CONFIG_REFUSE_TO_FETCH_THIRD_PARTY_URLS, false);
}
@@ -363,8 +363,8 @@ public class HapiProperties {
public static Set<String> getSupportedResourceTypes() {
String[] types = defaultString(getProperty("supported_resource_types")).split(",");
return Arrays.stream(types)
.map(t -> trim(t))
.filter(t -> isNotBlank(t))
.map(StringUtils::trim)
.filter(StringUtils::isNotBlank)
.collect(Collectors.toSet());
}
@@ -392,6 +392,23 @@ public class HapiProperties {
return HapiProperties.getBooleanProperty(SUBSCRIPTION_WEBSOCKET_ENABLED, false);
}
public static Boolean getEmpiEnabled() {
return HapiProperties.getBooleanProperty(EMPI_ENABLED, false);
}
public static Boolean getPartitioningEnabled() {
return HapiProperties.getBooleanProperty(PARTITIONING_ENABLED, false);
}
public static String getPartitioningCrossPartitionReferenceMode() {
return HapiProperties.getProperty(PARTITIONING_CROSS_PARTITION_REFERENCE_MODE, "NOT_ALLOWED");
}
public static Boolean getIncludePartitionInSearchHashes() {
return HapiProperties.getBooleanProperty(PARTITIONING_INCLUDE_PARTITION_IN_SEARCH_HASHES, true);
}
public static Boolean getAllowContainsSearches() {
return HapiProperties.getBooleanProperty(ALLOW_CONTAINS_SEARCHES, true);
}
@@ -512,5 +529,7 @@ public class HapiProperties {
public static boolean getPartitioningMultitenancyEnabled() {
return HapiProperties.getBooleanProperty(PARTITIONING_MULTITENANCY_ENABLED, false);
}
}

46
src/main/resources/empi-rules.json Normal file
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@@ -0,0 +1,46 @@
{
"candidateSearchParams": [
{
"resourceType": "Patient",
"searchParams": ["birthdate"]
},
{
"resourceType": "*",
"searchParams": ["identifier"]
},
{
"resourceType": "Patient",
"searchParams": ["general-practitioner"]
}
],
"candidateFilterSearchParams": [
{
"resourceType": "*",
"searchParam": "active",
"fixedValue": "true"
}
],
"matchFields": [
{
"name": "cosine-given-name",
"resourceType": "*",
"resourcePath": "name.given",
"metric": "COSINE",
"matchThreshold": 0.8,
"exact": true
},
{
"name": "jaro-last-name",
"resourceType": "*",
"resourcePath": "name.family",
"metric": "JARO_WINKLER",
"matchThreshold": 0.8,
"exact": true
}
],
"matchResultMap": {
"cosine-given-name" : "POSSIBLE_MATCH",
"cosine-given-name,jaro-last-name" : "MATCH"
},
"eidSystem": "http://company.io/fhir/NamingSystem/custom-eid-system"
}

10
src/main/resources/hapi.properties
View File

@@ -150,8 +150,18 @@ email.password=
# Enable Websocket Subscription Channel
subscription.websocket.enabled=false
###################################################
# EMPI
###################################################
empi.enabled=false
###################################################
# Partitioning And Multitenancy
###################################################
partitioning.enabled=false
partitioning.cross_partition_reference_mode=NOT_ALLOWED
partitioning.partitioning_include_in_search_hashes=true
partitioning.multitenancy.enabled=false
#daoconfig.client_id_strategy=ANY

19
src/main/resources/logback.xml
View File

@@ -9,6 +9,25 @@
</encoder>
</appender>
<appender name="EMPI_TROUBLESHOOTING" class="ch.qos.logback.core.rolling.RollingFileAppender">
<filter class="ch.qos.logback.classic.filter.ThresholdFilter"><level>DEBUG</level></filter>
<file>${smile.basedir}/log/empi-troubleshooting.log</file>
<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
<fileNamePattern>${smile.basedir}/log/empi-troubleshooting.log.%i.gz</fileNamePattern>
<minIndex>1</minIndex>
<maxIndex>9</maxIndex>
</rollingPolicy>
<triggeringPolicy class="ch.qos.logback.core.rolling.SizeBasedTriggeringPolicy">
<maxFileSize>5MB</maxFileSize>
</triggeringPolicy>
<encoder>
<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n${log.stackfilter.pattern}</pattern>
</encoder>
</appender>
<logger name="ca.uhn.fhir.log.empi_troubleshooting" level="TRACE">
<appender-ref ref="EMPI_TROUBLESHOOTING"/>
</logger>
<root level="INFO">
<appender-ref ref="STDOUT" />
</root>

40
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java
View File

@@ -8,6 +8,7 @@ import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.test.utilities.JettyUtil;
import ca.uhn.fhir.util.BundleUtil;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.webapp.WebAppContext;
import org.eclipse.jetty.websocket.api.Session;
@@ -17,6 +18,8 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Person;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Subscription;
import org.junit.AfterClass;
import org.junit.BeforeClass;
@@ -24,11 +27,16 @@ import org.junit.Test;
import java.net.URI;
import java.nio.file.Paths;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import static ca.uhn.fhir.util.TestUtil.waitForSize;
import static org.awaitility.Awaitility.await;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
public class ExampleServerR4IT {
@@ -43,6 +51,7 @@ public class ExampleServerR4IT {
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr4");
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R4");
HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
HapiProperties.setProperty(HapiProperties.EMPI_ENABLED, "true");
ourCtx = FhirContext.forR4();
}
@@ -57,9 +66,30 @@ public class ExampleServerR4IT {
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(methodName, pt2.getName().get(0).getFamily());
// Test EMPI
// Wait until the EMPI message has been processed
await().until(() -> getPeople().size() > 0);
List<Person> persons = getPeople();
// Verify a Person was created that links to our Patient
Optional<String> personLinkToCreatedPatient = persons.stream()
.map(Person::getLink)
.flatMap(Collection::stream)
.map(Person.PersonLinkComponent::getTarget)
.map(Reference::getReference)
.filter(pid -> id.toUnqualifiedVersionless().getValue().equals(pid))
.findAny();
assertTrue(personLinkToCreatedPatient.isPresent());
}
@Test
private List<Person> getPeople() {
Bundle bundle = ourClient.search().forResource(Person.class).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute();
return BundleUtil.toListOfResourcesOfType(ourCtx, bundle, Person.class);
}
@Test
public void testWebsocketSubscription() throws Exception {
/*
* Create subscription
@@ -78,7 +108,7 @@ public class ExampleServerR4IT {
IIdType mySubscriptionId = methodOutcome.getId();
// Wait for the subscription to be activated
waitForSize(1, () -> ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size());
await().until(() -> activeSubscriptionCount() == 3);
/*
* Attach websocket
@@ -117,7 +147,11 @@ public class ExampleServerR4IT {
ourClient.delete().resourceById(mySubscriptionId).execute();
}
@AfterClass
private int activeSubscriptionCount() {
return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size();
}
@AfterClass
public static void afterClass() throws Exception {
ourServer.stop();
}

196
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java
View File

@@ -34,132 +34,132 @@ import static org.junit.Assert.assertEquals;
public class ExampleServerR5IT {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR5IT.class);
private static IGenericClient ourClient;
private static FhirContext ourCtx;
private static int ourPort;
private static Server ourServer;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR5IT.class);
private static IGenericClient ourClient;
private static FhirContext ourCtx;
private static int ourPort;
private static Server ourServer;
static {
HapiProperties.forceReload();
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr5");
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R5");
HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
ourCtx = FhirContext.forR5();
}
static {
HapiProperties.forceReload();
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr5");
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R5");
HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
ourCtx = FhirContext.forR5();
}
@Test
public void testCreateAndRead() {
ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
String methodName = "testCreateResourceConditional";
@Test
public void testCreateAndRead() {
ourLog.info("Base URL is: " + HapiProperties.getServerAddress());
String methodName = "testCreateResourceConditional";
Patient pt = new Patient();
pt.addName().setFamily(methodName);
IIdType id = ourClient.create().resource(pt).execute().getId();
Patient pt = new Patient();
pt.addName().setFamily(methodName);
IIdType id = ourClient.create().resource(pt).execute().getId();
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(methodName, pt2.getName().get(0).getFamily());
}
Patient pt2 = ourClient.read().resource(Patient.class).withId(id).execute();
assertEquals(methodName, pt2.getName().get(0).getFamily());
}
@Test
public void testWebsocketSubscription() throws Exception {
@Test
public void testWebsocketSubscription() throws Exception {
/*
* Create topic
*/
SubscriptionTopic topic = new SubscriptionTopic();
topic.getResourceTrigger().getQueryCriteria().setCurrent("Observation?status=final");
/*
* Create topic
*/
SubscriptionTopic topic = new SubscriptionTopic();
topic.getResourceTrigger().getQueryCriteria().setCurrent("Observation?status=final");
/*
* Create subscription
*/
Subscription subscription = new Subscription();
subscription.getTopic().setResource(topic);
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
subscription.setStatus(Enumerations.SubscriptionState.REQUESTED);
/*
* Create subscription
*/
Subscription subscription = new Subscription();
subscription.getTopic().setResource(topic);
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
subscription.setStatus(Enumerations.SubscriptionState.REQUESTED);
subscription.getChannelType()
.setSystem("http://terminology.hl7.org/CodeSystem/subscription-channel-type")
.setCode("websocket");
subscription.setContentType("application/json");
subscription.setContentType("application/json");
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
IIdType mySubscriptionId = methodOutcome.getId();
MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();
IIdType mySubscriptionId = methodOutcome.getId();
// Wait for the subscription to be activated
waitForSize(1, () -> ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size());
// Wait for the subscription to be activated
waitForSize(1, () -> ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active")).cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry().size());
/*
* Attach websocket
*/
/*
* Attach websocket
*/
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
WebSocketClient myWebSocketClient = new WebSocketClient();
SocketImplementation mySocketImplementation = new SocketImplementation(mySubscriptionId.getIdPart(), EncodingEnum.JSON);
myWebSocketClient.start();
URI echoUri = new URI("ws://localhost:" + ourPort + "/hapi-fhir-jpaserver/websocket");
ClientUpgradeRequest request = new ClientUpgradeRequest();
ourLog.info("Connecting to : {}", echoUri);
Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
Session session = connection.get(2, TimeUnit.SECONDS);
myWebSocketClient.start();
URI echoUri = new URI("ws://localhost:" + ourPort + "/hapi-fhir-jpaserver/websocket");
ClientUpgradeRequest request = new ClientUpgradeRequest();
ourLog.info("Connecting to : {}", echoUri);
Future<Session> connection = myWebSocketClient.connect(mySocketImplementation, echoUri, request);
Session session = connection.get(2, TimeUnit.SECONDS);
ourLog.info("Connected to WS: {}", session.isOpen());
ourLog.info("Connected to WS: {}", session.isOpen());
/*
* Create a matching resource
*/
Observation obs = new Observation();
obs.setStatus(Enumerations.ObservationStatus.FINAL);
ourClient.create().resource(obs).execute();
/*
* Create a matching resource
*/
Observation obs = new Observation();
obs.setStatus(Enumerations.ObservationStatus.FINAL);
ourClient.create().resource(obs).execute();
// Give some time for the subscription to deliver
Thread.sleep(2000);
// Give some time for the subscription to deliver
Thread.sleep(2000);
/*
* Ensure that we receive a ping on the websocket
*/
waitForSize(1, () -> mySocketImplementation.myPingCount);
/*
* Ensure that we receive a ping on the websocket
*/
waitForSize(1, () -> mySocketImplementation.myPingCount);
/*
* Clean up
*/
ourClient.delete().resourceById(mySubscriptionId).execute();
}
/*
* Clean up
*/
ourClient.delete().resourceById(mySubscriptionId).execute();
}
@AfterClass
public static void afterClass() throws Exception {
ourServer.stop();
}
@AfterClass
public static void afterClass() throws Exception {
ourServer.stop();
}
@BeforeClass
public static void beforeClass() throws Exception {
String path = Paths.get("").toAbsolutePath().toString();
@BeforeClass
public static void beforeClass() throws Exception {
String path = Paths.get("").toAbsolutePath().toString();
ourLog.info("Project base path is: {}", path);
ourLog.info("Project base path is: {}", path);
ourServer = new Server(0);
ourServer = new Server(0);
WebAppContext webAppContext = new WebAppContext();
webAppContext.setContextPath("/hapi-fhir-jpaserver");
webAppContext.setDisplayName("HAPI FHIR");
webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
webAppContext.setParentLoaderPriority(true);
WebAppContext webAppContext = new WebAppContext();
webAppContext.setContextPath("/hapi-fhir-jpaserver");
webAppContext.setDisplayName("HAPI FHIR");
webAppContext.setDescriptor(path + "/src/main/webapp/WEB-INF/web.xml");
webAppContext.setResourceBase(path + "/target/hapi-fhir-jpaserver-starter");
webAppContext.setParentLoaderPriority(true);
ourServer.setHandler(webAppContext);
ourServer.start();
ourServer.setHandler(webAppContext);
ourServer.start();
ourPort = JettyUtil.getPortForStartedServer(ourServer);
ourPort = JettyUtil.getPortForStartedServer(ourServer);
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
String ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
String ourServerBase = "http://localhost:" + ourPort + "/hapi-fhir-jpaserver/fhir/";
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
ourClient = ourCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
}
public static void main(String[] theArgs) throws Exception {
ourPort = 8080;
beforeClass();
}
public static void main(String[] theArgs) throws Exception {
ourPort = 8080;
beforeClass();
}
}

3
src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java
View File

@@ -1,12 +1,12 @@
package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.model.util.ProviderConstants;
import ca.uhn.fhir.rest.api.CacheControlDirective;
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.client.interceptor.UrlTenantSelectionInterceptor;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.test.utilities.JettyUtil;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.webapp.WebAppContext;
@@ -37,6 +37,7 @@ public class MultitenantServerR4IT {
HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr4-mt");
HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R4");
HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true");
HapiProperties.setProperty(HapiProperties.PARTITIONING_ENABLED, "true");
HapiProperties.setProperty(HapiProperties.PARTITIONING_MULTITENANCY_ENABLED, "true");
ourCtx = FhirContext.forR4();
}