diff --git a/README.md b/README.md index a46218c..25464fd 100644 --- a/README.md +++ b/README.md @@ -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) diff --git a/pom.xml b/pom.xml index dca8630..6f5a2a1 100644 --- a/pom.xml +++ b/pom.xml @@ -1,4 +1,4 @@ - 4.0.0 @@ -11,7 +11,7 @@ ca.uhn.hapi.fhir hapi-fhir - 5.0.2 + 5.1.0 hapi-fhir-jpaserver-starter @@ -20,6 +20,20 @@ 3.5.0 + war + + HAPI FHIR JPA Server - Starter Project + + + + oss-snapshots + + true + + https://oss.sonatype.org/content/repositories/snapshots/ + + + org.eclipse.jetty.websocket @@ -84,7 +98,12 @@ - + + + ca.uhn.hapi.fhir + hapi-fhir-jpaserver-empi + ${project.version} + ca.uhn.hapi.fhir @@ -249,23 +268,23 @@ test + + org.awaitility + awaitility + 4.0.0-rc1 + test + + + + + junit + junit + 4.12 + test + - war - - HAPI FHIR JPA Server - Starter Project - - - - oss-snapshots - - false - - https://oss.sonatype.org/content/repositories/snapshots/ - - - @@ -276,7 +295,7 @@ org.eclipse.jetty jetty-maven-plugin - ${jetty_version} + ${jetty_version} /hapi-fhir-jpaserver @@ -421,6 +440,7 @@ .*\.txt$ .*\.html$ + config/favicon.ico diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/ApplicationContext.java b/src/main/java/ca/uhn/fhir/jpa/starter/ApplicationContext.java index c177603..c4d2919 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/ApplicationContext.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/ApplicationContext.java @@ -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); + } + } } diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java b/src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java index 9eafd27..5b482c8 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java @@ -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; diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/EmpiConfig.java b/src/main/java/ca/uhn/fhir/jpa/starter/EmpiConfig.java new file mode 100644 index 0000000..107aa97 --- /dev/null +++ b/src/main/java/ca/uhn/fhir/jpa/starter/EmpiConfig.java @@ -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); + } + +} diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java index 344da8d..123b7a0 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java @@ -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"); diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java index dc91099..d80e70f 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java @@ -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; diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java index 3344952..2a93154 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java @@ -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; diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java index 77a798e..5f3f8a9 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java @@ -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; diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java index 6d9e45b..d6cf537 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java @@ -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; diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java b/src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java index 312ba7e..20628e5 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java @@ -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 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); } + + } diff --git a/src/main/resources/empi-rules.json b/src/main/resources/empi-rules.json new file mode 100644 index 0000000..ad549d8 --- /dev/null +++ b/src/main/resources/empi-rules.json @@ -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" +} diff --git a/src/main/resources/hapi.properties b/src/main/resources/hapi.properties index 2d199d1..b7ef0f8 100644 --- a/src/main/resources/hapi.properties +++ b/src/main/resources/hapi.properties @@ -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 \ No newline at end of file + +#daoconfig.client_id_strategy=ANY + diff --git a/src/main/resources/logback.xml b/src/main/resources/logback.xml index ffec8d3..9364495 100644 --- a/src/main/resources/logback.xml +++ b/src/main/resources/logback.xml @@ -9,6 +9,25 @@ + + DEBUG + ${smile.basedir}/log/empi-troubleshooting.log + + ${smile.basedir}/log/empi-troubleshooting.log.%i.gz + 1 + 9 + + + 5MB + + + %d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n${log.stackfilter.pattern} + + + + + + diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java index 1eedafd..22b5656 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java @@ -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 persons = getPeople(); + + // Verify a Person was created that links to our Patient + Optional 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 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(); } diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java index 3c02375..62ac1a3 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java @@ -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 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 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(); + } } diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java index 6db05fb..a2a6148 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java @@ -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(); }