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Merge branch 'master' of ssh://github.com/hapifhir/hapi-fhir-jpaserver-starter

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This commit is contained in:
Sean McIlvenna
2021-05-27 14:07:12 -07:00
parent a150aeb4d2 af6208c1f1
commit 7b97ed78eb
14 changed files with 174 additions and 56 deletions
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4
README.md
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@@ -317,11 +317,11 @@ It is important to use MySQL5Dialect when using MySQL version 5+.
The server may be configured with subscription support by enabling properties in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file:
- `hapi.fhir.subscription.resthook.enabled` - Enables REST Hook subscriptions, where the server will make an outgoing connection to a remote REST server
- `hapi.fhir.subscription.resthook_enabled` - Enables REST Hook subscriptions, where the server will make an outgoing connection to a remote REST server
- `hapi.fhir.subscription.email.*` - Enables email subscriptions. Note that you must also provide the connection details for a usable SMTP server.
- `hapi.fhir.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/websocket](ws://localhost:8080/websocket)
- `hapi.fhir.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/websocket](ws://localhost:8080/websocket)
## Enabling CQL

10
pom.xml
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@@ -14,8 +14,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<!-- FIMXME KBD Change this to 5.3.0 BEFORE merging this code to master ! -->
<version>5.3.0</version>
<version>5.4.0</version>
</parent>
<artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -148,6 +147,13 @@
<artifactId>thymeleaf</artifactId>
</dependency>
<!-- Needed for parsing the config -->
<dependency>
<groupId>org.yaml</groupId>
<artifactId>snakeyaml</artifactId>
<version>1.28</version>
</dependency>
<!-- Used for CORS support -->
<!-- Spring Web is used to deploy the server to a web container. -->
<dependency>

6
src/main/java/ca/uhn/fhir/jpa/mdm/MdmConfig.java
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@@ -7,7 +7,7 @@ import ca.uhn.fhir.jpa.starter.AppProperties;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.rules.config.MdmRuleValidator;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.rest.server.util.ISearchParamRetriever;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import org.springframework.beans.factory.annotation.Autowired;
@@ -30,8 +30,8 @@ import java.io.IOException;
public class MdmConfig {
@Bean
MdmRuleValidator mdmRuleValidator(FhirContext theFhirContext, ISearchParamRetriever theSearchParamRetriever) {
return new MdmRuleValidator(theFhirContext, theSearchParamRetriever);
MdmRuleValidator mdmRuleValidator(FhirContext theFhirContext, ISearchParamRegistry theSearchParamRegistry) {
return new MdmRuleValidator(theFhirContext, theSearchParamRegistry);
}
@Bean

29
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -30,6 +30,7 @@ public class AppProperties {
private Boolean allow_override_default_search_params = true;
private Boolean auto_create_placeholder_reference_targets = false;
private Boolean enable_index_missing_fields = false;
private Boolean enable_index_contained_resource = false;
private Boolean enable_repository_validating_interceptor = false;
private Boolean enforce_referential_integrity_on_delete = true;
private Boolean enforce_referential_integrity_on_write = true;
@@ -66,6 +67,9 @@ public class AppProperties {
private Boolean lastn_enabled = false;
private NormalizedQuantitySearchLevel normalized_quantity_search_level = NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_NOT_SUPPORTED;
private Integer search_coord_core_pool_size = 20;
private Integer search_coord_max_pool_size = 100;
private Integer search_coord_queue_capacity = 200;
private Boolean use_apache_address_strategy = false;
private Boolean use_apache_address_strategy_https = false;
@@ -264,6 +268,14 @@ public class AppProperties {
this.enable_index_missing_fields = enable_index_missing_fields;
}
public Boolean getEnable_index_contained_resource() {
return enable_index_contained_resource;
}
public void setEnable_index_contained_resource(Boolean enable_index_contained_resource) {
this.enable_index_contained_resource = enable_index_contained_resource;
}
public Boolean getEnable_repository_validating_interceptor() {
return enable_repository_validating_interceptor;
}
@@ -432,6 +444,23 @@ public class AppProperties {
this.normalized_quantity_search_level = normalized_quantity_search_level;
}
public Integer getSearch_coord_core_pool_size() { return search_coord_core_pool_size; }
public void setSearch_coord_core_pool_size(Integer search_coord_core_pool_size) {
this.search_coord_core_pool_size = search_coord_core_pool_size;
}
public Integer getSearch_coord_max_pool_size() { return search_coord_max_pool_size; }
public void setSearch_coord_max_pool_size(Integer search_coord_max_pool_size) {
this.search_coord_max_pool_size = search_coord_max_pool_size;
}
public Integer getSearch_coord_queue_capacity() { return search_coord_queue_capacity; }
public void setSearch_coord_queue_capacity(Integer search_coord_queue_capacity) {
this.search_coord_queue_capacity = search_coord_queue_capacity;
}
public static class Cors {
private Boolean allow_Credentials = true;

63
src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java
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@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.starter;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.cql.common.provider.CqlProviderLoader;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
@@ -9,31 +10,38 @@ 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.binstore.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.bulk.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.bulk.export.provider.BulkDataExportProvider;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc;
import ca.uhn.fhir.jpa.packages.PackageInstallOutcomeJson;
import ca.uhn.fhir.jpa.packages.PackageInstallationSpec;
import ca.uhn.fhir.jpa.partition.PartitionManagementProvider;
import ca.uhn.fhir.jpa.provider.*;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.provider.IJpaSystemProvider;
import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4;
import ca.uhn.fhir.jpa.provider.r5.JpaConformanceProviderR5;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.narrative.INarrativeGenerator;
import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
import ca.uhn.fhir.rest.server.ApacheProxyAddressStrategy;
import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
import ca.uhn.fhir.rest.server.ApacheProxyAddressStrategy;
import ca.uhn.fhir.rest.server.IncomingRequestAddressStrategy;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.*;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.rest.server.interceptor.FhirPathFilterInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
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.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import com.google.common.base.Strings;
@@ -44,74 +52,61 @@ import org.springframework.http.HttpHeaders;
import org.springframework.web.cors.CorsConfiguration;
import javax.servlet.ServletException;
import java.util.*;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.stream.Collectors;
public class BaseJpaRestfulServer extends RestfulServer {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaRestfulServer.class);
private static final long serialVersionUID = 1L;
@Autowired
DaoRegistry daoRegistry;
@Autowired
DaoConfig daoConfig;
@Autowired
ISearchParamRegistry searchParamRegistry;
@Autowired
IFhirSystemDao fhirSystemDao;
@Autowired
ResourceProviderFactory resourceProviders;
@Autowired
IJpaSystemProvider jpaSystemProvider;
@Autowired
IInterceptorBroadcaster interceptorBroadcaster;
@Autowired
DatabaseBackedPagingProvider databaseBackedPagingProvider;
@Autowired
IInterceptorService interceptorService;
@Autowired
IValidatorModule validatorModule;
@Autowired
Optional<GraphQLProvider> graphQLProvider;
@Autowired
BulkDataExportProvider bulkDataExportProvider;
@Autowired
PartitionManagementProvider partitionManagementProvider;
@Autowired
BinaryStorageInterceptor binaryStorageInterceptor;
@Autowired
IPackageInstallerSvc packageInstallerSvc;
@Autowired
AppProperties appProperties;
@Autowired
ApplicationContext myApplicationContext;
@Autowired(required = false)
IRepositoryValidationInterceptorFactory factory;
// These are set only if the features are enabled
private CqlProviderLoader cqlProviderLoader;
@Autowired
private IValidationSupport myValidationSupport;
public BaseJpaRestfulServer() {
}
private static final long serialVersionUID = 1L;
@SuppressWarnings("unchecked")
@Override
protected void initialize() throws ServletException {
@@ -159,14 +154,14 @@ public class BaseJpaRestfulServer extends RestfulServer {
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.R4) {
JpaConformanceProviderR4 confProvider = new JpaConformanceProviderR4(this, fhirSystemDao,
daoConfig, searchParamRegistry);
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(this, fhirSystemDao,
daoConfig, searchParamRegistry, myValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R4 Server");
setServerConformanceProvider(confProvider);
} else if (fhirVersion == FhirVersionEnum.R5) {
JpaConformanceProviderR5 confProvider = new JpaConformanceProviderR5(this, fhirSystemDao,
daoConfig, searchParamRegistry);
JpaCapabilityStatementProvider confProvider = new JpaCapabilityStatementProvider(this, fhirSystemDao,
daoConfig, searchParamRegistry, myValidationSupport);
confProvider.setImplementationDescription("HAPI FHIR R5 Server");
setServerConformanceProvider(confProvider);
} else {
@@ -389,5 +384,7 @@ public class BaseJpaRestfulServer extends RestfulServer {
}
daoConfig.getModelConfig().setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
daoConfig.getModelConfig().setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
}
}

6
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java
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@@ -61,6 +61,10 @@ public class FhirServerConfigCommon {
if (appProperties.getSubscription().getEmail() != null) {
ourLog.info("Email subscriptions enabled");
}
if (appProperties.getEnable_index_contained_resource() == Boolean.TRUE) {
ourLog.info("Indexed on contained resource enabled");
}
}
/**
@@ -163,6 +167,8 @@ public class FhirServerConfigCommon {
}
modelConfig.setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
modelConfig.setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
return modelConfig;
}

14
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java
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@@ -13,6 +13,7 @@ import org.springframework.core.env.ConfigurableEnvironment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
@@ -31,6 +32,19 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 {
@Autowired
AppProperties appProperties;
@PostConstruct
public void initSettings() {
if(appProperties.getSearch_coord_core_pool_size() != null) {
setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
}
if(appProperties.getSearch_coord_max_pool_size() != null) {
setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
}
if(appProperties.getSearch_coord_queue_capacity() != null) {
setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
}
}
@Override
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();

22
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java
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@@ -11,6 +11,7 @@ import org.springframework.core.env.ConfigurableEnvironment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
@@ -29,6 +30,20 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
@Autowired
AppProperties appProperties;
@PostConstruct
public void initSettings() {
if(appProperties.getSearch_coord_core_pool_size() != null) {
setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
}
if(appProperties.getSearch_coord_max_pool_size() != null) {
setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
}
if(appProperties.getSearch_coord_queue_capacity() != null) {
setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
}
}
@Override
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
@@ -68,7 +83,12 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
public ElasticsearchSvcImpl elasticsearchSvc() {
if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":"));
String elasticsearchHost;
if (elasticsearchUrl.startsWith("http")) {
elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://") + 3, elasticsearchUrl.lastIndexOf(":"));
} else {
elasticsearchHost = elasticsearchUrl.substring(0, elasticsearchUrl.indexOf(":"));
}
String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));

14
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java
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@@ -12,6 +12,7 @@ import org.springframework.core.env.ConfigurableEnvironment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
@@ -31,6 +32,19 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
@Autowired
AppProperties appProperties;
@PostConstruct
public void initSettings() {
if(appProperties.getSearch_coord_core_pool_size() != null) {
setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
}
if(appProperties.getSearch_coord_max_pool_size() != null) {
setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
}
if(appProperties.getSearch_coord_queue_capacity() != null) {
setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
}
}
@Override
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();

21
src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java
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@@ -14,6 +14,7 @@ import org.springframework.core.env.ConfigurableEnvironment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
@@ -32,6 +33,19 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
@Autowired
AppProperties appProperties;
@PostConstruct
public void initSettings() {
if(appProperties.getSearch_coord_core_pool_size() != null) {
setSearchCoordCorePoolSize(appProperties.getSearch_coord_core_pool_size());
}
if(appProperties.getSearch_coord_max_pool_size() != null) {
setSearchCoordMaxPoolSize(appProperties.getSearch_coord_max_pool_size());
}
if(appProperties.getSearch_coord_queue_capacity() != null) {
setSearchCoordQueueCapacity(appProperties.getSearch_coord_queue_capacity());
}
}
@Override
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
DatabaseBackedPagingProvider pagingProvider = super.databaseBackedPagingProvider();
@@ -71,7 +85,12 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 {
public ElasticsearchSvcImpl elasticsearchSvc() {
if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) {
String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment);
String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":"));
String elasticsearchHost;
if (elasticsearchUrl.startsWith("http")) {
elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://") + 3, elasticsearchUrl.lastIndexOf(":"));
} else {
elasticsearchHost = elasticsearchUrl.substring(0, elasticsearchUrl.indexOf(":"));
}
String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment);
String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment);
int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1));

11
src/main/resources/application.yaml
View File

@@ -6,6 +6,10 @@ spring:
password: null
driverClassName: org.h2.Driver
max-active: 15
# database connection pool size
hikari:
maximum-pool-size: 10
jpa:
properties:
hibernate.format_sql: false
@@ -65,6 +69,7 @@ hapi:
# default_page_size: 20
# enable_repository_validating_interceptor: false
# enable_index_missing_fields: false
# enable_index_contained_resource: false
# enforce_referential_integrity_on_delete: false
# enforce_referential_integrity_on_write: false
# etag_support_enabled: true
@@ -83,6 +88,12 @@ hapi:
# These are allowed_origin patterns, see: https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/cors/CorsConfiguration.html#setAllowedOriginPatterns-java.util.List-
allowed_origin:
- '*'
# Search coordinator thread pool sizes
search-coord-core-pool-size: 20
search-coord-max-pool-size: 100
search-coord-queue-capacity: 200
# logger:
# error_format: 'ERROR - ${requestVerb} ${requestUrl}'
# format: >-

2
src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java
View File

@@ -60,7 +60,7 @@ public class ElasticsearchLastNR4IT {
private IGenericClient ourClient;
private FhirContext ourCtx;
private static final String ELASTIC_VERSION = "7.10.1";
private static final String ELASTIC_VERSION = "7.10.2";
private static final String ELASTIC_IMAGE = "docker.elastic.co/elasticsearch/elasticsearch:" + ELASTIC_VERSION;
private static ElasticsearchContainer embeddedElastic;

8
src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java
View File

@@ -67,16 +67,18 @@ public class ExampleServerR5IT {
public void testWebsocketSubscription() throws Exception {
/*
* Create topic
* Create topic (will be contained in subscription)
*/
SubscriptionTopic topic = new SubscriptionTopic();
topic.getResourceTrigger().getQueryCriteria().setCurrent("Observation?status=final");
topic.setId("#1");
topic.getResourceTriggerFirstRep().getQueryCriteria().setCurrent("Observation?status=final");
/*
* Create subscription
*/
Subscription subscription = new Subscription();
subscription.getTopic().setResource(topic);
subscription.getContained().add(topic);
subscription.setTopic("#1");
subscription.setReason("Monitor new neonatal function (note, age will be determined by the monitor)");
subscription.setStatus(Enumerations.SubscriptionState.REQUESTED);
subscription.getChannelType()