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Merge pull request #220 from hapifhir/rel_5_4_0

Browse Source 
Release 5.4.0
This commit is contained in:
James Agnew
2021-05-19 08:50:33 -04:00
committed by GitHub
parent 9760e586b6 44e6c65d08
commit a7fa1caea0
13 changed files with 170 additions and 57 deletions
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3
pom.xml
View File

@@ -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>

24
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;
@@ -29,17 +29,17 @@ import java.io.IOException;
@Import({MdmConsumerConfig.class, MdmSubmitterConfig.class})
public class MdmConfig {
@Bean
MdmRuleValidator mdmRuleValidator(FhirContext theFhirContext, ISearchParamRetriever theSearchParamRetriever) {
return new MdmRuleValidator(theFhirContext, theSearchParamRetriever);
}
@Bean
MdmRuleValidator mdmRuleValidator(FhirContext theFhirContext, ISearchParamRegistry theSearchParamRegistry) {
return new MdmRuleValidator(theFhirContext, theSearchParamRegistry);
}
@Bean
IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties) throws IOException {
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
Resource resource = resourceLoader.getResource("mdm-rules.json");
String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
return new MdmSettings(theMdmRuleValidator).setEnabled(appProperties.getMdm_enabled()).setScriptText(json);
}
@Bean
IMdmSettings mdmSettings(@Autowired MdmRuleValidator theMdmRuleValidator, AppProperties appProperties) throws IOException {
DefaultResourceLoader resourceLoader = new DefaultResourceLoader();
Resource resource = resourceLoader.getResource("mdm-rules.json");
String json = IOUtils.toString(resource.getInputStream(), Charsets.UTF_8);
return new MdmSettings(theMdmRuleValidator).setEnabled(appProperties.getMdm_enabled()).setScriptText(json);
}
}

29
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java
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@@ -31,6 +31,7 @@ public class AppProperties {
private Boolean allow_placeholder_references = 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;
@@ -67,6 +68,9 @@ 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;
@@ -273,6 +277,14 @@ 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;
}
@@ -441,6 +453,23 @@ 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;

61
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;
@@ -44,67 +52,56 @@ 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 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() {
}
@@ -158,14 +155,14 @@ 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 {
@@ -384,5 +381,7 @@ public class BaseJpaRestfulServer extends RestfulServer {
}
daoConfig.getModelConfig().setNormalizedQuantitySearchLevel(appProperties.getNormalized_quantity_search_level());
daoConfig.getModelConfig().setIndexOnContainedResources(appProperties.getEnable_index_contained_resource());
}
}

2
src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java
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@@ -183,4 +183,4 @@ public class EnvironmentHelper {
aBase.put(entry.getKey(), entry.getValue());
}
}
}
}

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
View File

@@ -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
View File

@@ -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));

21
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
@@ -66,6 +70,7 @@ 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
@@ -79,11 +84,17 @@ hapi:
# partitioning:
# allow_references_across_partitions: false
# partitioning_include_in_search_hashes: false
cors:
allow_Credentials: true
# 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:
- '*'
cors:
allow_Credentials: true
# 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()