diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml new file mode 100644 index 0000000..74c342f --- /dev/null +++ b/.github/workflows/maven.yml @@ -0,0 +1,24 @@ +# This workflow will build a Java project with Maven +# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven + +name: Java CI with Maven + +on: + push: + branches: [ master ] + pull_request: + branches: [ master ] + +jobs: + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + - name: Set up JDK 11 + uses: actions/setup-java@v1 + with: + java-version: 11 + - name: Build with Maven + run: mvn -B package --file pom.xml diff --git a/README.md b/README.md index 7ee6092..09c080d 100644 --- a/README.md +++ b/README.md @@ -42,15 +42,23 @@ docker run -p 8080:8080 -e hapi.fhir.default_encoding=xml hapiproject/hapi:lates HAPI looks in the environment variables for properties in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file for defaults. -### Configuration via overridden application.yaml file +### Configuration via overridden application.yaml file and using Docker You can customize HAPI by telling HAPI to look for the configuration file in a different location, eg.: +``` +docker run -p 8090:8080 -v $(pwd)/yourLocalFolder:/configs -e "--spring.config.location=file:///configs/another.application.yaml" hapiproject/hapi:latest +``` +Here, the configuration file (*another.application.yaml*) is placed locally in the folder *yourLocalFolder*. + + + ``` docker run -p 8090:8080 -e "--spring.config.location=classpath:/another.application.yaml" hapiproject/hapi:latest ``` +Here, the configuration file (*another.application.yaml*) is part of the compiled set of resources. -### Example docker-compose.yml +### Example using docker-compose.yml for docker-compose ``` version: '3.7' @@ -314,6 +322,10 @@ elasticsearch.required_index_status=YELLOW elasticsearch.schema_management_strategy=CREATE ``` +## Enabling LastN + +Set `hapi.fhir.lastn_enabled=true` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to enable the $lastn operation on this server. Note that the $lastn operation relies on Elasticsearch, so for $lastn to work, indexing must be enabled using Elasticsearch. + ## Example of a Dockerfile based on distroless images (for lower footprint and improved security) ```code diff --git a/pom.xml b/pom.xml index e17c0cc..ecf437a 100644 --- a/pom.xml +++ b/pom.xml @@ -14,7 +14,7 @@ ca.uhn.hapi.fhir hapi-fhir - 5.1.0 + 5.2.0 hapi-fhir-jpaserver-starter @@ -177,37 +177,30 @@ org.webjars Eonasdan-bootstrap-datetimepicker - 4.17.43 org.webjars font-awesome - 5.8.2 org.webjars.bower awesome-bootstrap-checkbox - 1.0.1 org.webjars jstimezonedetect - 1.0.6 org.webjars select2 - 4.0.3 org.webjars.bower jquery - 3.3.1 org.webjars.bower moment - 2.15.1 diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java b/src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java index 2835656..30df010 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java @@ -7,8 +7,10 @@ import ca.uhn.fhir.rest.api.EncodingEnum; import java.util.ArrayList; import java.util.List; +import java.util.Map; import com.google.common.collect.ImmutableList; +import com.google.common.collect.ImmutableMap; import org.hl7.fhir.r4.model.Bundle; import org.springframework.boot.context.properties.ConfigurationProperties; @@ -52,14 +54,17 @@ public class AppProperties { private ClientIdStrategyEnum client_id_strategy = ClientIdStrategyEnum.ALPHANUMERIC; private List supported_resource_types = new ArrayList<>(); private List allowed_bundle_types = null; + private Boolean narrative_enabled = true; private Validation validation = new Validation(); - private List tester = ImmutableList.of(new Tester()); + private Map tester = ImmutableMap.of("home", new Tester()); private Logger logger = new Logger(); private Subscription subscription = new Subscription(); private Cors cors = null; private Partitioning partitioning = null; - private List implementationGuides = null; + private Map implementationGuides = null; + + private Boolean lastn_enabled = false; public Integer getDefer_indexing_for_codesystems_of_size() { return defer_indexing_for_codesystems_of_size; @@ -69,11 +74,11 @@ public class AppProperties { this.defer_indexing_for_codesystems_of_size = defer_indexing_for_codesystems_of_size; } - public List getImplementationGuides() { + public Map getImplementationGuides() { return implementationGuides; } - public void setImplementationGuides(List implementationGuides) { + public void setImplementationGuides(Map implementationGuides) { this.implementationGuides = implementationGuides; } @@ -363,14 +368,32 @@ public class AppProperties { this.reuse_cached_search_results_millis = reuse_cached_search_results_millis; } - public List getTester() { + public Map getTester() { return tester; } - public void setTester(List tester) { + public void setTester(Map tester) { this.tester = tester; } + public Boolean getNarrative_enabled() + { + return narrative_enabled; + } + + public void setNarrative_enabled(Boolean narrative_enabled) + { + this.narrative_enabled = narrative_enabled; + } + + public Boolean getLastn_enabled() { + return lastn_enabled; + } + + public void setLastn_enabled(Boolean lastn_enabled) { + this.lastn_enabled = lastn_enabled; + } + public static class Cors { private Boolean allow_Credentials = true; private List allowed_origin = ImmutableList.of("*"); @@ -437,7 +460,6 @@ public class AppProperties { public static class Tester { - private String id = "home"; private String name = "Local Tester"; private String server_address = "http://localhost:8080/fhir"; private Boolean refuse_to_fetch_third_party_urls = true; @@ -451,14 +473,6 @@ public class AppProperties { this.fhir_version = fhir_version; } - public String getId() { - return id; - } - - public void setId(String id) { - this.id = id; - } - public String getName() { return name; } diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/Application.java b/src/main/java/ca/uhn/fhir/jpa/starter/Application.java index fab5481..272feb6 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/Application.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/Application.java @@ -1,6 +1,7 @@ package ca.uhn.fhir.jpa.starter; import ca.uhn.fhir.jpa.empi.EmpiConfig; +import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion; 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; @@ -15,6 +16,7 @@ import org.springframework.boot.web.servlet.ServletComponentScan; import org.springframework.boot.web.servlet.ServletRegistrationBean; import org.springframework.boot.web.servlet.support.SpringBootServletInitializer; import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Import; import org.springframework.web.context.support.AnnotationConfigWebApplicationContext; import org.springframework.web.servlet.DispatcherServlet; @@ -44,6 +46,7 @@ public class Application extends SpringBootServletInitializer { AutowireCapableBeanFactory beanFactory; @Bean + @Conditional(OnEitherVersion.class) public ServletRegistrationBean hapiServletRegistration() { ServletRegistrationBean servletRegistrationBean = new ServletRegistrationBean(); JpaRestfulServer jpaRestfulServer = new JpaRestfulServer(); 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 2f7c044..dfbe8c8 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java @@ -13,11 +13,7 @@ import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor; import ca.uhn.fhir.jpa.packages.IPackageInstallerSvc; import ca.uhn.fhir.jpa.packages.PackageInstallationSpec; import ca.uhn.fhir.jpa.partition.PartitionManagementProvider; -import ca.uhn.fhir.jpa.provider.GraphQLProvider; -import ca.uhn.fhir.jpa.provider.IJpaSystemProvider; -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.*; import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3; import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4; import ca.uhn.fhir.jpa.provider.r5.JpaConformanceProviderR5; @@ -25,6 +21,8 @@ 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.ETagSupportEnum; import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy; import ca.uhn.fhir.rest.server.RestfulServer; @@ -42,10 +40,7 @@ import org.springframework.http.HttpHeaders; import org.springframework.web.cors.CorsConfiguration; import javax.servlet.ServletException; -import java.util.Arrays; -import java.util.Collections; -import java.util.List; -import java.util.Optional; +import java.util.*; import java.util.stream.Collectors; public class BaseJpaRestfulServer extends RestfulServer { @@ -181,7 +176,11 @@ public class BaseJpaRestfulServer extends RestfulServer { * This server tries to dynamically generate narratives */ FhirContext ctx = getFhirContext(); - ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator()); + INarrativeGenerator theNarrativeGenerator = + appProperties.getNarrative_enabled() ? + new DefaultThymeleafNarrativeGenerator() : + new NullNarrativeGenerator(); + ctx.setNarrativeGenerator(theNarrativeGenerator); /* * Default to JSON and pretty printing @@ -349,15 +348,21 @@ public class BaseJpaRestfulServer extends RestfulServer { } if (appProperties.getImplementationGuides() != null) { - List guides = appProperties.getImplementationGuides(); - for (AppProperties.ImplementationGuide guide : guides) { + Map guides = appProperties.getImplementationGuides(); + for (Map.Entry guide : guides.entrySet()) { packageInstallerSvc.install(new PackageInstallationSpec() - .setPackageUrl(guide.getUrl()) - .setName(guide.getName()) - .setVersion(guide.getVersion()) + .setPackageUrl(guide.getValue().getUrl()) + .setName(guide.getValue().getName()) + .setVersion(guide.getValue().getVersion()) .setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL)); } } + + if (appProperties.getLastn_enabled()) { + daoConfig.setLastNEnabled(true); + } + + } diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java b/src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java index 4dbc122..6dd8311 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java @@ -1,5 +1,8 @@ package ca.uhn.fhir.jpa.starter; +import ca.uhn.fhir.jpa.search.elastic.ElasticsearchHibernatePropertiesBuilder; +import org.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus; +import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy; import org.springframework.core.env.CompositePropertySource; import org.springframework.core.env.ConfigurableEnvironment; import org.springframework.core.env.EnumerablePropertySource; @@ -35,9 +38,66 @@ public class EnvironmentHelper { properties.put(values[0], values[1]); }); } + + if (environment.getProperty("elasticsearch.enabled", Boolean.class) != null + && environment.getProperty("elasticsearch.enabled", Boolean.class) == true ){ + ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder(); + ElasticsearchIndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", ElasticsearchIndexStatus.class); + if (requiredIndexStatus == null) { + builder.setRequiredIndexStatus(ElasticsearchIndexStatus.YELLOW); + } else { + builder.setRequiredIndexStatus(requiredIndexStatus); + } + + builder.setRestUrl(getElasticsearchServerUrl(environment)); + builder.setUsername(getElasticsearchServerUsername(environment)); + builder.setPassword(getElasticsearchServerPassword(environment)); + IndexSchemaManagementStrategy indexSchemaManagementStrategy = environment.getProperty("elasticsearch.schema_management_strategy", IndexSchemaManagementStrategy.class); + if (indexSchemaManagementStrategy == null) { + builder.setIndexSchemaManagementStrategy(IndexSchemaManagementStrategy.CREATE); + } else { + builder.setIndexSchemaManagementStrategy(indexSchemaManagementStrategy); + } + // pretty_print_json_log: false + Boolean refreshAfterWrite = environment.getProperty("elasticsearch.debug.refresh_after_write", Boolean.class); + if (refreshAfterWrite == null) { + builder.setDebugRefreshAfterWrite(false); + } else { + builder.setDebugRefreshAfterWrite(refreshAfterWrite); + } + // pretty_print_json_log: false + Boolean prettyPrintJsonLog = environment.getProperty("elasticsearch.debug.pretty_print_json_log", Boolean.class); + if (prettyPrintJsonLog == null) { + builder.setDebugPrettyPrintJsonLog(false); + } else { + builder.setDebugPrettyPrintJsonLog(prettyPrintJsonLog); + } + builder.apply(properties); + } + return properties; } + public static String getElasticsearchServerUrl(ConfigurableEnvironment environment) { + return environment.getProperty("elasticsearch.rest_url", String.class); + } + + public static String getElasticsearchServerUsername(ConfigurableEnvironment environment) { + return environment.getProperty("elasticsearch.username"); + } + + public static String getElasticsearchServerPassword(ConfigurableEnvironment environment) { + return environment.getProperty("elasticsearch.password"); + } + + public static Boolean isElasticsearchEnabled(ConfigurableEnvironment environment) { + if (environment.getProperty("elasticsearch.enabled", Boolean.class) != null) { + return environment.getProperty("elasticsearch.enabled", Boolean.class); + } else { + return false; + } + } + public static Map getPropertiesStartingWith(ConfigurableEnvironment aEnv, String aKeyPrefix) { Map result = new HashMap<>(); 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 cfe9bde..4b7d721 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigCommon.java @@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.starter; import ca.uhn.fhir.jpa.api.config.DaoConfig; import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl; import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc; +import ca.uhn.fhir.jpa.config.HibernateDialectProvider; import ca.uhn.fhir.jpa.model.config.PartitionSettings; import ca.uhn.fhir.jpa.model.entity.ModelConfig; import ca.uhn.fhir.jpa.subscription.channel.subscription.SubscriptionDeliveryHandlerFactory; @@ -10,9 +11,12 @@ import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender; import ca.uhn.fhir.jpa.subscription.match.deliver.email.JavaMailEmailSender; import com.google.common.base.Strings; import org.hl7.fhir.dstu2.model.Subscription; +import org.springframework.boot.env.YamlPropertySourceLoader; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Lazy; +import org.springframework.context.annotation.Primary; +import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean; import org.springframework.transaction.annotation.EnableTransactionManagement; import java.util.Optional; @@ -110,6 +114,11 @@ public class FhirServerConfigCommon { return retVal; } + @Bean + public YamlPropertySourceLoader yamlPropertySourceLoader() { + return new YamlPropertySourceLoader(); + } + @Bean public PartitionSettings partitionSettings(AppProperties appProperties) { PartitionSettings retVal = new PartitionSettings(); @@ -123,6 +132,12 @@ public class FhirServerConfigCommon { } + @Primary + @Bean + public HibernateDialectProvider jpaStarterDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) { + return new JpaHibernateDialectProvider(myEntityManagerFactory); + } + @Bean public ModelConfig modelConfig(AppProperties appProperties) { ModelConfig modelConfig = new ModelConfig(); 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 8efc81f..5674d2a 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java @@ -3,24 +3,21 @@ package ca.uhn.fhir.jpa.starter; import ca.uhn.fhir.context.ConfigurationException; import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; +import ca.uhn.fhir.jpa.starter.annotations.OnDSTU2Condition; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Primary; -import org.springframework.context.annotation.Profile; import org.springframework.core.env.ConfigurableEnvironment; -import org.springframework.core.env.Environment; import org.springframework.orm.jpa.JpaTransactionManager; import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean; import javax.persistence.EntityManagerFactory; import javax.sql.DataSource; -import java.util.HashMap; -import java.util.Map; -import java.util.Properties; @Configuration -@Profile("dstu2") +@Conditional(OnDSTU2Condition.class) public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 { @Autowired 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 ace88af..07406b2 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java @@ -3,11 +3,10 @@ package ca.uhn.fhir.jpa.starter; import ca.uhn.fhir.context.ConfigurationException; import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; +import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl; +import ca.uhn.fhir.jpa.starter.annotations.OnDSTU3Condition; 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.context.annotation.Profile; +import org.springframework.context.annotation.*; import org.springframework.core.env.ConfigurableEnvironment; import org.springframework.orm.jpa.JpaTransactionManager; import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean; @@ -16,7 +15,7 @@ import javax.persistence.EntityManagerFactory; import javax.sql.DataSource; @Configuration -@Profile("dstu3") +@Conditional(OnDSTU3Condition.class) public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 { @Autowired @@ -65,4 +64,18 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 { return retVal; } + @Bean() + public ElasticsearchSvcImpl elasticsearchSvc() { + if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) { + String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment); + String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":")); + String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment); + String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment); + int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1)); + return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword); + } else { + return null; + } + } + } 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 8d8e699..e415fea 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java @@ -3,23 +3,22 @@ package ca.uhn.fhir.jpa.starter; import ca.uhn.fhir.context.ConfigurationException; import ca.uhn.fhir.jpa.config.BaseJavaConfigR4; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; +import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl; +import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Primary; -import org.springframework.context.annotation.Profile; import org.springframework.core.env.ConfigurableEnvironment; -import org.springframework.core.env.Environment; import org.springframework.orm.jpa.JpaTransactionManager; import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean; import javax.persistence.EntityManagerFactory; import javax.sql.DataSource; -import java.util.Arrays; -import java.util.Properties; @Configuration -@Profile("r4") +@Conditional(OnR4Condition.class) public class FhirServerConfigR4 extends BaseJavaConfigR4 { @Autowired @@ -68,4 +67,18 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 { return retVal; } + @Bean() + public ElasticsearchSvcImpl elasticsearchSvc() { + if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) { + String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment); + String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":")); + String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment); + String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment); + int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1)); + return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword); + } else { + return null; + } + } + } 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 5a5145b..6e5bd98 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java @@ -3,11 +3,13 @@ package ca.uhn.fhir.jpa.starter; import ca.uhn.fhir.context.ConfigurationException; import ca.uhn.fhir.jpa.config.BaseJavaConfigR5; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; +import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl; +import ca.uhn.fhir.jpa.starter.annotations.OnR5Condition; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Bean; +import org.springframework.context.annotation.Conditional; import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Primary; -import org.springframework.context.annotation.Profile; import org.springframework.core.env.ConfigurableEnvironment; import org.springframework.orm.jpa.JpaTransactionManager; import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean; @@ -16,7 +18,7 @@ import javax.persistence.EntityManagerFactory; import javax.sql.DataSource; @Configuration -@Profile("r5") +@Conditional(OnR5Condition.class) public class FhirServerConfigR5 extends BaseJavaConfigR5 { @Autowired @@ -65,4 +67,19 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 { return retVal; } + @Bean() + public ElasticsearchSvcImpl elasticsearchSvc() { + if (EnvironmentHelper.isElasticsearchEnabled(configurableEnvironment)) { + String elasticsearchUrl = EnvironmentHelper.getElasticsearchServerUrl(configurableEnvironment); + String elasticsearchHost = elasticsearchUrl.substring(elasticsearchUrl.indexOf("://")+3, elasticsearchUrl.lastIndexOf(":")); + String elasticsearchUsername = EnvironmentHelper.getElasticsearchServerUsername(configurableEnvironment); + String elasticsearchPassword = EnvironmentHelper.getElasticsearchServerPassword(configurableEnvironment); + int elasticsearchPort = Integer.parseInt(elasticsearchUrl.substring(elasticsearchUrl.lastIndexOf(":")+1)); + return new ElasticsearchSvcImpl(elasticsearchHost, elasticsearchPort, elasticsearchUsername, elasticsearchPassword); + } else { + return null; + } + } + + } diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/FhirTesterConfig.java b/src/main/java/ca/uhn/fhir/jpa/starter/FhirTesterConfig.java index 45a7808..7adf8bf 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirTesterConfig.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirTesterConfig.java @@ -36,15 +36,15 @@ public class FhirTesterConfig { @Bean public TesterConfig testerConfig(AppProperties appProperties) { TesterConfig retVal = new TesterConfig(); - appProperties.getTester().stream().forEach(t -> { + appProperties.getTester().entrySet().stream().forEach(t -> { retVal .addServer() - .withId(t.getId()) - .withFhirVersion(t.getFhir_version()) - .withBaseUrl(t.getServer_address()) - .withName(t.getName()); + .withId(t.getKey()) + .withFhirVersion(t.getValue().getFhir_version()) + .withBaseUrl(t.getValue().getServer_address()) + .withName(t.getValue().getName()); retVal.setRefuseToFetchThirdPartyUrls( - t.getRefuse_to_fetch_third_party_urls()); + t.getValue().getRefuse_to_fetch_third_party_urls()); }); return retVal; diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/JpaHibernateDialectProvider.java b/src/main/java/ca/uhn/fhir/jpa/starter/JpaHibernateDialectProvider.java new file mode 100644 index 0000000..49d31ee --- /dev/null +++ b/src/main/java/ca/uhn/fhir/jpa/starter/JpaHibernateDialectProvider.java @@ -0,0 +1,31 @@ +package ca.uhn.fhir.jpa.starter; + +import ca.uhn.fhir.context.ConfigurationException; +import ca.uhn.fhir.jpa.config.HibernateDialectProvider; +import org.hibernate.dialect.Dialect; +import org.hibernate.engine.jdbc.dialect.internal.StandardDialectResolver; +import org.hibernate.engine.jdbc.dialect.spi.DatabaseMetaDataDialectResolutionInfoAdapter; +import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean; + +import javax.sql.DataSource; +import java.sql.SQLException; + +public class JpaHibernateDialectProvider extends HibernateDialectProvider { + + private final Dialect dialect; + + public JpaHibernateDialectProvider(LocalContainerEntityManagerFactoryBean myEntityManagerFactory) { + DataSource connection = myEntityManagerFactory.getDataSource(); + try { + dialect = new StandardDialectResolver() + .resolveDialect(new DatabaseMetaDataDialectResolutionInfoAdapter(connection.getConnection().getMetaData())); + } catch (SQLException sqlException) { + throw new ConfigurationException(sqlException.getMessage(), sqlException); + } + } + + @Override + public Dialect getDialect() { + return dialect; + } +} diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU2Condition.java b/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU2Condition.java new file mode 100644 index 0000000..2c2419c --- /dev/null +++ b/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU2Condition.java @@ -0,0 +1,19 @@ +package ca.uhn.fhir.jpa.starter.annotations; + +import ca.uhn.fhir.context.FhirVersionEnum; +import org.springframework.context.annotation.Condition; +import org.springframework.context.annotation.ConditionContext; +import org.springframework.core.type.AnnotatedTypeMetadata; + +public class OnDSTU2Condition implements Condition { + @Override + public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) { + FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext. + getEnvironment() + .getProperty("hapi.fhir.fhir_version") + .toUpperCase()); + + return version == FhirVersionEnum.DSTU2; + + } +} diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU3Condition.java b/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU3Condition.java new file mode 100644 index 0000000..1196245 --- /dev/null +++ b/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnDSTU3Condition.java @@ -0,0 +1,19 @@ +package ca.uhn.fhir.jpa.starter.annotations; + +import ca.uhn.fhir.context.FhirVersionEnum; +import org.springframework.context.annotation.Condition; +import org.springframework.context.annotation.ConditionContext; +import org.springframework.core.type.AnnotatedTypeMetadata; + +public class OnDSTU3Condition implements Condition { + @Override + public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) { + FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext. + getEnvironment() + .getProperty("hapi.fhir.fhir_version") + .toUpperCase()); + + return version == FhirVersionEnum.DSTU3; + + } +} diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnEitherVersion.java b/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnEitherVersion.java new file mode 100644 index 0000000..abf564f --- /dev/null +++ b/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnEitherVersion.java @@ -0,0 +1,35 @@ +package ca.uhn.fhir.jpa.starter.annotations; + +import org.springframework.boot.autoconfigure.condition.AnyNestedCondition; +import org.springframework.boot.autoconfigure.condition.ConditionOutcome; +import org.springframework.context.annotation.Conditional; + +public class OnEitherVersion extends AnyNestedCondition { + + OnEitherVersion() { + super(ConfigurationPhase.REGISTER_BEAN); + } + + @Override + protected ConditionOutcome getFinalMatchOutcome(MemberMatchOutcomes memberOutcomes) { + ConditionOutcome result = super.getFinalMatchOutcome(memberOutcomes); + return result; + } + + @Conditional(OnDSTU2Condition.class) + static class OnDSTU2 { + } + + @Conditional(OnDSTU3Condition.class) + static class OnDSTU3 { + } + + @Conditional(OnR4Condition.class) + static class OnR4 { + } + + @Conditional(OnR5Condition.class) + static class OnR5 { + } + +} \ No newline at end of file diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR4Condition.java b/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR4Condition.java new file mode 100644 index 0000000..e362aea --- /dev/null +++ b/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR4Condition.java @@ -0,0 +1,19 @@ +package ca.uhn.fhir.jpa.starter.annotations; + +import ca.uhn.fhir.context.FhirVersionEnum; +import org.springframework.context.annotation.Condition; +import org.springframework.context.annotation.ConditionContext; +import org.springframework.core.type.AnnotatedTypeMetadata; + +public class OnR4Condition implements Condition { + @Override + public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) { + FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext. + getEnvironment() + .getProperty("hapi.fhir.fhir_version") + .toUpperCase()); + + return version == FhirVersionEnum.R4; + + } +} diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR5Condition.java b/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR5Condition.java new file mode 100644 index 0000000..1ecca66 --- /dev/null +++ b/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnR5Condition.java @@ -0,0 +1,19 @@ +package ca.uhn.fhir.jpa.starter.annotations; + +import ca.uhn.fhir.context.FhirVersionEnum; +import org.springframework.context.annotation.Condition; +import org.springframework.context.annotation.ConditionContext; +import org.springframework.core.type.AnnotatedTypeMetadata; + +public class OnR5Condition implements Condition { + @Override + public boolean matches(ConditionContext conditionContext, AnnotatedTypeMetadata metadata) { + FhirVersionEnum version = FhirVersionEnum.forVersionString(conditionContext. + getEnvironment() + .getProperty("hapi.fhir.fhir_version") + .toUpperCase()); + + return version == FhirVersionEnum.R5; + + } +} diff --git a/src/main/resources/application.yaml b/src/main/resources/application.yaml index b7ec776..d081516 100644 --- a/src/main/resources/application.yaml +++ b/src/main/resources/application.yaml @@ -1,28 +1,26 @@ spring: datasource: url: 'jdbc:h2:file:./target/database/h2' + #url: jdbc:h2:mem:test_mem username: sa password: null driverClassName: org.h2.Driver max-active: 15 - profiles: - ### This is the FHIR version. Choose between, dstu2, dstu3, r4 or r5 - active: r4 - jpa: - properties: - hibernate.dialect: org.hibernate.dialect.H2Dialect - hibernate.search.model_mapping: ca.uhn.fhir.jpa.search.LuceneSearchMappingFactory - hibernate.format_sql: false - hibernate.show_sql: false - hibernate.hbm2ddl.auto: update - hibernate.jdbc.batch_size: 20 - hibernate.cache.use_query_cache: false - hibernate.cache.use_second_level_cache: false - hibernate.cache.use_structured_entries: false - hibernate.cache.use_minimal_puts: false - hibernate.search.default.directory_provider: filesystem - hibernate.search.default.indexBase: target/lucenefiles - hibernate.search.lucene_version: LUCENE_CURRENT +# jpa: +# properties: +# hibernate.dialect: org.hibernate.dialect.h2dialect +# hibernate.search.model_mapping: ca.uhn.fhir.jpa.search.lucenesearchmappingfactory +# hibernate.format_sql: false +# hibernate.show_sql: false +# hibernate.hbm2ddl.auto: update +# hibernate.jdbc.batch_size: 20 +# hibernate.cache.use_query_cache: false +# hibernate.cache.use_second_level_cache: false +# hibernate.cache.use_structured_entries: false +# hibernate.cache.use_minimal_puts: false +# hibernate.search.default.directory_provider: filesystem +# hibernate.search.default.indexbase: target/lucenefiles +# hibernate.search.lucene_version: lucene_current batch: job: @@ -30,15 +28,21 @@ spring: hapi: fhir: - defer_indexing_for_codesystems_of_size: 101 -# implementationguides: -# - -# url: https://build.fhir.org/ig/hl7dk/dk-medcom/branches/corrections/package.tgz -# name: dk.fhir.ig.medcom-core -# version: 0.8.0 -# - -# name: hl7.fhir.uv.ips -# version: 0.3.0 + ### enable to set the Server URL +# server_address: http://hapi.fhir.org/baseR4 + ### This is the FHIR version. Choose between, DSTU2, DSTU3, R4 or R5 + fhir_version: R4 +# defer_indexing_for_codesystems_of_size: 101 + #implementationguides: + #example from registry (packages.fhir.org) + #swiss: + #name: swiss.mednet.fhir + #version: 0.8.0 + #example not from registry + #ips_1_0_0: + #url: https://build.fhir.org/ig/HL7/fhir-ips/package.tgz + #name: hl7.fhir.uv.ips + #version: 1.0.0 #supported_resource_types: # - Patient @@ -62,6 +66,7 @@ hapi: # fhirpath_interceptor_enabled: false # filter_search_enabled: true # graphql_enabled: true +# narrative_enabled: true #partitioning: # cross_partition_reference_mode: true # multitenancy_enabled: true @@ -87,14 +92,14 @@ hapi: # retain_cached_searches_mins: 60 # reuse_cached_search_results_millis: 60000 tester: - - - id: home + + home: name: Local Tester server_address: 'http://localhost:8080/fhir' refuse_to_fetch_third_party_urls: false fhir_version: R4 - - - id: global + + global: name: Global Tester server_address: "http://hapi.fhir.org/baseR4" refuse_to_fetch_third_party_urls: false @@ -118,6 +123,7 @@ hapi: # startTlsEnable: # startTlsRequired: # quitWait: +# lastn_enabled: true # diff --git a/src/main/resources/empi-rules.json b/src/main/resources/empi-rules.json index 9f2706a..cb1d710 100644 --- a/src/main/resources/empi-rules.json +++ b/src/main/resources/empi-rules.json @@ -26,17 +26,17 @@ "name": "cosine-given-name", "resourceType": "*", "resourcePath": "name.given", - "metric": "COSINE", - "matchThreshold": 0.8, - "exact": true + "matcher": { + "algorithm": "COLOGNE" + } }, { "name": "jaro-last-name", "resourceType": "*", "resourcePath": "name.family", - "metric": "JARO_WINKLER", - "matchThreshold": 0.8, - "exact": true + "matcher": { + "algorithm": "SOUNDEX" + } } ], "matchResultMap": { diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java new file mode 100644 index 0000000..c3fb7f7 --- /dev/null +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ElasticsearchLastNR4IT.java @@ -0,0 +1,144 @@ +package ca.uhn.fhir.jpa.starter; + +import ca.uhn.fhir.context.ConfigurationException; +import ca.uhn.fhir.context.FhirContext; +import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl; +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 org.hl7.fhir.instance.model.api.IIdType; +import org.hl7.fhir.r4.model.Bundle; +import org.hl7.fhir.r4.model.DateTimeType; +import org.hl7.fhir.r4.model.IntegerType; +import org.hl7.fhir.r4.model.Observation; +import org.hl7.fhir.r4.model.Parameters; +import org.hl7.fhir.r4.model.Patient; +import org.hl7.fhir.r4.model.StringType; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.util.TestPropertyValues; +import org.springframework.boot.web.server.LocalServerPort; +import org.springframework.context.ApplicationContextInitializer; +import org.springframework.context.ConfigurableApplicationContext; +import org.springframework.test.context.ContextConfiguration; +import org.springframework.test.context.junit.jupiter.SpringExtension; +import pl.allegro.tech.embeddedelasticsearch.EmbeddedElastic; +import pl.allegro.tech.embeddedelasticsearch.PopularProperties; + +import javax.annotation.PreDestroy; +import java.io.IOException; +import java.util.Date; +import java.util.GregorianCalendar; +import java.util.UUID; +import java.util.concurrent.TimeUnit; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +@ExtendWith(SpringExtension.class) +@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = + { + "spring.batch.job.enabled=false", + "spring.datasource.url=jdbc:h2:mem:dbr4", + "hapi.fhir.fhir_version=r4", + "hapi.fhir.lastn_enabled=true", + "elasticsearch.enabled=true", + // Because the port is set randomly, we will set the rest_url using the Initializer. + // "elasticsearch.rest_url='http://localhost:9200'", + "elasticsearch.username=SomeUsername", + "elasticsearch.password=SomePassword" + }) +@ContextConfiguration(initializers = ElasticsearchLastNR4IT.Initializer.class) +public class ElasticsearchLastNR4IT { + + private IGenericClient ourClient; + private FhirContext ourCtx; + + private static final String ELASTIC_VERSION = "6.5.4"; + private static EmbeddedElastic embeddedElastic; + + @Autowired + private ElasticsearchSvcImpl myElasticsearchSvc; + + @BeforeAll + public static void beforeClass() { + + embeddedElastic = null; + try { + embeddedElastic = EmbeddedElastic.builder() + .withElasticVersion(ELASTIC_VERSION) + .withSetting(PopularProperties.TRANSPORT_TCP_PORT, 0) + .withSetting(PopularProperties.HTTP_PORT, 0) + .withSetting(PopularProperties.CLUSTER_NAME, UUID.randomUUID()) + .withStartTimeout(60, TimeUnit.SECONDS) + .build() + .start(); + } catch (IOException | InterruptedException e) { + throw new ConfigurationException(e); + } + } + + @PreDestroy + public void stop() { + embeddedElastic.stop(); + } + + @LocalServerPort + private int port; + + @Test + void testLastN() throws IOException { + + Patient pt = new Patient(); + pt.addName().setFamily("Lastn").addGiven("Arthur"); + IIdType id = ourClient.create().resource(pt).execute().getId().toUnqualifiedVersionless(); + + Observation obs = new Observation(); + obs.getSubject().setReferenceElement(id); + String observationCode = "testobservationcode"; + String codeSystem = "http://testobservationcodesystem"; + obs.getCode().addCoding().setCode(observationCode).setSystem(codeSystem); + obs.setValue(new StringType(observationCode)); + Date effectiveDtm = new GregorianCalendar().getTime(); + obs.setEffective(new DateTimeType(effectiveDtm)); + obs.getCategoryFirstRep().addCoding().setCode("testcategorycode").setSystem("http://testcategorycodesystem"); + IIdType obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless(); + + myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX); + + Parameters output = ourClient.operation().onType(Observation.class).named("lastn") + .withParameter(Parameters.class, "max", new IntegerType(1)) + .andParameter("subject", new StringType("Patient/" + id.getIdPart())) + .execute(); + Bundle b = (Bundle) output.getParameter().get(0).getResource(); + assertEquals(1, b.getTotal()); + assertEquals(obsId, b.getEntry().get(0).getResource().getIdElement().toUnqualifiedVersionless()); + } + + @BeforeEach + void beforeEach() { + + ourCtx = FhirContext.forR4(); + ourCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER); + ourCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000); + String ourServerBase = "http://localhost:" + port + "/fhir/"; + ourClient = ourCtx.newRestfulGenericClient(ourServerBase); + ourClient.registerInterceptor(new LoggingInterceptor(true)); + } + + static class Initializer + implements ApplicationContextInitializer { + + @Override + public void initialize( + ConfigurableApplicationContext configurableApplicationContext) { + // Since the port is dynamically generated, replace the URL with one that has the correct port + TestPropertyValues.of("elasticsearch.rest_url=http://localhost:" + embeddedElastic.getHttpPort()) + .applyTo(configurableApplicationContext.getEnvironment()); + } + + } +} diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java index b99ea65..3aa1556 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu2IT.java @@ -19,7 +19,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals; @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = { "spring.batch.job.enabled=false", - "spring.profiles.active=dstu2", + "hapi.fhir.fhir_version=dstu2", "spring.datasource.url=jdbc:h2:mem:dbr2" }) public class ExampleServerDstu2IT { diff --git a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java index ca1cbf1..f190697 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerDstu3IT.java @@ -33,8 +33,8 @@ import static org.junit.jupiter.api.Assertions.assertEquals; @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = { "spring.batch.job.enabled=false", - "spring.profiles.active=dstu3", "spring.datasource.url=jdbc:h2:mem:dbr3", + "hapi.fhir.fhir_version=dstu3", "hapi.fhir.subscription.websocket_enabled=true", "hapi.fhir.allow_external_references=true", "hapi.fhir.allow_placeholder_references=true", 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 6fc36b3..8a011be 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java @@ -36,8 +36,8 @@ import static org.junit.jupiter.api.Assertions.assertTrue; @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = { "spring.batch.job.enabled=false", - "spring.profiles.active=r4", "spring.datasource.url=jdbc:h2:mem:dbr4", + "hapi.fhir.fhir_version=r4", "hapi.fhir.subscription.websocket_enabled=true", "hapi.fhir.empi_enabled=true", //Override is currently required when using Empi as the construction of the Empi beans are ambiguous as they are constructed multiple places. This is evident when running in a spring boot environment 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 3a52ec7..9ac9997 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java @@ -35,8 +35,8 @@ import org.springframework.test.context.junit.jupiter.SpringExtension; @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = { "spring.batch.job.enabled=false", - "spring.profiles.active=r5", "spring.datasource.url=jdbc:h2:mem:dbr5", + "hapi.fhir.fhir_version=r5", "hapi.fhir.subscription.websocket_enabled=true" }) public class ExampleServerR5IT { 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 66fb4df..f13a11a 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/MultitenantServerR4IT.java @@ -21,8 +21,8 @@ import static org.junit.jupiter.api.Assertions.assertEquals; @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = Application.class, properties = { "spring.batch.job.enabled=false", - "spring.profiles.active=r4", "spring.datasource.url=jdbc:h2:mem:dbr4-mt", + "hapi.fhir.fhir_version=r4", "hapi.fhir.subscription.websocket_enabled=true", "hapi.fhir.partitioning.partitioning_include_in_search_hashes=false"