From 88e2b6d4a708e7450a22a5d63719667b214024cd Mon Sep 17 00:00:00 2001 From: James Agnew Date: Mon, 30 Sep 2019 18:38:30 -0400 Subject: [PATCH 1/6] Adjust configs --- README.md | 15 ++++ pom.xml | 3 +- .../jpa/starter/FhirServerConfigDstu2.java | 2 +- .../jpa/starter/FhirServerConfigDstu3.java | 2 +- .../fhir/jpa/starter/FhirServerConfigR4.java | 2 +- .../fhir/jpa/starter/FhirServerConfigR5.java | 3 +- .../uhn/fhir/jpa/starter/HapiProperties.java | 74 +++++++++++++++---- src/main/resources/hapi.properties | 18 +++++ 8 files changed, 97 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index 60bc4ae..949ff9d 100644 --- a/README.md +++ b/README.md @@ -115,3 +115,18 @@ The server may be configured with subscription support by enabling properties in * `subscription.email.enabled` - Enables email subscriptions. Note that you must also provide the connection details for a usable SMTP server. * `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) + +# 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) + +For example: + +```properties +elasticsearch.enabled=true +elasticsearch.rest_url=http://localhost:9200 +elasticsearch.username=SomeUsername +elasticsearch.password=SomePassword +elasticsearch.required_index_status=YELLOW +elasticsearch.schema_management_strategy=CREATE +``` \ No newline at end of file diff --git a/pom.xml b/pom.xml index 6816519..c0219df 100644 --- a/pom.xml +++ b/pom.xml @@ -11,10 +11,9 @@ ca.uhn.hapi.fhir hapi-fhir - 4.0.0 + 4.1.0-SNAPSHOT - ca.uhn.hapi.fhir hapi-fhir-jpaserver-starter 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 3255de7..dc91099 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu2.java @@ -43,7 +43,7 @@ public class FhirServerConfigDstu2 extends BaseJavaConfigDstu2 { throw new ConfigurationException("Could not set the data source due to a configuration issue", e); } - retVal.setJpaProperties(HapiProperties.getProperties()); + retVal.setJpaProperties(HapiProperties.getJpaProperties()); 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 7cf6996..3344952 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigDstu3.java @@ -43,7 +43,7 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 { throw new ConfigurationException("Could not set the data source due to a configuration issue", e); } - retVal.setJpaProperties(HapiProperties.getProperties()); + retVal.setJpaProperties(HapiProperties.getJpaProperties()); 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 abf6938..77a798e 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR4.java @@ -43,7 +43,7 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 { throw new ConfigurationException("Could not set the data source due to a configuration issue", e); } - retVal.setJpaProperties(HapiProperties.getProperties()); + retVal.setJpaProperties(HapiProperties.getJpaProperties()); 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 e176080..6d9e45b 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/FhirServerConfigR5.java @@ -1,7 +1,6 @@ package ca.uhn.fhir.jpa.starter; import ca.uhn.fhir.context.ConfigurationException; -import ca.uhn.fhir.jpa.config.BaseJavaConfigR4; import ca.uhn.fhir.jpa.config.BaseJavaConfigR5; import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider; import org.springframework.beans.factory.annotation.Autowired; @@ -44,7 +43,7 @@ public class FhirServerConfigR5 extends BaseJavaConfigR5 { throw new ConfigurationException("Could not set the data source due to a configuration issue", e); } - retVal.setJpaProperties(HapiProperties.getProperties()); + retVal.setJpaProperties(HapiProperties.getJpaProperties()); 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 3dac8f4..4ddd31e 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/HapiProperties.java @@ -2,9 +2,13 @@ package ca.uhn.fhir.jpa.starter; import ca.uhn.fhir.context.ConfigurationException; import ca.uhn.fhir.context.FhirVersionEnum; +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.hibernate.search.elasticsearch.cfg.ElasticsearchIndexStatus; +import org.hibernate.search.elasticsearch.cfg.IndexSchemaManagementStrategy; +import org.jetbrains.annotations.NotNull; import java.io.FileInputStream; import java.io.InputStream; @@ -57,13 +61,17 @@ public class HapiProperties { private static final String VALIDATE_RESPONSES_ENABLED = "validation.responses.enabled"; private static final String FILTER_SEARCH_ENABLED = "filter_search.enabled"; private static final String GRAPHQL_ENABLED = "graphql.enabled"; - private static Properties properties; + private static Properties ourProperties; + + public static boolean isElasticSearchEnabled() { + return HapiProperties.getPropertyBoolean("elasticsearch.enabled", false); + } /* * Force the configuration to be reloaded */ public static void forceReload() { - properties = null; + ourProperties = null; getProperties(); } @@ -76,22 +84,48 @@ public class HapiProperties { getProperties().setProperty(theKey, theValue); } - public static Properties getProperties() { - if (properties == null) { - // Load the configurable properties file - try (InputStream in = HapiProperties.class.getClassLoader().getResourceAsStream(HAPI_PROPERTIES)) { - HapiProperties.properties = new Properties(); - HapiProperties.properties.load(in); - } catch (Exception e) { - throw new ConfigurationException("Could not load HAPI properties", e); - } + public static Properties getJpaProperties() { + Properties retVal = loadProperties(); - Properties overrideProps = loadOverrideProperties(); - if (overrideProps != null) { - properties.putAll(overrideProps); - } + if (isElasticSearchEnabled()) { + ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder(); + builder.setRequiredIndexStatus(getPropertyEnum("elasticsearch.required_index_status", ElasticsearchIndexStatus.class, ElasticsearchIndexStatus.YELLOW)); + builder.setRestUrl(getProperty("elasticsearch.rest_url")); + builder.setUsername(getProperty("elasticsearch.username")); + builder.setPassword(getProperty("elasticsearch.password")); + builder.setIndexSchemaManagementStrategy(getPropertyEnum("elasticsearch.schema_management_strateg", IndexSchemaManagementStrategy.class, IndexSchemaManagementStrategy.CREATE)); + builder.setDebugRefreshAfterWrite(getPropertyBoolean("elasticsearch.debug.refresh_after_write", false)); + builder.setDebugPrettyPrintJsonLog(getPropertyBoolean("elasticsearch.debug.pretty_print_json_log", false)); + builder.apply(retVal); } + return retVal; + } + + private static Properties getProperties() { + if (ourProperties == null) { + Properties properties = loadProperties(); + HapiProperties.ourProperties = properties; + } + + return ourProperties; + } + + @NotNull + private static Properties loadProperties() { + // Load the configurable properties file + Properties properties; + try (InputStream in = HapiProperties.class.getClassLoader().getResourceAsStream(HAPI_PROPERTIES)) { + properties = new Properties(); + properties.load(in); + } catch (Exception e) { + throw new ConfigurationException("Could not load HAPI properties", e); + } + + Properties overrideProps = loadOverrideProperties(); + if (overrideProps != null) { + properties.putAll(overrideProps); + } return properties; } @@ -375,5 +409,15 @@ public class HapiProperties { return HapiProperties.getBooleanProperty(GRAPHQL_ENABLED, true); } + private static boolean getPropertyBoolean(String thePropertyName, boolean theDefaultValue) { + String value = getProperty(thePropertyName, Boolean.toString(theDefaultValue)); + return Boolean.parseBoolean(value); + } + + private static T getPropertyEnum(String thePropertyName, Class theEnumType, T theDefaultValue) { + String value = getProperty(thePropertyName, theDefaultValue.name()); + return (T) Enum.valueOf(theEnumType, value); + } + } diff --git a/src/main/resources/hapi.properties b/src/main/resources/hapi.properties index 0f9bd81..5cbb918 100644 --- a/src/main/resources/hapi.properties +++ b/src/main/resources/hapi.properties @@ -78,6 +78,24 @@ hibernate.search.default.indexBase=target/lucenefiles hibernate.search.lucene_version=LUCENE_CURRENT tester.config.refuse_to_fetch_third_party_urls=false +################################################## +# ElasticSearch +# Note that using ElasticSearch is disabled by +# default and the server will use Lucene instead. +################################################## +elasticsearch.enabled=false +elasticsearch.rest_url=http://localhost:9200 +elasticsearch.username=SomeUsername +elasticsearch.password=SomePassword +elasticsearch.rest_url=http://localhost:9200 +elasticsearch.required_index_status=YELLOW +elasticsearch.schema_management_strategy=CREATE +# Immediately refresh indexes after every write. This is very bad for +# performance, but can be helpful for testing. +elasticsearch.debug.refresh_after_write=false +elasticsearch.debug.pretty_print_json_log=false + + ################################################## # Binary Storage Operations ################################################## From 4f060b9efb209b2cf73e30fd263f75d314c52f40 Mon Sep 17 00:00:00 2001 From: James Agnew Date: Mon, 30 Sep 2019 18:56:28 -0400 Subject: [PATCH 2/6] Exclude commons-logging --- pom.xml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pom.xml b/pom.xml index c0219df..3ebf100 100644 --- a/pom.xml +++ b/pom.xml @@ -67,6 +67,10 @@ org.springframework spring-jcl + + commons-logging + commons-logging + From 9d8d7489be949c1484566089f455dc2c5a882b92 Mon Sep 17 00:00:00 2001 From: seanmcilvenna Date: Mon, 4 Nov 2019 11:34:39 -0800 Subject: [PATCH 3/6] Fixing build error because namespace changed on SubscriptionDeliveryHandler Adding missing webjar dependencies --- pom.xml | 44 ++++++++++++++++++- .../jpa/starter/FhirServerConfigCommon.java | 2 +- 2 files changed, 44 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 3ebf100..6ec0cfa 100644 --- a/pom.xml +++ b/pom.xml @@ -148,6 +148,48 @@ h2 + + + org.webjars + bootstrap + 3.3.7 + + + 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 + + org.eclipse.jetty @@ -178,7 +220,7 @@ org.eclipse.jetty jetty-webapp test - + ca.uhn.hapi.fhir diff --git a/src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java b/src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java index 9f88f5e..ce7cf55 100644 --- a/src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java +++ b/src/main/java/ca/uhn/fhir/jpa/starter/JpaRestfulServer.java @@ -5,11 +5,16 @@ import ca.uhn.fhir.context.FhirVersionEnum; import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster; import ca.uhn.fhir.interceptor.api.IInterceptorService; import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor; +import ca.uhn.fhir.jpa.bulk.BulkDataExportProvider; import ca.uhn.fhir.jpa.dao.DaoConfig; import ca.uhn.fhir.jpa.dao.DaoRegistry; import ca.uhn.fhir.jpa.dao.IFhirSystemDao; import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor; -import ca.uhn.fhir.jpa.provider.*; +import ca.uhn.fhir.jpa.provider.GraphQLProvider; +import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2; +import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2; +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.dstu3.JpaSystemProviderDstu3; import ca.uhn.fhir.jpa.provider.r4.JpaConformanceProviderR4; @@ -24,7 +29,11 @@ import ca.uhn.fhir.model.dstu2.composite.MetaDt; import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator; import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy; 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.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.validation.IValidatorModule; import ca.uhn.fhir.validation.ResultSeverityEnum; import org.hl7.fhir.dstu3.model.Bundle; @@ -257,6 +266,9 @@ public class JpaRestfulServer extends RestfulServer { // Validation IValidatorModule validatorModule; switch (fhirVersion) { + case DSTU2: + validatorModule = appCtx.getBean("myInstanceValidatorDstu2", IValidatorModule.class); + break; case DSTU3: validatorModule = appCtx.getBean("myInstanceValidatorDstu3", IValidatorModule.class); break; @@ -266,6 +278,9 @@ public class JpaRestfulServer extends RestfulServer { case R5: validatorModule = appCtx.getBean("myInstanceValidatorR5", IValidatorModule.class); break; + // These versions are not supported by HAPI FHIR JPA + case DSTU2_HL7ORG: + case DSTU2_1: default: validatorModule = null; break; 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 04aee05..7eff8b0 100644 --- a/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java +++ b/src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR5IT.java @@ -14,10 +14,12 @@ import org.eclipse.jetty.websocket.api.Session; import org.eclipse.jetty.websocket.client.ClientUpgradeRequest; import org.eclipse.jetty.websocket.client.WebSocketClient; 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.Subscription; +import org.hl7.fhir.r5.model.Bundle; +import org.hl7.fhir.r5.model.Observation; +import org.hl7.fhir.r5.model.Patient; +import org.hl7.fhir.r5.model.Subscription; +import org.hl7.fhir.r5.model.Topic; +import org.hl7.fhir.r5.model.codesystems.SubscriptionChannelType; import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.Test; @@ -43,7 +45,7 @@ public class ExampleServerR5IT { HapiProperties.setProperty(HapiProperties.DATASOURCE_URL, "jdbc:h2:mem:dbr5"); HapiProperties.setProperty(HapiProperties.FHIR_VERSION, "R5"); HapiProperties.setProperty(HapiProperties.SUBSCRIPTION_WEBSOCKET_ENABLED, "true"); - ourCtx = FhirContext.forR4(); + ourCtx = FhirContext.forR5(); } @Test @@ -61,17 +63,26 @@ public class ExampleServerR5IT { @Test public void testWebsocketSubscription() throws Exception { + + /* + * Create topic + */ + Topic topic = new Topic(); + 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(Subscription.SubscriptionStatus.REQUESTED); - subscription.setCriteria("Observation?status=final"); Subscription.SubscriptionChannelComponent channel = new Subscription.SubscriptionChannelComponent(); - channel.setType(Subscription.SubscriptionChannelType.WEBSOCKET); - channel.setPayload("application/json"); + channel.getType().addCoding() + .setSystem(SubscriptionChannelType.WEBSOCKET.getSystem()) + .setCode(SubscriptionChannelType.WEBSOCKET.toCode()); + channel.getPayload().setContentType("application/json"); subscription.setChannel(channel); MethodOutcome methodOutcome = ourClient.create().resource(subscription).execute();