feature swap to non javax clinical reasoning (#5463)
* Update to a version of Clinical Reasoning/CQL that no longer includes javax dependencies * Rev to CR 3.0.0-PRE10 * version bump, pom changes for jakarta conflicts * undo exclusions from other modules * Rework exclusions * Fix type in dependency * new cr version, exclude conflicts in cr and cds-hooks * remove exclusions * pom update * Redo the exclusions * add retrieveSettings config * new CR retrieve settings and config * update config to new enums and parameters * update unit tests and config for new cql and terminology properties * bump CR to 3.0.0-PRE12 * spotless edits, update class path for CR config * missing dependencies * swap for jakarta * moving conflicting dependencies * Fix a couple code review items --------- Co-authored-by: Jonathan Percival <jonathan.i.percival@gmail.com>
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---
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type: add
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issue: 5436
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title: "Moving clinical reasoning to non-javax dependency for alignment with incoming hapi-fhir changes, bumping CR version and updating impacted classes and services"
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|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<artifactId>hapi-fhir-serviceloaders</artifactId>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
@ -21,7 +21,7 @@
|
|||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-caching-api</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
</dependency>
|
||||
<dependency>
|
||||
|
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<artifactId>hapi-fhir-serviceloaders</artifactId>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
</parent>
|
||||
|
||||
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
</parent>
|
||||
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
</parent>
|
||||
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-spring-boot</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
</parent>
|
||||
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
@ -19,7 +19,6 @@
|
|||
|
||||
<properties>
|
||||
<org.antlr-version>4.10.1</org.antlr-version>
|
||||
<xpp3-version>1.1.6</xpp3-version>
|
||||
<spring-security-core.version>5.7.8</spring-security-core.version>
|
||||
</properties>
|
||||
|
||||
|
@ -66,6 +65,31 @@
|
|||
<artifactId>hapi-fhir-base</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.icegreen</groupId>
|
||||
<artifactId>greenmail</artifactId>
|
||||
<version>1.6.4</version>
|
||||
<scope>compile</scope>
|
||||
<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>com.sun.activation</groupId>
|
||||
<artifactId>jakarta.activation</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.simplejavamail</groupId>
|
||||
<artifactId>simple-java-mail</artifactId>
|
||||
<version>6.6.1</version>
|
||||
<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>com.sun.activation</groupId>
|
||||
<artifactId>jakarta.activation</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
</dependencyManagement>
|
||||
|
||||
|
@ -84,52 +108,23 @@
|
|||
<groupId>org.opencds.cqf.fhir</groupId>
|
||||
<artifactId>cqf-fhir-jackson</artifactId>
|
||||
<version>${clinical-reasoning.version}</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>xpp3</groupId>
|
||||
<artifactId>xpp3_min</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xmlpull</groupId>
|
||||
<artifactId>xmlpull</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xmlpull</groupId>
|
||||
<artifactId>xmlpull</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
<type>pom</type>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.opencds.cqf.fhir</groupId>
|
||||
<artifactId>cqf-fhir-cql</artifactId>
|
||||
<version>${clinical-reasoning.version}</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>xpp3</groupId>
|
||||
<artifactId>xpp3_min</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xmlpull</groupId>
|
||||
<artifactId>xmlpull</artifactId>
|
||||
</exclusion>
|
||||
<exclusion>
|
||||
<groupId>xmlpull</groupId>
|
||||
<artifactId>xmlpull</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
<type>pom</type>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.ogce</groupId>
|
||||
<artifactId>xpp3</artifactId>
|
||||
<version>${xpp3-version}</version>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-storage</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>com.sun.activation</groupId>
|
||||
<artifactId>jakarta.activation</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
|
||||
<dependency>
|
||||
<groupId>org.apache.poi</groupId>
|
||||
<artifactId>poi</artifactId>
|
||||
</dependency>
|
||||
|
||||
<!-- This is needed for the threaded execution -->
|
||||
|
@ -139,11 +134,23 @@
|
|||
<version>${spring-security-core.version}</version>
|
||||
</dependency>
|
||||
|
||||
<!-- This is needed for the CqlExceptionHandlingInterceptor -->
|
||||
<!--
|
||||
START Jakarta CR Swap
|
||||
|
||||
These dependencies are added/swapped because the
|
||||
Clinical Reasoning components no longer include it.
|
||||
These will need to be adjusted / removed as soon as
|
||||
the HAPI Jakarta PR hits -->
|
||||
<dependency>
|
||||
<groupId>javax.servlet</groupId>
|
||||
<artifactId>javax.servlet-api</artifactId>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>javax.xml.bind</groupId>
|
||||
<artifactId>jaxb-api</artifactId>
|
||||
<version>2.3.1</version>
|
||||
</dependency>
|
||||
<!-- END Jakarta CR Swap -->
|
||||
|
||||
<!-- test -->
|
||||
<dependency>
|
||||
|
@ -185,10 +192,6 @@
|
|||
<version>${project.version}</version>
|
||||
<scope>test</scope>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.apache.poi</groupId>
|
||||
<artifactId>poi</artifactId>
|
||||
</dependency>
|
||||
</dependencies>
|
||||
<profiles>
|
||||
<profile>
|
||||
|
|
|
@ -43,7 +43,7 @@ public class CrProcessorConfig {
|
|||
@Bean
|
||||
ca.uhn.fhir.cr.dstu3.IQuestionnaireProcessorFactory dstu3QuestionnaireProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.questionnaire.dstu3.QuestionnaireProcessor(
|
||||
return rd -> new org.opencds.cqf.fhir.cr.questionnaire.dstu3.processor.QuestionnaireProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
|
|
|
@ -43,7 +43,7 @@ public class CrProcessorConfig {
|
|||
@Bean
|
||||
ca.uhn.fhir.cr.r4.IQuestionnaireProcessorFactory r4QuestionnaireProcessorFactory(
|
||||
IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
|
||||
return rd -> new org.opencds.cqf.fhir.cr.questionnaire.r4.QuestionnaireProcessor(
|
||||
return rd -> new org.opencds.cqf.fhir.cr.questionnaire.r4.processor.QuestionnaireProcessor(
|
||||
theRepositoryFactory.create(rd), theEvaluationSettings);
|
||||
}
|
||||
|
||||
|
|
|
@ -20,7 +20,7 @@
|
|||
package ca.uhn.fhir.cr.dstu3;
|
||||
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.opencds.cqf.fhir.cr.questionnaire.dstu3.QuestionnaireProcessor;
|
||||
import org.opencds.cqf.fhir.cr.questionnaire.dstu3.processor.QuestionnaireProcessor;
|
||||
|
||||
@FunctionalInterface
|
||||
public interface IQuestionnaireProcessorFactory {
|
||||
|
|
|
@ -31,6 +31,7 @@ import org.hl7.fhir.dstu3.model.Endpoint;
|
|||
import org.hl7.fhir.dstu3.model.IdType;
|
||||
import org.hl7.fhir.dstu3.model.Measure;
|
||||
import org.hl7.fhir.dstu3.model.MeasureReport;
|
||||
import org.hl7.fhir.dstu3.model.Parameters;
|
||||
import org.hl7.fhir.exceptions.FHIRException;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.stereotype.Component;
|
||||
|
@ -76,6 +77,7 @@ public class MeasureOperationsProvider {
|
|||
@OperationParam(name = "productLine") String theProductLine,
|
||||
@OperationParam(name = "additionalData") Bundle theAdditionalData,
|
||||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
@OperationParam(name = "parameters") Parameters theParameters,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return myDstu3MeasureProcessorFactory
|
||||
|
@ -90,6 +92,7 @@ public class MeasureOperationsProvider {
|
|||
theLastReceivedOn,
|
||||
theProductLine,
|
||||
theAdditionalData,
|
||||
theParameters,
|
||||
theTerminologyEndpoint);
|
||||
}
|
||||
}
|
||||
|
|
|
@ -20,7 +20,7 @@
|
|||
package ca.uhn.fhir.cr.r4;
|
||||
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.opencds.cqf.fhir.cr.questionnaire.r4.QuestionnaireProcessor;
|
||||
import org.opencds.cqf.fhir.cr.questionnaire.r4.processor.QuestionnaireProcessor;
|
||||
|
||||
@FunctionalInterface
|
||||
public interface IQuestionnaireProcessorFactory {
|
||||
|
|
|
@ -32,6 +32,7 @@ import org.hl7.fhir.r4.model.Endpoint;
|
|||
import org.hl7.fhir.r4.model.IdType;
|
||||
import org.hl7.fhir.r4.model.Measure;
|
||||
import org.hl7.fhir.r4.model.MeasureReport;
|
||||
import org.hl7.fhir.r4.model.Parameters;
|
||||
import org.opencds.cqf.fhir.utility.monad.Eithers;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
|
@ -74,6 +75,7 @@ public class MeasureOperationsProvider {
|
|||
@OperationParam(name = "productLine") String theProductLine,
|
||||
@OperationParam(name = "additionalData") Bundle theAdditionalData,
|
||||
@OperationParam(name = "terminologyEndpoint") Endpoint theTerminologyEndpoint,
|
||||
@OperationParam(name = "parameters") Parameters theParameters,
|
||||
RequestDetails theRequestDetails)
|
||||
throws InternalErrorException, FHIRException {
|
||||
return myR4MeasureServiceFactory
|
||||
|
@ -89,6 +91,7 @@ public class MeasureOperationsProvider {
|
|||
theTerminologyEndpoint,
|
||||
null,
|
||||
theAdditionalData,
|
||||
theParameters,
|
||||
theProductLine,
|
||||
thePractitioner);
|
||||
}
|
||||
|
|
|
@ -3,21 +3,17 @@ package ca.uhn.fhir.cr;
|
|||
import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.support.IValidationSupport;
|
||||
|
||||
import ca.uhn.fhir.cr.common.CodeCacheResourceChangeListener;
|
||||
import ca.uhn.fhir.cr.common.ElmCacheResourceChangeListener;
|
||||
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
|
||||
import ca.uhn.fhir.jpa.cache.IResourceChangeListener;
|
||||
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerCacheRefresher;
|
||||
import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
|
||||
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCache;
|
||||
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheFactory;
|
||||
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerCacheRefresherImpl;
|
||||
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryImpl;
|
||||
import ca.uhn.fhir.jpa.cache.ResourceChangeListenerRegistryInterceptor;
|
||||
import ca.uhn.fhir.jpa.cache.ResourceVersionMap;
|
||||
import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
|
||||
import ca.uhn.fhir.jpa.provider.DiffProvider;
|
||||
import ca.uhn.fhir.jpa.provider.IJpaSystemProvider;
|
||||
|
@ -34,32 +30,22 @@ import ca.uhn.fhir.rest.server.RestfulServer;
|
|||
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
|
||||
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
|
||||
import com.google.common.base.Strings;
|
||||
import org.cqframework.cql.cql2elm.LibraryManager;
|
||||
import org.cqframework.cql.cql2elm.ModelManager;
|
||||
import org.cqframework.cql.cql2elm.model.CompiledLibrary;
|
||||
import org.cqframework.cql.cql2elm.model.Model;
|
||||
|
||||
import org.hl7.cql.model.ModelIdentifier;
|
||||
import org.hl7.elm.r1.VersionedIdentifier;
|
||||
import org.opencds.cqf.cql.engine.runtime.Code;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.beans.factory.annotation.Qualifier;
|
||||
import org.springframework.context.ApplicationContext;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
import org.springframework.context.annotation.Configuration;
|
||||
import org.springframework.context.annotation.Import;
|
||||
import org.springframework.context.annotation.Primary;
|
||||
import org.springframework.context.annotation.Scope;
|
||||
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.concurrent.ConcurrentHashMap;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
|
||||
@Configuration
|
||||
@Import({SubscriptionSubmitterConfig.class, SubscriptionChannelConfig.class})
|
||||
|
@ -168,4 +154,6 @@ public class TestCrConfig {
|
|||
return new ResourceChangeListenerRegistryInterceptor();
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
|
@ -16,6 +16,8 @@ import org.opencds.cqf.cql.engine.execution.CqlEngine;
|
|||
|
||||
import org.opencds.cqf.cql.engine.runtime.Code;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings;
|
||||
import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings;
|
||||
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
|
||||
import org.opencds.cqf.fhir.utility.ValidationProfile;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
|
@ -43,11 +45,31 @@ public class TestCrDstu3Config {
|
|||
}
|
||||
return measureEvalOptions;
|
||||
}
|
||||
@Bean
|
||||
public TerminologySettings terminologySettings(){
|
||||
var termSettings = new TerminologySettings();
|
||||
termSettings.setCodeLookupMode(TerminologySettings.CODE_LOOKUP_MODE.USE_CODESYSTEM_URL);
|
||||
termSettings.setValuesetExpansionMode(TerminologySettings.VALUESET_EXPANSION_MODE.PERFORM_NAIVE_EXPANSION);
|
||||
termSettings.setValuesetMembershipMode(TerminologySettings.VALUESET_MEMBERSHIP_MODE.USE_EXPANSION);
|
||||
termSettings.setValuesetPreExpansionMode(TerminologySettings.VALUESET_PRE_EXPANSION_MODE.USE_IF_PRESENT);
|
||||
|
||||
return termSettings;
|
||||
}
|
||||
@Bean
|
||||
public RetrieveSettings retrieveSettings(){
|
||||
var retrieveSettings = new RetrieveSettings();
|
||||
retrieveSettings.setSearchParameterMode(RetrieveSettings.SEARCH_FILTER_MODE.USE_SEARCH_PARAMETERS);
|
||||
retrieveSettings.setTerminologyParameterMode(RetrieveSettings.TERMINOLOGY_FILTER_MODE.FILTER_IN_MEMORY);
|
||||
retrieveSettings.setProfileMode(RetrieveSettings.PROFILE_MODE.OFF);
|
||||
|
||||
return retrieveSettings;
|
||||
}
|
||||
@Bean
|
||||
public EvaluationSettings evaluationSettings(TestCqlProperties theCqlProperties, Map<VersionedIdentifier,
|
||||
CompiledLibrary> theGlobalLibraryCache, Map<ModelIdentifier, Model> theGlobalModelCache,
|
||||
Map<String, List<Code>> theGlobalValueSetCache) {
|
||||
Map<String, List<Code>> theGlobalValueSetCache,
|
||||
RetrieveSettings theRetrieveSettings,
|
||||
TerminologySettings theTerminologySettings) {
|
||||
var evaluationSettings = EvaluationSettings.getDefault();
|
||||
var cqlOptions = evaluationSettings.getCqlOptions();
|
||||
|
||||
|
@ -112,6 +134,8 @@ public class TestCrDstu3Config {
|
|||
cqlCompilerOptions.setCollapseDataRequirements(theCqlProperties.isCqlCompilerCollapseDataRequirements());
|
||||
|
||||
cqlOptions.setCqlCompilerOptions(cqlCompilerOptions);
|
||||
evaluationSettings.setTerminologySettings(theTerminologySettings);
|
||||
evaluationSettings.setRetrieveSettings(theRetrieveSettings);
|
||||
evaluationSettings.setLibraryCache(theGlobalLibraryCache);
|
||||
evaluationSettings.setModelCache(theGlobalModelCache);
|
||||
evaluationSettings.setValueSetCache(theGlobalValueSetCache);
|
||||
|
|
|
@ -59,7 +59,7 @@ public class CrResourceListenerTests extends BaseCrR4TestServer {
|
|||
myResourceChangeListenerCacheRefresher.refreshExpiredCachesAndNotifyListeners();
|
||||
|
||||
//cached valueSets
|
||||
assertEquals(11, myEvaluationSettings.getValueSetCache().size());
|
||||
assertEquals(7, myEvaluationSettings.getValueSetCache().size());
|
||||
|
||||
//remove valueset from server
|
||||
var id = new IdType("ValueSet/2.16.840.1.113883.3.464.1003.101.12.1001");
|
||||
|
@ -158,7 +158,7 @@ public class CrResourceListenerTests extends BaseCrR4TestServer {
|
|||
runEvaluateMeasure("2019-01-01", "2019-12-31", "Patient/numer-EXM130", "ColorectalCancerScreeningsFHIR", "Individual", null);
|
||||
|
||||
//cached valueset from bundle
|
||||
assertEquals(11, myEvaluationSettings.getValueSetCache().size());
|
||||
assertEquals(8, myEvaluationSettings.getValueSetCache().size());
|
||||
|
||||
// manually refresh cache
|
||||
myResourceChangeListenerCacheRefresher.refreshExpiredCachesAndNotifyListeners();
|
||||
|
@ -170,7 +170,7 @@ public class CrResourceListenerTests extends BaseCrR4TestServer {
|
|||
myResourceChangeListenerCacheRefresher.refreshExpiredCachesAndNotifyListeners();
|
||||
|
||||
//cache should be invalidated for valueset url and removed
|
||||
assertEquals(10, myEvaluationSettings.getValueSetCache().size());
|
||||
assertEquals(7, myEvaluationSettings.getValueSetCache().size());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -3,11 +3,8 @@ package ca.uhn.fhir.cr.r4;
|
|||
import ca.uhn.fhir.cr.TestCqlProperties;
|
||||
import ca.uhn.fhir.cr.TestCrConfig;
|
||||
import ca.uhn.fhir.cr.common.CqlThreadFactory;
|
||||
import ca.uhn.fhir.cr.config.r4.ApplyOperationConfig;
|
||||
import ca.uhn.fhir.cr.config.r4.ExtractOperationConfig;
|
||||
import ca.uhn.fhir.cr.config.r4.PackageOperationConfig;
|
||||
import ca.uhn.fhir.cr.config.r4.PopulateOperationConfig;
|
||||
import ca.uhn.fhir.cr.config.r4.CrR4Config;
|
||||
import ca.uhn.fhir.rest.api.SearchStyleEnum;
|
||||
import org.cqframework.cql.cql2elm.CqlCompilerOptions;
|
||||
import org.cqframework.cql.cql2elm.model.CompiledLibrary;
|
||||
import org.cqframework.cql.cql2elm.model.Model;
|
||||
|
@ -16,6 +13,9 @@ import org.hl7.elm.r1.VersionedIdentifier;
|
|||
import org.opencds.cqf.cql.engine.execution.CqlEngine;
|
||||
import org.opencds.cqf.cql.engine.runtime.Code;
|
||||
import org.opencds.cqf.fhir.cql.EvaluationSettings;
|
||||
import org.opencds.cqf.fhir.cql.engine.retrieve.BaseRetrieveProvider;
|
||||
import org.opencds.cqf.fhir.cql.engine.retrieve.RetrieveSettings;
|
||||
import org.opencds.cqf.fhir.cql.engine.terminology.TerminologySettings;
|
||||
import org.opencds.cqf.fhir.cr.measure.CareGapsProperties;
|
||||
import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
|
||||
import org.opencds.cqf.fhir.utility.ValidationProfile;
|
||||
|
@ -64,10 +64,32 @@ public class TestCrR4Config {
|
|||
}
|
||||
return measureEvalOptions;
|
||||
}
|
||||
|
||||
@Bean
|
||||
public TerminologySettings terminologySettings(){
|
||||
var termSettings = new TerminologySettings();
|
||||
termSettings.setCodeLookupMode(TerminologySettings.CODE_LOOKUP_MODE.USE_CODESYSTEM_URL);
|
||||
termSettings.setValuesetExpansionMode(TerminologySettings.VALUESET_EXPANSION_MODE.PERFORM_NAIVE_EXPANSION);
|
||||
termSettings.setValuesetMembershipMode(TerminologySettings.VALUESET_MEMBERSHIP_MODE.USE_EXPANSION);
|
||||
termSettings.setValuesetPreExpansionMode(TerminologySettings.VALUESET_PRE_EXPANSION_MODE.USE_IF_PRESENT);
|
||||
|
||||
return termSettings;
|
||||
}
|
||||
@Bean
|
||||
public RetrieveSettings retrieveSettings(){
|
||||
var retrieveSettings = new RetrieveSettings();
|
||||
retrieveSettings.setSearchParameterMode(RetrieveSettings.SEARCH_FILTER_MODE.USE_SEARCH_PARAMETERS);
|
||||
retrieveSettings.setTerminologyParameterMode(RetrieveSettings.TERMINOLOGY_FILTER_MODE.FILTER_IN_MEMORY);
|
||||
retrieveSettings.setProfileMode(RetrieveSettings.PROFILE_MODE.OFF);
|
||||
|
||||
return retrieveSettings;
|
||||
}
|
||||
@Bean
|
||||
public EvaluationSettings evaluationSettings(TestCqlProperties theCqlProperties, Map<VersionedIdentifier,
|
||||
CompiledLibrary> theGlobalLibraryCache, Map<ModelIdentifier, Model> theGlobalModelCache,
|
||||
Map<String, List<Code>> theGlobalValueSetCache) {
|
||||
Map<String, List<Code>> theGlobalValueSetCache,
|
||||
RetrieveSettings theRetrieveSettings,
|
||||
TerminologySettings theTerminologySettings) {
|
||||
var evaluationSettings = EvaluationSettings.getDefault();
|
||||
var cqlOptions = evaluationSettings.getCqlOptions();
|
||||
|
||||
|
@ -132,6 +154,8 @@ public class TestCrR4Config {
|
|||
cqlCompilerOptions.setCollapseDataRequirements(theCqlProperties.isCqlCompilerCollapseDataRequirements());
|
||||
|
||||
cqlOptions.setCqlCompilerOptions(cqlCompilerOptions);
|
||||
evaluationSettings.setTerminologySettings(theTerminologySettings);
|
||||
evaluationSettings.setRetrieveSettings(theRetrieveSettings);
|
||||
evaluationSettings.setLibraryCache(theGlobalLibraryCache);
|
||||
evaluationSettings.setModelCache(theGlobalModelCache);
|
||||
evaluationSettings.setValueSetCache(theGlobalValueSetCache);
|
||||
|
|
File diff suppressed because one or more lines are too long
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -4,7 +4,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -4,7 +4,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -4,7 +4,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -4,7 +4,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -4,7 +4,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -4,7 +4,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -4,7 +4,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-deployable-pom</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -4,7 +4,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
27
pom.xml
27
pom.xml
|
@ -9,7 +9,7 @@
|
|||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<packaging>pom</packaging>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<name>HAPI-FHIR</name>
|
||||
<description>An open-source implementation of the FHIR specification in Java.</description>
|
||||
|
@ -983,7 +983,7 @@
|
|||
<ucum_version>1.0.8</ucum_version>
|
||||
|
||||
<!-- CQL Support -->
|
||||
<clinical-reasoning.version>3.0.0-PRE9</clinical-reasoning.version>
|
||||
<clinical-reasoning.version>3.0.0-PRE12</clinical-reasoning.version>
|
||||
|
||||
<!-- Site properties -->
|
||||
<fontawesomeVersion>5.4.1</fontawesomeVersion>
|
||||
|
@ -1179,11 +1179,6 @@
|
|||
<artifactId>javax.activation</artifactId>
|
||||
<version>${activation_api_version}</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>com.sun.activation</groupId>
|
||||
<artifactId>jakarta.activation</artifactId>
|
||||
<version>2.0.0</version>
|
||||
</dependency>
|
||||
<!-- Architecture Test -->
|
||||
<dependency>
|
||||
<groupId>com.tngtech.archunit</groupId>
|
||||
|
@ -1288,6 +1283,11 @@
|
|||
<artifactId>jakarta.annotation-api</artifactId>
|
||||
<version>1.3.5</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>jakarta.activation</groupId>
|
||||
<artifactId>jakarta.activation-api</artifactId>
|
||||
<version>2.1.0</version>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>jakarta.transaction</groupId>
|
||||
<artifactId>jakarta.transaction-api</artifactId>
|
||||
|
@ -1738,6 +1738,13 @@
|
|||
<groupId>org.glassfish.jaxb</groupId>
|
||||
<artifactId>jaxb-runtime</artifactId>
|
||||
<version>${jaxb_runtime_version}</version>
|
||||
<!-- Excluded in favor of jakarta.activation:jakarta.activation-api -->
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>com.sun.activation</groupId>
|
||||
<artifactId>jakarta.activation</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.glassfish.jersey.core</groupId>
|
||||
|
@ -2192,6 +2199,12 @@
|
|||
<groupId>org.ogce</groupId>
|
||||
<artifactId>xpp3</artifactId>
|
||||
<version>1.1.6</version>
|
||||
<exclusions>
|
||||
<exclusion>
|
||||
<groupId>junit</groupId>
|
||||
<artifactId>junt</artifactId>
|
||||
</exclusion>
|
||||
</exclusions>
|
||||
</dependency>
|
||||
<dependency>
|
||||
<groupId>org.flywaydb</groupId>
|
||||
|
|
|
@ -7,7 +7,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -4,7 +4,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
|
@ -5,7 +5,7 @@
|
|||
<parent>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir</artifactId>
|
||||
<version>6.11.0-SNAPSHOT</version>
|
||||
<version>6.11.1-SNAPSHOT</version>
|
||||
|
||||
<relativePath>../../pom.xml</relativePath>
|
||||
</parent>
|
||||
|
|
Loading…
Reference in New Issue