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hapi-fhir
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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
James Agnew 2017-03-29 15:29:10 +08:00
parent c6555ddd4f 4748c8ba74
commit 14d861992c
6 changed files with 164 additions and 84 deletions
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30
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java
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@ -20,6 +20,16 @@ package ca.uhn.fhir.jpa.config;
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu2;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.validation.IValidatorModule;
import org.hl7.fhir.instance.hapi.validation.DefaultProfileValidationSupport;
import org.hl7.fhir.instance.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.instance.hapi.validation.ValidationSupportChain;
import org.hl7.fhir.instance.validation.IResourceValidator.BestPracticeWarningLevel;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@ -27,17 +37,6 @@ import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
import ca.uhn.fhir.jpa.dao.SearchParamExtractorDstu2;
import ca.uhn.fhir.jpa.dao.SearchParamRegistryDstu2;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu2;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
@Configuration
@EnableTransactionManagement
public class BaseDstu2Config extends BaseConfig {
@ -75,6 +74,15 @@ public class BaseDstu2Config extends BaseConfig {
return retVal;
}
@Bean(name = "myInstanceValidatorDstu2")
@Lazy
public IValidatorModule instanceValidatorDstu2() {
FhirInstanceValidator retVal = new FhirInstanceValidator();
retVal.setBestPracticeWarningLevel(BestPracticeWarningLevel.Warning);
retVal.setValidationSupport(new ValidationSupportChain(new DefaultProfileValidationSupport(), jpaValidationSupportDstu2()));
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
public IFulltextSearchSvc searchDao() {
FulltextSearchSvcImpl searchDao = new FulltextSearchSvcImpl();

78
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2.java
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@ -1,43 +1,5 @@
package ca.uhn.fhir.jpa.dao;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.ArrayList;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.util.Collections;
import java.util.List;
import org.hl7.fhir.instance.hapi.validation.DefaultProfileValidationSupport;
import org.hl7.fhir.instance.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.hl7.fhir.instance.hapi.validation.ValidationSupportChain;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.validation.IResourceValidator.BestPracticeWarningLevel;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.entity.ResourceTable;
@ -64,6 +26,38 @@ import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.IValidatorModule;
import ca.uhn.fhir.validation.ValidationResult;
import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2017 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
public class FhirResourceDaoDstu2<T extends IResource> extends BaseHapiFhirResourceDao<T> {
@ -71,6 +65,9 @@ public class FhirResourceDaoDstu2<T extends IResource> extends BaseHapiFhirResou
@Qualifier("myJpaValidationSupportDstu2")
private IValidationSupport myJpaValidationSupport;
@Autowired()
@Qualifier("myInstanceValidatorDstu2")
private IValidatorModule myInstanceValidator;
@Override
protected List<Object> getIncludeValues(FhirTerser theTerser, Include theInclude, IBaseResource theResource, RuntimeResourceDefinition theResourceDef) {
@ -124,10 +121,7 @@ public class FhirResourceDaoDstu2<T extends IResource> extends BaseHapiFhirResou
FhirValidator validator = getContext().newValidator();
FhirInstanceValidator val = new FhirInstanceValidator();
val.setBestPracticeWarningLevel(BestPracticeWarningLevel.Warning);
val.setValidationSupport(new ValidationSupportChain(new DefaultProfileValidationSupport(), myJpaValidationSupport));
validator.registerValidatorModule(val);
validator.registerValidatorModule(myInstanceValidator);
validator.registerValidatorModule(new IdChecker(theMode));

30
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java
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@ -1,21 +1,20 @@
package ca.uhn.fhir.jpa.config;
import java.util.Properties;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Primary;
import org.springframework.context.annotation.Lazy;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.util.Properties;
@Configuration
@EnableTransactionManagement()
@ -65,4 +64,19 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
return extraProperties;
}
/**
* Bean which validates incoming requests
*/
@Bean
@Lazy
public RequestValidatingInterceptor requestValidatingInterceptor() {
RequestValidatingInterceptor requestValidator = new RequestValidatingInterceptor();
requestValidator.setFailOnSeverity(ResultSeverityEnum.ERROR);
requestValidator.setAddResponseHeaderOnSeverity(null);
requestValidator.setAddResponseOutcomeHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
requestValidator.addValidatorModule(instanceValidatorDstu2());
return requestValidator;
}
}

67
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TdlDstu2Config.java
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@ -1,10 +1,14 @@
package ca.uhn.fhirtest.config;
import java.util.Properties;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseValidatingInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import ca.uhn.fhirtest.interceptor.TdlSecurityInterceptor;
import org.apache.commons.dbcp2.BasicDataSource;
import org.apache.commons.lang3.time.DateUtils;
import org.hibernate.dialect.DerbyTenSevenDialect;
@ -13,18 +17,16 @@ import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.DependsOn;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhirtest.interceptor.TdlSecurityInterceptor;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.util.Properties;
@Configuration
@Import(CommonConfig.class)
@ -113,6 +115,49 @@ public class TdlDstu2Config extends BaseJavaConfigDstu2 {
return extraProperties;
}
/**
* Bean which validates incoming requests
*/
@Bean
@Lazy
public RequestValidatingInterceptor requestValidatingInterceptor() {
RequestValidatingInterceptor requestValidator = new RequestValidatingInterceptor();
requestValidator.setFailOnSeverity(null);
requestValidator.setAddResponseHeaderOnSeverity(null);
requestValidator.setAddResponseOutcomeHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
requestValidator.addValidatorModule(instanceValidatorDstu2());
requestValidator.setIgnoreValidatorExceptions(true);
return requestValidator;
}
/**
* Bean which validates outgoing responses
*/
@Bean
@Lazy
public ResponseValidatingInterceptor responseValidatingInterceptor() {
ResponseValidatingInterceptor responseValidator = new ResponseValidatingInterceptor();
responseValidator.setResponseHeaderValueNoIssues("Validation did not detect any issues");
responseValidator.setFailOnSeverity(null);
responseValidator.setAddResponseHeaderOnSeverity(null);
responseValidator.setAddResponseOutcomeHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
responseValidator.addExcludeOperationType(RestOperationTypeEnum.METADATA);
responseValidator.addExcludeOperationType(RestOperationTypeEnum.EXTENDED_OPERATION_INSTANCE);
responseValidator.addExcludeOperationType(RestOperationTypeEnum.EXTENDED_OPERATION_SERVER);
responseValidator.addExcludeOperationType(RestOperationTypeEnum.EXTENDED_OPERATION_TYPE);
responseValidator.addExcludeOperationType(RestOperationTypeEnum.GET_PAGE);
responseValidator.addExcludeOperationType(RestOperationTypeEnum.HISTORY_INSTANCE);
responseValidator.addExcludeOperationType(RestOperationTypeEnum.HISTORY_SYSTEM);
responseValidator.addExcludeOperationType(RestOperationTypeEnum.HISTORY_TYPE);
responseValidator.addExcludeOperationType(RestOperationTypeEnum.SEARCH_SYSTEM);
responseValidator.addExcludeOperationType(RestOperationTypeEnum.SEARCH_TYPE);
responseValidator.addValidatorModule(instanceValidatorDstu2());
responseValidator.setIgnoreValidatorExceptions(true);
return responseValidator;
}
@Bean(autowire=Autowire.BY_TYPE)
public IServerInterceptor subscriptionSecurityInterceptor() {
return new SubscriptionsRequireManualActivationInterceptorDstu2();

38
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java
View File

@ -1,30 +1,28 @@
package ca.uhn.fhirtest.config;
import java.util.Properties;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
import org.apache.commons.dbcp2.BasicDataSource;
import org.apache.commons.lang3.time.DateUtils;
import org.hibernate.dialect.PostgreSQL94Dialect;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.DependsOn;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhirtest.interceptor.PublicSecurityInterceptor;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.util.Properties;
@Configuration
@Import(CommonConfig.class)
@ -114,6 +112,22 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
return extraProperties;
}
/**
* Bean which validates incoming requests
*/
@Bean
@Lazy
public RequestValidatingInterceptor requestValidatingInterceptor() {
RequestValidatingInterceptor requestValidator = new RequestValidatingInterceptor();
requestValidator.setFailOnSeverity(null);
requestValidator.setAddResponseHeaderOnSeverity(null);
requestValidator.setAddResponseOutcomeHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
requestValidator.addValidatorModule(instanceValidatorDstu2());
requestValidator.setIgnoreValidatorExceptions(true);
return requestValidator;
}
// @Bean(autowire = Autowire.BY_TYPE)
// public IServerInterceptor subscriptionSecurityInterceptor() {
// return new SubscriptionsRequireManualActivationInterceptorDstu2();

5
src/changes/changes.xml
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@ -32,6 +32,11 @@
are now a part of the FHIR specification. Thanks to Jan Dědek for
pointing this out!
</action>
<action type="add" issue="609">
hapi-fhir-jpaserver-base now exposes a
<![CDATA[<code>FhirInstanceValidator</code> bean named <code>"myInstanceValidatorDstu2"</code>]]>
for DSTU2. A similar bean for DSTU3 was previously implemented.
</action>
</release>
<release version="2.3" date="2017-03-18">
<action type="add">