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hapi-fhir
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Code Issues Packages Projects Releases Wiki Activity

remove hapi jpa spring config hierarchy (#3390) 

* initial refactor to remove hapi jpa spring config hierarchy

* fix poms

* fix batch config

* dependency rearrangement arising from further testing

* fix searchDao bean name

* fixed dstu2 tests

* consolidate validation config

* dstu2 validation regression (man dstu2 support is expensive)

* fix test (with WIP comment)

* restore poms

* fix demo projects

* fix build

* bumping version

* rename generated config class
This commit is contained in:
Ken Stevens 2022-02-16 20:44:03 -05:00 committed by GitHub
parent 1c82d0933c
commit 631391819b
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
290 changed files with 3134 additions and 3590 deletions
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2
hapi-deployable-pom/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/api/IResourceSupportedSvc.java Normal file
View File

@ -0,0 +1,5 @@
package ca.uhn.fhir.rest.api;
public interface IResourceSupportedSvc {
boolean isSupported(String theResourceName);
}

2
hapi-fhir-batch/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-bom/pom.xml
View File

@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-checkstyle/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

20
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfig.java
View File

@ -20,14 +20,15 @@ package ca.uhn.fhir.jpa.demo;
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu2;
import ca.uhn.fhir.jpa.config.HapiJpaConfig;
import ca.uhn.fhir.jpa.config.JpaDstu2Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu2;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.apache.commons.lang3.time.DateUtils;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
@ -45,8 +46,8 @@ import java.util.Properties;
@Configuration
@EnableTransactionManagement()
@Import(CommonConfig.class)
public class FhirServerConfig extends BaseJavaConfigDstu2 {
@Import({CommonConfig.class, JpaDstu2Config.class, HapiJpaConfig.class})
public class FhirServerConfig {
@Autowired
private DataSource myDataSource;
@ -64,10 +65,9 @@ public class FhirServerConfig extends BaseJavaConfigDstu2 {
return retVal;
}
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(myDataSource);
retVal.setJpaProperties(myJpaProperties);
@ -92,13 +92,13 @@ public class FhirServerConfig extends BaseJavaConfigDstu2 {
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
* @return
*/
@Bean(autowire = Autowire.BY_TYPE)
@Bean
public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
@Bean
public IServerInterceptor subscriptionSecurityInterceptor() {
SubscriptionsRequireManualActivationInterceptorDstu2 retVal = new SubscriptionsRequireManualActivationInterceptorDstu2();
return retVal;

21
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu3.java
View File

@ -20,14 +20,14 @@ package ca.uhn.fhir.jpa.demo;
* #L%
*/
import ca.uhn.fhir.jpa.binstore.DatabaseBlobBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.config.BaseJavaConfigDstu3;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.HapiJpaConfig;
import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorDstu3;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
@ -52,8 +52,8 @@ import java.util.Properties;
*/
@Configuration
@EnableTransactionManagement()
@Import(CommonConfig.class)
public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
@Import({CommonConfig.class, JpaDstu3Config.class, HapiJpaConfig.class,})
public class FhirServerConfigDstu3 {
@Autowired
private DataSource myDataSource;
@ -61,10 +61,9 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
@Qualifier("jpaProperties")
private Properties myJpaProperties;
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(myDataSource);
retVal.setJpaProperties(myJpaProperties);
@ -89,13 +88,13 @@ public class FhirServerConfigDstu3 extends BaseJavaConfigDstu3 {
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
* @return
*/
@Bean(autowire = Autowire.BY_TYPE)
@Bean
public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
@Bean
public IServerInterceptor subscriptionSecurityInterceptor() {
SubscriptionsRequireManualActivationInterceptorDstu3 retVal = new SubscriptionsRequireManualActivationInterceptorDstu3();
return retVal;

19
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigR4.java
View File

@ -20,12 +20,14 @@ package ca.uhn.fhir.jpa.demo;
* #L%
*/
import ca.uhn.fhir.jpa.config.BaseJavaConfigR4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.HapiJpaConfig;
import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.util.SubscriptionsRequireManualActivationInterceptorR4;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
@ -50,8 +52,8 @@ import java.util.Properties;
*/
@Configuration
@EnableTransactionManagement()
@Import(CommonConfig.class)
public class FhirServerConfigR4 extends BaseJavaConfigR4 {
@Import({CommonConfig.class, JpaR4Config.class, HapiJpaConfig.class})
public class FhirServerConfigR4 {
@Autowired
private DataSource myDataSource;
@ -59,10 +61,9 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
@Qualifier("jpaProperties")
private Properties myJpaProperties;
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("HAPI_PU");
retVal.setDataSource(myDataSource);
retVal.setJpaProperties(myJpaProperties);
@ -87,13 +88,13 @@ public class FhirServerConfigR4 extends BaseJavaConfigR4 {
* This interceptor adds some pretty syntax highlighting in responses when a browser is detected
* @return
*/
@Bean(autowire = Autowire.BY_TYPE)
@Bean
public ResponseHighlighterInterceptor responseHighlighterInterceptor() {
ResponseHighlighterInterceptor retVal = new ResponseHighlighterInterceptor();
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
@Bean
public IServerInterceptor subscriptionSecurityInterceptor() {
SubscriptionsRequireManualActivationInterceptorR4 retVal = new SubscriptionsRequireManualActivationInterceptorR4();
return retVal;

12
hapi-fhir-cli/hapi-fhir-cli-jpaserver/src/main/java/ca/uhn/fhir/jpa/demo/JpaServerDemo.java
View File

@ -20,25 +20,24 @@ package ca.uhn.fhir.jpa.demo;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.binstore.BinaryAccessProvider;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.interceptor.CascadingDeleteInterceptor;
import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
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.JpaCapabilityStatementProvider;
import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
@ -47,8 +46,9 @@ import ca.uhn.fhir.rest.server.ETagSupportEnum;
import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.CorsInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
@ -109,7 +109,7 @@ public class JpaServerDemo extends RestfulServer {
} else if (fhirVersion == FhirVersionEnum.R4) {
systemProvider.add(myAppCtx.getBean("mySystemProviderR4", JpaSystemProviderR4.class));
systemProvider.add(myAppCtx.getBean(TerminologyUploaderProvider.class));
systemProvider.add(myAppCtx.getBean(BaseConfig.GRAPHQL_PROVIDER_NAME));
systemProvider.add(myAppCtx.getBean(JpaConfig.GRAPHQL_PROVIDER_NAME));
} else {
throw new IllegalStateException(Msg.code(1533));
}

2
hapi-fhir-cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jacoco/pom.xml
View File

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpa/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

14
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.0.0-PRE2-SNAPSHOT</version>
<version>6.0.0-PRE3-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -556,6 +556,18 @@
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<goals>
<goal>test-jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/BatchJobsConfig.java
View File

@ -20,19 +20,29 @@ package ca.uhn.fhir.jpa.batch;
* #L%
*/
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.batch.mdm.job.MdmClearJobConfig;
import ca.uhn.fhir.jpa.batch.svc.BatchJobSubmitterImpl;
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.imprt.job.BulkImportJobConfig;
import ca.uhn.fhir.jpa.config.BatchJobRegisterer;
import ca.uhn.fhir.jpa.delete.job.DeleteExpungeJobConfig;
import ca.uhn.fhir.jpa.reindex.job.ReindexEverythingJobConfig;
import ca.uhn.fhir.jpa.reindex.job.ReindexJobConfig;
import ca.uhn.fhir.jpa.term.job.TermCodeSystemDeleteJobConfig;
import ca.uhn.fhir.jpa.term.job.TermCodeSystemVersionDeleteJobConfig;
import org.springframework.batch.core.configuration.JobRegistry;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.batch.core.launch.JobLauncher;
import org.springframework.batch.core.launch.support.SimpleJobOperator;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@Configuration
//When you define a new batch job, add it here.
@EnableBatchProcessing
@Import({
CommonBatchJobConfig.class,
BulkExportJobConfig.class,
@ -43,6 +53,28 @@ import org.springframework.context.annotation.Import;
MdmClearJobConfig.class,
TermCodeSystemDeleteJobConfig.class,
TermCodeSystemVersionDeleteJobConfig.class
// When you define a new batch job, add it here.
})
public class BatchJobsConfig {
@Bean
public IBatchJobSubmitter batchJobSubmitter() {
return new BatchJobSubmitterImpl();
}
@Bean
public BatchJobRegisterer batchJobRegisterer() {
return new BatchJobRegisterer();
}
@Bean
public SimpleJobOperator jobOperator(JobExplorer theJobExplorer, JobRepository theJobRepository, JobRegistry theJobRegistry, JobLauncher theJobLauncher) {
SimpleJobOperator jobOperator = new SimpleJobOperator();
jobOperator.setJobExplorer(theJobExplorer);
jobOperator.setJobRepository(theJobRepository);
jobOperator.setJobRegistry(theJobRegistry);
jobOperator.setJobLauncher(theJobLauncher);
return jobOperator;
}
}

126
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfigDstu3Plus.java
View File

@ -1,126 +0,0 @@
package ca.uhn.fhir.jpa.config;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* 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 ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.JpaPersistedResourceValidationSupport;
import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
import ca.uhn.fhir.jpa.validation.ValidatorPolicyAdvisor;
import ca.uhn.fhir.jpa.validation.ValidatorResourceFetcher;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
@Configuration
public abstract class BaseConfigDstu3Plus extends BaseConfig {
@Bean
public ITermCodeSystemStorageSvc termCodeSystemStorageSvc() {
return new TermCodeSystemStorageSvcImpl();
}
@Bean
public ITermDeferredStorageSvc termDeferredStorageSvc() {
return new TermDeferredStorageSvcImpl();
}
@Bean
public ITermReindexingSvc termReindexingSvc() {
return new TermReindexingSvcImpl();
}
@Bean
public abstract ITermVersionAdapterSvc terminologyVersionAdapterSvc();
@Bean(name = "myDefaultProfileValidationSupport")
public DefaultProfileValidationSupport defaultProfileValidationSupport(DaoConfig theDaoConfig) {
return new DefaultProfileValidationSupport(fhirContext());
}
@Bean(name = JPA_VALIDATION_SUPPORT_CHAIN)
public JpaValidationSupportChain jpaValidationSupportChain() {
return new JpaValidationSupportChain(fhirContext());
}
@Bean(name = JPA_VALIDATION_SUPPORT)
public IValidationSupport jpaValidationSupport() {
return new JpaPersistedResourceValidationSupport(fhirContext());
}
@Primary
@Bean
public IValidationSupport validationSupportChain() {
// Short timeout for code translation because TermConceptMappingSvcImpl has its own caching
CachingValidationSupport.CacheTimeouts cacheTimeouts = CachingValidationSupport.CacheTimeouts.defaultValues()
.setTranslateCodeMillis(1000);
return new CachingValidationSupport(jpaValidationSupportChain(), cacheTimeouts);
}
@Bean(name = "myInstanceValidator")
@Lazy
public IInstanceValidatorModule instanceValidator() {
FhirInstanceValidator val = new FhirInstanceValidator(validationSupportChain());
val.setValidatorResourceFetcher(jpaValidatorResourceFetcher());
val.setValidatorPolicyAdvisor(jpaValidatorPolicyAdvisor());
val.setBestPracticeWarningLevel(BestPracticeWarningLevel.Warning);
val.setValidationSupport(validationSupportChain());
return val;
}
@Bean
@Lazy
public ValidatorResourceFetcher jpaValidatorResourceFetcher() {
return new ValidatorResourceFetcher();
}
@Bean
@Lazy
public ValidatorPolicyAdvisor jpaValidatorPolicyAdvisor() {
return new ValidatorPolicyAdvisor();
}
@Bean
public abstract ITermReadSvc terminologyService();
@Bean
public ObservationLastNIndexPersistSvc baseObservationLastNIndexpersistSvc() {
return new ObservationLastNIndexPersistSvc();
}
}

155
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java
View File

@ -1,155 +0,0 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
import ca.uhn.fhir.jpa.dao.JpaPersistedResourceValidationSupport;
import ca.uhn.fhir.jpa.dao.TransactionProcessorVersionAdapterDstu2;
import ca.uhn.fhir.jpa.term.TermReadSvcDstu2;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.common.hapi.validation.validator.HapiToHl7OrgDstu2ValidatingSupportWrapper;
import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;
import org.springframework.beans.factory.annotation.Autowire;
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.transaction.annotation.EnableTransactionManagement;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* 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%
*/
@Configuration
@EnableTransactionManagement
public class BaseDstu2Config extends BaseConfig {
private static FhirContext ourFhirContextDstu2;
private static FhirContext ourFhirContextDstu2Hl7Org;
@Bean
@Primary
public FhirContext defaultFhirContext() {
return fhirContextDstu2();
}
@Override
public FhirContext fhirContext() {
return fhirContextDstu2();
}
@Bean(name = "myFhirContextDstu2")
@Lazy
public FhirContext fhirContextDstu2() {
if (ourFhirContextDstu2 == null) {
ourFhirContextDstu2 = FhirContext.forDstu2();
}
return ourFhirContextDstu2;
}
@Bean(name = "myFhirContextDstu2Hl7Org")
@Lazy
public FhirContext fhirContextDstu2Hl7Org() {
if (ourFhirContextDstu2Hl7Org == null) {
ourFhirContextDstu2Hl7Org = FhirContext.forDstu2Hl7Org();
}
return ourFhirContextDstu2Hl7Org;
}
@Bean(name = "myInstanceValidator")
@Lazy
public IInstanceValidatorModule instanceValidator(ValidationSupportChain theValidationSupportChain) {
CachingValidationSupport cachingValidationSupport = new CachingValidationSupport(new HapiToHl7OrgDstu2ValidatingSupportWrapper(theValidationSupportChain));
FhirInstanceValidator retVal = new FhirInstanceValidator(cachingValidationSupport);
retVal.setBestPracticeWarningLevel(BestPracticeWarningLevel.Warning);
return retVal;
}
@Bean
public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
return new TransactionProcessorVersionAdapterDstu2();
}
@Bean(name = "myDefaultProfileValidationSupport")
public DefaultProfileValidationSupport defaultProfileValidationSupport() {
return new DefaultProfileValidationSupport(fhirContext());
}
@Bean(name = JPA_VALIDATION_SUPPORT_CHAIN)
public ValidationSupportChain validationSupportChain(DefaultProfileValidationSupport theDefaultProfileValidationSupport) {
InMemoryTerminologyServerValidationSupport inMemoryTerminologyServer = new InMemoryTerminologyServerValidationSupport(fhirContextDstu2());
IValidationSupport jpaValidationSupport = jpaValidationSupportDstu2();
CommonCodeSystemsTerminologyService commonCodeSystemsTermSvc = new CommonCodeSystemsTerminologyService(fhirContext());
return new ValidationSupportChain(theDefaultProfileValidationSupport, jpaValidationSupport, inMemoryTerminologyServer, commonCodeSystemsTermSvc);
}
@Primary
@Bean(name = JPA_VALIDATION_SUPPORT)
public IValidationSupport jpaValidationSupportDstu2() {
return new JpaPersistedResourceValidationSupport(fhirContextDstu2());
}
@Bean(name = "myResourceCountsCache")
public ResourceCountCache resourceCountsCache() {
ResourceCountCache retVal = new ResourceCountCache(() -> systemDaoDstu2().getResourceCounts());
retVal.setCacheMillis(4 * DateUtils.MILLIS_PER_HOUR);
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
public IFulltextSearchSvc searchDao() {
FulltextSearchSvcImpl searchDao = new FulltextSearchSvcImpl();
return searchDao;
}
@Bean(name = "mySystemDaoDstu2", autowire = Autowire.BY_NAME)
public IFhirSystemDao<Bundle, MetaDt> systemDaoDstu2() {
ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu2 retVal = new ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu2();
return retVal;
}
@Bean(name = "mySystemProviderDstu2")
public ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2 systemProviderDstu2() {
ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2 retVal = new ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2();
retVal.setDao(systemDaoDstu2());
retVal.setContext(fhirContextDstu2());
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
public ITermReadSvc terminologyService() {
return new TermReadSvcDstu2();
}
}

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BatchJobRegisterer.java
View File

@ -24,7 +24,6 @@ import org.springframework.batch.core.Job;
import org.springframework.batch.core.configuration.DuplicateJobException;
import org.springframework.batch.core.configuration.JobFactory;
import org.springframework.batch.core.configuration.JobRegistry;
import org.springframework.batch.core.configuration.support.ApplicationContextJobFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BeanPostProcessorConfig.java Normal file
View File

@ -0,0 +1,20 @@
package ca.uhn.fhir.jpa.config;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor;
@Configuration
// TODO KHS do we even need this class?
// TODO KHS find out why this Spring Config produces the message and if there's anything we can do about it:
// o.s.c.s.PostProcessorRegistrationDelegate$BeanPostProcessorChecker [PostProcessorRegistrationDelegate.java:376]
// Bean 'ca.uhn.fhir.jpa.config.BeanPostProcessorConfig'
// of type [ca.uhn.fhir.jpa.config.BeanPostProcessorConfig$$EnhancerBySpringCGLIB$$8d867950]
// is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
public class BeanPostProcessorConfig {
@Bean
public PersistenceExceptionTranslationPostProcessor persistenceExceptionTranslationPostProcessor() {
return new PersistenceExceptionTranslationPostProcessor();
}
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/FhirContextDstu2Config.java Normal file
View File

@ -0,0 +1,13 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Primary;
public class FhirContextDstu2Config {
@Primary
@Bean(name = "primaryFhirContext")
public FhirContext fhirContextDstu2() {
return FhirContext.forDstu2();
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HapiFhirHibernateJpaDialect.java
View File

@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.config;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.i18n.HapiLocalizer;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.model.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedComboStringUnique;

62
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HapiJpaConfig.java Normal file
View File

@ -0,0 +1,62 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.jpa.api.IDaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;
import ca.uhn.fhir.jpa.config.util.ResourceCountCacheUtil;
import ca.uhn.fhir.jpa.config.util.ValidationSupportConfigUtil;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.provider.DaoRegistryResourceSupportedSvc;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
import ca.uhn.fhir.rest.api.IResourceSupportedSvc;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Primary;
@Configuration
@Import({JpaConfig.class})
public class HapiJpaConfig {
@Bean
public IFulltextSearchSvc fullTextSearchSvc() {
return new FulltextSearchSvcImpl();
}
@Bean
public IStaleSearchDeletingSvc staleSearchDeletingSvc() {
return new StaleSearchDeletingSvcImpl();
}
@Primary
@Bean
public CachingValidationSupport validationSupportChain(JpaValidationSupportChain theJpaValidationSupportChain) {
return ValidationSupportConfigUtil.newCachingValidationSupport(theJpaValidationSupportChain);
}
@Bean
public BatchConfigurer batchConfigurer() {
return new NonPersistedBatchConfigurer();
}
@Bean
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
return new DatabaseBackedPagingProvider();
}
@Bean
public IResourceSupportedSvc resourceSupportedSvc(IDaoRegistry theDaoRegistry) {
return new DaoRegistryResourceSupportedSvc(theDaoRegistry);
}
@Bean(name = "myResourceCountsCache")
public ResourceCountCache resourceCountsCache(IFhirSystemDao<?, ?> theSystemDao) {
return ResourceCountCacheUtil.newResourceCountCache(theSystemDao);
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HibernatePropertiesProvider.java
View File

@ -21,8 +21,8 @@ package ca.uhn.fhir.jpa.config;
*/
import ca.uhn.fhir.util.ReflectionUtil;
import org.apache.commons.lang3.StringUtils;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hibernate.dialect.Dialect;
import org.hibernate.search.engine.cfg.BackendSettings;

150
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java
View File

@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.i18n.HapiLocalizer;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.interceptor.executor.InterceptorService;
@ -12,13 +11,10 @@ import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.batch.config.BatchConstants;
import ca.uhn.fhir.jpa.batch.config.NonPersistedBatchConfigurer;
import ca.uhn.fhir.jpa.batch.job.PartitionedUrlValidator;
import ca.uhn.fhir.jpa.batch.mdm.MdmClearJobSubmitterImpl;
import ca.uhn.fhir.jpa.batch.reader.BatchResourceSearcher;
import ca.uhn.fhir.jpa.batch.svc.BatchJobSubmitterImpl;
import ca.uhn.fhir.jpa.binstore.BinaryAccessProvider;
import ca.uhn.fhir.jpa.binstore.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
@ -88,13 +84,10 @@ import ca.uhn.fhir.jpa.provider.r4.MemberMatcherR4Helper;
import ca.uhn.fhir.jpa.reindex.ReindexJobSubmitterImpl;
import ca.uhn.fhir.jpa.sched.AutowiringSpringBeanJobFactory;
import ca.uhn.fhir.jpa.sched.HapiSchedulerServiceImpl;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProviderFactory;
import ca.uhn.fhir.jpa.search.PersistedJpaSearchFirstPageBundleProvider;
import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import ca.uhn.fhir.jpa.search.builder.QueryStack;
import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
import ca.uhn.fhir.jpa.search.builder.predicate.ComboNonUniqueSearchParameterPredicateBuilder;
@ -148,20 +141,10 @@ import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInter
import ca.uhn.fhir.rest.server.provider.DeleteExpungeProvider;
import ca.uhn.fhir.rest.server.provider.ReindexProvider;
import ca.uhn.fhir.util.ThreadPoolUtil;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.npm.PackageClient;
import org.springframework.batch.core.configuration.JobRegistry;
import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.batch.core.launch.JobLauncher;
import org.springframework.batch.core.launch.support.SimpleJobOperator;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.ApplicationContext;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@ -169,18 +152,14 @@ import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
import org.springframework.context.annotation.Scope;
import org.springframework.core.env.Environment;
import org.springframework.core.task.AsyncTaskExecutor;
import org.springframework.core.task.TaskExecutor;
import org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor;
import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.scheduling.TaskScheduler;
import org.springframework.scheduling.concurrent.ConcurrentTaskScheduler;
import org.springframework.scheduling.concurrent.ScheduledExecutorFactoryBean;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import java.util.Date;
/*
@ -203,15 +182,15 @@ import java.util.Date;
* #L%
*/
@Configuration
@EnableJpaRepositories(basePackages = "ca.uhn.fhir.jpa.dao.data", enableDefaultTransactions=true)
@EnableJpaRepositories(basePackages = "ca.uhn.fhir.jpa.dao.data")
@Import({
SearchParamConfig.class, BatchJobsConfig.class
BeanPostProcessorConfig.class,
BatchJobsConfig.class,
SearchParamConfig.class,
ValidationSupportConfig.class
})
@EnableBatchProcessing
public abstract class BaseConfig {
public class JpaConfig {
public static final String JPA_VALIDATION_SUPPORT_CHAIN = "myJpaValidationSupportChain";
public static final String JPA_VALIDATION_SUPPORT = "myJpaValidationSupport";
public static final String TASK_EXECUTOR_NAME = "hapiJpaTaskExecutor";
@ -222,100 +201,24 @@ public abstract class BaseConfig {
public static final String SEARCH_BUILDER = "SearchBuilder";
public static final String HISTORY_BUILDER = "HistoryBuilder";
private static final String HAPI_DEFAULT_SCHEDULER_GROUP = "HAPI";
@Autowired
protected Environment myEnv;
@Autowired
private DaoRegistry myDaoRegistry;
private Integer searchCoordCorePoolSize = 20;
private Integer searchCoordMaxPoolSize = 100;
private Integer searchCoordQueueCapacity = 200;
@Autowired
private JobLauncher myJobLauncher;
/**
* Subclasses may override this method to provide settings such as search coordinator pool sizes.
*/
@PostConstruct
public void initSettings() {
}
public void setSearchCoordCorePoolSize(Integer searchCoordCorePoolSize) {
this.searchCoordCorePoolSize = searchCoordCorePoolSize;
}
public void setSearchCoordMaxPoolSize(Integer searchCoordMaxPoolSize) {
this.searchCoordMaxPoolSize = searchCoordMaxPoolSize;
}
public void setSearchCoordQueueCapacity(Integer searchCoordQueueCapacity) {
this.searchCoordQueueCapacity = searchCoordQueueCapacity;
}
@Bean
public BatchConfigurer batchConfigurer() {
return new NonPersistedBatchConfigurer();
}
@Bean("myDaoRegistry")
public DaoRegistry daoRegistry() {
return new DaoRegistry();
}
@Bean
public DatabaseBackedPagingProvider databaseBackedPagingProvider() {
return new DatabaseBackedPagingProvider();
}
@Bean
public IBatchJobSubmitter batchJobSubmitter() {
return new BatchJobSubmitterImpl();
}
@Bean
public BatchJobRegisterer batchJobRegisterer() {
return new BatchJobRegisterer();
}
@Lazy
@Bean
public CascadingDeleteInterceptor cascadingDeleteInterceptor(FhirContext theFhirContext, DaoRegistry theDaoRegistry, IInterceptorBroadcaster theInterceptorBroadcaster) {
return new CascadingDeleteInterceptor(theFhirContext, theDaoRegistry, theInterceptorBroadcaster);
}
@Bean
public SimpleJobOperator jobOperator(JobExplorer jobExplorer, JobRepository jobRepository, JobRegistry jobRegistry) {
SimpleJobOperator jobOperator = new SimpleJobOperator();
jobOperator.setJobExplorer(jobExplorer);
jobOperator.setJobRepository(jobRepository);
jobOperator.setJobRegistry(jobRegistry);
jobOperator.setJobLauncher(myJobLauncher);
return jobOperator;
}
@Lazy
@Bean
public ResponseTerminologyTranslationInterceptor responseTerminologyTranslationInterceptor(IValidationSupport theValidationSupport) {
return new ResponseTerminologyTranslationInterceptor(theValidationSupport);
}
/**
* This method should be overridden to provide an actual completed
* bean, but it provides a partially completed entity manager
* factory with HAPI FHIR customizations
*/
protected LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory);
configureEntityManagerFactory(retVal, fhirContext());
return retVal;
}
public abstract FhirContext fhirContext();
@Bean
@Lazy
public IGraphQLStorageServices graphqlStorageServices() {
@ -420,7 +323,7 @@ public abstract class BaseConfig {
return retVal;
}
@Bean(name= BatchConstants.JOB_LAUNCHING_TASK_EXECUTOR)
@Bean(name = BatchConstants.JOB_LAUNCHING_TASK_EXECUTOR)
public TaskExecutor jobLaunchingTaskExecutor() {
return ThreadPoolUtil.newThreadPool(0, 10, "job-launcher-");
}
@ -441,13 +344,8 @@ public abstract class BaseConfig {
}
@Bean
public IStaleSearchDeletingSvc staleSearchDeletingSvc() {
return new StaleSearchDeletingSvcImpl();
}
@Bean
public HapiFhirHibernateJpaDialect hibernateJpaDialect() {
return new HapiFhirHibernateJpaDialect(fhirContext().getLocalizer());
public HapiFhirHibernateJpaDialect hibernateJpaDialect(FhirContext theFhirContext) {
return new HapiFhirHibernateJpaDialect(theFhirContext.getLocalizer());
}
@Bean
@ -461,11 +359,6 @@ public abstract class BaseConfig {
return new RequestPartitionHelperSvc();
}
@Bean
public PersistenceExceptionTranslationPostProcessor persistenceExceptionTranslationPostProcessor() {
return new PersistenceExceptionTranslationPostProcessor();
}
@Bean
public HapiTransactionService hapiTransactionService() {
return new HapiTransactionService();
@ -476,13 +369,6 @@ public abstract class BaseConfig {
return new InterceptorService("JPA");
}
/**
* Subclasses may override
*/
protected boolean isSupported(String theResourceType) {
return myDaoRegistry.getResourceDaoOrNull(theResourceType) != null;
}
@Bean
public IPackageInstallerSvc npmInstallerSvc() {
return new PackageInstallerSvcImpl();
@ -593,6 +479,7 @@ public abstract class BaseConfig {
return new BulkDataImportSvcImpl();
}
@Bean
public PersistedJpaBundleProviderFactory persistedJpaBundleProviderFactory() {
return new PersistedJpaBundleProviderFactory();
@ -623,6 +510,7 @@ public abstract class BaseConfig {
return new ResourceVersionSvcDaoImpl();
}
/* **************************************************************** *
* Prototype Beans Below *
* **************************************************************** */
@ -927,8 +815,8 @@ public abstract class BaseConfig {
}
@Bean
public UnknownCodeSystemWarningValidationSupport unknownCodeSystemWarningValidationSupport() {
return new UnknownCodeSystemWarningValidationSupport(fhirContext());
public UnknownCodeSystemWarningValidationSupport unknownCodeSystemWarningValidationSupport(FhirContext theFhirContext) {
return new UnknownCodeSystemWarningValidationSupport(theFhirContext);
}
@Lazy
@ -936,16 +824,4 @@ public abstract class BaseConfig {
public MemberMatcherR4Helper memberMatcherR4Helper(FhirContext theFhirContext) {
return new MemberMatcherR4Helper(theFhirContext);
}
public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) {
theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer()));
theFactory.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");
theFactory.setPersistenceProvider(new HibernatePersistenceProvider());
}
private static HapiFhirHibernateJpaDialect hibernateJpaDialect(HapiLocalizer theLocalizer) {
return new HapiFhirHibernateJpaDialect(theLocalizer);
}
}

67
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaDstu2Config.java Normal file
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@ -0,0 +1,67 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
import ca.uhn.fhir.jpa.dao.TransactionProcessorVersionAdapterDstu2;
import ca.uhn.fhir.jpa.term.TermReadSvcDstu2;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.transaction.annotation.EnableTransactionManagement;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* 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%
*/
@Configuration
@EnableTransactionManagement
@Import({
FhirContextDstu2Config.class,
GeneratedDaoAndResourceProviderConfigDstu2.class,
JpaConfig.class
})
public class JpaDstu2Config {
@Bean
public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
return new TransactionProcessorVersionAdapterDstu2();
}
@Bean(name = "mySystemDaoDstu2")
public IFhirSystemDao<Bundle, MetaDt> systemDaoDstu2() {
ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu2 retVal = new ca.uhn.fhir.jpa.dao.FhirSystemDaoDstu2();
return retVal;
}
@Bean(name = "mySystemProviderDstu2")
public ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2 systemProviderDstu2(FhirContext theFhirContext) {
ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2 retVal = new ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2();
retVal.setDao(systemDaoDstu2());
retVal.setContext(theFhirContext);
return retVal;
}
@Bean
public ITermReadSvc terminologyService() {
return new TermReadSvcDstu2();
}
}

57
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/SharedConfigDstu3Plus.java Normal file
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@ -0,0 +1,57 @@
package ca.uhn.fhir.jpa.config;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2022 Smile CDR, Inc.
* %%
* 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 ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@Configuration
public class SharedConfigDstu3Plus {
@Bean
public ITermCodeSystemStorageSvc termCodeSystemStorageSvc() {
return new TermCodeSystemStorageSvcImpl();
}
@Bean
public ITermDeferredStorageSvc termDeferredStorageSvc() {
return new TermDeferredStorageSvcImpl();
}
@Bean
public ITermReindexingSvc termReindexingSvc() {
return new TermReindexingSvcImpl();
}
@Bean
public ObservationLastNIndexPersistSvc baseObservationLastNIndexpersistSvc() {
return new ObservationLastNIndexPersistSvc();
}
}

67
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/ValidationSupportConfig.java Normal file
View File

@ -0,0 +1,67 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.dao.JpaPersistedResourceValidationSupport;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
import ca.uhn.fhir.jpa.validation.ValidatorPolicyAdvisor;
import ca.uhn.fhir.jpa.validation.ValidatorResourceFetcher;
import ca.uhn.fhir.validation.IInstanceValidatorModule;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.common.hapi.validation.validator.HapiToHl7OrgDstu2ValidatingSupportWrapper;
import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
@Configuration
public class ValidationSupportConfig {
@Bean(name = "myDefaultProfileValidationSupport")
public DefaultProfileValidationSupport defaultProfileValidationSupport(FhirContext theFhirContext) {
return new DefaultProfileValidationSupport(theFhirContext);
}
@Bean(name = JpaConfig.JPA_VALIDATION_SUPPORT_CHAIN)
public JpaValidationSupportChain jpaValidationSupportChain(FhirContext theFhirContext) {
return new JpaValidationSupportChain(theFhirContext);
}
@Bean(name = JpaConfig.JPA_VALIDATION_SUPPORT)
public IValidationSupport jpaValidationSupport(FhirContext theFhirContext) {
return new JpaPersistedResourceValidationSupport(theFhirContext);
}
@Bean(name = "myInstanceValidator")
public IInstanceValidatorModule instanceValidator(FhirContext theFhirContext, CachingValidationSupport theCachingValidationSupport, ValidationSupportChain theValidationSupportChain) {
if (theFhirContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3)) {
FhirInstanceValidator val = new FhirInstanceValidator(theCachingValidationSupport);
val.setValidatorResourceFetcher(jpaValidatorResourceFetcher());
val.setValidatorPolicyAdvisor(jpaValidatorPolicyAdvisor());
val.setBestPracticeWarningLevel(BestPracticeWarningLevel.Warning);
val.setValidationSupport(theCachingValidationSupport);
return val;
} else {
CachingValidationSupport cachingValidationSupport = new CachingValidationSupport(new HapiToHl7OrgDstu2ValidatingSupportWrapper(theValidationSupportChain));
FhirInstanceValidator retVal = new FhirInstanceValidator(cachingValidationSupport);
retVal.setBestPracticeWarningLevel(BestPracticeWarningLevel.Warning);
return retVal;
}
}
@Bean
@Lazy
public ValidatorResourceFetcher jpaValidatorResourceFetcher() {
return new ValidatorResourceFetcher();
}
@Bean
@Lazy
public ValidatorPolicyAdvisor jpaValidatorPolicyAdvisor() {
return new ValidatorPolicyAdvisor();
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/FhirContextDstu3Config.java Normal file
View File

@ -0,0 +1,20 @@
package ca.uhn.fhir.jpa.config.dstu3;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.ParserOptions;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Primary;
public class FhirContextDstu3Config {
@Primary
@Bean(name = "primaryFhirContext")
public FhirContext fhirContextDstu3() {
FhirContext retVal = FhirContext.forDstu3();
// Don't strip versions in some places
ParserOptions parserOptions = retVal.getParserOptions();
parserOptions.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
return retVal;
}
}

65
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/JpaDstu3Config.java
View File

@ -1,11 +1,11 @@
package ca.uhn.fhir.jpa.config.dstu3;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.ParserOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigDstu3;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.config.SharedConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
import ca.uhn.fhir.jpa.dao.dstu3.TransactionProcessorVersionAdapterDstu3;
import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
@ -17,14 +17,13 @@ import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
import org.springframework.transaction.annotation.EnableTransactionManagement;
/*
@ -49,37 +48,22 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
@Configuration
@EnableTransactionManagement
public class BaseDstu3Config extends BaseConfigDstu3Plus {
public static FhirContext ourFhirContext = FhirContext.forDstu3();
@Override
public FhirContext fhirContext() {
return fhirContextDstu3();
}
@Import({
FhirContextDstu3Config.class,
GeneratedDaoAndResourceProviderConfigDstu3.class,
SharedConfigDstu3Plus.class,
JpaConfig.class
})
public class JpaDstu3Config {
@Bean
@Override
public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
return new TermVersionAdapterSvcDstu3();
}
@Bean
@Primary
public FhirContext fhirContextDstu3() {
FhirContext retVal = ourFhirContext;
// Don't strip versions in some places
ParserOptions parserOptions = retVal.getParserOptions();
parserOptions.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
return retVal;
}
@Bean(name = GRAPHQL_PROVIDER_NAME)
@Bean(name = JpaConfig.GRAPHQL_PROVIDER_NAME)
@Lazy
public GraphQLProvider graphQLProvider() {
return new GraphQLProvider(fhirContextDstu3(), validationSupportChain(), graphqlStorageServices());
public GraphQLProvider graphQLProvider(FhirContext theFhirContext, IGraphQLStorageServices theGraphqlStorageServices, IValidationSupport theValidationSupport) {
return new GraphQLProvider(theFhirContext, theValidationSupport, theGraphqlStorageServices);
}
@Bean
@ -87,27 +71,15 @@ public class BaseDstu3Config extends BaseConfigDstu3Plus {
return new TransactionProcessorVersionAdapterDstu3();
}
@Bean(name = "myResourceCountsCache")
public ResourceCountCache resourceCountsCache() {
ResourceCountCache retVal = new ResourceCountCache(() -> systemDaoDstu3().getResourceCounts());
retVal.setCacheMillis(4 * DateUtils.MILLIS_PER_HOUR);
return retVal;
}
@Bean
public IFulltextSearchSvc searchDaoDstu3() {
return new FulltextSearchSvcImpl();
}
@Bean(name = "mySystemDaoDstu3")
public IFhirSystemDao<Bundle, Meta> systemDaoDstu3() {
return new ca.uhn.fhir.jpa.dao.dstu3.FhirSystemDaoDstu3();
}
@Bean(name = "mySystemProviderDstu3")
public ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3 systemProviderDstu3() {
public ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3 systemProviderDstu3(FhirContext theFhirContext) {
ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3 retVal = new ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3();
retVal.setContext(fhirContextDstu3());
retVal.setContext(theFhirContext);
retVal.setDao(systemDaoDstu3());
return retVal;
}
@ -117,7 +89,6 @@ public class BaseDstu3Config extends BaseConfigDstu3Plus {
return new TermLoaderSvcImpl(theDeferredStorageSvc, theCodeSystemStorageSvc);
}
@Override
@Bean
public ITermReadSvcDstu3 terminologyService() {
return new TermReadSvcDstu3();

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/FhirContextR4Config.java Normal file
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@ -0,0 +1,20 @@
package ca.uhn.fhir.jpa.config.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.ParserOptions;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Primary;
public class FhirContextR4Config {
@Bean(name = "primaryFhirContext")
@Primary
public FhirContext fhirContextR4() {
FhirContext retVal = FhirContext.forR4();
// Don't strip versions in some places
ParserOptions parserOptions = retVal.getParserOptions();
parserOptions.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.what");
return retVal;
}
}

144
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/JpaR4Config.java
View File

@ -1,11 +1,11 @@
package ca.uhn.fhir.jpa.config.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.ParserOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigR4;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.config.SharedConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
@ -17,17 +17,67 @@ import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Meta;
import org.springframework.beans.factory.annotation.Autowire;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
import org.springframework.transaction.annotation.EnableTransactionManagement;
@Configuration
@EnableTransactionManagement
@Import({
FhirContextR4Config.class,
GeneratedDaoAndResourceProviderConfigR4.class,
SharedConfigDstu3Plus.class,
JpaConfig.class
})
public class JpaR4Config {
@Bean
public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
return new TermVersionAdapterSvcR4();
}
@Bean
public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
return new TransactionProcessorVersionAdapterR4();
}
@Bean(name = JpaConfig.GRAPHQL_PROVIDER_NAME)
@Lazy
public GraphQLProvider graphQLProvider(FhirContext theFhirContext, IGraphQLStorageServices theGraphqlStorageServices, IValidationSupport theValidationSupport) {
return new GraphQLProvider(theFhirContext, theValidationSupport, theGraphqlStorageServices);
}
@Bean(name = "mySystemDaoR4")
public IFhirSystemDao<Bundle, Meta> systemDaoR4() {
ca.uhn.fhir.jpa.dao.r4.FhirSystemDaoR4 retVal = new ca.uhn.fhir.jpa.dao.r4.FhirSystemDaoR4();
return retVal;
}
@Bean(name = "mySystemProviderR4")
public ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4 systemProviderR4(FhirContext theFhirContext) {
ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4 retVal = new ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4();
retVal.setContext(theFhirContext);
retVal.setDao(systemDaoR4());
return retVal;
}
@Bean
public ITermLoaderSvc termLoaderService(ITermDeferredStorageSvc theDeferredStorageSvc, ITermCodeSystemStorageSvc theCodeSystemStorageSvc) {
return new TermLoaderSvcImpl(theDeferredStorageSvc, theCodeSystemStorageSvc);
}
@Bean
public ITermReadSvcR4 terminologyService() {
return new TermReadSvcR4();
}
}
/*
* #%L
* HAPI FHIR JPA Server
@ -47,81 +97,3 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
* limitations under the License.
* #L%
*/
@Configuration
@EnableTransactionManagement
public class BaseR4Config extends BaseConfigDstu3Plus {
@Override
public FhirContext fhirContext() {
return fhirContextR4();
}
@Bean
@Override
public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
return new TermVersionAdapterSvcR4();
}
@Bean
@Primary
public FhirContext fhirContextR4() {
FhirContext retVal = FhirContext.forR4();
// Don't strip versions in some places
ParserOptions parserOptions = retVal.getParserOptions();
parserOptions.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.what");
return retVal;
}
@Bean
public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
return new TransactionProcessorVersionAdapterR4();
}
@Bean(name = GRAPHQL_PROVIDER_NAME)
@Lazy
public GraphQLProvider graphQLProvider() {
return new GraphQLProvider(fhirContextR4(), validationSupportChain(), graphqlStorageServices());
}
@Bean(name = "myResourceCountsCache")
public ResourceCountCache resourceCountsCache() {
ResourceCountCache retVal = new ResourceCountCache(() -> systemDaoR4().getResourceCounts());
retVal.setCacheMillis(4 * DateUtils.MILLIS_PER_HOUR);
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
public IFulltextSearchSvc searchDaoR4() {
FulltextSearchSvcImpl searchDao = new FulltextSearchSvcImpl();
return searchDao;
}
@Bean(name = "mySystemDaoR4", autowire = Autowire.BY_NAME)
public IFhirSystemDao<Bundle, Meta> systemDaoR4() {
ca.uhn.fhir.jpa.dao.r4.FhirSystemDaoR4 retVal = new ca.uhn.fhir.jpa.dao.r4.FhirSystemDaoR4();
return retVal;
}
@Bean(name = "mySystemProviderR4")
public ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4 systemProviderR4() {
ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4 retVal = new ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4();
retVal.setContext(fhirContextR4());
retVal.setDao(systemDaoR4());
return retVal;
}
@Bean
public ITermLoaderSvc termLoaderService(ITermDeferredStorageSvc theDeferredStorageSvc, ITermCodeSystemStorageSvc theCodeSystemStorageSvc) {
return new TermLoaderSvcImpl(theDeferredStorageSvc, theCodeSystemStorageSvc);
}
@Override
@Bean(autowire = Autowire.BY_TYPE)
public ITermReadSvcR4 terminologyService() {
return new TermReadSvcR4();
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/FhirContextR5Config.java Normal file
View File

@ -0,0 +1,20 @@
package ca.uhn.fhir.jpa.config.r5;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.ParserOptions;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Primary;
public class FhirContextR5Config {
@Bean(name = "primaryFhirContext")
@Primary
public FhirContext fhirContextR5() {
FhirContext retVal = FhirContext.forR5();
// Don't strip versions in some places
ParserOptions parserOptions = retVal.getParserOptions();
parserOptions.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.what");
return retVal;
}
}

68
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/JpaR5Config.java
View File

@ -1,11 +1,11 @@
package ca.uhn.fhir.jpa.config.r5;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.ParserOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigR5;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.config.SharedConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
import ca.uhn.fhir.jpa.dao.r5.TransactionProcessorVersionAdapterR5;
import ca.uhn.fhir.jpa.graphql.GraphQLProvider;
@ -17,15 +17,13 @@ import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Meta;
import org.springframework.beans.factory.annotation.Autowire;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
import org.springframework.transaction.annotation.EnableTransactionManagement;
/*
@ -50,65 +48,40 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
@Configuration
@EnableTransactionManagement
public class BaseR5Config extends BaseConfigDstu3Plus {
@Override
public FhirContext fhirContext() {
return fhirContextR5();
}
@Import({
FhirContextR5Config.class,
GeneratedDaoAndResourceProviderConfigR5.class,
SharedConfigDstu3Plus.class,
JpaConfig.class
})
public class JpaR5Config {
@Bean
@Override
public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
return new TermVersionAdapterSvcR5();
}
@Bean
@Primary
public FhirContext fhirContextR5() {
FhirContext retVal = FhirContext.forR5();
// Don't strip versions in some places
ParserOptions parserOptions = retVal.getParserOptions();
parserOptions.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.what");
return retVal;
}
@Bean
public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
return new TransactionProcessorVersionAdapterR5();
}
@Bean(name = GRAPHQL_PROVIDER_NAME)
@Bean(name = JpaConfig.GRAPHQL_PROVIDER_NAME)
@Lazy
public GraphQLProvider graphQLProvider() {
return new GraphQLProvider(fhirContextR5(), validationSupportChain(), graphqlStorageServices());
public GraphQLProvider graphQLProvider(FhirContext theFhirContext, IGraphQLStorageServices theGraphqlStorageServices, IValidationSupport theValidationSupport) {
return new GraphQLProvider(theFhirContext, theValidationSupport, theGraphqlStorageServices);
}
@Bean(name = "myResourceCountsCache")
public ResourceCountCache resourceCountsCache() {
ResourceCountCache retVal = new ResourceCountCache(() -> systemDaoR5().getResourceCounts());
retVal.setCacheMillis(4 * DateUtils.MILLIS_PER_HOUR);
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
public IFulltextSearchSvc searchDaoR5() {
FulltextSearchSvcImpl searchDao = new FulltextSearchSvcImpl();
return searchDao;
}
@Bean(name = "mySystemDaoR5", autowire = Autowire.BY_NAME)
@Bean(name = "mySystemDaoR5")
public IFhirSystemDao<Bundle, Meta> systemDaoR5() {
ca.uhn.fhir.jpa.dao.r5.FhirSystemDaoR5 retVal = new ca.uhn.fhir.jpa.dao.r5.FhirSystemDaoR5();
return retVal;
}
@Bean(name = "mySystemProviderR5")
public ca.uhn.fhir.jpa.provider.r5.JpaSystemProviderR5 systemProviderR5() {
public ca.uhn.fhir.jpa.provider.r5.JpaSystemProviderR5 systemProviderR5(FhirContext theFhirContext) {
ca.uhn.fhir.jpa.provider.r5.JpaSystemProviderR5 retVal = new ca.uhn.fhir.jpa.provider.r5.JpaSystemProviderR5();
retVal.setContext(fhirContextR5());
retVal.setContext(theFhirContext);
retVal.setDao(systemDaoR5());
return retVal;
}
@ -118,8 +91,7 @@ public class BaseR5Config extends BaseConfigDstu3Plus {
return new TermLoaderSvcImpl(theDeferredStorageSvc, theCodeSystemStorageSvc);
}
@Override
@Bean(autowire = Autowire.BY_TYPE)
@Bean
public ITermReadSvcR5 terminologyService() {
return new TermReadSvcR5();
}

28
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/util/HapiEntityManagerFactoryUtil.java Normal file
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@ -0,0 +1,28 @@
package ca.uhn.fhir.jpa.config.util;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect;
import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
public final class HapiEntityManagerFactoryUtil {
private HapiEntityManagerFactoryUtil() {}
/**
* This method provides a partially completed entity manager
* factory with HAPI FHIR customizations
*/
public static LocalContainerEntityManagerFactoryBean newEntityManagerFactory(ConfigurableListableBeanFactory myConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory);
configureEntityManagerFactory(retVal, theFhirContext);
return retVal;
}
public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theFhirContext) {
theFactory.setJpaDialect(new HapiFhirHibernateJpaDialect(theFhirContext.getLocalizer()));
theFactory.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");
theFactory.setPersistenceProvider(new HibernatePersistenceProvider());
}
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/util/ResourceCountCacheUtil.java Normal file
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@ -0,0 +1,14 @@
package ca.uhn.fhir.jpa.config.util;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import org.apache.commons.lang3.time.DateUtils;
public final class ResourceCountCacheUtil {
private ResourceCountCacheUtil() {}
public static ResourceCountCache newResourceCountCache(IFhirSystemDao<?, ?> theSystemDao) {
ResourceCountCache retVal = new ResourceCountCache(() -> theSystemDao.getResourceCounts());
retVal.setCacheMillis(4 * DateUtils.MILLIS_PER_HOUR);
return retVal;
}
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/util/ValidationSupportConfigUtil.java Normal file
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@ -0,0 +1,16 @@
package ca.uhn.fhir.jpa.config.util;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChain;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
public final class ValidationSupportConfigUtil {
private ValidationSupportConfigUtil() {}
public static CachingValidationSupport newCachingValidationSupport(JpaValidationSupportChain theJpaValidationSupportChain) {
// Short timeout for code translation because TermConceptMappingSvcImpl has its own caching
CachingValidationSupport.CacheTimeouts cacheTimeouts = CachingValidationSupport.CacheTimeouts.defaultValues()
.setTranslateCodeMillis(1000);
return new CachingValidationSupport(theJpaValidationSupportChain, cacheTimeouts);
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
View File

@ -7,14 +7,13 @@ import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.ApplicationContext;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
@ -48,11 +47,11 @@ import java.util.Map;
public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends BaseHapiFhirDao<IBaseResource> implements IFhirSystemDao<T, MT> {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirSystemDao.class);
@Autowired
@Qualifier("myResourceCountsCache")
public ResourceCountCache myResourceCountsCache;
@Autowired
private TransactionProcessor myTransactionProcessor;
@Autowired
private ApplicationContext myApplicationContext;
@VisibleForTesting
public void setTransactionProcessorForUnitTest(TransactionProcessor theTransactionProcessor) {
@ -89,6 +88,10 @@ public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends B
@Nullable
@Override
public Map<String, Long> getResourceCountsFromCache() {
if (myResourceCountsCache == null) {
// Lazy load this to avoid a circular dependency
myResourceCountsCache = myApplicationContext.getBean("myResourceCountsCache", ResourceCountCache.class);
}
return myResourceCountsCache.get();
}

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
View File

@ -20,12 +20,12 @@ package ca.uhn.fhir.jpa.dao;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
@ -51,7 +51,6 @@ import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import javax.annotation.Nonnull;
import javax.annotation.PostConstruct;
@ -69,14 +68,13 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueSet>
implements IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt>, IFhirResourceDaoCodeSystem<ValueSet, CodingDt, CodeableConceptDt> {
private static FhirContext ourRiCtx;
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
@Autowired
private IValidationSupport myJpaValidationSupport;
@Autowired
@Qualifier("myFhirContextDstu2Hl7Org")
private FhirContext myRiCtx;
@Autowired
private FhirContext myFhirContext;
@ -160,7 +158,7 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
ValueSet defaultValueSet = myDefaultProfileValidationSupport.fetchResource(ValueSet.class, theUri);
if (defaultValueSet != null) {
source = getContext().newJsonParser().parseResource(ValueSet.class, myRiCtx.newJsonParser().encodeResourceToString(defaultValueSet));
source = getContext().newJsonParser().parseResource(ValueSet.class, getRiCtx().newJsonParser().encodeResourceToString(defaultValueSet));
} else {
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronousUpTo(1);
@ -195,7 +193,7 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
if (theId.getValue().startsWith("http://hl7.org/fhir/")) {
org.hl7.fhir.dstu2.model.ValueSet valueSet = myValidationSupport.fetchResource(org.hl7.fhir.dstu2.model.ValueSet.class, theId.getValue());
if (valueSet != null) {
return getContext().newJsonParser().parseResource(ValueSet.class, myRiCtx.newJsonParser().encodeResourceToString(valueSet));
return getContext().newJsonParser().parseResource(ValueSet.class, getRiCtx().newJsonParser().encodeResourceToString(valueSet));
}
}
BaseHasResource sourceEntity = readEntity(theId, theRequest);
@ -206,6 +204,13 @@ public class FhirResourceDaoValueSetDstu2 extends BaseHapiFhirResourceDao<ValueS
return source;
}
private FhirContext getRiCtx() {
if (ourRiCtx == null) {
ourRiCtx = FhirContext.forDstu2Hl7Org();
}
return ourRiCtx;
}
private IValidationSupport.LookupCodeResult lookup(List<ExpansionContains> theContains, String theSystem, String theCode) {
for (ExpansionContains nextCode : theContains) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/HistoryBuilderFactory.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.dao;
* #L%
*/
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.JpaConfig;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
@ -33,7 +33,7 @@ public class HistoryBuilderFactory {
private ApplicationContext myApplicationContext;
public HistoryBuilder newHistoryBuilder(@Nullable String theResourceType, @Nullable Long theResourceId, @Nullable Date theRangeStartInclusive, @Nullable Date theRangeEndInclusive) {
return (HistoryBuilder) myApplicationContext.getBean(BaseConfig.HISTORY_BUILDER, theResourceType, theResourceId, theRangeStartInclusive, theRangeEndInclusive);
return (HistoryBuilder) myApplicationContext.getBean(JpaConfig.HISTORY_BUILDER, theResourceType, theResourceId, theRangeStartInclusive, theRangeEndInclusive);
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilderFactory.java
View File

@ -22,7 +22,7 @@ package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.JpaConfig;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
@ -35,7 +35,7 @@ public class SearchBuilderFactory {
private DaoConfig myDaoConfig;
public ISearchBuilder newSearchBuilder(IDao theDao, String theResourceName, Class<? extends IBaseResource> theResourceType) {
return (ISearchBuilder) myApplicationContext.getBean(BaseConfig.SEARCH_BUILDER, theDao, theResourceName, theResourceType, myDaoConfig);
return (ISearchBuilder) myApplicationContext.getBean(JpaConfig.SEARCH_BUILDER, theDao, theResourceName, theResourceType, myDaoConfig);
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/ValueSetOperationProvider.java
View File

@ -28,7 +28,7 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.search.autocomplete.ValueSetAutocompleteOptions;
@ -69,7 +69,7 @@ public class ValueSetOperationProvider extends BaseJpaProvider {
@Autowired
private ITermReadSvc myTermReadSvc;
@Autowired
@Qualifier(BaseConfig.JPA_VALIDATION_SUPPORT_CHAIN)
@Qualifier(JpaConfig.JPA_VALIDATION_SUPPORT_CHAIN)
private ValidationSupportChain myValidationSupportChain;
@Autowired
private IValidationSupport myValidationSupport;

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java
View File

@ -1,11 +1,11 @@
package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
@ -53,7 +53,7 @@ import java.util.List;
public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4<CodeSystem> {
@Autowired
@Qualifier(BaseConfig.JPA_VALIDATION_SUPPORT_CHAIN)
@Qualifier(JpaConfig.JPA_VALIDATION_SUPPORT_CHAIN)
private ValidationSupportChain myValidationSupportChain;
@Autowired

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProviderFactory.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.search;
* #L%
*/
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.rest.api.server.RequestDetails;
@ -33,16 +33,16 @@ public class PersistedJpaBundleProviderFactory {
private ApplicationContext myApplicationContext;
public PersistedJpaBundleProvider newInstance(RequestDetails theRequest, String theUuid) {
Object retVal = myApplicationContext.getBean(BaseConfig.PERSISTED_JPA_BUNDLE_PROVIDER, theRequest, theUuid);
Object retVal = myApplicationContext.getBean(JpaConfig.PERSISTED_JPA_BUNDLE_PROVIDER, theRequest, theUuid);
return (PersistedJpaBundleProvider) retVal;
}
public PersistedJpaBundleProvider newInstance(RequestDetails theRequest, Search theSearch) {
Object retVal = myApplicationContext.getBean(BaseConfig.PERSISTED_JPA_BUNDLE_PROVIDER_BY_SEARCH, theRequest, theSearch);
Object retVal = myApplicationContext.getBean(JpaConfig.PERSISTED_JPA_BUNDLE_PROVIDER_BY_SEARCH, theRequest, theSearch);
return (PersistedJpaBundleProvider) retVal;
}
public PersistedJpaSearchFirstPageBundleProvider newInstanceFirstPage(RequestDetails theRequestDetails, Search theSearch, SearchCoordinatorSvcImpl.SearchTask theTask, ISearchBuilder theSearchBuilder) {
return (PersistedJpaSearchFirstPageBundleProvider) myApplicationContext.getBean(BaseConfig.PERSISTED_JPA_SEARCH_FIRST_PAGE_BUNDLE_PROVIDER, theRequestDetails, theSearch, theTask, theSearchBuilder);
return (PersistedJpaSearchFirstPageBundleProvider) myApplicationContext.getBean(JpaConfig.PERSISTED_JPA_SEARCH_FIRST_PAGE_BUNDLE_PROVIDER, theRequestDetails, theSearch, theTask, theSearchBuilder);
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu2.java
View File

@ -20,10 +20,10 @@ package ca.uhn.fhir.jpa.term;
* #L%
*/
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/BulkDataExportSvcImplR4Test.java
View File

@ -774,7 +774,7 @@ public class BulkDataExportSvcImplR4Test extends BaseJpaR4Test {
}
private <T extends IBaseResource> List<T> readBulkExportContentsIntoResources(String theContents, Class<T> theClass) {
IParser iParser = myFhirCtx.newJsonParser();
IParser iParser = myFhirContext.newJsonParser();
return Arrays.stream(theContents.split("\n"))
.map(iParser::parseResource)
.map(theClass::cast)

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/imprt/svc/BulkDataImportR4Test.java
View File

@ -203,10 +203,10 @@ public class BulkDataImportR4Test extends BaseJpaR4Test implements ITestDataBuil
StringBuilder fileContents = new StringBuilder();
for (int transactionIdx = 0; transactionIdx < transactionsPerFile; transactionIdx++) {
BundleBuilder bundleBuilder = new BundleBuilder(myFhirCtx);
BundleBuilder bundleBuilder = new BundleBuilder(myFhirContext);
IBaseResource patient = buildPatient(withFamily("FAM " + fileIndex + " " + transactionIdx), withIdentifier(null, "patient" + counter++));
bundleBuilder.addTransactionCreateEntry(patient);
fileContents.append(myFhirCtx.newJsonParser().setPrettyPrint(false).encodeResourceToString(bundleBuilder.getBundle()));
fileContents.append(myFhirContext.newJsonParser().setPrettyPrint(false).encodeResourceToString(bundleBuilder.getBundle()));
fileContents.append("\n");
}

20
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java
View File

@ -1,5 +1,8 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
@ -8,7 +11,6 @@ import ca.uhn.fhir.validation.ResultSeverityEnum;
import net.ttddyy.dsproxy.listener.ThreadQueryCountHolder;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -18,7 +20,6 @@ import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.sql.DataSource;
import java.sql.Connection;
@ -29,9 +30,13 @@ import java.util.concurrent.TimeUnit;
import static org.junit.jupiter.api.Assertions.fail;
@Configuration
@Import({TestJPAConfig.class, TestHibernateSearchAddInConfig.DefaultLuceneHeap.class})
@EnableTransactionManagement()
public class TestDstu2Config extends BaseJavaConfigDstu2 {
@Import({
JpaDstu2Config.class,
HapiJpaConfig.class,
TestJPAConfig.class,
TestHibernateSearchAddInConfig.DefaultLuceneHeap.class
})
public class TestDstu2Config {
private static final Logger ourLog = LoggerFactory.getLogger(TestDstu2Config.class);
private static int ourMaxThreads;
@ -129,10 +134,9 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
return dataSource;
}
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu2");
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());

26
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu3Config.java
View File

@ -1,5 +1,9 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.dstu3.JpaDstu3Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.EmailSenderImpl;
import ca.uhn.fhir.jpa.subscription.match.deliver.email.IEmailSender;
import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
@ -11,7 +15,7 @@ import ca.uhn.fhir.rest.server.mail.MailSvc;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
@ -21,7 +25,6 @@ import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.sql.DataSource;
import java.sql.Connection;
@ -31,9 +34,13 @@ import java.util.concurrent.TimeUnit;
import static org.junit.jupiter.api.Assertions.fail;
@Configuration
@Import({TestJPAConfig.class, TestHibernateSearchAddInConfig.DefaultLuceneHeap.class})
@EnableTransactionManagement()
public class TestDstu3Config extends BaseJavaConfigDstu3 {
@Import({
JpaDstu3Config.class,
HapiJpaConfig.class,
TestJPAConfig.class,
TestHibernateSearchAddInConfig.DefaultLuceneHeap.class
})
public class TestDstu3Config {
static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestDstu3Config.class);
private Exception myLastStackTrace;
@ -139,10 +146,9 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
return new EmailSenderImpl(mailSvc);
}
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("PU_HapiFhirJpaDstu3");
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());
@ -172,12 +178,12 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
*/
@Bean
@Lazy
public RequestValidatingInterceptor requestValidatingInterceptor() {
public RequestValidatingInterceptor requestValidatingInterceptor(FhirInstanceValidator theFhirInstanceValidator) {
RequestValidatingInterceptor requestValidator = new RequestValidatingInterceptor();
requestValidator.setFailOnSeverity(ResultSeverityEnum.ERROR);
requestValidator.setAddResponseHeaderOnSeverity(null);
requestValidator.setAddResponseOutcomeHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
requestValidator.addValidatorModule(instanceValidator());
requestValidator.addValidatorModule(theFhirInstanceValidator);
return requestValidator;
}

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestHibernateSearchAddInConfig.java
View File

@ -68,8 +68,8 @@ public class TestHibernateSearchAddInConfig {
}
@Bean(name={"searchDao", "searchDaoDstu2", "searchDaoDstu3", "searchDaoR4", "searchDaoR5"})
public IFulltextSearchSvc searchDao() {
@Bean
public IFulltextSearchSvc fullTextSearchSvc() {
ourLog.info("Hibernate Search: FulltextSearchSvcImpl present");
return new FulltextSearchSvcImpl();
}
@ -88,9 +88,9 @@ public class TestHibernateSearchAddInConfig {
};
}
@Primary // force override of default bean which might have a variety of names
@Bean(name={"searchDao", "searchDaoDstu2", "searchDaoDstu3", "searchDaoR4", "searchDaoR5"})
public IFulltextSearchSvc searchDao() {
@Primary
@Bean
public IFulltextSearchSvc fullTextSearchSvc() {
ourLog.info("Hibernate Search: FulltextSearchSvcImpl not available");
return null;
}

38
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
View File

@ -1,10 +1,10 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.batch.svc.BatchJobSubmitterImpl;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.config.r4.JpaR4Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
@ -14,7 +14,7 @@ import net.ttddyy.dsproxy.listener.SingleQueryCountHolder;
import net.ttddyy.dsproxy.listener.logging.SLF4JLogLevel;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
@ -22,7 +22,6 @@ import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.sql.DataSource;
import java.sql.Connection;
@ -32,9 +31,13 @@ import java.util.concurrent.TimeUnit;
import static org.junit.jupiter.api.Assertions.fail;
@Configuration
@Import({TestJPAConfig.class, BatchJobsConfig.class, TestHibernateSearchAddInConfig.DefaultLuceneHeap.class})
@EnableTransactionManagement()
public class TestR4Config extends BaseJavaConfigR4 {
@Import({
JpaR4Config.class,
HapiJpaConfig.class,
TestJPAConfig.class,
TestHibernateSearchAddInConfig.DefaultLuceneHeap.class
})
public class TestR4Config {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestR4Config.class);
public static Integer ourMaxThreads;
@ -60,12 +63,6 @@ public class TestR4Config extends BaseJavaConfigR4 {
private Exception myLastStackTrace;
@Override
@Bean
public IBatchJobSubmitter batchJobSubmitter() {
return new BatchJobSubmitterImpl();
}
@Bean
public CircularQueueCaptureQueriesListener captureQueriesListener() {
return new CircularQueueCaptureQueriesListener();
@ -144,14 +141,9 @@ public class TestR4Config extends BaseJavaConfigR4 {
}
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = new HapiFhirLocalContainerEntityManagerFactoryBean(theConfigurableListableBeanFactory);
configureEntityManagerFactory(retVal, fhirContext());
retVal.setJpaDialect(new HapiFhirHibernateJpaDialect(fhirContext().getLocalizer()));
retVal.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");
retVal.setPersistenceProvider(new HibernatePersistenceProvider());
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("PU_HapiFhirJpaR4");
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());
@ -180,12 +172,12 @@ public class TestR4Config extends BaseJavaConfigR4 {
*/
@Bean
@Lazy
public RequestValidatingInterceptor requestValidatingInterceptor() {
public RequestValidatingInterceptor requestValidatingInterceptor(FhirInstanceValidator theFhirInstanceValidator) {
RequestValidatingInterceptor requestValidator = new RequestValidatingInterceptor();
requestValidator.setFailOnSeverity(ResultSeverityEnum.ERROR);
requestValidator.setAddResponseHeaderOnSeverity(null);
requestValidator.setAddResponseOutcomeHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
requestValidator.addValidatorModule(instanceValidator());
requestValidator.addValidatorModule(theFhirInstanceValidator);
return requestValidator;
}

26
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR5Config.java
View File

@ -1,7 +1,11 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.config.r5.JpaR5Config;
import ca.uhn.fhir.jpa.config.util.HapiEntityManagerFactoryUtil;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import ca.uhn.fhir.jpa.util.CircularQueueCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
@ -9,7 +13,7 @@ import ca.uhn.fhir.validation.ResultSeverityEnum;
import net.ttddyy.dsproxy.listener.SingleQueryCountHolder;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource;
import ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.annotation.Bean;
@ -18,7 +22,6 @@ import org.springframework.context.annotation.Import;
import org.springframework.context.annotation.Lazy;
import org.springframework.core.env.Environment;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.sql.DataSource;
import java.sql.Connection;
@ -27,9 +30,13 @@ import java.util.Properties;
import static org.junit.jupiter.api.Assertions.fail;
@Configuration
@Import({TestJPAConfig.class, TestHibernateSearchAddInConfig.DefaultLuceneHeap.class})
@EnableTransactionManagement()
public class TestR5Config extends BaseJavaConfigR5 {
@Import({
JpaR5Config.class,
HapiJpaConfig.class,
TestJPAConfig.class,
TestHibernateSearchAddInConfig.DefaultLuceneHeap.class
})
public class TestR5Config {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestR5Config.class);
public static Integer ourMaxThreads;
@ -134,10 +141,9 @@ public class TestR5Config extends BaseJavaConfigR5 {
return new SingleQueryCountHolder();
}
@Override
@Bean
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory) {
LocalContainerEntityManagerFactoryBean retVal = super.entityManagerFactory(theConfigurableListableBeanFactory);
public LocalContainerEntityManagerFactoryBean entityManagerFactory(ConfigurableListableBeanFactory theConfigurableListableBeanFactory, FhirContext theFhirContext) {
LocalContainerEntityManagerFactoryBean retVal = HapiEntityManagerFactoryUtil.newEntityManagerFactory(theConfigurableListableBeanFactory, theFhirContext);
retVal.setPersistenceUnitName("PU_HapiFhirJpaR5");
retVal.setDataSource(dataSource());
retVal.setJpaProperties(jpaProperties());
@ -166,12 +172,12 @@ public class TestR5Config extends BaseJavaConfigR5 {
*/
@Bean
@Lazy
public RequestValidatingInterceptor requestValidatingInterceptor() {
public RequestValidatingInterceptor requestValidatingInterceptor(FhirInstanceValidator theFhirInstanceValidator) {
RequestValidatingInterceptor requestValidator = new RequestValidatingInterceptor();
requestValidator.setFailOnSeverity(ResultSeverityEnum.ERROR);
requestValidator.setAddResponseHeaderOnSeverity(null);
requestValidator.setAddResponseOutcomeHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
requestValidator.addValidatorModule(instanceValidator());
requestValidator.addValidatorModule(theFhirInstanceValidator);
return requestValidator;
}

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -10,7 +10,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceIndexedComboTokensNonUniqueDao;
@ -194,7 +194,7 @@ public abstract class BaseJpaTest extends BaseTest {
private IdHelperService myIdHelperService;
@Autowired
private MemoryCacheService myMemoryCacheService;
@Qualifier(BaseConfig.JPA_VALIDATION_SUPPORT)
@Qualifier(JpaConfig.JPA_VALIDATION_SUPPORT)
@Autowired
private IValidationSupport myJpaPersistedValidationSupport;
@Autowired
@ -305,7 +305,7 @@ public abstract class BaseJpaTest extends BaseTest {
});
}
protected abstract FhirContext getContext();
protected abstract FhirContext getFhirContext();
protected abstract PlatformTransactionManager getTxManager();
@ -458,7 +458,7 @@ public abstract class BaseJpaTest extends BaseTest {
protected List<String> toUnqualifiedIdValues(IBaseBundle theFound) {
List<String> retVal = new ArrayList<>();
List<IBaseResource> res = BundleUtil.toListOfResources(getContext(), theFound);
List<IBaseResource> res = BundleUtil.toListOfResources(getFhirContext(), theFound);
int size = res.size();
ourLog.info("Found {} results", size);
for (IBaseResource next : res) {
@ -481,7 +481,7 @@ public abstract class BaseJpaTest extends BaseTest {
protected List<String> toUnqualifiedVersionlessIdValues(IBaseBundle theFound) {
List<String> retVal = new ArrayList<>();
List<IBaseResource> res = BundleUtil.toListOfResources(getContext(), theFound);
List<IBaseResource> res = BundleUtil.toListOfResources(getFhirContext(), theFound);
int size = res.size();
ourLog.info("Found {} results", size);
for (IBaseResource next : res) {

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2SystemTest.java
View File

@ -4,8 +4,6 @@ import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.jpa.rp.dstu2.PatientResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeEach;
import javax.servlet.ServletConfig;
@ -26,7 +24,7 @@ public abstract class BaseJpaDstu2SystemTest extends BaseJpaDstu2Test {
when(mySrd.getInterceptorBroadcaster()).thenReturn(mock(IInterceptorBroadcaster.class));
if (myServer == null) {
myServer = new RestfulServer(myFhirCtx);
myServer = new RestfulServer(myFhirContext);
PatientResourceProvider patientRp = new PatientResourceProvider();
patientRp.setDao(myPatientDao);

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java
View File

@ -21,7 +21,6 @@ import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistryController;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.subscription.match.registry.SubscriptionLoader;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
@ -59,8 +58,8 @@ import ca.uhn.fhir.model.dstu2.resource.ValueSet;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.jupiter.api.AfterEach;
@ -133,8 +132,7 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
@Autowired
protected EntityManager myEntityManager;
@Autowired
@Qualifier("myFhirContextDstu2")
protected FhirContext myFhirCtx;
protected FhirContext myFhirContext;
@Autowired
@Qualifier("myImmunizationDaoDstu2")
protected IFhirResourceDao<Immunization> myImmunizationDao;
@ -248,8 +246,8 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
}
@Override
protected FhirContext getContext() {
return myFhirCtx;
public FhirContext getFhirContext() {
return myFhirContext;
}
@Override
@ -263,7 +261,7 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
fail("Unable to load resource: " + resourceName);
}
String string = IOUtils.toString(stream, StandardCharsets.UTF_8);
IParser newJsonParser = EncodingEnum.detectEncodingNoDefault(string).newParser(myFhirCtx);
IParser newJsonParser = EncodingEnum.detectEncodingNoDefault(string).newParser(myFhirContext);
return newJsonParser.parseResource(type, string);
}

47
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java
View File

@ -2,11 +2,16 @@ package ca.uhn.fhir.jpa.dao.dstu2;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.config.TestHibernateSearchAddInConfig;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.util.TestUtil;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.Include;
@ -20,7 +25,23 @@ import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu2.composite.PeriodDt;
import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu2.resource.*;
import ca.uhn.fhir.model.dstu2.resource.Appointment;
import ca.uhn.fhir.model.dstu2.resource.ConceptMap;
import ca.uhn.fhir.model.dstu2.resource.Device;
import ca.uhn.fhir.model.dstu2.resource.DiagnosticOrder;
import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
import ca.uhn.fhir.model.dstu2.resource.Encounter;
import ca.uhn.fhir.model.dstu2.resource.Immunization;
import ca.uhn.fhir.model.dstu2.resource.Location;
import ca.uhn.fhir.model.dstu2.resource.Medication;
import ca.uhn.fhir.model.dstu2.resource.MedicationOrder;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.model.dstu2.resource.Organization;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.resource.Practitioner;
import ca.uhn.fhir.model.dstu2.resource.Subscription;
import ca.uhn.fhir.model.dstu2.resource.Substance;
import ca.uhn.fhir.model.dstu2.resource.ValueSet;
import ca.uhn.fhir.model.dstu2.valueset.ContactPointSystemEnum;
import ca.uhn.fhir.model.dstu2.valueset.SubscriptionChannelTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.SubscriptionStatusEnum;
@ -34,7 +55,21 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.CompositeParam;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.NumberParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -2112,7 +2147,7 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
value = myDeviceDao.search(new SearchParameterMap());
if (value.size() > 0) {
ourLog.info("Found: " + (value.getResources(0, 1).get(0).getIdElement()));
fail(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(value.getResources(0, 1).get(0)));
fail(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(value.getResources(0, 1).get(0)));
}
assertEquals(0, value.size().intValue());

18
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
View File

@ -1510,7 +1510,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
int initial = val.size();
Organization org = myFhirCtx.newJsonParser().parseResource(Organization.class, inputStr);
Organization org = myFhirContext.newJsonParser().parseResource(Organization.class, inputStr);
myOrganizationDao.create(org, mySrd);
val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
@ -2084,7 +2084,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.info("Observation: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -2096,7 +2096,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
oid2 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.info("Observation: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -2108,7 +2108,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
oid3 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.info("Observation: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -2120,7 +2120,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
oid4 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.info("Observation: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
@ -2681,7 +2681,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
IIdType orgId = myOrganizationDao.create(org, mySrd).getId();
Organization returned = myOrganizationDao.read(orgId, mySrd);
String val = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(returned);
String val = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(returned);
ourLog.info(val);
assertThat(val, containsString("<name value=\"測試醫院\"/>"));
@ -2842,16 +2842,16 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
String stream = IOUtils.toString(getClass().getResourceAsStream("/binu_testpatient_structuredefinition_dstu2.xml"), StandardCharsets.UTF_8);
StructureDefinition sd = myFhirCtx.newXmlParser().parseResource(StructureDefinition.class, stream);
StructureDefinition sd = myFhirContext.newXmlParser().parseResource(StructureDefinition.class, stream);
myStructureDefinitionDao.create(sd, mySrd);
String rawResource = IOUtils.toString(getClass().getResourceAsStream("/binu_testpatient_resource.json"), StandardCharsets.UTF_8);
IBaseResource parsedResource = myFhirCtx.newJsonParser().parseResource(rawResource);
IBaseResource parsedResource = myFhirContext.newJsonParser().parseResource(rawResource);
try {
myPatientDao.validate((Patient) parsedResource, null, rawResource, EncodingEnum.JSON, ValidationModeEnum.UPDATE, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
}
}

22
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2ValidateTest.java
View File

@ -18,19 +18,17 @@ import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.util.Collections;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.junit.jupiter.api.Assertions.fail;
public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
@ -51,7 +49,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
String methodName = "testValidateResourceContainingProfileDeclarationJson";
OperationOutcome outcome = doTestValidateResourceContainingProfileDeclaration(methodName, EncodingEnum.JSON);
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
String ooString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(ooString);
assertThat(ooString, containsString("Observation.subject: minimum required = 1, but only found 0"));
assertThat(ooString, containsString("Observation.encounter: max allowed = 0, but found 1"));
@ -63,7 +61,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
String methodName = "testValidateResourceContainingProfileDeclarationXml";
OperationOutcome outcome = doTestValidateResourceContainingProfileDeclaration(methodName, EncodingEnum.XML);
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
String ooString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(ooString);
assertThat(ooString, containsString("Observation.subject: minimum required = 1, but only found 0"));
assertThat(ooString, containsString("Observation.encounter: max allowed = 0, but found 1"));
@ -99,7 +97,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
ValidationModeEnum mode = ValidationModeEnum.CREATE;
switch (enc) {
case JSON:
encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input);
encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(input);
ourLog.info(encoded);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
@ -109,7 +107,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
}
break;
case XML:
encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
encoded = myFhirContext.newXmlParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
fail();
@ -136,13 +134,13 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
ValidationModeEnum mode = ValidationModeEnum.CREATE;
String encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
String encoded = myFhirContext.newJsonParser().encodeResourceToString(input);
ourLog.info(encoded);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome());
String ooString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome());
ourLog.info(ooString);
assertThat(ooString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' has not been checked because it is unknown"));
}
@ -204,7 +202,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
} catch (PreconditionFailedException e) {
// should not happen
IBaseOperationOutcome oo = e.getOperationOutcome();
fail(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
fail(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
}
pat.setId("");
@ -238,7 +236,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
outcome = (OperationOutcome) e.getOperationOutcome();
}
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
String ooString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(ooString);
assertThat(ooString, containsString("Unable to delete Organization"));
@ -247,7 +245,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
myPatientDao.update(pat, mySrd);
outcome = (OperationOutcome) myOrganizationDao.validate(null, orgId, null, null, ValidationModeEnum.DELETE, null, mySrd).getOperationOutcome();
ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ooString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(ooString);
assertThat(ooString, containsString("Ok to delete"));

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java
View File

@ -157,7 +157,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
String resp;
ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null, mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
// @formatter:off
assertThat(resp,
@ -182,7 +182,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
*/
expanded = myValueSetDao.expand(myExtensionalVsId, new ValueSetExpansionOptions().setFilter("systolic"), mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off
assertThat(resp, stringContainsInOrder(
@ -195,7 +195,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
*/
expanded = myValueSetDao.expand(myExtensionalVsId, new ValueSetExpansionOptions().setFilter("11378"), mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off
assertThat(resp, stringContainsInOrder(
@ -207,7 +207,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
@Test
public void testExpandByIdentifier() {
ValueSet expanded = myValueSetDao.expandByIdentifier("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", new ValueSetExpansionOptions().setFilter("11378"));
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
String resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off
assertThat(resp, stringContainsInOrder(
@ -222,7 +222,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
public void testExpandByValueSet() throws IOException {
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-2.xml");
ValueSet expanded = myValueSetDao.expand(toExpand, new ValueSetExpansionOptions().setFilter("11378"));
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
String resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off
assertThat(resp, stringContainsInOrder(

67
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirSystemDaoDstu2Test.java
View File

@ -50,7 +50,16 @@ import java.util.ArrayList;
import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.*;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.emptyString;
import static org.hamcrest.Matchers.endsWith;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.is;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.startsWith;
import static org.junit.jupiter.api.Assertions.assertArrayEquals;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
@ -168,7 +177,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
assertEquals(2, resp.getEntry().size());
assertEquals(BundleTypeEnum.BATCH_RESPONSE, resp.getTypeElement().getValueAsEnum());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
EntryResponse respEntry;
// Bundle.entry[1] is create response
@ -200,11 +209,11 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
@Test
public void testTransactionBug638() throws Exception {
String input = loadClasspath("/bug638.xml");
Bundle request = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle request = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
Bundle resp = mySystemDao.transaction(mySrd, request);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(18, resp.getEntry().size());
}
@ -1045,11 +1054,11 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve.xml");
String bundleStr = IOUtils.toString(bundleRes);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, bundleStr);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, bundleStr);
Bundle resp = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
assertThat(resp.getEntry().get(0).getResponse().getLocation(), startsWith("Patient/a555-44-4444/_history/"));
assertThat(resp.getEntry().get(1).getResponse().getLocation(), startsWith("Patient/temp6789/_history/"));
@ -1063,8 +1072,8 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
public void testTransactionFromBundle6() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle3.xml");
String bundle = IOUtils.toString(bundleRes);
Bundle output = mySystemDao.transaction(mySrd, myFhirCtx.newXmlParser().parseResource(Bundle.class, bundle));
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
Bundle output = mySystemDao.transaction(mySrd, myFhirContext.newXmlParser().parseResource(Bundle.class, bundle));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
}
@Test
@ -1072,11 +1081,11 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/josh-bundle.json");
String bundleStr = IOUtils.toString(bundleRes);
Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, bundleStr);
Bundle bundle = myFhirContext.newJsonParser().parseResource(Bundle.class, bundleStr);
Bundle resp = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
assertEquals("201 Created", resp.getEntry().get(1).getResponse().getStatus());
@ -1137,7 +1146,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
}
private void testTransactionOrderingValidateResponse(int pass, Bundle resp) {
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(4, resp.getEntry().size());
assertEquals("200 OK", resp.getEntry().get(0).getResponse().getStatus());
if (pass == 0) {
@ -1291,7 +1300,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
Bundle resp = mySystemDao.transaction(mySrd, request);
assertEquals(2, resp.getEntry().size());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
Entry nextEntry = resp.getEntry().get(0);
assertEquals("200 OK", nextEntry.getResponse().getStatus());
@ -1435,7 +1444,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
Bundle initialBundleResponse = mySystemDao.transaction(mySrd, request);
assertEquals(1, initialBundleResponse.getEntry().size());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(initialBundleResponse));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(initialBundleResponse));
Entry initialBundleResponseEntry = initialBundleResponse.getEntry().get(0);
assertEquals("201 Created", initialBundleResponseEntry.getResponse().getStatus());
@ -1445,7 +1454,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
Bundle secondBundleResponse = mySystemDao.transaction(mySrd, request);
assertEquals(1, secondBundleResponse.getEntry().size());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(secondBundleResponse));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(secondBundleResponse));
Entry secondBundleResponseEntry = secondBundleResponse.getEntry().get(0);
assertEquals("200 OK", secondBundleResponseEntry.getResponse().getStatus());
@ -1464,7 +1473,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
Bundle initialBundleResponse = mySystemDao.transaction(mySrd, request);
assertEquals(1, initialBundleResponse.getEntry().size());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(initialBundleResponse));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(initialBundleResponse));
Entry initialBundleResponseEntry = initialBundleResponse.getEntry().get(0);
assertEquals("201 Created", initialBundleResponseEntry.getResponse().getStatus());
@ -1472,7 +1481,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
Bundle secondBundleResponse = mySystemDao.transaction(mySrd, request);
assertEquals(1, secondBundleResponse.getEntry().size());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(secondBundleResponse));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(secondBundleResponse));
Entry secondBundleResponseEntry = secondBundleResponse.getEntry().get(0);
assertEquals("200 OK", secondBundleResponseEntry.getResponse().getStatus());
@ -1591,9 +1600,9 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
"}";
//@formatter:on
Bundle inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
Bundle inputBundle = myFhirContext.newJsonParser().parseResource(Bundle.class, input);
Bundle outputBundle = mySystemDao.transaction(mySrd, inputBundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
}
@Test
@ -1657,7 +1666,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
//@formatter:on
Bundle outputBundle = mySystemDao.transaction(mySrd, inputBundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
assertEquals(3, outputBundle.getEntry().size());
IdDt id0 = new IdDt(outputBundle.getEntry().get(0).getResponse().getLocation());
@ -1680,9 +1689,9 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
// First bundle (name is Joshua)
String input = IOUtils.toString(getClass().getResource("/dstu3-post1.xml"), StandardCharsets.UTF_8);
Bundle request = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle request = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
Bundle response = mySystemDao.transaction(mySrd, request);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
assertEquals(1, response.getEntry().size());
assertEquals("201 Created", response.getEntry().get(0).getResponse().getStatus());
@ -1692,9 +1701,9 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
// Now the second (name is Adam, shouldn't get used)
input = IOUtils.toString(getClass().getResource("/dstu3-post2.xml"), StandardCharsets.UTF_8);
request = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
request = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
response = mySystemDao.transaction(mySrd, request);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
assertEquals(1, response.getEntry().size());
assertEquals("200 OK", response.getEntry().get(0).getResponse().getStatus());
@ -1703,7 +1712,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
assertEquals(id, id2);
Patient patient = myPatientDao.read(new IdType(id), mySrd);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals("Joshua", patient.getNameFirstRep().getGivenAsSingleString());
}
@ -1722,10 +1731,10 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
mo.setMedication(new ResourceReferenceDt(medId));
bundle.addEntry().setResource(mo).setFullUrl(mo.getId().getValue()).getRequest().setMethod(HTTPVerbEnum.POST);
ourLog.info("Request:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
ourLog.info("Request:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
Bundle outcome = mySystemDao.transaction(mySrd, bundle);
ourLog.info("Response:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
ourLog.info("Response:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
IdDt medId1 = new IdDt(outcome.getEntry().get(0).getResponse().getLocation());
IdDt medOrderId1 = new IdDt(outcome.getEntry().get(1).getResponse().getLocation());
@ -1782,7 +1791,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
Bundle resp = mySystemDao.transaction(mySrd, res);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(BundleTypeEnum.TRANSACTION_RESPONSE, resp.getTypeElement().getValueAsEnum());
assertEquals(3, resp.getEntry().size());
@ -1823,7 +1832,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
Bundle resp = mySystemDao.transaction(mySrd, res);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(BundleTypeEnum.TRANSACTION_RESPONSE, resp.getTypeElement().getValueAsEnum());
assertEquals(3, resp.getEntry().size());
@ -1973,7 +1982,7 @@ public class FhirSystemDaoDstu2Test extends BaseJpaDstu2SystemTest {
drEntry.setResource(dr).setFullUrl(dr.getId()).getRequest().setUrl("DiagnosticReport").setMethod(HTTPVerbEnum.POST);
transactionBundle.addEntry(drEntry);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(transactionBundle));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(transactionBundle));
Bundle transactionResp = mySystemDao.transaction(mySrd, transactionBundle);

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3SystemTest.java
View File

@ -25,7 +25,7 @@ public abstract class BaseJpaDstu3SystemTest extends BaseJpaDstu3Test {
when(mySrd.getInterceptorBroadcaster()).thenReturn(mock(IInterceptorBroadcaster.class));
if (myServer == null) {
myServer = new RestfulServer(myFhirCtx);
myServer = new RestfulServer(myFhirContext);
PatientResourceProvider patientRp = new PatientResourceProvider();
patientRp.setDao(myPatientDao);

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -105,7 +105,6 @@ import org.hl7.fhir.dstu3.model.Task;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.extension.ExtendWith;
@ -196,11 +195,10 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Autowired
@Qualifier("myEncounterDaoDstu3")
protected IFhirResourceDao<Encounter> myEncounterDao;
// @PersistenceContext()
@Autowired
protected EntityManager myEntityManager;
@Autowired
protected FhirContext myFhirCtx;
protected FhirContext myFhirContext;
@Autowired
@Qualifier("myGroupDaoDstu3")
protected IFhirResourceDao<Group> myGroupDao;
@ -395,12 +393,12 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@BeforeEach
public void beforeResetConfig() {
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
myFhirContext.setParserErrorHandler(new StrictErrorHandler());
}
@Override
protected FhirContext getContext() {
return myFhirCtx;
public FhirContext getFhirContext() {
return myFhirContext;
}
@Override
@ -414,7 +412,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
fail("Unable to load resource: " + resourceName);
}
String string = IOUtils.toString(stream, StandardCharsets.UTF_8);
IParser newJsonParser = EncodingEnum.detectEncodingNoDefault(string).newParser(myFhirCtx);
IParser newJsonParser = EncodingEnum.detectEncodingNoDefault(string).newParser(myFhirContext);
return newJsonParser.parseResource(type, string);
}

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCustomTypeDstu3Test.java
View File

@ -4,9 +4,9 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ -17,7 +17,7 @@ public class FhirResourceDaoCustomTypeDstu3Test extends BaseJpaDstu3Test {
@BeforeEach
public void before() {
myFhirCtx.setDefaultTypeForProfile(CustomObservationDstu3.PROFILE, CustomObservationDstu3.class);
myFhirContext.setDefaultTypeForProfile(CustomObservationDstu3.PROFILE, CustomObservationDstu3.class);
}
@Test
@ -39,6 +39,6 @@ public class FhirResourceDaoCustomTypeDstu3Test extends BaseJpaDstu3Test {
@AfterEach
public void after() {
myFhirCtx.setDefaultTypeForProfile(CustomObservationDstu3.PROFILE, null);
myFhirContext.setDefaultTypeForProfile(CustomObservationDstu3.PROFILE, null);
}
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDocumentDstu3Test.java
View File

@ -1,10 +1,8 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.Bundle;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import java.nio.charset.StandardCharsets;
@ -16,7 +14,7 @@ public class FhirResourceDaoDocumentDstu3Test extends BaseJpaDstu3Test {
@Test
public void testPostDocument() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/sample-document.xml"), StandardCharsets.UTF_8);
Bundle inputBundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle inputBundle = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
DaoMethodOutcome responseBundle = myBundleDao.create(inputBundle, mySrd);
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java
View File

@ -34,7 +34,7 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
String input = IOUtils.toString(getClass().getResource("/dstu3_codesystem_complete.json"), StandardCharsets.UTF_8);
CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);
CodeSystem cs = myFhirContext.newJsonParser().parseResource(CodeSystem.class, input);
myCodeSystemDao.create(cs, mySrd);

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ConceptMapTest.java
View File

@ -1,8 +1,8 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.context.support.TranslateConceptResult;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.context.support.TranslateConceptResults;
import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.entity.TermConceptMap;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
@ -62,7 +62,7 @@ public class FhirResourceDaoDstu3ConceptMapTest extends BaseJpaDstu3Test {
public void testTranslateByCodeSystemsAndSourceCodeOneToMany() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ContainedTest.java
View File

@ -36,7 +36,7 @@ public class FhirResourceDaoDstu3ContainedTest extends BaseJpaDstu3Test {
p2.addName().setFamily("MYFAMILY").addGiven("MYGIVEN");
IIdType pid2 = myPatientDao.create(p2, mySrd).getId().toUnqualifiedVersionless();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(o2));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(o2));
SearchParameterMap map = new SearchParameterMap();

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3PhoneticSearchNoFtTest.java
View File

@ -96,7 +96,7 @@ public class FhirResourceDaoDstu3PhoneticSearchNoFtTest extends BaseJpaDstu3Test
patient.addName().addGiven(GALE);
patient.addAddress().addLine(ADDRESS);
patient.addTelecom().setValue(PHONE);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
IIdType pId = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
@ -150,7 +150,7 @@ public class FhirResourceDaoDstu3PhoneticSearchNoFtTest extends BaseJpaDstu3Test
searchParameter.addExtension()
.setUrl(HapiExtensions.EXT_SEARCHPARAM_PHONETIC_ENCODER)
.setValue(new StringType(theEncoder.name()));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(searchParameter));
mySearchParameterDao.create(searchParameter, mySrd).getId().toUnqualifiedVersionless();
}

31
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchCustomSearchParamTest.java
View File

@ -14,13 +14,34 @@ import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Appointment;
import org.hl7.fhir.dstu3.model.Appointment.AppointmentStatus;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Communication;
import org.hl7.fhir.dstu3.model.Condition;
import org.hl7.fhir.dstu3.model.DateTimeType;
import org.hl7.fhir.dstu3.model.DateType;
import org.hl7.fhir.dstu3.model.DecimalType;
import org.hl7.fhir.dstu3.model.Enumerations;
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Medication;
import org.hl7.fhir.dstu3.model.MedicationAdministration;
import org.hl7.fhir.dstu3.model.MedicationRequest;
import org.hl7.fhir.dstu3.model.MedicationStatement;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Practitioner;
import org.hl7.fhir.dstu3.model.ProcedureRequest;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.dstu3.model.SearchParameter;
import org.hl7.fhir.dstu3.model.Specimen;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
@ -158,7 +179,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
pract.addName().setFamily("PRACT");
myPractitionerDao.update(pract);
Patient pat = myFhirCtx.newJsonParser().parseResource(Patient.class, loadClasspath("/dstu3_custom_resource_patient.json"));
Patient pat = myFhirContext.newJsonParser().parseResource(Patient.class, loadClasspath("/dstu3_custom_resource_patient.json"));
IIdType pid = myPatientDao.create(pat, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap params = new SearchParameterMap();
@ -928,7 +949,7 @@ public class FhirResourceDaoDstu3SearchCustomSearchParamTest extends BaseJpaDstu
sp.setExpression("Observation.specimen.resolve().receivedTime");
sp.setXpathUsage(SearchParameter.XPathUsageType.NORMAL);
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(sp));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(sp));
mySearchParameterDao.create(sp);
mySearchParamRegistry.forceRefresh();

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchDistanceTest.java
View File

@ -40,7 +40,7 @@ public class FhirResourceDaoDstu3SearchDistanceTest extends BaseJpaDstu3Test {
SearchParameterMap map = myMatchUrlService.translateMatchUrl(
"Location?" +
Location.SP_NEAR + "=" + latitude + ":" + longitude,
myFhirCtx.getResourceDefinition("Location"));
myFhirContext.getResourceDefinition("Location"));
List<String> ids = toUnqualifiedVersionlessIdValues(myLocationDao.search(map));
assertThat(ids, contains(locId));
@ -60,7 +60,7 @@ public class FhirResourceDaoDstu3SearchDistanceTest extends BaseJpaDstu3Test {
Location.SP_NEAR + "=" + latitude + ":" + longitude +
"&" +
Location.SP_NEAR_DISTANCE + "=0||",
myFhirCtx.getResourceDefinition("Location"));
myFhirContext.getResourceDefinition("Location"));
List<String> ids = toUnqualifiedVersionlessIdValues(myLocationDao.search(map));
assertThat(ids, contains(locId));
@ -81,7 +81,7 @@ public class FhirResourceDaoDstu3SearchDistanceTest extends BaseJpaDstu3Test {
"Location?" +
Location.SP_NEAR + "=" + CoordCalculatorTest.LATITUDE_CHIN + ":" + CoordCalculatorTest.LONGITUDE_CHIN +
"&" +
Location.SP_NEAR_DISTANCE + "=" + bigEnoughDistance + "|http://unitsofmeasure.org|km", myFhirCtx.getResourceDefinition("Location"));
Location.SP_NEAR_DISTANCE + "=" + bigEnoughDistance + "|http://unitsofmeasure.org|km", myFhirContext.getResourceDefinition("Location"));
List<String> ids = toUnqualifiedVersionlessIdValues(myLocationDao.search(map));
assertThat(ids, contains(locId));
@ -93,7 +93,7 @@ public class FhirResourceDaoDstu3SearchDistanceTest extends BaseJpaDstu3Test {
"Location?" +
Location.SP_NEAR + "=" + CoordCalculatorTest.LATITUDE_CHIN + ":" + CoordCalculatorTest.LONGITUDE_CHIN +
"&" +
Location.SP_NEAR_DISTANCE + "=" + tooSmallDistance + "|http://unitsofmeasure.org|km", myFhirCtx.getResourceDefinition("Location"));
Location.SP_NEAR_DISTANCE + "=" + tooSmallDistance + "|http://unitsofmeasure.org|km", myFhirContext.getResourceDefinition("Location"));
List<String> ids = toUnqualifiedVersionlessIdValues(myLocationDao.search(map));
assertThat(ids.size(), is(0));

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java
View File

@ -261,10 +261,10 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
*/
@Test
public void testEverythingWithLargeSet() throws Exception {
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
myFhirContext.setParserErrorHandler(new StrictErrorHandler());
String inputString = IOUtils.toString(getClass().getResourceAsStream("/david_big_bundle.json"), StandardCharsets.UTF_8);
Bundle inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, inputString);
Bundle inputBundle = myFhirContext.newJsonParser().parseResource(Bundle.class, inputString);
inputBundle.setType(BundleType.TRANSACTION);
Set<String> allIds = new TreeSet<>();
@ -329,7 +329,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
map.setLoadSynchronous(true);
ReferenceParam referenceParam = new ReferenceParam();
referenceParam.setValueAsQueryToken(myFhirCtx, "subject", "._has:Group:member:_id", "Group/G");
referenceParam.setValueAsQueryToken(myFhirContext, "subject", "._has:Group:member:_id", "Group/G");
map.add("subject", referenceParam);
List<String> actual = toUnqualifiedVersionlessIdValues(myDiagnosticReportDao.search(map));
assertThat(actual, containsInAnyOrder("DiagnosticReport/DR"));
@ -671,7 +671,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
public void testIndexWithUtf8Chars() throws IOException {
String input = IOUtils.toString(getClass().getResourceAsStream("/bug454_utf8.json"), StandardCharsets.UTF_8);
CodeSystem cs = (CodeSystem) myFhirCtx.newJsonParser().parseResource(input);
CodeSystem cs = (CodeSystem) myFhirContext.newJsonParser().parseResource(input);
myCodeSystemDao.create(cs);
}
@ -2920,7 +2920,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
value = myDeviceDao.search(new SearchParameterMap());
if (value.size() > 0) {
ourLog.info("Found: " + (value.getResources(0, 1).get(0).getIdElement()));
fail(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(value.getResources(0, 1).get(0)));
fail(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(value.getResources(0, 1).get(0)));
}
assertEquals(0, value.size().intValue());
@ -3252,7 +3252,7 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
@Test
public void testSearchWithUriParamBelow() throws Exception {
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
myFhirContext.setParserErrorHandler(new StrictErrorHandler());
Class<ValueSet> type = ValueSet.class;
String resourceName = "/valueset-dstu2.json";

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3StructureDefinitionTest.java
View File

@ -1,8 +1,6 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Test;
@ -24,7 +22,7 @@ public class FhirResourceDaoDstu3StructureDefinitionTest extends BaseJpaDstu3Tes
assertEquals(0, sd.getSnapshot().getElement().size());
StructureDefinition output = myStructureDefinitionDao.generateSnapshot(sd, "http://foo", null, "THE BEST PROFILE");
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(output));
assertEquals(54, output.getSnapshot().getElement().size());
}

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -221,11 +221,11 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
private void logAndValidateValueSet(ValueSet theResult) {
IParser parser = myFhirCtx.newXmlParser().setPrettyPrint(true);
IParser parser = myFhirContext.newXmlParser().setPrettyPrint(true);
String encoded = parser.encodeResourceToString(theResult);
ourLog.info(encoded);
FhirValidator validator = myFhirCtx.newValidator();
FhirValidator validator = myFhirContext.newValidator();
validator.setValidateAgainstStandardSchema(true);
validator.setValidateAgainstStandardSchematron(true);
ValidationResult result = validator.validateWithResult(theResult);
@ -332,7 +332,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
ValueSet result = myValueSetDao.expandByIdentifier("http://hl7.org/fhir/ValueSet/doc-typecodes", new ValueSetExpansionOptions().setFilter(""));
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(result));
}
@ -673,7 +673,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
assertEquals(4, result.getExpansion().getContains().size());
String encoded = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result);
String encoded = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(result);
assertThat(encoded, containsStringIgnoringCase("<code value=\"childAAB\"/>"));
}

21
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
View File

@ -32,7 +32,6 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.RandomStringUtils;
@ -100,6 +99,7 @@ import java.util.List;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
@ -114,7 +114,6 @@ import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ -464,11 +463,11 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
String vsContents;
vsContents = IOUtils.toString(FhirResourceDaoDstu3Test.class.getResourceAsStream("/org/hl7/fhir/dstu3/model/profile/" + name + ".xml"), StandardCharsets.UTF_8);
bundle = myFhirCtx.newXmlParser().parseResource(org.hl7.fhir.dstu3.model.Bundle.class, vsContents);
bundle = myFhirContext.newXmlParser().parseResource(org.hl7.fhir.dstu3.model.Bundle.class, vsContents);
for (BundleEntryComponent i : bundle.getEntry()) {
org.hl7.fhir.dstu3.model.Resource next = i.getResource();
ourLog.debug(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(next));
ourLog.debug(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(next));
if (next instanceof StructureDefinition) {
myStructureDefinitionDao.update((StructureDefinition) next, mySrd);
} else if (next instanceof CompartmentDefinition) {
@ -617,7 +616,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
" </NamingSystem>";
//@formatter:on
NamingSystem res = myFhirCtx.newXmlParser().parseResource(NamingSystem.class, input);
NamingSystem res = myFhirContext.newXmlParser().parseResource(NamingSystem.class, input);
IIdType id = myNamingSystemDao.create(res, mySrd).getId().toUnqualifiedVersionless();
assertThat(toUnqualifiedVersionlessIdValues(myNamingSystemDao.search(new SearchParameterMap(NamingSystem.SP_NAME, new StringParam("NDF")).setLoadSynchronous(true))), org.hamcrest.Matchers.contains(id.getValue()));
@ -1918,7 +1917,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
Set<ResourcePersistentId> val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
int initial = val.size();
Organization org = myFhirCtx.newJsonParser().parseResource(Organization.class, inputStr);
Organization org = myFhirContext.newJsonParser().parseResource(Organization.class, inputStr);
myOrganizationDao.create(org, mySrd);
val = myOrganizationDao.searchForIds(new SearchParameterMap("name", new StringParam("P")), null);
@ -2555,7 +2554,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
oid1 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.info("Observation: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -2567,7 +2566,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
oid2 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.info("Observation: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -2579,7 +2578,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
oid3 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.info("Observation: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
{
@ -2591,7 +2590,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
oid4 = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
ourLog.info("Observation: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
}
@ -3150,7 +3149,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
IIdType orgId = myOrganizationDao.create(org, mySrd).getId();
Organization returned = myOrganizationDao.read(orgId, mySrd);
String val = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(returned);
String val = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(returned);
ourLog.info(val);
assertThat(val, containsString("<name value=\"測試醫院\"/>"));

80
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
View File

@ -1,9 +1,8 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.JpaConfig;
import ca.uhn.fhir.jpa.dao.JpaPersistedResourceValidationSupport;
import ca.uhn.fhir.jpa.util.TestUtil;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
@ -16,14 +15,27 @@ import ca.uhn.fhir.validation.IValidatorModule;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.common.hapi.validation.support.CachingValidationSupport;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Narrative;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.OperationOutcome;
import org.hl7.fhir.dstu3.model.Organization;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Questionnaire;
import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
@ -34,9 +46,9 @@ import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.jupiter.api.Assertions.fail;
public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
@ -48,7 +60,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
@Autowired
private FhirInstanceValidator myFhirInstanceValidator;
@Autowired
@Qualifier(BaseConfig.JPA_VALIDATION_SUPPORT)
@Qualifier(JpaConfig.JPA_VALIDATION_SUPPORT)
private IValidationSupport myPersistedResourceValidationSupport;
@Test
@ -65,9 +77,9 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
qr.addItem().setLinkId("A").addAnswer().setValue(new StringType("AAA"));
MethodOutcome results = myQuestionnaireResponseDao.validate(qr, null, null, null, null, null, null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(results.getOperationOutcome()));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(results.getOperationOutcome()));
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
fail(e.toString());
}
@ -83,7 +95,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
qr.addItem().setLinkId("A").addAnswer().setValue(new StringType("AAA"));
MethodOutcome results = myQuestionnaireResponseDao.validate(qr, null, null, null, null, null, null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(results.getOperationOutcome()));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(results.getOperationOutcome()));
ourLog.info("Clearing cache");
myValidationSupport.invalidateCaches();
@ -94,7 +106,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
myQuestionnaireResponseDao.validate(qr, null, null, null, null, null, null);
fail();
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
// good
}
@ -110,7 +122,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
myValueSetDao.create(vs);
ValueSet expansion = myValueSetDao.expandByIdentifier("http://ccim.on.ca/fhir/iar/ValueSet/iar-citizenship-status", null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
assertThat(expansion.getExpansion().getContains().stream().map(t->t.getCode()).collect(Collectors.toList()), containsInAnyOrder(
"CDN", "PR", "TR", "REF", "UNK", "ASKU"
@ -163,25 +175,25 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
try {
MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
fail();
} catch (PreconditionFailedException e) {
OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
String encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
ourLog.info(encoded);
assertThat(encoded, containsString("is not in the options value set"));
}
// Validate as string
try {
String raw = myFhirCtx.newJsonParser().encodeResourceToString(qr);
String raw = myFhirContext.newJsonParser().encodeResourceToString(qr);
MethodOutcome outcome = myQuestionnaireResponseDao.validate(qr, null, raw, EncodingEnum.JSON, ValidationModeEnum.CREATE, null, mySrd);
OperationOutcome oo = (OperationOutcome) outcome.getOperationOutcome();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
fail();
} catch (PreconditionFailedException e) {
OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
String encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
ourLog.info(encoded);
assertThat(encoded, containsString("is not in the options value set"));
}
@ -192,14 +204,14 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
@Test
public void testValidateStructureDefinition() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/sd-david-dhtest7.json"), StandardCharsets.UTF_8);
StructureDefinition sd = myFhirCtx.newJsonParser().parseResource(StructureDefinition.class, input);
StructureDefinition sd = myFhirContext.newJsonParser().parseResource(StructureDefinition.class, input);
ourLog.info("Starting validation");
try {
myStructureDefinitionDao.validate(sd, null, null, null, ValidationModeEnum.UPDATE, null, mySrd);
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
}
ourLog.info("Done validation");
@ -217,14 +229,14 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
@Test
public void testValidateDocument() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/document-bundle-dstu3.json"), StandardCharsets.UTF_8);
Bundle document = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
Bundle document = myFhirContext.newJsonParser().parseResource(Bundle.class, input);
ourLog.info("Starting validation");
try {
MethodOutcome outcome = myBundleDao.validate(document, null, null, null, ValidationModeEnum.CREATE, null, mySrd);
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
}
ourLog.info("Done validation");
@ -237,7 +249,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
String methodName = "testValidateResourceContainingProfileDeclarationJson";
OperationOutcome outcome = doTestValidateResourceContainingProfileDeclaration(methodName, EncodingEnum.JSON);
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
String ooString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(ooString);
assertThat(ooString, containsString("Element '.subject': minimum required = 1, but only found 0"));
assertThat(ooString, containsString("Element encounter @ : max allowed = 0, but found 1"));
@ -250,7 +262,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
String methodName = "testValidateResourceContainingProfileDeclarationXml";
OperationOutcome outcome = doTestValidateResourceContainingProfileDeclaration(methodName, EncodingEnum.XML);
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
String ooString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(ooString);
assertThat(ooString, containsString("Element '/f:Observation.subject': minimum required = 1, but only found 0"));
assertThat(ooString, containsString("Element encounter @ /f:Observation: max allowed = 0, but found 1"));
@ -287,7 +299,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
ValidationModeEnum mode = ValidationModeEnum.CREATE;
switch (enc) {
case JSON:
encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
encoded = myFhirContext.newJsonParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
fail();
@ -296,7 +308,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
}
break;
case XML:
encoded = myFhirCtx.newXmlParser().encodeResourceToString(input);
encoded = myFhirContext.newXmlParser().encodeResourceToString(input);
try {
myObservationDao.validate(input, null, encoded, EncodingEnum.XML, mode, null, mySrd);
fail();
@ -323,15 +335,15 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
ValidationModeEnum mode = ValidationModeEnum.CREATE;
String encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
String encoded = myFhirContext.newJsonParser().encodeResourceToString(input);
try {
// Expected to throw exception
MethodOutcome output = myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(output.getOperationOutcome()));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(output.getOperationOutcome()));
fail();
} catch (PreconditionFailedException e) {
OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
String outputString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
ourLog.info(outputString);
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' has not been checked because it is unknown"));
}
@ -421,7 +433,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
outcome = (OperationOutcome) e.getOperationOutcome();
}
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
String ooString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(ooString);
assertThat(ooString, containsString("Unable to delete Organization"));
@ -430,7 +442,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
myPatientDao.update(pat, mySrd);
outcome = (OperationOutcome) myOrganizationDao.validate(null, orgId, null, null, ValidationModeEnum.DELETE, null, mySrd).getOperationOutcome();
ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ooString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome);
ourLog.info(ooString);
assertThat(ooString, containsString("Ok to delete"));
@ -460,10 +472,10 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
try {
MethodOutcome results = myQuestionnaireDao.validate(null, null, input, EncodingEnum.XML, ValidationModeEnum.UPDATE, null, mySrd);
OperationOutcome oo = (OperationOutcome) results.getOperationOutcome();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
} catch (PreconditionFailedException e) {
// this is a failure of the test
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
throw e;
}
}
@ -479,16 +491,16 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
p.getMeta().addProfile("http://hl7.org/fhir/StructureDefinition/MyPatient421");
p.setActive(true);
String raw = myFhirCtx.newJsonParser().encodeResourceToString(p);
String raw = myFhirContext.newJsonParser().encodeResourceToString(p);
try {
MethodOutcome outcome = myPatientDao.validate(p, null, raw, EncodingEnum.JSON, null, null, mySrd);
String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome());
String encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome());
ourLog.info("OO: {}", encoded);
assertThat(encoded, containsString("No issues detected"));
} catch (PreconditionFailedException e) {
// not expected, but let's log the error
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
fail(e.toString());
}
}

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValueSetTest.java
View File

@ -128,7 +128,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
assertEquals("http://hl7.org/fhir/ValueSet/endpoint-payload-type", vs.getUrl());
ValueSet expansion = myValueSetDao.expand(vs.getIdElement(), null, mySrd);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expansion));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(expansion));
}
@Test
@ -136,7 +136,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
String resp;
ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null, mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
assertThat(resp, containsString("<expansion>"));
@ -157,7 +157,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
*/
expanded = myValueSetDao.expand(myExtensionalVsId, new ValueSetExpansionOptions().setFilter("systolic"), mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off
assertThat(resp, stringContainsInOrder(
@ -171,7 +171,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
@Disabled
public void testExpandByIdentifier() {
ValueSet expanded = myValueSetDao.expandByIdentifier("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", new ValueSetExpansionOptions().setFilter("11378"));
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
String resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off
assertThat(resp, stringContainsInOrder(
@ -190,7 +190,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
public void testExpandByValueSet() throws IOException {
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-3-vs.xml");
ValueSet expanded = myValueSetDao.expand(toExpand, new ValueSetExpansionOptions().setFilter("11378"));
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
String resp = myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off
assertThat(resp, stringContainsInOrder(

124
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSystemDaoDstu3Test.java
View File

@ -241,16 +241,16 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
private Bundle loadBundle(String theFileName) throws IOException {
String req = IOUtils.toString(FhirSystemDaoDstu3Test.class.getResourceAsStream(theFileName), StandardCharsets.UTF_8);
return myFhirCtx.newXmlParser().parseResource(Bundle.class, req);
return myFhirContext.newXmlParser().parseResource(Bundle.class, req);
}
@Test
public void testTransactionWithDuplicateConditionalCreates2() throws IOException {
Bundle request = myFhirCtx.newJsonParser().parseResource(Bundle.class, IOUtils.toString(FhirSystemDaoR4.class.getResourceAsStream("/dstu3/duplicate-conditional-create.json"), Constants.CHARSET_UTF8));
Bundle request = myFhirContext.newJsonParser().parseResource(Bundle.class, IOUtils.toString(FhirSystemDaoR4.class.getResourceAsStream("/dstu3/duplicate-conditional-create.json"), Constants.CHARSET_UTF8));
Bundle response = mySystemDao.transaction(null, request);
ourLog.info("Response:\n{}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(response));
ourLog.info("Response:\n{}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(response));
List<String> responseTypes = response
.getEntry()
@ -289,7 +289,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
assertEquals("404 Not Found", response.getEntry().get(1).getResponse().getStatus());
OperationOutcome oo = (OperationOutcome) response.getEntry().get(1).getResponse().getOutcome();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals(IssueSeverity.ERROR, oo.getIssue().get(0).getSeverity());
assertEquals(Msg.code(2001) + "Resource Patient/BABABABA is not known", oo.getIssue().get(0).getDiagnostics());
}
@ -323,7 +323,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
assertEquals("400 Bad Request", response.getEntry().get(1).getResponse().getStatus());
OperationOutcome oo = (OperationOutcome) response.getEntry().get(1).getResponse().getOutcome();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals(IssueSeverity.ERROR, oo.getIssue().get(0).getSeverity());
assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("Unknown search parameter"));
}
@ -362,7 +362,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
.getRequest().setMethod(HTTPVerb.POST);
Bundle resp = mySystemDao.transaction(mySrd, inputBundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
IdType epId = new IdType(resp.getEntry().get(0).getResponse().getLocation());
IdType condId = new IdType(resp.getEntry().get(1).getResponse().getLocation());
@ -394,9 +394,9 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
.getRequest().setMethod(HTTPVerb.DELETE)
.setUrl(condId.toUnqualifiedVersionless().getValue());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(inputBundle));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(inputBundle));
resp = mySystemDao.transaction(mySrd, inputBundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
// They should now be deleted
try {
@ -414,11 +414,11 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
public void testProcessCollectionAsBatch() throws IOException {
byte[] inputBytes = IOUtils.toByteArray(getClass().getResourceAsStream("/dstu3/Reilly_Libby_73.json.gz"));
String input = GZipUtil.decompress(inputBytes);
Bundle bundle = myFhirCtx.newJsonParser().setParserErrorHandler(new LenientErrorHandler()).parseResource(Bundle.class, input);
Bundle bundle = myFhirContext.newJsonParser().setParserErrorHandler(new LenientErrorHandler()).parseResource(Bundle.class, input);
ourLog.info("Bundle has {} resources", bundle);
Bundle output = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
}
@ -428,14 +428,14 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
@Test
public void testContainedArePreservedForBug410() throws IOException {
String input = IOUtils.toString(getClass().getResourceAsStream("/bug-410-bundle.xml"), StandardCharsets.UTF_8);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
Bundle output = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
IdType id = new IdType(output.getEntry().get(1).getResponse().getLocation());
MedicationRequest mo = myMedicationRequestDao.read(id);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(mo));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(mo));
}
@Test
@ -547,7 +547,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
@Test
public void testStructureDefinitionInBundle() throws IOException {
String input = IOUtils.toString(FhirSystemDaoDstu3Test.class.getResourceAsStream("/bug1044-bundle.xml"), Charsets.UTF_8);
Bundle inputBundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle inputBundle = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
mySystemDao.transaction(mySrd, inputBundle);
}
@ -630,10 +630,10 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
@Test
public void testTransaction1() throws IOException {
String inputBundleString = loadClasspath("/david-bundle-error.json");
Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, inputBundleString);
Bundle bundle = myFhirContext.newJsonParser().parseResource(Bundle.class, inputBundleString);
Bundle resp = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
}
@ -654,7 +654,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
assertEquals(2, resp.getEntry().size());
assertEquals(BundleType.BATCHRESPONSE, resp.getTypeElement().getValue());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
BundleEntryResponseComponent respEntry;
// Bundle.entry[0] is create response
@ -974,7 +974,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
assertEquals("404 Not Found", response.getEntry().get(1).getResponse().getStatus());
OperationOutcome oo = (OperationOutcome) response.getEntry().get(1).getResponse().getOutcome();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals(IssueSeverity.ERROR, oo.getIssue().get(0).getSeverity());
assertEquals(Msg.code(2001) + "Resource Patient/BABABABA is not known", oo.getIssue().get(0).getDiagnostics());
}
@ -1008,7 +1008,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
assertEquals("400 Bad Request", response.getEntry().get(1).getResponse().getStatus());
OperationOutcome oo = (OperationOutcome) response.getEntry().get(1).getResponse().getOutcome();
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(oo));
assertEquals(IssueSeverity.ERROR, oo.getIssue().get(0).getSeverity());
assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("Unknown search parameter"));
}
@ -1424,12 +1424,12 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
fail(e.toString());
return;
}
Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
Bundle bundle = myFhirContext.newJsonParser().parseResource(Bundle.class, input);
mySystemDao.transaction(mySrd, bundle);
IBundleProvider history = mySystemDao.history(null, null, null, null);
Bundle list = toBundle(history);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(list));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(list));
assertEquals(6, list.getEntry().size());
@ -1671,11 +1671,11 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/transaction_link_patient_eve.xml");
String bundleStr = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, bundleStr);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, bundleStr);
Bundle resp = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
assertThat(resp.getEntry().get(0).getResponse().getLocation(), startsWith("Patient/a555-44-4444/_history/"));
assertThat(resp.getEntry().get(1).getResponse().getLocation(), startsWith("Patient/temp6789/_history/"));
@ -1688,10 +1688,10 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
@Test
public void testTransactionFromBundle2() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/transaction-bundle.xml"), StandardCharsets.UTF_8);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
Bundle response = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
assertEquals("201 Created", response.getEntry().get(0).getResponse().getStatus());
assertThat(response.getEntry().get(0).getResponse().getLocation(), matchesPattern("Practitioner/[0-9]+/_history/1"));
@ -1699,10 +1699,10 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
* Now a second time
*/
bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
response = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
assertEquals("200 OK", response.getEntry().get(0).getResponse().getStatus());
assertThat(response.getEntry().get(0).getResponse().getLocation(), matchesPattern("Practitioner/[0-9]+/_history/1"));
@ -1712,8 +1712,8 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
public void testTransactionFromBundle6() throws Exception {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/simone_bundle3.xml");
String bundle = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
Bundle output = mySystemDao.transaction(mySrd, myFhirCtx.newXmlParser().parseResource(Bundle.class, bundle));
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
Bundle output = mySystemDao.transaction(mySrd, myFhirContext.newXmlParser().parseResource(Bundle.class, bundle));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
}
@Test
@ -1721,11 +1721,11 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/josh-bundle.json");
String bundleStr = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
Bundle bundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, bundleStr);
Bundle bundle = myFhirContext.newJsonParser().parseResource(Bundle.class, bundleStr);
Bundle resp = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
assertEquals("201 Created", resp.getEntry().get(1).getResponse().getStatus());
@ -1759,7 +1759,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
params.put(Constants.PARAMETER_CASCADE_DELETE, new String[]{Constants.CASCADE_DELETE});
mySrd.setParameters(params);
CascadingDeleteInterceptor deleteInterceptor = new CascadingDeleteInterceptor(myFhirCtx, myDaoRegistry, myInterceptorBroadcaster);
CascadingDeleteInterceptor deleteInterceptor = new CascadingDeleteInterceptor(myFhirContext, myDaoRegistry, myInterceptorBroadcaster);
myInterceptorBroadcaster.registerInterceptor(deleteInterceptor);
@ -1822,7 +1822,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
}
private void testTransactionOrderingValidateResponse(int pass, Bundle resp) {
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(4, resp.getEntry().size());
assertEquals("200 OK", resp.getEntry().get(0).getResponse().getStatus());
if (pass == 0) {
@ -1857,13 +1857,13 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
Bundle inputBundle;
Bundle outputBundle;
inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
inputBundle = myFhirContext.newJsonParser().parseResource(Bundle.class, input);
outputBundle = mySystemDao.transaction(mySrd, inputBundle);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
inputBundle = myFhirContext.newJsonParser().parseResource(Bundle.class, input);
outputBundle = mySystemDao.transaction(mySrd, inputBundle);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
IBundleProvider allPatients = myPatientDao.search(new SearchParameterMap());
assertEquals(1, allPatients.size().intValue());
@ -2225,14 +2225,14 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/questionnaire-sdc-profile-example-ussg-fht.xml");
String bundleStr = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, bundleStr);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, bundleStr);
Bundle resp = mySystemDao.transaction(mySrd, bundle);
String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp);
String encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp);
ourLog.info(encoded);
encoded = myFhirCtx.newJsonParser().setPrettyPrint(false).encodeResourceToString(resp);
encoded = myFhirContext.newJsonParser().setPrettyPrint(false).encodeResourceToString(resp);
//@formatter:off
assertThat(encoded, containsString("\"response\":{" +
"\"status\":\"201 Created\"," +
@ -2245,10 +2245,10 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
resp = mySystemDao.transaction(mySrd, bundle);
encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp);
encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp);
ourLog.info(encoded);
encoded = myFhirCtx.newJsonParser().setPrettyPrint(false).encodeResourceToString(resp);
encoded = myFhirContext.newJsonParser().setPrettyPrint(false).encodeResourceToString(resp);
//@formatter:off
assertThat(encoded, containsString("\"response\":{" +
"\"status\":\"200 OK\"," +
@ -2422,10 +2422,10 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
myPatientDao.create(patient, mySrd);
String input = IOUtils.toString(getClass().getResourceAsStream("/simone-conditional-url.xml"), StandardCharsets.UTF_8);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
Bundle response = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
}
@ -2442,7 +2442,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
myPatientDao.create(patient, mySrd);
String input = IOUtils.toString(getClass().getResourceAsStream("/simone-conditional-url.xml"), StandardCharsets.UTF_8);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
try {
mySystemDao.transaction(mySrd, bundle);
@ -2458,7 +2458,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
myDaoConfig.setAllowInlineMatchUrlReferences(true);
String input = IOUtils.toString(getClass().getResourceAsStream("/simone-conditional-url.xml"), StandardCharsets.UTF_8);
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
try {
mySystemDao.transaction(mySrd, bundle);
@ -2488,10 +2488,10 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
@Test
public void testTransactionWithMultiBundle() throws IOException {
String inputBundleString = loadClasspath("/batch-error.xml");
Bundle bundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, inputBundleString);
Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, inputBundleString);
Bundle resp = mySystemDao.transaction(mySrd, bundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
@ -2555,7 +2555,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
//@formatter:on
Bundle outputBundle = mySystemDao.transaction(mySrd, inputBundle);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(outputBundle));
assertEquals(3, outputBundle.getEntry().size());
IdDt id0 = new IdDt(outputBundle.getEntry().get(0).getResponse().getLocation());
@ -2590,7 +2590,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
Bundle input2 = createInputTransactionWithPlaceholderIdInMatchUrl(HTTPVerb.POST);
Bundle output2 = mySystemDao.transaction(null, input2);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output2));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(output2));
assertEquals("200 OK", output2.getEntry().get(0).getResponse().getStatus());
assertEquals("200 OK", output2.getEntry().get(1).getResponse().getStatus());
@ -2620,7 +2620,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
Bundle input2 = createInputTransactionWithPlaceholderIdInMatchUrl(HTTPVerb.PUT);
Bundle output2 = mySystemDao.transaction(null, input2);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output2));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(output2));
assertEquals("200 OK", output2.getEntry().get(0).getResponse().getStatus());
assertEquals("200 OK", output2.getEntry().get(1).getResponse().getStatus());
@ -2637,9 +2637,9 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
// First bundle (name is Joshua)
String input = IOUtils.toString(getClass().getResource("/dstu3-post1.xml"), StandardCharsets.UTF_8);
Bundle request = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle request = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
Bundle response = mySystemDao.transaction(mySrd, request);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
assertEquals(1, response.getEntry().size());
assertEquals("201 Created", response.getEntry().get(0).getResponse().getStatus());
@ -2649,9 +2649,9 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
// Now the second (name is Adam, shouldn't get used)
input = IOUtils.toString(getClass().getResource("/dstu3-post2.xml"), StandardCharsets.UTF_8);
request = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
request = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
response = mySystemDao.transaction(mySrd, request);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
assertEquals(1, response.getEntry().size());
assertEquals("200 OK", response.getEntry().get(0).getResponse().getStatus());
@ -2660,7 +2660,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
assertEquals(id, id2);
Patient patient = myPatientDao.read(new IdType(id), mySrd);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals("Joshua", patient.getNameFirstRep().getGivenAsSingleString());
}
@ -2679,7 +2679,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
Bundle resp = mySystemDao.transaction(mySrd, request);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
String patientId = new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualifiedVersionless().getValue();
assertThat(patientId, startsWith("Patient/"));
@ -2706,10 +2706,10 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
mo.setMedication(new Reference(medId));
bundle.addEntry().setResource(mo).setFullUrl(mo.getIdElement().getValue()).getRequest().setMethod(HTTPVerb.POST);
ourLog.info("Request:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
ourLog.info("Request:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(bundle));
Bundle outcome = mySystemDao.transaction(mySrd, bundle);
ourLog.info("Response:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
ourLog.info("Response:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome));
IdType medId1 = new IdType(outcome.getEntry().get(0).getResponse().getLocation());
IdType medOrderId1 = new IdType(outcome.getEntry().get(1).getResponse().getLocation());
@ -2759,7 +2759,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
request.addEntry().setResource(o).getRequest().setMethod(HTTPVerb.POST);
Bundle resp = mySystemDao.transaction(mySrd, request);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
String patientId = new IdType(resp.getEntry().get(0).getResponse().getLocation()).toUnqualifiedVersionless().getValue();
assertThat(patientId, startsWith("Patient/"));
@ -2793,7 +2793,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
Bundle resp = mySystemDao.transaction(mySrd, res);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(BundleType.TRANSACTIONRESPONSE, resp.getTypeElement().getValue());
assertEquals(3, resp.getEntry().size());
@ -2834,7 +2834,7 @@ public class FhirSystemDaoDstu3Test extends BaseJpaDstu3SystemTest {
Bundle resp = mySystemDao.transaction(mySrd, res);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(BundleType.TRANSACTIONRESPONSE, resp.getTypeElement().getValue());
assertEquals(3, resp.getEntry().size());

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/DeleteExpungeDaoTest.java
View File

@ -124,7 +124,7 @@ class DeleteExpungeDaoTest extends BaseJpaR4Test {
//See https://github.com/hapifhir/hapi-fhir/issues/2661
// setup
BundleBuilder builder = new BundleBuilder(myFhirCtx);
BundleBuilder builder = new BundleBuilder(myFhirContext);
for (int i = 0; i < 20; i++) {
Organization o = new Organization();
o.setId("Organization/O-" + i);

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4SystemTest.java
View File

@ -21,7 +21,7 @@ public abstract class BaseJpaR4SystemTest extends BaseJpaR4Test {
super.beforeInitMocks();
if (myServer == null) {
myServer = new RestfulServer(myFhirCtx, mySrdInterceptorService);
myServer = new RestfulServer(myFhirContext, mySrdInterceptorService);
PatientResourceProvider patientRp = new PatientResourceProvider();
patientRp.setDao(myPatientDao);

24
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -167,7 +167,6 @@ import org.hl7.fhir.r5.utils.validation.constants.BindingKind;
import org.hl7.fhir.r5.utils.validation.constants.CodedContentValidationPolicy;
import org.hl7.fhir.r5.utils.validation.constants.ContainedReferenceValidationPolicy;
import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.extension.ExtendWith;
@ -316,7 +315,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@Autowired
protected EntityManager myEntityManager;
@Autowired
protected FhirContext myFhirCtx;
protected FhirContext myFhirContext;
@Autowired
@Qualifier("myGroupDaoR4")
protected IFhirResourceDao<Group> myGroupDao;
@ -566,7 +565,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
@BeforeEach
public void beforeResetConfig() {
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
myFhirContext.setParserErrorHandler(new StrictErrorHandler());
myValidationSettings.setLocalReferenceValidationDefaultPolicy(new ValidationSettings().getLocalReferenceValidationDefaultPolicy());
}
@ -583,17 +582,12 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
}
protected String encode(IBaseResource theResource) {
return myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(theResource);
return myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(theResource);
}
@Override
public FhirContext getFhirContext() {
return myFhirCtx;
}
@Override
protected FhirContext getContext() {
return myFhirCtx;
return myFhirContext;
}
@Override
@ -602,25 +596,25 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
}
protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
return ClasspathUtil.loadResource(myFhirCtx, type, resourceName);
return ClasspathUtil.loadResource(myFhirContext, type, resourceName);
}
protected void validate(IBaseResource theResource) {
FhirValidator validatorModule = myFhirCtx.newValidator();
FhirValidator validatorModule = myFhirContext.newValidator();
FhirInstanceValidator instanceValidator = new FhirInstanceValidator(myValidationSupport);
instanceValidator.setBestPracticeWarningLevel(BestPracticeWarningLevel.Ignore);
instanceValidator.setValidatorPolicyAdvisor(new ValidationPolicyAdvisor());
validatorModule.registerValidatorModule(instanceValidator);
ValidationResult result = validatorModule.validateWithResult(theResource);
if (!result.isSuccessful()) {
fail(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome()));
fail(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome()));
}
}
@SuppressWarnings("unchecked")
protected void upload(String theClasspath) throws IOException {
String resource = loadResource(theClasspath);
IParser parser = EncodingEnum.detectEncoding(resource).newParser(myFhirCtx);
IParser parser = EncodingEnum.detectEncoding(resource).newParser(myFhirContext);
IBaseResource resourceParsed = parser.parseResource(resource);
IFhirResourceDao dao = myDaoRegistry.getResourceDao(resourceParsed.getIdElement().getResourceType());
dao.update(resourceParsed);
@ -690,7 +684,7 @@ public abstract class BaseJpaR4Test extends BaseJpaTest implements ITestDataBuil
Optional<ValueSet.ValueSetExpansionContainsComponent> first = stream.findFirst();
if (!first.isPresent()) {
String expandedValueSetString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(theValueSet);
String expandedValueSetString = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(theValueSet);
String failureMessage = String.format("Expanded ValueSet %s did not contain concept [%s|%s|%s] with [%d] designations. Outcome:\n%s", theValueSet.getId(), theSystem, theCode, theDisplay, theDesignationCount, expandedValueSetString);
fail(failureMessage);
return null;

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseR4SearchLastN.java
View File

@ -94,7 +94,7 @@ abstract public class BaseR4SearchLastN extends BaseJpaTest {
protected ElasticsearchSvcImpl myElasticsearchSvc;
@Override
protected FhirContext getContext() {
protected FhirContext getFhirContext() {
return myFhirCtx;
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/ChainingR4SearchTest.java
View File

@ -57,7 +57,7 @@ public class ChainingR4SearchTest extends BaseJpaR4Test {
@BeforeEach
public void before() throws Exception {
myFhirCtx.setParserErrorHandler(new StrictErrorHandler());
myFhirContext.setParserErrorHandler(new StrictErrorHandler());
myDaoConfig.setAllowMultipleDelete(true);
myDaoConfig.setSearchPreFetchThresholds(new DaoConfig().getSearchPreFetchThresholds());

55
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
View File

@ -34,7 +34,6 @@ import org.junit.jupiter.api.Test;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.CoreMatchers.startsWith;
@ -211,7 +210,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
// Read the Observation
Observation createdObs = myObservationDao.read(id);
ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info("\nObservation created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
/*
* Read the placeholder Patient referenced by the Observation
@ -219,7 +218,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
*/
Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
IIdType placeholderPatId = placeholderPat.getIdElement();
ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
ourLog.info("\nPlaceholder Patient created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
assertEquals(0, placeholderPat.getIdentifier().size());
Extension extension = placeholderPat.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
assertNotNull(extension);
@ -237,7 +236,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
* Placeholder extension should not exist
*/
Patient updatedPat = myPatientDao.read(updatedPatId);
ourLog.info("\nUpdated Patient:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedPat));
ourLog.info("\nUpdated Patient:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(updatedPat));
assertEquals(1, updatedPat.getIdentifier().size());
extension = updatedPat.getExtensionByUrl(HapiExtensions.EXT_RESOURCE_PLACEHOLDER);
assertNull(extension);
@ -256,10 +255,10 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
IIdType id = myObservationDao.create(obsToCreate, mySrd).getId();
Observation createdObs = myObservationDao.read(id);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
Patient patient = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(0, patient.getIdentifier().size());
}
@ -290,7 +289,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
//Read the Placeholder Patient
Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info("\nObservation created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
//Ensure the Obs has the right placeholder ID.
IIdType placeholderPatId = placeholderPat.getIdElement();
@ -299,7 +298,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
/*
* Should have a single identifier populated.
*/
ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
ourLog.info("\nPlaceholder Patient created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
assertEquals(1, placeholderPat.getIdentifier().size());
List<Identifier> identifiers = placeholderPat.getIdentifier();
Identifier identifier = identifiers.get(0);
@ -335,7 +334,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
//Read the Placeholder Patient
Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info("\nObservation created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
//Ensure the Obs has the right placeholder ID.
IIdType placeholderPatId = placeholderPat.getIdElement();
@ -344,7 +343,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
/*
* Should have a single identifier populated.
*/
ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
ourLog.info("\nPlaceholder Patient created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
assertEquals(1, placeholderPat.getIdentifier().size());
List<Identifier> identifiers = placeholderPat.getIdentifier();
Identifier identifier = identifiers.get(0);
@ -381,7 +380,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
//Read the Placeholder Patient
Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info("\nObservation created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
//Ensure the Obs has the right placeholder ID.
IIdType placeholderPatId = placeholderPat.getIdElement();
@ -390,7 +389,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
/*
* Should have a single identifier populated.
*/
ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
ourLog.info("\nPlaceholder Patient created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
assertEquals(1, placeholderPat.getIdentifier().size());
List<Identifier> identifiers = placeholderPat.getIdentifier();
Identifier identifier = identifiers.get(0);
@ -428,7 +427,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
//Read the Placeholder Patient
Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info("\nObservation created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
//Ensure the Obs has the right placeholder ID.
IIdType placeholderPatId = placeholderPat.getIdElement();
@ -437,7 +436,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
/*
* Placeholder Identifiers should both be populated since they were both provided, and did not match
*/
ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
ourLog.info("\nPlaceholder Patient created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
assertEquals(2, placeholderPat.getIdentifier().size());
List<Identifier> identifiers = placeholderPat.getIdentifier();
@ -458,7 +457,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
// Read the conditionally updated Patient
Patient conditionalUpdatePat = myPatientDao.read(conditionalUpdatePatId);
ourLog.info("\nConditionally updated Patient:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conditionalUpdatePat));
ourLog.info("\nConditionally updated Patient:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conditionalUpdatePat));
assertEquals(1, conditionalUpdatePat.getIdentifier().size());
/*
@ -466,7 +465,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
* ID of placeholder Patient should match ID of conditionally updated Patient
*/
createdObs = myObservationDao.read(obsId);
ourLog.info("\nObservation read after Patient update:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info("\nObservation read after Patient update:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
assertEquals(createdObs.getSubject().getReference(), conditionalUpdatePatId.toUnqualifiedVersionless().getValueAsString());
assertEquals(placeholderPatId.toUnqualifiedVersionless().getValueAsString(), conditionalUpdatePatId.toUnqualifiedVersionless().getValueAsString());
}
@ -488,7 +487,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
// Read the Observation
Observation createdObs = myObservationDao.read(obsId);
ourLog.info("\nObservation created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info("\nObservation created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
/*
* Read the placeholder Patient referenced by the Observation
@ -496,7 +495,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
*/
Patient placeholderPat = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
IIdType placeholderPatId = placeholderPat.getIdElement();
ourLog.info("\nPlaceholder Patient created:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
ourLog.info("\nPlaceholder Patient created:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(placeholderPat));
assertEquals(1, placeholderPat.getIdentifier().size());
assertEquals(createdObs.getSubject().getReference(), placeholderPatId.toUnqualifiedVersionless().getValueAsString());
@ -508,7 +507,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
// Read the conditionally updated Patient
Patient conditionalUpdatePat = myPatientDao.read(conditionalUpdatePatId);
ourLog.info("\nConditionally updated Patient:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conditionalUpdatePat));
ourLog.info("\nConditionally updated Patient:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conditionalUpdatePat));
assertEquals(1, conditionalUpdatePat.getIdentifier().size());
/*
@ -516,7 +515,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
* ID of placeholder Patient should match ID of conditionally updated Patient
*/
createdObs = myObservationDao.read(obsId);
ourLog.info("\nObservation read after Patient update:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info("\nObservation read after Patient update:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
assertEquals(createdObs.getSubject().getReference(), conditionalUpdatePatId.toUnqualifiedVersionless().getValueAsString());
assertEquals(placeholderPatId.toUnqualifiedVersionless().getValueAsString(), conditionalUpdatePatId.toUnqualifiedVersionless().getValueAsString());
}
@ -533,10 +532,10 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
IIdType id = myObservationDao.create(obsToCreate, mySrd).getId();
Observation createdObs = myObservationDao.read(id);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
Patient patient = myPatientDao.read(new IdType(createdObs.getSubject().getReference()));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(1, patient.getIdentifier().size());
assertEquals("http://foo", patient.getIdentifier().get(0).getSystem());
assertEquals("123", patient.getIdentifier().get(0).getValue());
@ -556,7 +555,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
IIdType id = myAuditEventDao.create(eventToCreate, mySrd).getId();
AuditEvent createdEvent = myAuditEventDao.read(id);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEvent));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEvent));
}
@Test
@ -587,7 +586,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
obs.setId("Observation/DEF");
Reference patientRef = new Reference("Patient/RED");
obs.setSubject(patientRef);
BundleBuilder builder = new BundleBuilder(myFhirCtx);
BundleBuilder builder = new BundleBuilder(myFhirContext);
builder.addTransactionUpdateEntry(obs);
mySystemDao.transaction(new SystemRequestDetails(), (Bundle) builder.getBundle());
@ -619,7 +618,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
obs.setId("Observation/DEF");
Reference patientRef = new Reference(patientId);
obs.setSubject(patientRef);
BundleBuilder builder = new BundleBuilder(myFhirCtx);
BundleBuilder builder = new BundleBuilder(myFhirContext);
builder.addTransactionUpdateEntry(obs);
Bundle transaction = mySystemDao.transaction(new SystemRequestDetails(), (Bundle) builder.getBundle());
@ -655,7 +654,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
obs.setId("Observation/DEF");
Reference patientRef = new Reference("Patient/" + ret.getId().getIdPart());
obs.setSubject(patientRef);
BundleBuilder builder = new BundleBuilder(myFhirCtx);
BundleBuilder builder = new BundleBuilder(myFhirContext);
builder.addTransactionUpdateEntry(obs);
Bundle transaction = mySystemDao.transaction(new SystemRequestDetails(), (Bundle) builder.getBundle());
@ -680,7 +679,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
obs1.setId("Observation/DEF1");
Reference patientRef = new Reference("Patient/RED");
obs1.setSubject(patientRef);
BundleBuilder builder = new BundleBuilder(myFhirCtx);
BundleBuilder builder = new BundleBuilder(myFhirContext);
Observation obs2 = new Observation();
obs2.setId("Observation/DEF2");
obs2.setSubject(patientRef);
@ -702,7 +701,7 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
obs1.setId("Observation/DEF1");
Reference patientRef = new Reference("Patient/RED");
obs1.setSubject(patientRef);
BundleBuilder builder = new BundleBuilder(myFhirCtx);
BundleBuilder builder = new BundleBuilder(myFhirContext);
Observation obs2 = new Observation();
obs2.setId("Observation/DEF2");
obs2.setSubject(patientRef);

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCustomTypeR4Test.java
View File

@ -4,9 +4,9 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.StringType;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ -17,7 +17,7 @@ public class FhirResourceDaoCustomTypeR4Test extends BaseJpaR4Test {
@BeforeEach
public void before() {
myFhirCtx.setDefaultTypeForProfile(CustomObservationR4.PROFILE, CustomObservationR4.class);
myFhirContext.setDefaultTypeForProfile(CustomObservationR4.PROFILE, CustomObservationR4.class);
}
@Test
@ -39,6 +39,6 @@ public class FhirResourceDaoCustomTypeR4Test extends BaseJpaR4Test {
@AfterEach
public void after() {
myFhirCtx.setDefaultTypeForProfile(CustomObservationR4.PROFILE, null);
myFhirContext.setDefaultTypeForProfile(CustomObservationR4.PROFILE, null);
}
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoDocumentR4Test.java
View File

@ -1,10 +1,8 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.r4.model.Bundle;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import java.nio.charset.StandardCharsets;
@ -16,7 +14,7 @@ public class FhirResourceDaoDocumentR4Test extends BaseJpaR4Test {
@Test
public void testPostDocument() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/sample-document.xml"), StandardCharsets.UTF_8);
Bundle inputBundle = myFhirCtx.newXmlParser().parseResource(Bundle.class, input);
Bundle inputBundle = myFhirContext.newXmlParser().parseResource(Bundle.class, input);
DaoMethodOutcome responseBundle = myBundleDao.create(inputBundle, mySrd);
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java
View File

@ -29,7 +29,7 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
String input = IOUtils.toString(getClass().getResource("/r4/codesystem_complete.json"), StandardCharsets.UTF_8);
CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);
CodeSystem cs = myFhirContext.newJsonParser().parseResource(CodeSystem.class, input);
myCodeSystemDao.create(cs, mySrd);
myResourceReindexingSvc.markAllResourcesForReindexing();

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ComboUniqueParamTest.java
View File

@ -492,7 +492,7 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
.setValue(new BooleanType(true));
mySearchParameterDao.create(sp);
mySearchParamRegistry.forceRefresh();
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(sp));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(sp));
// Now create matching/non-matching resources
Patient pt = new Patient();
@ -977,11 +977,11 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
" ]\n" +
"}";
Bundle inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(inputBundle));
Bundle inputBundle = myFhirContext.newJsonParser().parseResource(Bundle.class, input);
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(inputBundle));
mySystemDao.transaction(mySrd, inputBundle);
inputBundle = myFhirCtx.newJsonParser().parseResource(Bundle.class, input);
inputBundle = myFhirContext.newJsonParser().parseResource(Bundle.class, input);
mySystemDao.transaction(mySrd, inputBundle);
}

42
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConceptMapTest.java
View File

@ -81,7 +81,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateByCodeSystemsAndSourceCodeOneToMany() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -125,7 +125,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateByCodeSystemsAndSourceCodeOneToOne() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -160,7 +160,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateByCodeSystemsAndSourceCodeUnmapped() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -187,7 +187,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateUsingPredicatesWithCodeOnly() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -238,7 +238,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateUsingPredicatesWithSourceAndTargetSystem2() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -277,7 +277,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateUsingPredicatesWithSourceAndTargetSystem3() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -324,7 +324,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateUsingPredicatesWithSourceSystem() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -377,7 +377,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateUsingPredicatesWithSourceSystemAndVersion1() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -416,7 +416,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateUsingPredicatesWithSourceSystemAndVersion3() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -463,7 +463,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateUsingPredicatesWithSourceValueSet() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -516,7 +516,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateUsingPredicatesWithTargetValueSet() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -569,7 +569,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateWithReverse() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -717,7 +717,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateWithReverseHavingEquivalence() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -758,7 +758,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateWithReverseByCodeSystemsAndSourceCodeUnmapped() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -786,7 +786,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateWithReverseUsingPredicatesWithCodeOnly() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -831,7 +831,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateWithReverseUsingPredicatesWithSourceAndTargetSystem1() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -872,7 +872,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateWithReverseUsingPredicatesWithSourceAndTargetSystem4() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -913,7 +913,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateWithReverseUsingPredicatesWithSourceSystem() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -960,7 +960,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateWithReverseUsingPredicatesWithSourceSystemAndVersion() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -1009,7 +1009,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateWithReverseUsingPredicatesWithSourceValueSet() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override
@ -1056,7 +1056,7 @@ public class FhirResourceDaoR4ConceptMapTest extends BaseJpaR4Test {
public void testTranslateWithReverseUsingPredicatesWithTargetValueSet() {
ConceptMap conceptMap = myConceptMapDao.read(myConceptMapId);
ourLog.info("ConceptMap:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
ourLog.info("ConceptMap:\n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
@Override

28
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ConcurrentWriteTest.java
View File

@ -72,7 +72,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
myRetryInterceptor = new UserRequestRetryVersionConflictsInterceptor();
myConcurrencySemaphoreInterceptor = new TransactionConcurrencySemaphoreInterceptor(myMemoryCacheService);
RestfulServer server = new RestfulServer(myFhirCtx);
RestfulServer server = new RestfulServer(myFhirContext);
when(mySrd.getServer()).thenReturn(server);
}
@ -215,7 +215,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
myConcurrencySemaphoreInterceptor.setLogWaits(true);
Runnable creator = ()->{
BundleBuilder bb = new BundleBuilder(myFhirCtx);
BundleBuilder bb = new BundleBuilder(myFhirContext);
Patient patient1 = new Patient();
patient1.addIdentifier().setSystem("http://foo").setValue("1");
@ -276,7 +276,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
@Nonnull
private Runnable newTransactionTaskWithUpdatesAndConditionalUpdates(AtomicInteger theSetCounter, AtomicInteger theFuzzCounter) {
Runnable creator = () -> {
BundleBuilder bb = new BundleBuilder(myFhirCtx);
BundleBuilder bb = new BundleBuilder(myFhirContext);
String patientId = "Patient/PT" + theSetCounter.get();
IdType practitionerId = IdType.newRandomUuid();
IdType practitionerId2 = IdType.newRandomUuid();
@ -358,7 +358,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@ -391,7 +391,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@ -424,7 +424,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@ -578,7 +578,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@ -614,7 +614,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@ -654,7 +654,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@ -707,7 +707,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
// Make sure we saved the object
Patient patient = myPatientDao.read(pId);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals("6", patient.getMeta().getVersionId());
}
@ -721,7 +721,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
String value = UserRequestRetryVersionConflictsInterceptor.RETRY + "; " + UserRequestRetryVersionConflictsInterceptor.MAX_RETRIES + "=10";
when(srd.getHeaders(eq(UserRequestRetryVersionConflictsInterceptor.HEADER_NAME))).thenReturn(Collections.singletonList(value));
when(srd.getUserData()).thenReturn(new HashMap<>());
when(srd.getServer()).thenReturn(new RestfulServer(myFhirCtx));
when(srd.getServer()).thenReturn(new RestfulServer(myFhirContext));
when(srd.getInterceptorBroadcaster()).thenReturn(new InterceptorService());
List<Future<?>> futures = new ArrayList<>();
@ -759,7 +759,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
// Make sure we saved the object
Patient patient = myPatientDao.read(new IdType("Patient/ABC"));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info(myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
assertEquals(true, patient.getActive());
}
@ -774,7 +774,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
String value = UserRequestRetryVersionConflictsInterceptor.RETRY + "; " + UserRequestRetryVersionConflictsInterceptor.MAX_RETRIES + "=10";
when(srd.getHeaders(eq(UserRequestRetryVersionConflictsInterceptor.HEADER_NAME))).thenReturn(Collections.singletonList(value));
when(srd.getUserData()).thenReturn(new HashMap<>());
when(srd.getServer()).thenReturn(new RestfulServer(myFhirCtx));
when(srd.getServer()).thenReturn(new RestfulServer(myFhirContext));
when(srd.getInterceptorBroadcaster()).thenReturn(new InterceptorService());
List<Future<?>> futures = new ArrayList<>();
@ -783,7 +783,7 @@ public class FhirResourceDaoR4ConcurrentWriteTest extends BaseJpaR4Test {
String patientId = "PATIENT" + i;
Runnable task = () -> {
BundleBuilder bb = new BundleBuilder(myFhirCtx);
BundleBuilder bb = new BundleBuilder(myFhirContext);
Patient p = new Patient();
p.setId(patientId);

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ContainedTest.java
View File

@ -2,7 +2,6 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.SearchContainedModeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -57,13 +56,13 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
obs.getCode().setText("Some Observation");
obs.setSubject(new Reference(p));
ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Input: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
IIdType id = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
Observation createdObs = myObservationDao.read(id);
ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info("Output: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
runInTransaction(()->{
ourLog.info("String indexes:\n * {}", myResourceIndexedSearchParamStringDao.findAll().stream().map(t->t.toString()).collect(Collectors.joining("\n * ")));
@ -93,13 +92,13 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
obs.getContained().add(p);
obs.getSubject().setReference("#fooId");
ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Input: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
IIdType id = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
Observation createdObs = myObservationDao.read(id);
ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
ourLog.info("Output: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdObs));
runInTransaction(()->{
Long i = myEntityManager
@ -153,13 +152,13 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
patient.addGeneralPractitioner().setReference("#org1");
patient.getManagingOrganization().setReference("#org2");
ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
ourLog.info("Input: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient));
IIdType id = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
Patient createdPatient = myPatientDao.read(id);
ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdPatient));
ourLog.info("Output: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdPatient));
runInTransaction(()->{
Long i = myEntityManager
@ -224,13 +223,13 @@ public class FhirResourceDaoR4ContainedTest extends BaseJpaR4Test {
encounter.addReasonReference().setReference("#obs1");
encounter.getContained().add(obs);
ourLog.info("Input: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
ourLog.info("Input: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(encounter));
IIdType id = myEncounterDao.create(encounter, mySrd).getId().toUnqualifiedVersionless();
Encounter createdEncounter = myEncounterDao.read(id);
ourLog.info("Output: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
ourLog.info("Output: {}", myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(createdEncounter));
runInTransaction(()->{
// The practitioner

29
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CreateTest.java
View File

@ -67,7 +67,6 @@ import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ -340,7 +339,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
*/
@Test
public void testConditionalCreateFailsIfMatchUrlDoesntMatch_InTransaction() {
BundleBuilder bb = new BundleBuilder(myFhirCtx);
BundleBuilder bb = new BundleBuilder(myFhirContext);
Patient patient = new Patient();
patient.setId(IdType.newRandomUuid());
@ -363,7 +362,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
@Test
public void testCreateResourceWithKoreanText() throws IOException {
String input = loadClasspath("/r4/bug832-korean-text.xml");
Patient p = myFhirCtx.newXmlParser().parseResource(Patient.class, input);
Patient p = myFhirContext.newXmlParser().parseResource(Patient.class, input);
String id = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
SearchParameterMap map = new SearchParameterMap();
@ -619,11 +618,11 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
.getRequest()
.setMethod(Bundle.HTTPVerb.POST);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(input));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(input));
Bundle output = mySystemDao.transaction(mySrd, input);
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
ourLog.info(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(output));
assertThat(output.getEntry().get(0).getResponse().getLocation(), matchesPattern("Organization/[a-z0-9]{8}-.*"));
assertThat(output.getEntry().get(1).getResponse().getLocation(), matchesPattern("Patient/[a-z0-9]{8}-.*"));
@ -640,7 +639,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
o.getMeta().addTag("http://foo", "bar", "FOOBAR");
p.getManagingOrganization().setResource(o);
String encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
String encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
ourLog.info("Input: {}", encoded);
assertThat(encoded, containsString("#1"));
@ -648,7 +647,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
p = myPatientDao.read(id);
encoded = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
encoded = myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
ourLog.info("Output: {}", encoded);
assertThat(encoded, containsString("#1"));
@ -691,7 +690,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
q.setCode("cm");
obs.setValue(q);
ourLog.info("Observation1: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation1: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
assertTrue(myObservationDao.create(obs).getCreated());
@ -731,7 +730,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
q.setCode("mm");
obs.setValue(q);
ourLog.info("Observation1: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation1: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
myCaptureQueriesListener.clear();
assertTrue(myObservationDao.create(obs).getCreated());
@ -808,7 +807,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
q.setCode("mm");
obs.setValue(q);
ourLog.info("Observation1: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation1: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
assertTrue(myObservationDao.create(obs).getCreated());
@ -843,7 +842,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
assertEquals(1, ids.size());
ourLog.info("Observation2: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resources.get(0)));
ourLog.info("Observation2: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(resources.get(0)));
}
@ -860,7 +859,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
q.setCode("kg/dL");
obs.setValue(q);
ourLog.info("Observation1: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation1: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
assertTrue(myObservationDao.create(obs).getCreated());
@ -900,7 +899,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
q.setCode("kg/dL");
obs.setValue(q);
ourLog.info("Observation1: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation1: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
assertTrue(myObservationDao.create(obs).getCreated());
@ -947,7 +946,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
q.setCode("mm");
obs.setValue(q);
ourLog.info("Observation1: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation1: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
myCaptureQueriesListener.clear();
assertTrue(myObservationDao.create(obs).getCreated());
@ -1080,7 +1079,7 @@ public class FhirResourceDaoR4CreateTest extends BaseJpaR4Test {
q.setCode("mm");
obs.setValue(q);
ourLog.info("Observation1: \n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
ourLog.info("Observation1: \n" + myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs));
myCaptureQueriesListener.clear();
assertTrue(myObservationDao.create(obs).getCreated());

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