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

This commit is contained in:
jamesagnew 2018-07-15 15:23:11 -04:00
parent 43ac912033 84b57f04d3
commit 116b9e335d
10 changed files with 205 additions and 114 deletions
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64
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -92,9 +92,9 @@ import static org.apache.commons.lang3.StringUtils.*;
* 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.
@ -1167,7 +1167,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
public SearchBuilder newSearchBuilder() {
SearchBuilder builder = new SearchBuilder(
getContext(), myEntityManager, myFulltextSearchSvc, this, myResourceIndexedSearchParamUriDao,
myForcedIdDao, myTerminologySvc, mySerarchParamRegistry, myResourceTagDao, myResourceViewDao);
myForcedIdDao, myTerminologySvc, mySerarchParamRegistry, myResourceTagDao, myResourceViewDao);
return builder;
}
@ -1301,20 +1301,24 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
}
// Don't keep duplicate tags
Set<ResourceTag> allTagsNew = getAllTagDefinitions(theEntity);
Set<TagDefinition> allDefsPresent = new HashSet<>();
theEntity.getTags().removeIf(theResourceTag -> !allDefsPresent.add(theResourceTag.getTag()));
allTagsNew.forEach(tag -> {
// Remove any tags that have been removed
for (ResourceTag next : allTagsOld) {
if (!allDefs.contains(next)) {
if (shouldDroppedTagBeRemovedOnUpdate(theRequest, next)) {
theEntity.getTags().remove(next);
// Don't keep duplicate tags
if (!allDefsPresent.add(tag.getTag())) {
theEntity.getTags().remove(tag);
}
// Drop any tags that have been removed
if (!allDefs.contains(tag)) {
if (shouldDroppedTagBeRemovedOnUpdate(theRequest, tag)) {
theEntity.getTags().remove(tag);
}
}
}
Set<ResourceTag> allTagsNew = getAllTagDefinitions(theEntity);
});
if (!allTagsOld.equals(allTagsNew)) {
changed = true;
}
@ -1473,6 +1477,15 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
return retVal;
}
/**
* Subclasses may override to provide behaviour. Called when a pre-existing resource has been updated in the database
*
* @param theEntity The resource
*/
protected void postDelete(ResourceTable theEntity) {
// nothing
}
/**
* Subclasses may override to provide behaviour. Called when a resource has been inserted into the database for the first time.
*
@ -1483,15 +1496,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
// nothing
}
/**
* Subclasses may override to provide behaviour. Called when a pre-existing resource has been updated in the database
*
* @param theEntity The resource
*/
protected void postDelete(ResourceTable theEntity) {
// nothing
}
/**
* Subclasses may override to provide behaviour. Called when a pre-existing resource has been updated in the database
*
@ -1626,20 +1630,20 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
@SuppressWarnings("unchecked")
@Override
public <R extends IBaseResource> R toResource(Class<R> theResourceType, IBaseResourceEntity theEntity, Collection<ResourceTag> theTagList, boolean theForHistoryOperation) {
// 1. get resource, it's encoding and the tags if any
byte[] resourceBytes = null;
ResourceEncodingEnum resourceEncoding = null;
Collection<? extends BaseTag> myTagList = null;
if (theEntity instanceof ResourceHistoryTable) {
ResourceHistoryTable history = (ResourceHistoryTable) theEntity;
resourceBytes = history.getResource();
resourceEncoding = history.getEncoding();
myTagList = history.getTags();
} else if (theEntity instanceof ResourceTable) {
ResourceTable resource = (ResourceTable)theEntity;
ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(theEntity.getId(), theEntity.getVersion());
ResourceTable resource = (ResourceTable) theEntity;
ResourceHistoryTable history = myResourceHistoryTableDao.findForIdAndVersion(theEntity.getId(), theEntity.getVersion());
if (history == null) {
return null;
}
@ -1648,7 +1652,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
myTagList = resource.getTags();
} else if (theEntity instanceof ResourceSearchView) {
// This is the search View
ResourceSearchView myView = (ResourceSearchView)theEntity;
ResourceSearchView myView = (ResourceSearchView) theEntity;
resourceBytes = myView.getResource();
resourceEncoding = myView.getEncoding();
if (theTagList == null)
@ -1663,7 +1667,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
// 2. get The text
String resourceText = null;
switch (resourceEncoding) {
case JSON:
case JSON:
try {
resourceText = new String(resourceBytes, "UTF-8");
} catch (UnsupportedEncodingException e) {
@ -1676,7 +1680,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
case DEL:
break;
}
// 3. Use the appropriate custom type if one is specified in the context
Class<R> resourceType = theResourceType;
if (myContext.hasDefaultTypeForProfile()) {
@ -2046,6 +2050,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
postPersist(theEntity, (T) theResource);
} else if (theEntity.getDeleted() != null) {
theEntity = myEntityManager.merge(theEntity);
postDelete(theEntity);
@ -2191,12 +2196,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
} // if thePerformIndexing
theEntity = myEntityManager.merge(theEntity);
if (theResource != null) {
populateResourceIdFromEntity(theEntity, theResource);
}
return theEntity;
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -395,16 +395,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
"This server cannot create an entity with a user-specified numeric ID - Client should not specify an ID when creating a new resource, or should include at least one letter in the ID to force a client-defined ID");
}
createForcedIdIfNeeded(entity, theResource.getIdElement());
if (entity.getForcedId() != null) {
try {
translateForcedIdToPid(getResourceName(), theResource.getIdElement().getIdPart());
throw new UnprocessableEntityException(getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "duplicateCreateForcedId", theResource.getIdElement().getIdPart()));
} catch (ResourceNotFoundException e) {
// good, this ID doesn't exist so we can create it
}
}
}
// Notify interceptors
@ -1211,7 +1201,9 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
} else {
/*
* Note: resourcdeId will not be null or empty here, because we check it and reject requests in BaseOutcomeReturningMethodBindingWithResourceParam
* Note: resourceId will not be null or empty here, because we
* check it and reject requests in
* BaseOutcomeReturningMethodBindingWithResourceParam
*/
resourceId = theResource.getIdElement();

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ForcedId.java
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@ -27,7 +27,6 @@ import javax.persistence.*;
@Entity()
@Table(name = "HFJ_FORCED_ID", uniqueConstraints = {
@UniqueConstraint(name = "IDX_FORCEDID_RESID", columnNames = {"RESOURCE_PID"}),
@UniqueConstraint(name = "IDX_FORCEDID_TYPE_RESID", columnNames = {"RESOURCE_TYPE", "RESOURCE_PID"}),
@UniqueConstraint(name = "IDX_FORCEDID_TYPE_FID", columnNames = {"RESOURCE_TYPE", "FORCED_ID"})
}, indexes = {
/*

16
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java
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@ -12,6 +12,7 @@ import org.slf4j.LoggerFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.core.env.Environment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.transaction.annotation.EnableTransactionManagement;
@ -43,11 +44,6 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
private Exception myLastStackTrace;
private String myLastStackTraceThreadName;
@Bean(name="maxDatabaseThreadsForTest")
public Integer getMaxThread(){
return ourMaxThreads;
}
@Bean()
public DaoConfig daoConfig() {
return new DaoConfig();
@ -131,6 +127,11 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
return retVal;
}
@Bean(name = "maxDatabaseThreadsForTest")
public Integer getMaxThread() {
return ourMaxThreads;
}
private Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.format_sql", "true");
@ -165,4 +166,9 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
return retVal;
}
@Bean
public UnregisterScheduledProcessor unregisterScheduledProcessor(Environment theEnv) {
return new UnregisterScheduledProcessor(theEnv);
}
}

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

@ -6,14 +6,9 @@ import ca.uhn.fhir.jpa.subscription.email.IEmailSender;
import ca.uhn.fhir.jpa.subscription.email.JavaMailEmailSender;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.validation.ResultSeverityEnum;
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.springframework.beans.BeansException;
import org.springframework.beans.factory.config.BeanFactoryPostProcessor;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.beans.factory.support.DefaultListableBeanFactory;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
@ -22,13 +17,11 @@ import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
import org.springframework.core.env.Environment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.scheduling.annotation.ScheduledAnnotationBeanPostProcessor;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.persistence.EntityManagerFactory;
import javax.sql.DataSource;
import java.sql.Connection;
import java.sql.SQLException;
import java.util.Properties;
import java.util.concurrent.TimeUnit;
@ -194,23 +187,4 @@ public class TestDstu3Config extends BaseJavaConfigDstu3 {
}
public class UnregisterScheduledProcessor implements BeanFactoryPostProcessor {
private final Environment myEnvironment;
public UnregisterScheduledProcessor(Environment theEnv) {
myEnvironment = theEnv;
}
@Override
public void postProcessBeanFactory(final ConfigurableListableBeanFactory beanFactory) throws BeansException {
String schedulingDisabled = myEnvironment.getProperty("scheduling_disabled");
if ("true".equals(schedulingDisabled)) {
for (String beanName : beanFactory.getBeanNamesForType(ScheduledAnnotationBeanPostProcessor.class)) {
((DefaultListableBeanFactory) beanFactory).removeBeanDefinition(beanName);
}
}
}
}
}

9
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
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@ -7,15 +7,13 @@ import net.ttddyy.dsproxy.listener.ThreadQueryCountHolder;
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.hibernate.query.criteria.LiteralHandlingMode;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.orm.hibernate5.HibernateExceptionTranslator;
import org.springframework.core.env.Environment;
import org.springframework.orm.jpa.JpaTransactionManager;
import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
import org.springframework.orm.jpa.vendor.HibernateJpaDialect;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.persistence.EntityManagerFactory;
@ -163,6 +161,11 @@ public class TestR4Config extends BaseJavaConfigR4 {
return retVal;
}
@Bean
public UnregisterScheduledProcessor unregisterScheduledProcessor(Environment theEnv) {
return new UnregisterScheduledProcessor(theEnv);
}
public static int getMaxThreads() {
return ourMaxThreads;
}

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/UnregisterScheduledProcessor.java Normal file
View File

@ -0,0 +1,39 @@
package ca.uhn.fhir.jpa.config;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.config.BeanFactoryPostProcessor;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.beans.factory.support.DefaultListableBeanFactory;
import org.springframework.core.env.Environment;
import org.springframework.scheduling.annotation.ScheduledAnnotationBeanPostProcessor;
import org.springframework.scheduling.concurrent.ExecutorConfigurationSupport;
/**
* This bean postprocessor disables all scheduled tasks. It is intended
* only to be used in unit tests in circumstances where scheduled
* tasks cause issues.
*/
public class UnregisterScheduledProcessor implements BeanFactoryPostProcessor {
private final Environment myEnvironment;
public UnregisterScheduledProcessor(Environment theEnv) {
myEnvironment = theEnv;
}
@Override
public void postProcessBeanFactory(final ConfigurableListableBeanFactory beanFactory) throws BeansException {
String schedulingDisabled = myEnvironment.getProperty("scheduling_disabled");
if ("true".equals(schedulingDisabled)) {
for (String beanName : beanFactory.getBeanNamesForType(ScheduledAnnotationBeanPostProcessor.class)) {
((DefaultListableBeanFactory) beanFactory).removeBeanDefinition(beanName);
}
for (String beanName : beanFactory.getBeanNamesForType(ExecutorConfigurationSupport.class)) {
ExecutorConfigurationSupport executorConfigSupport = ((DefaultListableBeanFactory) beanFactory).getBean(beanName, ExecutorConfigurationSupport.class);
executorConfigSupport.shutdown();
}
}
}
}

109
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java Normal file
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@ -0,0 +1,109 @@
package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.util.TestUtil;
import net.ttddyy.dsproxy.QueryCountHolder;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Patient;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Test;
import org.springframework.test.context.TestPropertySource;
import static org.junit.Assert.*;
@TestPropertySource(properties = {
"scheduling_disabled=true"
})
public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4QueryCountTest.class);
@After
public void afterResetDao() {
myDaoConfig.setResourceMetaCountHardLimit(new DaoConfig().getResourceMetaCountHardLimit());
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
}
@Test
public void testCreateClientAssignedId() {
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
QueryCountHolder.clear();
ourLog.info("** Starting Update Non-Existing resource with client assigned ID");
Patient p = new Patient();
p.setId("A");
p.getPhotoFirstRep().setCreationElement(new DateTimeType("2011")); // non-indexed field
myPatientDao.update(p).getId().toUnqualifiedVersionless();
assertEquals(1, QueryCountHolder.getGrandTotal().getSelect());
assertEquals(4, QueryCountHolder.getGrandTotal().getInsert());
assertEquals(0, QueryCountHolder.getGrandTotal().getDelete());
// Because of the forced ID's bidirectional link HFJ_RESOURCE <-> HFJ_FORCED_ID
assertEquals(1, QueryCountHolder.getGrandTotal().getUpdate());
runInTransaction(() -> {
assertEquals(1, myResourceTableDao.count());
assertEquals(1, myResourceHistoryTableDao.count());
assertEquals(1, myForcedIdDao.count());
assertEquals(1, myResourceIndexedSearchParamTokenDao.count());
});
// Ok how about an update
QueryCountHolder.clear();
ourLog.info("** Starting Update Existing resource with client assigned ID");
p = new Patient();
p.setId("A");
p.getPhotoFirstRep().setCreationElement(new DateTimeType("2012")); // non-indexed field
myPatientDao.update(p).getId().toUnqualifiedVersionless();
assertEquals(5, QueryCountHolder.getGrandTotal().getSelect());
assertEquals(1, QueryCountHolder.getGrandTotal().getInsert());
assertEquals(0, QueryCountHolder.getGrandTotal().getDelete());
assertEquals(1, QueryCountHolder.getGrandTotal().getUpdate());
runInTransaction(() -> {
assertEquals(1, myResourceTableDao.count());
assertEquals(2, myResourceHistoryTableDao.count());
assertEquals(1, myForcedIdDao.count());
assertEquals(1, myResourceIndexedSearchParamTokenDao.count());
});
}
@Test
public void testOneRowPerUpdate() {
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
QueryCountHolder.clear();
Patient p = new Patient();
p.getPhotoFirstRep().setCreationElement(new DateTimeType("2011")); // non-indexed field
IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
assertEquals(3, QueryCountHolder.getGrandTotal().getInsert());
runInTransaction(() -> {
assertEquals(1, myResourceTableDao.count());
assertEquals(1, myResourceHistoryTableDao.count());
});
QueryCountHolder.clear();
p = new Patient();
p.setId(id);
p.getPhotoFirstRep().setCreationElement(new DateTimeType("2012")); // non-indexed field
myPatientDao.update(p).getId().toUnqualifiedVersionless();
assertEquals(1, QueryCountHolder.getGrandTotal().getInsert());
runInTransaction(() -> {
assertEquals(1, myResourceTableDao.count());
assertEquals(2, myResourceHistoryTableDao.count());
});
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTagSnapshotTest.java
View File

@ -39,9 +39,7 @@ public class FhirResourceDaoR4UpdateTagSnapshotTest extends BaseJpaR4Test {
myPatientDao.update(p, mySrd);
p = myPatientDao.read(new IdType("A"), mySrd);
// It would be nice if this didn't trigger a version update but
// i guess it's not so bad that it does
assertEquals("2", p.getIdElement().getVersionIdPart());
assertEquals("1", p.getIdElement().getVersionIdPart());
assertEquals(true, p.getActive());
assertEquals(1, p.getMeta().getTag().size());
}
@ -86,9 +84,7 @@ public class FhirResourceDaoR4UpdateTagSnapshotTest extends BaseJpaR4Test {
myPatientDao.update(p, mySrd);
p = myPatientDao.read(new IdType("A"), mySrd);
// It would be nice if this didn't trigger a version update but
// i guess it's not so bad that it does
assertEquals("2", p.getIdElement().getVersionIdPart());
assertEquals("1", p.getIdElement().getVersionIdPart());
assertEquals(true, p.getActive());
assertEquals(1, p.getMeta().getTag().size());
assertEquals("urn:foo", p.getMeta().getTag().get(0).getSystem());
@ -136,9 +132,7 @@ public class FhirResourceDaoR4UpdateTagSnapshotTest extends BaseJpaR4Test {
p = myPatientDao.read(new IdType("A"), mySrd);
assertEquals(true, p.getActive());
assertEquals(0, p.getMeta().getTag().size());
// It would be nice if this didn't trigger a version update but
// i guess it's not so bad that it does
assertEquals("2", p.getIdElement().getVersionIdPart());
assertEquals("1", p.getIdElement().getVersionIdPart());
}
@AfterClass

29
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UpdateTest.java
View File

@ -39,35 +39,6 @@ public class FhirResourceDaoR4UpdateTest extends BaseJpaR4Test {
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
}
@Test
public void testOneRowPerUpdate(){
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
QueryCountHolder.clear();
Patient p = new Patient();
p.getPhotoFirstRep().setCreationElement(new DateTimeType("2011")); // non-indexed field
IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
assertEquals(3, QueryCountHolder.getGrandTotal().getInsert());
runInTransaction(()->{
assertEquals(1, myResourceTableDao.count());
assertEquals(1, myResourceHistoryTableDao.count());
});
QueryCountHolder.clear();
p = new Patient();
p.setId(id);
p.getPhotoFirstRep().setCreationElement(new DateTimeType("2012")); // non-indexed field
myPatientDao.update(p).getId().toUnqualifiedVersionless();
assertEquals(1, QueryCountHolder.getGrandTotal().getInsert());
runInTransaction(()->{
assertEquals(1, myResourceTableDao.count());
assertEquals(2, myResourceHistoryTableDao.count());
});
}
@Test
public void testCreateAndUpdateWithoutRequest() {
String methodName = "testUpdateByUrl";