diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
index da6826ab588001a1ff779b8cb0a30c5bab7237de..f6ed78e85b6ee2059d51bafb93ebfd4a63cca30f 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
@@ -169,7 +169,7 @@ public class UploadingCommandTest extends AssertJUnit
DataSetTypePE dataSetTypePE = new DataSetTypePE();
dataSetTypePE.setCode("D");
externalData.setDataSetType(dataSetTypePE);
- externalData.setupExperiment(createExperiment());
+ externalData.setExperiment(createExperiment());
// TODO 2009-09-15, Piotr Buczek: write a test with no parents but with sample connection
// Does it make any difference how many parents are added here?
externalData.addParent(createParent("parent1"));
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
index cc55fa8421dab973cfb05feb017825a03c9d15d1..264f839c7c459d4888ccd7e8d84710fd92a68ff4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
@@ -140,7 +140,7 @@ public class ExternalDataBO extends AbstractExternalDataBusinessObject implement
define(data, sourceType);
externalData.setSample(sample);
- externalData.setupExperiment(sample.getExperiment());
+ externalData.setExperiment(sample.getExperiment());
}
public void define(NewExternalData data, ExperimentPE experiment, SourceType sourceType)
@@ -148,7 +148,7 @@ public class ExternalDataBO extends AbstractExternalDataBusinessObject implement
assert experiment != null : "Undefined experiment.";
DataStorePE dataStore = define(data, sourceType);
- externalData.setupExperiment(experiment);
+ externalData.setExperiment(experiment);
final List<String> parentDataSetCodes = data.getParentDataSetCodes();
if (parentDataSetCodes != null)
{
@@ -250,7 +250,7 @@ public class ExternalDataBO extends AbstractExternalDataBusinessObject implement
parent.setCode(parentDataSetCode);
String code = DataSetTypeCode.UNKNOWN.getCode();
parent.setDataSetType(getDataSetTypeDAO().tryToFindDataSetTypeByCode(code));
- parent.setupExperiment(experiment);
+ parent.setExperiment(experiment);
parent.setPlaceholder(true);
dataDAO.createDataSet(parent);
}
@@ -513,7 +513,7 @@ public class ExternalDataBO extends AbstractExternalDataBusinessObject implement
// move dataset to the experiment if needed
if (experiment.equals(externalData.getExperiment()) == false)
{
- externalData.setupExperiment(experiment);
+ externalData.setExperiment(experiment);
}
externalData.setSample(newSample);
}
@@ -522,7 +522,7 @@ public class ExternalDataBO extends AbstractExternalDataBusinessObject implement
{
assert experimentIdentifierOrNull != null;
ExperimentPE experiment = getExperimentByIdentifier(experimentIdentifierOrNull);
- externalData.setupExperiment(experiment);
+ externalData.setExperiment(experiment);
}
private ExperimentPE getExperimentByIdentifier(final ExperimentIdentifier identifier)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
index 33f053db4a1f868139db023e8d6a852a734ed74a..68bad133eabc543846967447d0bb5a7bbe043157 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
@@ -33,7 +33,6 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.IDataStoreServiceFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
-import ch.systemsx.cisd.openbis.generic.server.util.HibernateTransformer;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
@@ -323,9 +322,7 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
{
IDataStoreService service = dssFactory.create(dataStore.getRemoteUrl());
String sessionToken = dataStore.getSessionToken();
- List<ExternalData> cleanDataSets =
- ExternalDataTranslator.translate(HibernateTransformer.HIBERNATE_BEAN_REPLICATOR
- .get().copy(dataSets), "?", "?");
+ List<ExternalData> cleanDataSets = ExternalDataTranslator.translate(dataSets, "?", "?");
service.uploadDataSetsToCIFEX(sessionToken, cleanDataSets, context);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
index 8d5a180590c9b0d18f4d24f520ede0a81531b3e4..cd8f86dbfa698938a6098982bdf1dd6ea54dac8f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
@@ -340,7 +340,7 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
{
for (DataPE dataset : datasets)
{
- dataset.setupExperiment(experiment);
+ dataset.setExperiment(experiment);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/HibernateTransformer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/HibernateTransformer.java
deleted file mode 100644
index f0cee14925fd5bb5d71f92de97c32ef582b5e62d..0000000000000000000000000000000000000000
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/util/HibernateTransformer.java
+++ /dev/null
@@ -1,188 +0,0 @@
-/*
- * Copyright 2008 ETH Zuerich, CISD
- *
- * 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.
- */
-
-package ch.systemsx.cisd.openbis.generic.server.util;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import net.sf.beanlib.hibernate.HibernateBeanReplicator;
-import net.sf.beanlib.hibernate3.Hibernate3BeanTransformer;
-import net.sf.beanlib.hibernate3.Hibernate3CollectionReplicator;
-import net.sf.beanlib.hibernate3.Hibernate3JavaBeanReplicator;
-import net.sf.beanlib.spi.BeanTransformerSpi;
-import net.sf.beanlib.spi.replicator.BeanReplicatorSpi;
-import net.sf.beanlib.spi.replicator.CollectionReplicatorSpi;
-import net.sf.beanlib.spi.replicator.CollectionReplicatorSpi.Factory;
-
-import org.aopalliance.intercept.MethodInterceptor;
-import org.aopalliance.intercept.MethodInvocation;
-import org.hibernate.Hibernate;
-import org.hibernate.collection.PersistentCollection;
-import org.hibernate.proxy.HibernateProxy;
-
-import ch.systemsx.cisd.common.collections.UnmodifiableCollectionDecorator;
-import ch.systemsx.cisd.common.exceptions.NotImplementedException;
-
-/**
- * A {@link MethodInterceptor} implementation to get rid of <i>Hibernate</i> proxy classes like
- * {@link PersistentCollection} or {@link HibernateProxy}.
- * <p>
- * Note that this interceptor should only be used on the service layer (when the object is
- * <i>detached</i> and when database transactions are closed). Otherwise they might trigger <i>SQL</i>
- * calls.
- * </p>
- *
- * @author Christian Ribeaud
- */
-public final class HibernateTransformer implements MethodInterceptor
-{
-
- public final static ThreadLocal<HibernateBeanReplicator> HIBERNATE_BEAN_REPLICATOR =
- new ThreadLocal<HibernateBeanReplicator>()
- {
-
- private final HibernateBeanReplicator createHibernateBeanReplicator()
- {
- final Hibernate3BeanTransformer beanTransformer =
- Hibernate3BeanTransformer.newBeanTransformer();
- beanTransformer
- .initCollectionReplicatable(new CollectionReplicatorSpiFactory());
- beanTransformer.initBeanReplicatable(new BeanReplicatorSpiFactory());
- return new HibernateBeanReplicator(beanTransformer);
- }
-
- //
- // ThreadLocal
- //
-
- @Override
- protected final HibernateBeanReplicator initialValue()
- {
- return createHibernateBeanReplicator();
- }
- };
-
- //
- // MethodInterceptor
- //
-
- public final Object invoke(final MethodInvocation methodInvocation) throws Throwable
- {
- final Object proceed = methodInvocation.proceed();
- if (proceed != null)
- {
- return HIBERNATE_BEAN_REPLICATOR.get().copy(proceed);
- }
- return null;
- }
-
- //
- // Helper classes
- //
-
- private static final class BeanReplicatorSpiFactory implements BeanReplicatorSpi.Factory
- {
-
- //
- // Factory
- //
-
- public final BeanReplicatorSpi newBeanReplicatable(final BeanTransformerSpi beanTransformer)
- {
- return new NoInitializationHibernate3JavaBeanReplicator(beanTransformer);
- }
- }
-
- private static final class CollectionReplicatorSpiFactory implements Factory
- {
-
- //
- // Factory
- //
-
- public final CollectionReplicatorSpi newCollectionReplicatable(
- final BeanTransformerSpi beanTransformerSpi)
- {
- return new NoInitializationHibernate3CollectionReplicator(beanTransformerSpi);
- }
- }
-
- private static final class NoInitializationHibernate3CollectionReplicator extends
- Hibernate3CollectionReplicator
- {
-
- NoInitializationHibernate3CollectionReplicator(final BeanTransformerSpi beanTransformer)
- {
- super(beanTransformer);
- }
-
- //
- // Hibernate3CollectionReplicator
- //
-
- @SuppressWarnings("unchecked")
- @Override
- public final <V, T> T replicateCollection(final Collection<V> from, final Class<T> toClass)
- {
- final boolean unmodifiable = (from instanceof UnmodifiableCollectionDecorator);
- final Collection<V> realFrom =
- (unmodifiable) ? ((UnmodifiableCollectionDecorator<V>) from).getDecorated()
- : from;
- if (Hibernate.isInitialized(realFrom) == false)
- {
- if (realFrom instanceof Set)
- {
- return (T) new HashSet(0);
- } else if (realFrom instanceof List)
- {
- return (T) new ArrayList(0);
- } else
- {
- throw new NotImplementedException();
- }
- }
- return super.replicateCollection(realFrom, toClass);
- }
- }
-
- private static final class NoInitializationHibernate3JavaBeanReplicator extends
- Hibernate3JavaBeanReplicator
- {
-
- NoInitializationHibernate3JavaBeanReplicator(final BeanTransformerSpi beanTransformer)
- {
- super(beanTransformer);
- }
-
- //
- // Hibernate3JavaBeanReplicator
- //
-
- @Override
- public final <V, T> T replicateBean(final V from, final Class<T> toClass)
- {
- if (Hibernate.isInitialized(from) == false)
- {
- return null;
- }
- return super.replicateBean(from, toClass);
- }
- }
-}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
index 5c46b9999a20be14e240ef79418c4432bd0950b2..dfa6968a2e38c1cb50a431769579cc755d34ba1c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
@@ -387,7 +387,7 @@ public class DataPE extends AbstractIdAndCodeHolder<DataPE> implements IEntityPr
return code;
}
- public void setupExperiment(final ExperimentPE experiment)
+ public void setExperiment(final ExperimentPE experiment)
{
if (experiment != null)
{
diff --git a/openbis/source/java/genericApplicationContext.xml b/openbis/source/java/genericApplicationContext.xml
index e2e6b8a51a9643197975b367ac44d652a7f5bde1..9b10be83ea9da2c18504ee5fa695d239ab6401c5 100644
--- a/openbis/source/java/genericApplicationContext.xml
+++ b/openbis/source/java/genericApplicationContext.xml
@@ -111,7 +111,6 @@
<property name="interceptorNames">
<list>
<value>exception-translator</value>
- <value>hibernate-transformer</value>
</list>
</property>
</bean>
@@ -125,8 +124,6 @@
</property>
</bean>
- <bean id="hibernate-transformer" class="ch.systemsx.cisd.openbis.generic.server.util.HibernateTransformer" />
-
<!--
// Transaction
-->
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
index e9325e997c7fca7180d187ba893685ad8cdbbc57..f51a82e6ddba5424fd7d449f33c4566c64db7018 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
@@ -211,7 +211,7 @@ public class ExternalDataBOTest extends AbstractBOTest
final DataPE parentData = new DataPE();
parentData.setCode(PARENT_CODE);
parentData.setDataSetType(dataSetTypeUnknown);
- parentData.setupExperiment(createExperiment("EXP1"));
+ parentData.setExperiment(createExperiment("EXP1"));
parentData.setPlaceholder(true);
context.checking(new Expectations()
{
@@ -258,7 +258,7 @@ public class ExternalDataBOTest extends AbstractBOTest
parentData.setCode(PARENT_CODE);
parentData.setDataSetType(dataSetTypeUnknown);
ExperimentPE experiment = createExperiment("EXP1");
- parentData.setupExperiment(experiment);
+ parentData.setExperiment(experiment);
parentData.setPlaceholder(true);
context.checking(new Expectations()
{
@@ -454,7 +454,7 @@ public class ExternalDataBOTest extends AbstractBOTest
dataSet.setCode(DATA_SET_CODE);
dataSet.setModificationDate(PRODUCTION_DATE);
dataSet.setSample(sampleOrNull);
- dataSet.setupExperiment(experimentOrNull);
+ dataSet.setExperiment(experimentOrNull);
return dataSet;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
index f3230a245dc34575b490db1f1282a1aecf46a420..b14970ad9bedd4e3db964d29608b5d7ebbda0891 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
@@ -406,7 +406,7 @@ public final class ExternalDataTableTest extends AbstractBOTest
group.setDatabaseInstance(instance);
project.setGroup(group);
experiment.setProject(project);
- data.setupExperiment(experiment);
+ data.setExperiment(experiment);
return data;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAOTest.java
index f116b2f5acff7472cc4a171644b704cddbf00283..d49930050bfa507d8303f66fd2c2c31852310674 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAOTest.java
@@ -252,7 +252,7 @@ public class ExperimentDAOTest extends AbstractDAOTest
// Currently there is no such experiment in test DB so we first add a data set
// to an empty experiment (with no connections).
final ExternalDataPE dataSet = findExternalData("20081105092158673-1");
- dataSet.setupExperiment(deletedExperiment);
+ dataSet.setExperiment(deletedExperiment);
daoFactory.getExternalDataDAO().validateAndSaveUpdatedEntity(dataSet);
assertTrue(deletedExperiment.getAttachments().isEmpty());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAOTest.java
index cc1d3cc094cd232bd1233e67d61b98bd2355ae99..ccfdc1cf2081a2a4d663660beefca7e7b9e9e55e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAOTest.java
@@ -115,7 +115,7 @@ public final class ExternalDataDAOTest extends AbstractDAOTest
externalData.setCode(dataSetCode);
externalData.setDataSetType(getDataSetType(DataSetTypeCode.UNKNOWN));
- externalData.setupExperiment(pickAnExperiment());
+ externalData.setExperiment(pickAnExperiment());
if (sampleOrNull != null)
{
externalData.setSampleAcquiredFrom(sampleOrNull);
@@ -156,7 +156,7 @@ public final class ExternalDataDAOTest extends AbstractDAOTest
String dataSetCode = daoFactory.getPermIdDAO().createPermId();
data.setCode(dataSetCode);
data.setDataSetType(getDataSetType(DataSetTypeCode.UNKNOWN));
- data.setupExperiment(pickAnExperiment());
+ data.setExperiment(pickAnExperiment());
data.setSampleAcquiredFrom(pickASample());
data.setPlaceholder(true);
data.setDataStore(pickADataStore());
@@ -168,7 +168,7 @@ public final class ExternalDataDAOTest extends AbstractDAOTest
externalData.setCode(dataSetCode);
externalData.setDataSetType(getDataSetType(DataSetTypeCode.UNKNOWN));
externalData.setDataStore(pickADataStore());
- externalData.setupExperiment(pickAnExperiment());
+ externalData.setExperiment(pickAnExperiment());
externalData.setSampleAcquiredFrom(pickASample());
externalData.setFileFormatType(pickAFileFormatType());
externalData.setLocatorType(pickALocatorType());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/scalability/DBCreator.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/scalability/DBCreator.java
index bc361f9ce9b215ea1a6df910c644a4de0c825651..01f72627f56c8762c6b16517794f6b4b07e1dcec 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/scalability/DBCreator.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/scalability/DBCreator.java
@@ -324,7 +324,7 @@ public final class DBCreator extends AbstractDAOTest
String dataSetCode = daoFactory.getPermIdDAO().createPermId();
externalData.setCode(dataSetCode);
externalData.setDataSetType(defaultDataSetType);
- externalData.setupExperiment(sample.getExperiment());
+ externalData.setExperiment(sample.getExperiment());
externalData.setSampleAcquiredFrom(sample);
externalData.setFileFormatType(pickAFileFormatType());
externalData.setLocatorType(pickALocatorType());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java
index 9711c424ac4c3019bc7d0645d218e8e3339a62f1..8a1392cace9a1b781b4b7201777dffc2d9923d9e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslatorTest.java
@@ -98,7 +98,7 @@ public class ExternalDataTranslatorTest extends AssertJUnit
groupPE.setDatabaseInstance(databaseInstancePE);
projectPE.setGroup(groupPE);
experimentPE.setProject(projectPE);
- externalDataPE.setupExperiment(experimentPE);
+ externalDataPE.setExperiment(experimentPE);
externalDataPE.setProductionDate(new Date(1));
externalDataPE.setRegistrationDate(new Date(2));
SamplePE samplePE = new SamplePE();
@@ -163,7 +163,7 @@ public class ExternalDataTranslatorTest extends AssertJUnit
groupPE.setDatabaseInstance(databaseInstancePE);
projectPE.setGroup(groupPE);
experimentPE.setProject(projectPE);
- externalDataPE.setupExperiment(experimentPE);
+ externalDataPE.setExperiment(experimentPE);
externalDataPE.addParent(createParent("parent-1"));
externalDataPE.addParent(createParent("parent-2"));