diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
index 10a25de603ee055c7fe9006b832ed3c919d04680..9949b4a770392bcbc846f494e6906c994d8268b4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
@@ -546,7 +546,7 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
sample.getIdentifier(), parentToAdd.getIdentifier());
} else
{
- final Set<TechId> nextToVisit = getSampleDAO().listParents(toVisit, relationship);
+ final Set<TechId> nextToVisit = getSampleDAO().listSampleIdsByChildrenIds(toVisit, relationship);
visited.addAll(toVisit);
nextToVisit.removeAll(visited);
toVisit = nextToVisit;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
index 170707cc51d3ea5f7c6a69e91f8c260dbcfa784c..4c73d12f65ee6c42c4b804447f2393eec07ea8db 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
@@ -235,15 +235,17 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
dataSets.addAll(getDataDAO().listDataSets(experiment));
}
- public void trashLoadedDataSets(DeletionPE deletion)
+ public int trashByTechIds(List<TechId> dataSetIds, DeletionPE deletion)
+ throws UserFailureException
{
try
{
- getDataDAO().trash(dataSets, deletion);
+ return getDataDAO().trash(dataSetIds, deletion);
} catch (final DataAccessException ex)
{
throwException(ex, "Data Set", EntityKind.DATA_SET);
}
+ return -1; // not possible
}
public void deleteLoadedDataSets(String reason)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
index 3a4d955105c3596eace446586f098daec1bedd6e..20348f239ed3d73dd30ab3cd3bff3bbc1fbfcb18 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
@@ -39,6 +39,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DeletionPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
@@ -47,7 +48,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DeletionPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -208,19 +208,17 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
+ "') not found in experiment '" + experiment.getIdentifier() + "'.");
}
- public void trashByTechIds(List<TechId> experimentIds, DeletionPE deletion)
+ public int trashByTechIds(List<TechId> experimentIds, DeletionPE deletion)
throws UserFailureException
{
try
{
- getSessionFactory().getCurrentSession().flush();
- getSessionFactory().getCurrentSession().clear();
-
- getExperimentDAO().trash(experimentIds, deletion);
+ return getExperimentDAO().trash(experimentIds, deletion);
} catch (final DataAccessException ex)
{
throwException(ex, "Experiment", EntityKind.EXPERIMENT);
}
+ return -1; // not possible
}
public void deleteByTechIds(List<TechId> experimentIds, String reason)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java
index 270b74eb5b4454d862f8cd84f2a6dce453f5ebcc..d3bb6d8ffc3b250dc0510a97d772153eb2f84c7c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataSetTable.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.List;
import java.util.Map;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LinkModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewDataSet;
@@ -70,9 +71,13 @@ public interface IDataSetTable
void setDataSets(List<DataPE> dataSets);
/**
- * Moves loaded data sets to trash for specified reason.
+ * Moves data sets to trash with given deletion.
+ *
+ * @param dataSetIds data set technical identifiers
+ * @throws UserFailureException if one of the data sets can not be moved to trash.
*/
- void trashLoadedDataSets(DeletionPE deletion);
+ public int trashByTechIds(List<TechId> dataSetIds, DeletionPE deletion)
+ throws UserFailureException;
/**
* Permanently Deletes loaded data sets for specified reason.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExperimentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExperimentBO.java
index 668340e2f37c6a41d1d6433e42b6efd2e035bdf1..6d4512b92111263d5aad09625e277872afa28b63 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExperimentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExperimentBO.java
@@ -89,7 +89,7 @@ public interface IExperimentBO extends IEntityBusinessObject
* @param experimentIds experiment technical identifiers
* @throws UserFailureException if one of the experiments can not be moved to trash.
*/
- void trashByTechIds(List<TechId> experimentIds, DeletionPE deletion);
+ int trashByTechIds(List<TechId> experimentIds, DeletionPE deletion);
/**
* Changes the value of a managed property.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
index 68a1b38f937e42961ef7112126130bd8a0493e3e..1fa3e8fcc176a2e41fd8a798af9e8c37dc0eacea 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleTable.java
@@ -78,7 +78,7 @@ public interface ISampleTable
* @param sampleIds sample technical identifiers
* @throws UserFailureException if one of the samples can not be moved to trash.
*/
- public void trashByTechIds(List<TechId> sampleIds, DeletionPE deletion)
+ public int trashByTechIds(List<TechId> sampleIds, DeletionPE deletion)
throws UserFailureException;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ITrashBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ITrashBO.java
index e155d2689ded13ac1660d7158bef12212b6f3679..300a60a559c61ebed9107362d109208016bb6b07 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ITrashBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ITrashBO.java
@@ -19,7 +19,6 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
/**
* Handles the trash of entities.
@@ -34,7 +33,7 @@ public interface ITrashBO
public void trashExperiments(List<TechId> experimentIds);
- public void trashDataSets(List<DataPE> dataSets);
+ public void trashDataSets(List<TechId> dataSetIds);
/** Puts back all entities moved to trash in deletion with specified id. */
public void revertDeletion(TechId deletionId);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
index 5c2f74eb54047a9a8a3ee3839d950c91b4ac53cb..5942b4b7f07601b0d445a63e0f49033243de4a01 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
@@ -31,10 +31,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleBatchUpdateDetails;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DeletionPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DeletionPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
@@ -341,19 +341,17 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
}
}
- public void trashByTechIds(List<TechId> sampleIds, DeletionPE deletion)
+ public int trashByTechIds(List<TechId> sampleIds, DeletionPE deletion)
throws UserFailureException
{
try
{
- getSessionFactory().getCurrentSession().flush();
- getSessionFactory().getCurrentSession().clear();
-
- getSampleDAO().trash(sampleIds, deletion);
+ return getSampleDAO().trash(sampleIds, deletion);
} catch (final DataAccessException ex)
{
throwException(ex, "Sample", EntityKind.SAMPLE);
}
+ return -1; // not possible
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBO.java
index 8132222cf562894f429ceb86e3e8dccb9080f7b2..de43071759f206b50b0b0052c9f2359ef3d67efe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/TrashBO.java
@@ -16,13 +16,15 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
+import java.util.ArrayList;
import java.util.List;
import org.springframework.dao.DataAccessException;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DeletionPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -60,22 +62,57 @@ public class TrashBO extends AbstractBusinessObject implements ITrashBO
{
assert deletion != null;
ISampleTable sampleTableBO = boFactory.createSampleTable(session);
- sampleTableBO.trashByTechIds(sampleIds, deletion);
+ int trashedCount = sampleTableBO.trashByTechIds(sampleIds, deletion);
+ if (trashedCount > 0)
+ {
+ trashSampleDependentChildrenAndComponents(sampleIds);
+ trashSampleDependentDataSets(sampleIds);
+ }
}
public void trashExperiments(List<TechId> experimentIds)
{
assert deletion != null;
IExperimentBO experimentBO = boFactory.createExperimentBO(session);
- experimentBO.trashByTechIds(experimentIds, deletion);
+ int trashedCount = experimentBO.trashByTechIds(experimentIds, deletion);
+ if (trashedCount > 0)
+ {
+ trashExperimentDependentDataSets(experimentIds);
+ trashExperimentDependentSamples(experimentIds);
+ }
}
- public void trashDataSets(List<DataPE> dataSets)
+ public void trashDataSets(List<TechId> dataSetIds)
{
assert deletion != null;
IDataSetTable dataSetTable = boFactory.createDataSetTable(session);
- dataSetTable.setDataSets(dataSets);
- dataSetTable.trashLoadedDataSets(deletion);
+ dataSetTable.trashByTechIds(dataSetIds, deletion);
+ // NOTE: data set children are not cascade trashed - a conscious decision made by Tomek
+ }
+
+ private void trashSampleDependentChildrenAndComponents(List<TechId> sampleIds)
+ {
+ ISampleDAO sampleDAO = getSampleDAO();
+ trashSamples(new ArrayList<TechId>(sampleDAO.listSampleIdsByParentIds(sampleIds)));
+ trashSamples(sampleDAO.listSampleIdsByContainerIds(sampleIds));
+ }
+
+ private void trashSampleDependentDataSets(List<TechId> sampleIds)
+ {
+ IDataDAO dataDAO = getDataDAO();
+ trashDataSets(dataDAO.listDataSetIdsBySampleIds(sampleIds));
+ }
+
+ private void trashExperimentDependentSamples(List<TechId> experimentIds)
+ {
+ ISampleDAO sampleDAO = getSampleDAO();
+ trashSamples(sampleDAO.listSampleIdsByExperimentIds(experimentIds));
+ }
+
+ private void trashExperimentDependentDataSets(List<TechId> experimentIds)
+ {
+ IDataDAO dataDAO = getDataDAO();
+ trashDataSets(dataDAO.listDataSetIdsByExperimentIds(experimentIds));
}
public void revertDeletion(TechId deletionId)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataDAO.java
index 67fb17eb21e8355559a9645c9701feb5810a2f64..d79f4e2a933a9ca0249a3b1a7c01281071add610 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataDAO.java
@@ -120,9 +120,13 @@ public interface IDataDAO extends IGenericDAO<DataPE>
public void updateDataSets(List<DataPE> externalData);
- /**
- * Move given data sets to trash using specified deletion.
- */
- public void trash(List<DataPE> dataSets, DeletionPE deletion) throws DataAccessException;
+ /** Move given data sets to trash using specified deletion. */
+ public int trash(List<TechId> dataSetIds, DeletionPE deletion) throws DataAccessException;
+
+ /** Returns ids of data sets connected with samples specified by given ids. */
+ public List<TechId> listDataSetIdsBySampleIds(final Collection<TechId> samples);
+
+ /** Returns ids of data sets connected with experiments specified by given ids. */
+ public List<TechId> listDataSetIdsByExperimentIds(final Collection<TechId> samples);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java
index 8a52959b90e4255d20bf7fb37df99c1007f345b1..924057cf6fef822f38fdf30449993a4e34091136 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java
@@ -110,6 +110,6 @@ public interface IExperimentDAO extends IGenericDAO<ExperimentPE>
/**
* Move experiments with given ids to trash using specified deletion.
*/
- public void trash(List<TechId> experimentIds, DeletionPE deletion);
+ public int trash(List<TechId> experimentIds, DeletionPE deletion);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java
index b136bfeafa3c809a7084504f7fd22acc23c7ad7d..bb35bce72172e509518765e730103512adb72c43 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ISampleDAO.java
@@ -93,16 +93,25 @@ public interface ISampleDAO extends IGenericDAO<SamplePE>
List<SamplePE> listSamplesByGeneratedFrom(final SamplePE sample) throws DataAccessException;
/**
- * @return Unique set of ids of parents of data sets specified by ids.
- * <p>
- * NOTE: does not check if specified ids are proper data set ids.
+ * Returns ids of parents of samples specified by given ids and connected by chosen relationship
+ * type.
*/
+ public Set<TechId> listSampleIdsByChildrenIds(Collection<TechId> children, TechId relationship);
/**
- * Returns ids of parents of samples specified by given ids and connected by chosen relationship
- * type.
+ * Returns ids of children of samples specified by given ids.
+ * <p>
+ * NOTES:
+ * <li>we don't use relationship type as don't really support different relationship types
+ * <li>we need a set as the connection is many-to-many and we want unique ids
*/
- public Set<TechId> listParents(Collection<TechId> children, TechId relationship);
+ public Set<TechId> listSampleIdsByParentIds(Collection<TechId> parentIds);
+
+ /** Returns ids of components of samples specified by given ids. */
+ public List<TechId> listSampleIdsByContainerIds(Collection<TechId> containerIds);
+
+ /** Returns ids of samples connected with experiments specified by given ids. */
+ List<TechId> listSampleIdsByExperimentIds(Collection<TechId> experimentIds);
/**
* Lists samples (with minimal additional information) belonging to the given <code>space</code>
@@ -126,5 +135,6 @@ public interface ISampleDAO extends IGenericDAO<SamplePE>
/**
* Move samples with given ids to trash using specified deletion.
*/
- void trash(List<TechId> sampleIds, DeletionPE deletion) throws DataAccessException;
+ int trash(List<TechId> sampleIds, DeletionPE deletion) throws DataAccessException;
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
index 8eb96cea9308f049b95304d55d145a6d785cf630..650a1753641d783cfefadfb6e4123483daf25dcb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
@@ -464,18 +464,40 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
super.delete(entity);
}
- public void trash(List<DataPE> dataSets, DeletionPE deletion) throws DataAccessException
+ public int trash(final List<TechId> dataSetIds, final DeletionPE deletion)
+ throws DataAccessException
{
- // TODO 2011-06-16, Piotr Buczek: could be done faster with bulk update
- for (DataPE dataSet : dataSets)
+ if (dataSetIds.isEmpty())
{
- if (dataSet.getDeletion() == null)
- {
- dataSet.setDeletion(deletion);
- }
+ return 0;
}
+ final HibernateTemplate hibernateTemplate = getHibernateTemplate();
+ int updatedRows = (Integer) hibernateTemplate.execute(new HibernateCallback()
+ {
+
+ //
+ // HibernateCallback
+ //
- getHibernateTemplate().flush();
+ public final Object doInHibernate(final Session session) throws HibernateException,
+ SQLException
+ {
+ // NOTE: 'VERSIONED' makes modification time modified too
+ return session
+ .createQuery(
+ "UPDATE VERSIONED "
+ + DataPE.class.getSimpleName()
+ + " SET deletion = :deletion WHERE deletion IS NULL AND id IN (:ids) ")
+ .setParameter("deletion", deletion)
+ .setParameterList("ids", TechId.asLongs(dataSetIds)).executeUpdate();
+ }
+ });
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info(String.format("trashing %d data sets", updatedRows));
+ }
+ hibernateTemplate.flush();
+ return updatedRows;
}
@SuppressWarnings("unchecked")
@@ -556,4 +578,33 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
scheduleDynamicPropertiesEvaluation(Arrays.asList(entity));
}
+ public List<TechId> listDataSetIdsBySampleIds(final Collection<TechId> samples)
+ {
+ final DetachedCriteria criteria = DetachedCriteria.forClass(DataPE.class);
+ final List<Long> longIds = TechId.asLongs(samples);
+ criteria.setProjection(Projections.id());
+ criteria.add(Restrictions.in("sampleInternal.id", longIds));
+ final List<Long> results = cast(getHibernateTemplate().findByCriteria(criteria));
+ if (operationLog.isDebugEnabled())
+ {
+ operationLog.info(String.format("found %s data sets for given samples", results.size()));
+ }
+ return transformNumbers2TechIdList(results);
+ }
+
+ public List<TechId> listDataSetIdsByExperimentIds(final Collection<TechId> experiments)
+ {
+ final DetachedCriteria criteria = DetachedCriteria.forClass(DataPE.class);
+ final List<Long> longIds = TechId.asLongs(experiments);
+ criteria.setProjection(Projections.id());
+ criteria.add(Restrictions.in("experimentInternal.id", longIds));
+ final List<Long> results = cast(getHibernateTemplate().findByCriteria(criteria));
+ if (operationLog.isDebugEnabled())
+ {
+ operationLog
+ .info(String.format("found %s data sets for given experiments", results.size()));
+ }
+ return transformNumbers2TechIdList(results);
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java
index 98d6a1632c93460dc3b1db32d461d0a4f89e3592..756de7db2665d3725ad1962b9ddb996c30eb814a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.db;
+import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
@@ -25,9 +26,12 @@ import java.util.Set;
import org.apache.log4j.Logger;
import org.hibernate.Criteria;
import org.hibernate.FetchMode;
+import org.hibernate.HibernateException;
+import org.hibernate.Session;
import org.hibernate.criterion.DetachedCriteria;
import org.hibernate.criterion.Restrictions;
import org.springframework.dao.DataAccessException;
+import org.springframework.orm.hibernate3.HibernateCallback;
import org.springframework.orm.hibernate3.HibernateTemplate;
import ch.systemsx.cisd.common.logging.LogCategory;
@@ -38,10 +42,10 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DeletionPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DeletionPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
@@ -300,20 +304,40 @@ public class ExperimentDAO extends AbstractGenericEntityWithPropertiesDAO<Experi
}
}
- public void trash(final List<TechId> experimentIds, final DeletionPE deletion)
+ public int trash(final List<TechId> experimentIds, final DeletionPE deletion)
throws DataAccessException
{
- // TODO 2011-06-16, Piotr Buczek: could be done faster with bulk update
- for (TechId experimentId : experimentIds)
+ if (experimentIds.isEmpty())
{
- ExperimentPE experiment = loadByTechId(experimentId);
- if (experiment.getDeletion() == null)
- {
- experiment.setDeletion(deletion);
- }
+ return 0;
}
+ final HibernateTemplate hibernateTemplate = getHibernateTemplate();
+ int updatedRows = (Integer) hibernateTemplate.execute(new HibernateCallback()
+ {
- getHibernateTemplate().flush();
+ //
+ // HibernateCallback
+ //
+
+ public final Object doInHibernate(final Session session) throws HibernateException,
+ SQLException
+ {
+ // NOTE: 'VERSIONED' makes modification time modified too
+ return session
+ .createQuery(
+ "UPDATE VERSIONED "
+ + ExperimentPE.class.getSimpleName()
+ + " SET deletion = :deletion WHERE deletion IS NULL AND id IN (:ids) ")
+ .setParameter("deletion", deletion)
+ .setParameterList("ids", TechId.asLongs(experimentIds)).executeUpdate();
+ }
+ });
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info(String.format("trashing %d experiments", updatedRows));
+ }
+ hibernateTemplate.flush();
+ return updatedRows;
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
index 2c6e7f8067616c9568e0d6a5ad9ceb290377d58f..5f1d9619aad0886bbb01b4c2de48bb0fbbd20a97 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAO.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.db;
+import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
@@ -25,11 +26,13 @@ import java.util.Set;
import org.apache.log4j.Logger;
import org.hibernate.Criteria;
import org.hibernate.FetchMode;
+import org.hibernate.HibernateException;
import org.hibernate.SQLQuery;
import org.hibernate.Session;
import org.hibernate.StatelessSession;
import org.hibernate.criterion.Criterion;
import org.hibernate.criterion.DetachedCriteria;
+import org.hibernate.criterion.Projections;
import org.hibernate.criterion.Restrictions;
import org.springframework.dao.DataAccessException;
import org.springframework.jdbc.support.JdbcAccessor;
@@ -464,27 +467,48 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
scheduleRemoveFromFullTextIndex(ids);
}
- public void trash(final List<TechId> sampleIds, final DeletionPE deletion)
+ public int trash(final List<TechId> sampleIds, final DeletionPE deletion)
throws DataAccessException
{
- // TODO 2011-06-16, Piotr Buczek: could be done faster with bulk update
- for (TechId sampleId : sampleIds)
+ if (sampleIds.isEmpty())
{
- SamplePE sample = loadByTechId(sampleId);
- if (sample.getDeletion() == null)
- {
- sample.setDeletion(deletion);
- }
+ return 0;
}
+ final HibernateTemplate hibernateTemplate = getHibernateTemplate();
+ int updatedRows = (Integer) hibernateTemplate.execute(new HibernateCallback()
+ {
- getHibernateTemplate().flush();
+ //
+ // HibernateCallback
+ //
+
+ public final Object doInHibernate(final Session session) throws HibernateException,
+ SQLException
+ {
+ // NOTE: 'VERSIONED' makes modification time modified too
+ return session
+ .createQuery(
+ "UPDATE VERSIONED "
+ + SamplePE.class.getSimpleName()
+ + " SET deletion = :deletion WHERE deletion IS NULL AND id IN (:ids) ")
+ .setParameter("deletion", deletion)
+ .setParameterList("ids", TechId.asLongs(sampleIds)).executeUpdate();
+ }
+ });
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info(String.format("trashing %d samples", updatedRows));
+ }
+ hibernateTemplate.flush();
+ return updatedRows;
}
- @SuppressWarnings("unchecked")
- public Set<TechId> listParents(final Collection<TechId> children, final TechId relationship)
+ public Set<TechId> listSampleIdsByChildrenIds(final Collection<TechId> children,
+ final TechId relationship)
{
final String query =
"select sample_id_parent from sample_relationships where sample_id_child in (:ids) and relationship_id = :r ";
+ @SuppressWarnings("unchecked")
final List<? extends Number> results =
(List<? extends Number>) getHibernateTemplate().execute(new HibernateCallback()
{
@@ -499,10 +523,65 @@ public class SampleDAO extends AbstractGenericEntityWithPropertiesDAO<SamplePE>
Set<TechId> result = transformNumbers2TechIdSet(results);
if (operationLog.isDebugEnabled())
{
- operationLog.debug(String.format("%d sample parents(s) have been found.",
+ operationLog.debug(String.format("found %d sample parents for given children",
results.size()));
}
return result;
}
+ public Set<TechId> listSampleIdsByParentIds(final Collection<TechId> parents)
+ {
+ final String query =
+ "SELECT sample_id_child FROM " + TableNames.SAMPLE_RELATIONSHIPS_TABLE
+ + " WHERE sample_id_parent IN (:ids)";
+ @SuppressWarnings("unchecked")
+ final List<? extends Number> results =
+ (List<? extends Number>) getHibernateTemplate().execute(new HibernateCallback()
+ {
+
+ public final Object doInHibernate(final Session session)
+ {
+ final List<Long> longIds = TechId.asLongs(parents);
+ return session.createSQLQuery(query).setParameterList("ids", longIds)
+ .list();
+ }
+ });
+ Set<TechId> result = transformNumbers2TechIdSet(results);
+ if (operationLog.isDebugEnabled())
+ {
+ operationLog.info(String.format("found %d sample children for given parents",
+ results.size()));
+ }
+ return result;
+ }
+
+ public List<TechId> listSampleIdsByContainerIds(final Collection<TechId> containers)
+ {
+ final DetachedCriteria criteria = DetachedCriteria.forClass(SamplePE.class);
+ final List<Long> longIds = TechId.asLongs(containers);
+ criteria.setProjection(Projections.id());
+ criteria.add(Restrictions.in("container.id", longIds));
+ final List<Long> results = cast(getHibernateTemplate().findByCriteria(criteria));
+ if (operationLog.isDebugEnabled())
+ {
+ operationLog.info(String.format("found %s sample components for given containers",
+ results.size()));
+ }
+ return transformNumbers2TechIdList(results);
+ }
+
+ public List<TechId> listSampleIdsByExperimentIds(final Collection<TechId> experiments)
+ {
+ final DetachedCriteria criteria = DetachedCriteria.forClass(SamplePE.class);
+ final List<Long> longIds = TechId.asLongs(experiments);
+ criteria.setProjection(Projections.id());
+ criteria.add(Restrictions.in("experimentInternal.id", longIds));
+ final List<Long> results = cast(getHibernateTemplate().findByCriteria(criteria));
+ // if (operationLog.isDebugEnabled())
+ // {
+ operationLog.info(String.format("found %s samples for given experiments", results.size()));
+ // }
+ return transformNumbers2TechIdList(results);
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetTypeSlaveServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetTypeSlaveServerPlugin.java
index ece3c1d0f9c516be8a828bbf09bbaad47825805b..6e4b59f02495a52bd1a7a9e62795973c88f09c19 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetTypeSlaveServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetTypeSlaveServerPlugin.java
@@ -27,6 +27,7 @@ import ch.systemsx.cisd.openbis.generic.server.batch.DataSetBatchUpdate;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ITrashBO;
import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewDataSet;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
@@ -61,7 +62,7 @@ public class GenericDataSetTypeSlaveServerPlugin implements IDataSetTypeSlaveSer
case TRASH:
ITrashBO trashBO = businessObjectFactory.createTrashBO(session);
trashBO.createDeletion(reason);
- trashBO.trashDataSets(dataSets);
+ trashBO.trashDataSets(TechId.createList(dataSets));
break;
}
}