From 838b7d84fc564164e8fa7410b9c5f5ba76a540f4 Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Tue, 14 Feb 2012 11:57:15 +0000
Subject: [PATCH] LMS-2768 fixing performance of sample_relationships and
dataset_relationships
SVN: 24448
---
.../dataaccess/db/DatabaseVersionHolder.java | 2 +-
.../server/dataaccess/db/DeletionDAO.java | 128 ++++++++++++++++++
.../shared/dto/DataSetRelationshipPE.java | 107 +++++++++++++++
.../dto/DeletedSampleRelationshipPE.java | 23 ++++
.../shared/dto/SampleRelationshipPE.java | 19 +++
.../shared/translator/DataSetTranslator.java | 3 +
openbis/source/java/hibernateContext.xml | 4 +-
7 files changed, 283 insertions(+), 3 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetRelationshipPE.java
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseVersionHolder.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseVersionHolder.java
index e0b79c6048b..59a7e5f6953 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseVersionHolder.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseVersionHolder.java
@@ -24,7 +24,7 @@ package ch.systemsx.cisd.openbis.generic.server.dataaccess.db;
public final class DatabaseVersionHolder
{
/** Current version of the database. */
- private static final String DATABASE_VERSION = "097"; // S125
+ private static final String DATABASE_VERSION = "098"; // S125
private DatabaseVersionHolder()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DeletionDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DeletionDAO.java
index b70533e81ef..75a166640ab 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DeletionDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DeletionDAO.java
@@ -47,6 +47,8 @@ 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.IDeletablePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleRelationshipPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
@@ -159,11 +161,46 @@ final class DeletionDAO extends AbstractGenericEntityDAO<DeletionPE> implements
});
+ switch (entityKind)
+ {
+ case SAMPLE:
+ revertDeletionOfRelationships(deletion, TableNames.SAMPLE_RELATIONSHIPS_ALL_TABLE);
+ break;
+ case DATA_SET:
+ revertDeletionOfRelationships(deletion, TableNames.DATA_SET_RELATIONSHIPS_ALL_TABLE);
+ break;
+ case EXPERIMENT:
+ break;
+ case MATERIAL:
+ break;
+ }
+
scheduleDynamicPropertiesEvaluationByIds(TechId.asLongs(ids), entityKind);
operationLog.info(String.format("%s %s(s) reverted", updatedRows, entityKind.name()));
}
+ private void revertDeletionOfRelationships(final DeletionPE deletion, final String tableName)
+ {
+ assert deletion != null : "Unspecified deletion";
+
+ int updatedRows = (Integer) executeStatelessAction(new StatelessHibernateCallback()
+ {
+
+ public Object doInStatelessSession(StatelessSession session)
+ {
+ String query =
+ String.format("UPDATE %s SET del_id = NULL WHERE del_id = :deletionId",
+ tableName);
+ final SQLQuery sqlQuery = session.createSQLQuery(query);
+ sqlQuery.setParameter("deletionId", HibernateUtils.getId(deletion));
+ return sqlQuery.executeUpdate();
+ }
+ });
+
+ operationLog.info(String.format("%s %s(s) reverted", updatedRows, tableName));
+ }
+
public List<TechId> findTrashedSampleIds(final List<TechId> deletionIds)
{
return findTrashedEntityIds(deletionIds, EntityKind.SAMPLE);
@@ -254,6 +291,21 @@ final class DeletionDAO extends AbstractGenericEntityDAO<DeletionPE> implements
.setParameterList("ids", TechId.asLongs(entityIds)).executeUpdate();
}
});
+
+ switch (entityKind)
+ {
+ case SAMPLE:
+ trashSampleRelationships(entityIds, deletion);
+ break;
+ case DATA_SET:
+ trashDataSetRelationships(entityIds, deletion);
+ break;
+ case EXPERIMENT:
+ break;
+ case MATERIAL:
+ break;
+ }
+
if (operationLog.isInfoEnabled())
{
operationLog.info(String.format("trashing %d %ss", updatedRows, entityKind.getLabel()));
@@ -266,6 +318,82 @@ final class DeletionDAO extends AbstractGenericEntityDAO<DeletionPE> implements
return updatedRows;
}
+ public int trashSampleRelationships(final List<TechId> samplesIds, final DeletionPE deletion)
+ throws DataAccessException
+ {
+ if (samplesIds.isEmpty())
+ {
+ return 0;
+ }
+ final HibernateTemplate hibernateTemplate = getHibernateTemplate();
+ int updatedRows = (Integer) hibernateTemplate.execute(new HibernateCallback()
+ {
+ //
+ // HibernateCallback
+ //
+ public final Object doInHibernate(final Session session) throws HibernateException,
+ SQLException
+ {
+ // NOTE: 'VERSIONED' makes modification time modified too
+ return session
+ .createQuery(
+ "UPDATE "
+ + SampleRelationshipPE.class.getSimpleName()
+ + " SET deletion = :deletion"
+ + " WHERE deletion IS NULL"
+ + " AND (parentSample.id IN (:ids) OR childSample.id in (:ids))")
+ .setParameter("deletion", deletion)
+ .setParameterList("ids", TechId.asLongs(samplesIds)).executeUpdate();
+ }
+ });
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info(String
+ .format("trashing %d %ss", updatedRows, "sample relationships."));
+ }
+ hibernateTemplate.flush();
+
+ return updatedRows;
+ }
+
+ public int trashDataSetRelationships(final List<TechId> dataSetIds, final DeletionPE deletion)
+ throws DataAccessException
+ {
+ if (dataSetIds.isEmpty())
+ {
+ return 0;
+ }
+ final HibernateTemplate hibernateTemplate = getHibernateTemplate();
+ int updatedRows = (Integer) hibernateTemplate.execute(new HibernateCallback()
+ {
+ //
+ // HibernateCallback
+ //
+ public final Object doInHibernate(final Session session) throws HibernateException,
+ SQLException
+ {
+ // NOTE: 'VERSIONED' makes modification time modified too
+ return session
+ .createQuery(
+ "UPDATE "
+ + SampleRelationshipPE.class.getSimpleName()
+ + " SET deletion = :deletion"
+ + " WHERE deletion IS NULL"
+ + " AND (parentDataSet.id IN (:ids) OR childDataSet.id in (:ids))")
+ .setParameter("deletion", deletion)
+ .setParameterList("ids", TechId.asLongs(dataSetIds)).executeUpdate();
+ }
+ });
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info(String.format("trashing %d %ss", updatedRows,
+ "data set relationships."));
+ }
+ hibernateTemplate.flush();
+
+ return updatedRows;
+ }
+
public List<DeletionPE> findAllById(List<Long> ids)
{
if (ids.isEmpty())
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetRelationshipPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetRelationshipPE.java
new file mode 100644
index 00000000000..76f1d092d13
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetRelationshipPE.java
@@ -0,0 +1,107 @@
+/*
+ * Copyright 2010 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.shared.dto;
+
+import java.io.Serializable;
+
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+import org.hibernate.validator.NotNull;
+
+import ch.systemsx.cisd.openbis.generic.shared.IServer;
+
+/**
+ * <i>Persistent Entity</i> object representing data set relationship.
+ *
+ * @author Pawel Glyzewski
+ */
+@Entity
+@Table(name = TableNames.DATA_SET_RELATIONSHIPS_VIEW, uniqueConstraints = @UniqueConstraint(columnNames =
+ { ColumnNames.DATA_PARENT_COLUMN, ColumnNames.DATA_CHILD_COLUMN }))
+public class DataSetRelationshipPE implements Serializable
+{
+ private static final long serialVersionUID = IServer.VERSION;
+
+ private DataPE parentDataSet;
+
+ private DataPE childDataSet;
+
+ /**
+ * Deletion information.
+ * <p>
+ * If not <code>null</code>, then this data set is considered <i>deleted</i> (moved to trash).
+ * </p>
+ */
+ private DeletionPE deletion;
+
+ @Deprecated
+ public DataSetRelationshipPE()
+ {
+ }
+
+ public DataSetRelationshipPE(DataPE parentDataSet, DataPE childDataSet)
+ {
+ this.parentDataSet = parentDataSet;
+ this.childDataSet = childDataSet;
+ }
+
+ @NotNull(message = ValidationMessages.PARENT_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATA_PARENT_COLUMN)
+ @Id
+ public DataPE getParentDataSet()
+ {
+ return parentDataSet;
+ }
+
+ public void setParentDataSet(DataPE parentDataSet)
+ {
+ this.parentDataSet = parentDataSet;
+ }
+
+ @NotNull(message = ValidationMessages.CHILD_NOT_NULL_MESSAGE)
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DATA_CHILD_COLUMN)
+ @Id
+ public DataPE getChildDataSet()
+ {
+ return childDataSet;
+ }
+
+ public void setChildDataSet(DataPE childDataSet)
+ {
+ this.childDataSet = childDataSet;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DELETION_COLUMN)
+ public DeletionPE getDeletion()
+ {
+ return deletion;
+ }
+
+ public void setDeletion(final DeletionPE deletion)
+ {
+ this.deletion = deletion;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DeletedSampleRelationshipPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DeletedSampleRelationshipPE.java
index d003243ac93..9ce620438db 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DeletedSampleRelationshipPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DeletedSampleRelationshipPE.java
@@ -18,9 +18,12 @@ package ch.systemsx.cisd.openbis.generic.shared.dto;
import javax.persistence.Column;
import javax.persistence.Entity;
+import javax.persistence.FetchType;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
@@ -42,6 +45,14 @@ public class DeletedSampleRelationshipPE
private Long parentId;
+ /**
+ * Deletion information.
+ * <p>
+ * If not <code>null</code>, then this data set is considered <i>deleted</i> (moved to trash).
+ * </p>
+ */
+ private DeletionPE deletion;
+
@Id
@SequenceGenerator(name = SequenceNames.SAMPLE_SEQUENCE, sequenceName = SequenceNames.SAMPLE_SEQUENCE, allocationSize = 1)
@GeneratedValue(strategy = GenerationType.SEQUENCE, generator = SequenceNames.SAMPLE_SEQUENCE)
@@ -66,4 +77,16 @@ public class DeletedSampleRelationshipPE
{
this.parentId = parentId;
}
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DELETION_COLUMN)
+ public DeletionPE getDeletion()
+ {
+ return deletion;
+ }
+
+ public void setDeletion(final DeletionPE deletion)
+ {
+ this.deletion = deletion;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationshipPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationshipPE.java
index eed7562e204..9ed337a498d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationshipPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleRelationshipPE.java
@@ -54,6 +54,14 @@ public class SampleRelationshipPE implements Serializable
private RelationshipTypePE relationship;
+ /**
+ * Deletion information.
+ * <p>
+ * If not <code>null</code>, then this data set is considered <i>deleted</i> (moved to trash).
+ * </p>
+ */
+ private DeletionPE deletion;
+
@Deprecated
public SampleRelationshipPE()
{
@@ -121,4 +129,15 @@ public class SampleRelationshipPE implements Serializable
this.id = id;
}
+ @ManyToOne(fetch = FetchType.EAGER)
+ @JoinColumn(name = ColumnNames.DELETION_COLUMN)
+ public DeletionPE getDeletion()
+ {
+ return deletion;
+ }
+
+ public void setDeletion(final DeletionPE deletion)
+ {
+ this.deletion = deletion;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
index bbf9df2d7f5..4dd70b494ba 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
@@ -142,6 +142,7 @@ public class DataSetTranslator
public static ExternalData translate(DataPE dataPE, String baseIndexURL, boolean withDetails,
final LoadableFields... withExperimentFields)
{
+ long start = System.currentTimeMillis();
ExternalData externalData = null;
if (dataPE.isContainer())
{
@@ -184,6 +185,8 @@ public class DataSetTranslator
externalData.setExperiment(ExperimentTranslator.translate(experiment, baseIndexURL,
withExperimentFields));
externalData.setDeletion(DeletionTranslator.translate(dataPE.getDeletion()));
+ long end = System.currentTimeMillis();
+ System.out.println("CCCCCCCCCCCCCCCC: " + (end - start));
return externalData;
}
diff --git a/openbis/source/java/hibernateContext.xml b/openbis/source/java/hibernateContext.xml
index cca7c8ee042..11a2d3c0a5c 100644
--- a/openbis/source/java/hibernateContext.xml
+++ b/openbis/source/java/hibernateContext.xml
@@ -91,6 +91,7 @@
<value>ch.systemsx.cisd.openbis.generic.shared.dto.DeletedSamplePE</value>
<value>ch.systemsx.cisd.openbis.generic.shared.dto.DeletedSampleRelationshipPE</value>
<value>ch.systemsx.cisd.openbis.generic.shared.dto.CorePluginPE</value>
+ <value>ch.systemsx.cisd.openbis.generic.shared.dto.DataSetRelationshipPE</value>
<value>ch.systemsx.cisd.openbis.generic.shared.dto.PostRegistrationPE</value>
</list>
@@ -125,8 +126,7 @@
<!-- Uncomment this for debugging the Hibernate sql queries
<prop key="hibernate.show_sql">true</prop>
<prop key="hibernate.use_sql_comments">true</prop>
-<prop key="hibernate.format_sql">true</prop>
- -->
+<prop key="hibernate.format_sql">true</prop> -->
</props>
</property>
--
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