From 14280b3d0d96b4a3faea6fbe4fc93570ee390b43 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Mon, 12 Nov 2012 22:40:45 +0000
Subject: [PATCH] Use a managed database connection where we used to get the
connection from the Hibernate session.
SVN: 27581
---
.../AuthorizationDataProvider.java | 7 ----
.../IAuthorizationDataProvider.java | 6 ----
.../predicate/ExperimentListPredicate.java | 35 ++++++++++---------
.../predicate/SampleListPredicate.java | 31 ++++++++--------
.../business/bo/AbstractBusinessObject.java | 7 ----
.../business/bo/EntityCodeGenerator.java | 3 +-
.../bo/common/DatabaseContextUtils.java | 10 ------
.../entity/ISecondaryEntityListingQuery.java | 4 +--
.../bo/common/entity/SecondaryEntityDAO.java | 7 +---
.../bo/datasetlister/DatasetListerDAO.java | 7 +---
.../datasetlister/IDatasetListingQuery.java | 3 +-
.../datasetlister/DataSetLister.java | 4 +--
.../experimentlister/ExperimentLister.java | 4 +--
.../samplelister/SampleLister.java | 4 +--
.../materiallister/IMaterialListingQuery.java | 3 +-
.../bo/materiallister/MaterialListerDAO.java | 7 +---
.../bo/samplelister/ISampleListingQuery.java | 3 +-
.../bo/samplelister/SampleListerDAO.java | 7 +---
.../dataaccess/IAuthorizationDAOFactory.java | 7 ----
.../db/AuthorizationDAOFactory.java | 10 ------
.../DatasetListingQueryTest.java | 11 ------
.../samplelister/SampleListingQueryTest.java | 10 ------
.../screening/server/ScreeningServer.java | 9 ++---
.../ScreeningPlateListReadOnlyPredicate.java | 27 +++++++-------
.../server/logic/AbstractContentLoader.java | 5 +--
.../server/logic/ScreeningApiImpl.java | 5 +--
26 files changed, 68 insertions(+), 168 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationDataProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationDataProvider.java
index 03d81825012..257451524c4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationDataProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/AuthorizationDataProvider.java
@@ -1,6 +1,5 @@
package ch.systemsx.cisd.openbis.generic.server.authorization;
-import java.sql.Connection;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
@@ -484,10 +483,4 @@ final public class AuthorizationDataProvider implements IAuthorizationDataProvid
{
return list;
}
-
- @Override
- public Connection getConnection()
- {
- return daoFactory.getConnection();
- }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAuthorizationDataProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAuthorizationDataProvider.java
index a8947eb59cb..9eee1176660 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAuthorizationDataProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/IAuthorizationDataProvider.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.authorization;
-import java.sql.Connection;
import java.util.List;
import java.util.Set;
@@ -155,9 +154,4 @@ public interface IAuthorizationDataProvider extends IDatabaseInstanceFinder
* Fetches metaproject with given tech id.
*/
public MetaprojectPE getMetaproject(TechId id);
-
- /**
- * Returns the JDBC connection.
- */
- public Connection getConnection();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExperimentListPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExperimentListPredicate.java
index 080a7aa5d9c..791df168cb1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExperimentListPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/ExperimentListPredicate.java
@@ -50,6 +50,21 @@ import ch.systemsx.cisd.openbis.generic.shared.util.SpaceCodeHelper;
@ShouldFlattenCollections(value = false)
public class ExperimentListPredicate extends AbstractSpacePredicate<List<Experiment>>
{
+ public static interface IExperimentToSpaceQuery extends BaseQuery
+ {
+ @Select(sql = "select distinct space_id from projects p left join experiments e on e.proj_id = p.id "
+ + "where e.id = any(?{1}) union "
+ + "select distinct space_id from projects p left join experiments e on e.proj_id = p.id "
+ + "where e.perm_id = any(?{2})", parameterBindings =
+ { LongArrayMapper.class, StringArrayMapper.class })
+ public List<Long> getExperimentSpaceIds(long[] experimentIds, String[] experimentPermIds);
+ }
+
+ private final static int ARRAY_SIZE_LIMIT = 999;
+
+ private final IExperimentToSpaceQuery experimentToSpaceQuery =
+ QueryTool.getManagedQuery(IExperimentToSpaceQuery.class);
+
//
// AbstractPredicate
//
@@ -105,18 +120,6 @@ public class ExperimentListPredicate extends AbstractSpacePredicate<List<Experim
return Status.OK;
}
- private final static int ARRAY_SIZE_LIMIT = 999;
-
- public static interface IExperimentToSpaceQuery extends BaseQuery
- {
- @Select(sql = "select distinct space_id from projects p left join experiments e on e.proj_id = p.id "
- + "where e.id = any(?{1}) union "
- + "select distinct space_id from projects p left join experiments e on e.proj_id = p.id "
- + "where e.perm_id = any(?{2})", parameterBindings =
- { LongArrayMapper.class, StringArrayMapper.class })
- public List<Long> getExperimentSpaceIds(long[] experimentIds, String[] experimentPermIds);
- }
-
private Collection<Long> getExperimentSpaceIds(final List<Long> ids, final List<String> permIds)
{
if (ids.size() != permIds.size())
@@ -128,9 +131,6 @@ public class ExperimentListPredicate extends AbstractSpacePredicate<List<Experim
{
return Collections.emptyList();
}
- final IExperimentToSpaceQuery query =
- QueryTool.getQuery(authorizationDataProvider.getConnection(),
- IExperimentToSpaceQuery.class);
if (size > ARRAY_SIZE_LIMIT)
{
final Set<Long> spaceIds = new HashSet<Long>(size);
@@ -140,13 +140,14 @@ public class ExperimentListPredicate extends AbstractSpacePredicate<List<Experim
Math.min(size, startIdx + ARRAY_SIZE_LIMIT));
final List<String> permIdSubList = permIds.subList(startIdx,
Math.min(size, startIdx + ARRAY_SIZE_LIMIT));
- spaceIds.addAll(query.getExperimentSpaceIds(toArray(idSubList),
+ spaceIds.addAll(experimentToSpaceQuery.getExperimentSpaceIds(toArray(idSubList),
permIdSubList.toArray(new String[permIdSubList.size()])));
}
return spaceIds;
} else
{
- return query.getExperimentSpaceIds(toArray(ids), permIds.toArray(new String[size]));
+ return experimentToSpaceQuery.getExperimentSpaceIds(toArray(ids),
+ permIds.toArray(new String[size]));
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleListPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleListPredicate.java
index 181e93efef2..6e797a91cb1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleListPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/predicate/SampleListPredicate.java
@@ -50,11 +50,24 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentif
@ShouldFlattenCollections(value = false)
public class SampleListPredicate extends AbstractSpacePredicate<List<Sample>>
{
+ private final static int ARRAY_SIZE_LIMIT = 999;
+
+ public static interface ISampleToSpaceQuery extends BaseQuery
+ {
+ @Select(sql = "select distinct space_id from samples where id = any(?{1}) "
+ + "union select distinct space_id from samples where perm_id = any(?{2})", parameterBindings =
+ { LongArrayMapper.class, StringArrayMapper.class })
+ public List<Long> getSampleSpaceIds(long[] sampleIds, String[] samplePermIds);
+ }
+
private final SampleOwnerIdentifierPredicate idOwnerPredicate;
+ private final ISampleToSpaceQuery sampleToSpaceQuery;
+
public SampleListPredicate()
{
idOwnerPredicate = new SampleOwnerIdentifierPredicate();
+ sampleToSpaceQuery = QueryTool.getManagedQuery(ISampleToSpaceQuery.class);
}
//
@@ -133,16 +146,6 @@ public class SampleListPredicate extends AbstractSpacePredicate<List<Sample>>
return Status.OK;
}
- private final static int ARRAY_SIZE_LIMIT = 999;
-
- public static interface ISampleToSpaceQuery extends BaseQuery
- {
- @Select(sql = "select distinct space_id from samples where id = any(?{1}) "
- + "union select distinct space_id from samples where perm_id = any(?{2})", parameterBindings =
- { LongArrayMapper.class, StringArrayMapper.class })
- public List<Long> getSampleSpaceIds(long[] sampleIds, String[] samplePermIds);
- }
-
private Collection<Long> getSampleSpaceIds(final List<Long> ids, final List<String> permIds)
{
if (ids.size() != permIds.size())
@@ -154,9 +157,6 @@ public class SampleListPredicate extends AbstractSpacePredicate<List<Sample>>
{
return Collections.emptyList();
}
- final ISampleToSpaceQuery query =
- QueryTool.getQuery(authorizationDataProvider.getConnection(),
- ISampleToSpaceQuery.class);
if (size > ARRAY_SIZE_LIMIT)
{
final Set<Long> spaceIds = new HashSet<Long>(size);
@@ -166,13 +166,14 @@ public class SampleListPredicate extends AbstractSpacePredicate<List<Sample>>
Math.min(size, startIdx + ARRAY_SIZE_LIMIT));
final List<String> permIdSubList = permIds.subList(startIdx,
Math.min(size, startIdx + ARRAY_SIZE_LIMIT));
- spaceIds.addAll(query.getSampleSpaceIds(toArray(idSubList),
+ spaceIds.addAll(sampleToSpaceQuery.getSampleSpaceIds(toArray(idSubList),
permIdSubList.toArray(new String[permIdSubList.size()])));
}
return spaceIds;
} else
{
- return query.getSampleSpaceIds(toArray(ids), permIds.toArray(new String[size]));
+ return sampleToSpaceQuery.getSampleSpaceIds(toArray(ids),
+ permIds.toArray(new String[size]));
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java
index 5b6b62a4ee8..b82887f6119 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObject.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
-import java.sql.Connection;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
@@ -512,12 +511,6 @@ abstract class AbstractBusinessObject implements IDAOFactory
return daoFactory.getExternalDataManagementSystemDAO();
}
- @Override
- public Connection getConnection()
- {
- return daoFactory.getConnection();
- }
-
@Override
public IMetaprojectDAO getMetaprojectDAO()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java
index 8b2ebe4d21b..694cb93a1a5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityCodeGenerator.java
@@ -23,7 +23,6 @@ import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.QueryTool;
import net.lemnik.eodsql.Select;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
@@ -67,7 +66,7 @@ public class EntityCodeGenerator
{
String[] codes = new String[numberOfCodes];
- query = QueryTool.getQuery(DatabaseContextUtils.getConnection(daoFactory), Query.class);
+ query = QueryTool.getManagedQuery(Query.class);
for (int i = 0; i < numberOfCodes; i++)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/DatabaseContextUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/DatabaseContextUtils.java
index 81a5242873d..96941b1a19e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/DatabaseContextUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/DatabaseContextUtils.java
@@ -16,11 +16,8 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.common;
-import java.sql.Connection;
-
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
@@ -31,13 +28,6 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
*/
public class DatabaseContextUtils
{
-
- @SuppressWarnings("deprecation")
- public static Connection getConnection(IAuthorizationDAOFactory daoFactory)
- {
- return daoFactory.getSessionFactory().getCurrentSession().connection();
- }
-
/**
* @return associated database configuration context
* @throws ConfigurationFailureException if it was impossible to get the context
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
index defe86fa58d..64ffe1bea36 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
@@ -17,9 +17,9 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity;
import it.unimi.dsi.fastutil.longs.LongSet;
+import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
-import net.lemnik.eodsql.TransactionQuery;
import ch.rinn.restrictions.Friend;
import ch.rinn.restrictions.Private;
@@ -36,7 +36,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
@Private
@Friend(toClasses =
{ SampleReferenceRecord.class })
-public interface ISecondaryEntityListingQuery extends TransactionQuery
+public interface ISecondaryEntityListingQuery extends BaseQuery
{
public static final int FETCH_SIZE = 1000;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
index ced273d33b7..c07a7a020f7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
@@ -20,9 +20,6 @@ import it.unimi.dsi.fastutil.longs.Long2ObjectMap;
import it.unimi.dsi.fastutil.longs.Long2ObjectOpenHashMap;
import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
import it.unimi.dsi.fastutil.longs.LongSet;
-
-import java.sql.Connection;
-
import net.lemnik.eodsql.QueryTool;
import org.springframework.dao.EmptyResultDataAccessException;
@@ -30,7 +27,6 @@ import org.springframework.dao.EmptyResultDataAccessException;
import ch.rinn.restrictions.Friend;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
@@ -62,9 +58,8 @@ public class SecondaryEntityDAO
*/
public static SecondaryEntityDAO create(IDAOFactory daoFactory)
{
- Connection connection = DatabaseContextUtils.getConnection(daoFactory);
ISecondaryEntityListingQuery query =
- QueryTool.getQuery(connection, ISecondaryEntityListingQuery.class);
+ QueryTool.getManagedQuery(ISecondaryEntityListingQuery.class);
return create(daoFactory, query);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java
index 0da2f9e89a1..a8c7f6dca79 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java
@@ -17,15 +17,11 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister;
import it.unimi.dsi.fastutil.longs.LongSet;
-
-import java.sql.Connection;
-
import net.lemnik.eodsql.QueryTool;
import ch.rinn.restrictions.Friend;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.AbstractDAO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.GenericEntityPropertyRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertySetListingQuery;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.MaterialEntityPropertyRecord;
@@ -50,8 +46,7 @@ public final class DatasetListerDAO extends AbstractDAO
*/
public static DatasetListerDAO create(IDAOFactory daoFactory)
{
- Connection connection = DatabaseContextUtils.getConnection(daoFactory);
- IDatasetListingQuery query = QueryTool.getQuery(connection, IDatasetListingQuery.class);
+ IDatasetListingQuery query = QueryTool.getManagedQuery(IDatasetListingQuery.class);
return create(daoFactory, query);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
index 5c114ce3e10..5f51859fbde 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
@@ -21,6 +21,7 @@ import it.unimi.dsi.fastutil.longs.LongSet;
import java.util.Date;
import java.util.List;
+import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.TransactionQuery;
@@ -49,7 +50,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.StringArrayMapper;
@Private
@Friend(toClasses =
{ DataStoreRecord.class })
-public interface IDatasetListingQuery extends TransactionQuery, IPropertyListingQuery
+public interface IDatasetListingQuery extends BaseQuery, IPropertyListingQuery
{
public static final int FETCH_SIZE = 1000;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java
index 650365334d2..4cd44087b68 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java
@@ -28,7 +28,6 @@ import net.lemnik.eodsql.QueryTool;
import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IAuthorizationDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer;
@@ -58,8 +57,7 @@ public class DataSetLister implements IDataSetLister
public DataSetLister(IAuthorizationDAOFactory daoFactory, PersonPE person)
{
- this(QueryTool.getQuery(DatabaseContextUtils.getConnection(daoFactory),
- IDataSetListingQuery.class), person);
+ this(QueryTool.getManagedQuery(IDataSetListingQuery.class), person);
}
public DataSetLister(IDataSetListingQuery query, PersonPE person)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/experimentlister/ExperimentLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/experimentlister/ExperimentLister.java
index 8c71af2587b..6f8db96ecdc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/experimentlister/ExperimentLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/experimentlister/ExperimentLister.java
@@ -29,7 +29,6 @@ import net.lemnik.eodsql.QueryTool;
import org.apache.commons.lang.StringUtils;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.PermlinkUtilities;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
@@ -60,8 +59,7 @@ public class ExperimentLister implements IExperimentLister
public ExperimentLister(IDAOFactory daoFactory, String baseIndexURL)
{
- this(daoFactory, baseIndexURL, QueryTool.getQuery(
- DatabaseContextUtils.getConnection(daoFactory), IExperimentListingQuery.class));
+ this(daoFactory, baseIndexURL, QueryTool.getManagedQuery(IExperimentListingQuery.class));
}
public ExperimentLister(IDAOFactory daoFactory, String baseIndexURL,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java
index a27da73de8d..87443cf3243 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java
@@ -34,7 +34,6 @@ import net.lemnik.eodsql.QueryTool;
import ch.systemsx.cisd.common.collection.IKeyExtractor;
import ch.systemsx.cisd.common.collection.TableMap;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.EntityMetaprojectRelationRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.MetaprojectCreator;
import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.MetaprojectRecord;
@@ -98,8 +97,7 @@ public class SampleLister implements ISampleLister
public SampleLister(IDAOFactory daoFactory, PersonPE person)
{
- this(QueryTool.getQuery(DatabaseContextUtils.getConnection(daoFactory),
- ISampleListingQuery.class), person);
+ this(QueryTool.getManagedQuery(ISampleListingQuery.class), person);
}
SampleLister(ISampleListingQuery query, PersonPE person)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
index 3bcee0a51e9..5811b838d08 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/IMaterialListingQuery.java
@@ -20,6 +20,7 @@ import it.unimi.dsi.fastutil.longs.LongSet;
import java.util.List;
+import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.TransactionQuery;
@@ -44,7 +45,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.StringArrayMapper;
* @author Tomasz Pylak
*/
@Private
-public interface IMaterialListingQuery extends TransactionQuery, IPropertyListingQuery
+public interface IMaterialListingQuery extends BaseQuery, IPropertyListingQuery
{
public static final int FETCH_SIZE = 1000;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialListerDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialListerDAO.java
index ff63d404a09..6d9d8480578 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialListerDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/materiallister/MaterialListerDAO.java
@@ -17,15 +17,11 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister;
import it.unimi.dsi.fastutil.longs.LongSet;
-
-import java.sql.Connection;
-
import net.lemnik.eodsql.QueryTool;
import ch.rinn.restrictions.Friend;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.AbstractDAO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.GenericEntityPropertyRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertySetListingQuery;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.MaterialEntityPropertyRecord;
@@ -50,8 +46,7 @@ public final class MaterialListerDAO extends AbstractDAO
*/
public static MaterialListerDAO create(IDAOFactory daoFactory)
{
- Connection connection = DatabaseContextUtils.getConnection(daoFactory);
- IMaterialListingQuery query = QueryTool.getQuery(connection, IMaterialListingQuery.class);
+ IMaterialListingQuery query = QueryTool.getManagedQuery(IMaterialListingQuery.class);
return create(daoFactory, query);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
index 6b7b3346ab8..1ddb6419239 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
@@ -22,6 +22,7 @@ import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.List;
+import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.EoDException;
import net.lemnik.eodsql.Select;
@@ -53,7 +54,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
@Friend(toClasses =
{ ExperimentProjectSpaceCodeRecord.class })
@Private
-public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQuery
+public interface ISampleListingQuery extends BaseQuery, IPropertyListingQuery
{
public static final int FETCH_SIZE = 1000;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListerDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListerDAO.java
index 412c171c699..69854945b2b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListerDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListerDAO.java
@@ -17,15 +17,11 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister;
import it.unimi.dsi.fastutil.longs.LongSet;
-
-import java.sql.Connection;
-
import net.lemnik.eodsql.QueryTool;
import ch.rinn.restrictions.Friend;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.AbstractDAO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.GenericEntityPropertyRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertySetListingQuery;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.MaterialEntityPropertyRecord;
@@ -50,8 +46,7 @@ public final class SampleListerDAO extends AbstractDAO
*/
public static SampleListerDAO create(IDAOFactory daoFactory)
{
- Connection connection = DatabaseContextUtils.getConnection(daoFactory);
- ISampleListingQuery query = QueryTool.getQuery(connection, ISampleListingQuery.class);
+ ISampleListingQuery query = QueryTool.getManagedQuery(ISampleListingQuery.class);
return create(daoFactory, query);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationDAOFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationDAOFactory.java
index 85d8eed5277..8577615b99d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationDAOFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IAuthorizationDAOFactory.java
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess;
-import java.sql.Connection;
-
import org.hibernate.SessionFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
@@ -78,9 +76,4 @@ public interface IAuthorizationDAOFactory
public IDeletionDAO getDeletionDAO();
public IMetaprojectDAO getMetaprojectDAO();
-
- /**
- * Returns the JDBC connection.
- */
- public Connection getConnection();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AuthorizationDAOFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AuthorizationDAOFactory.java
index c625d1486c8..b3659cb455b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AuthorizationDAOFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AuthorizationDAOFactory.java
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.db;
-import java.sql.Connection;
-
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.hibernate.SessionFactory;
@@ -291,12 +289,4 @@ public class AuthorizationDAOFactory implements IAuthorizationDAOFactory
Session currentSession = sessionFactory.getCurrentSession();
HibernateUtils.setBatchUpdateMode(currentSession, batchMode);
}
-
- @SuppressWarnings("deprecation")
- @Override
- public Connection getConnection()
- {
- final SessionFactory sessionFactory = persistencyResources.getSessionFactory();
- return sessionFactory.getCurrentSession().connection();
- }
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
index a6cb850221e..d81132c8994 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
@@ -31,7 +31,6 @@ import java.util.List;
import java.util.Set;
import org.apache.commons.lang.builder.EqualsBuilder;
-import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@@ -79,16 +78,6 @@ public class DatasetListingQueryTest extends AbstractDAOTest
query = dao.getQuery();
}
- @AfterClass(alwaysRun = true)
- public void cleanUp() throws SQLException
- {
- if (query != null)
- {
- query.commit();
- }
-
- }
-
public static DatasetListerDAO createDatasetListerDAO(IDAOFactory daoFactory)
{
IDatasetListingQuery query =
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingQueryTest.java
index f593bf42084..802d94716e5 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingQueryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingQueryTest.java
@@ -32,7 +32,6 @@ import java.util.Arrays;
import java.util.List;
import org.apache.commons.lang.builder.EqualsBuilder;
-import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@@ -124,15 +123,6 @@ public class SampleListingQueryTest extends AbstractDAOTest
parentChildRelationshipTypeId = query.getRelationshipTypeId("PARENT_CHILD", true);
}
- @AfterClass(alwaysRun = true)
- public void cleanUp() throws SQLException
- {
- if (query != null)
- {
- query.commit();
- }
- }
-
public static SampleListerDAO createSampleListerDAO(IDAOFactory daoFactory)
{
ISampleListingQuery query =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 98639ad83f3..df12948a571 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.server;
-import java.sql.Connection;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
@@ -38,14 +37,13 @@ import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.Authoriz
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.Capability;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.ReturnValueFilter;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.DataSetTechIdPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetCodeCollectionPredicate;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetCodePredicate;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.SampleTechIdPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.DataSetTechIdPredicate;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IVocabularyDAO;
import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
@@ -654,8 +652,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
private static IScreeningQuery createDAO(IDAOFactory daoFactory)
{
- Connection connection = DatabaseContextUtils.getConnection(daoFactory);
- return QueryTool.getQuery(connection, IScreeningQuery.class);
+ return QueryTool.getManagedQuery(IScreeningQuery.class);
}
private ScreeningApiImpl createScreeningApiImpl(String sessionToken)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/authorization/ScreeningPlateListReadOnlyPredicate.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/authorization/ScreeningPlateListReadOnlyPredicate.java
index 6b2099af7a7..ccb10d1cc71 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/authorization/ScreeningPlateListReadOnlyPredicate.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/authorization/ScreeningPlateListReadOnlyPredicate.java
@@ -49,6 +49,17 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifi
public class ScreeningPlateListReadOnlyPredicate extends
AbstractSpacePredicate<List<? extends PlateIdentifier>>
{
+ private final static int ARRAY_SIZE_LIMIT = 999;
+
+ private final ISampleToSpaceQuery sampleToSpaceQuery = QueryTool
+ .getManagedQuery(ISampleToSpaceQuery.class);
+
+ interface ISampleToSpaceQuery extends BaseQuery
+ {
+ @Select(sql = "select distinct space_id from samples where perm_id = any(?{1})", parameterBindings =
+ { StringArrayMapper.class })
+ public List<Long> getSampleSpaceIds(String[] samplePermIds);
+ }
@Override
public String getCandidateDescription()
@@ -106,20 +117,8 @@ public class ScreeningPlateListReadOnlyPredicate extends
return Status.OK;
}
- private final static int ARRAY_SIZE_LIMIT = 999;
-
- interface ISampleToSpaceQuery extends BaseQuery
- {
- @Select(sql = "select distinct space_id from samples where perm_id = any(?{1})", parameterBindings =
- { StringArrayMapper.class })
- public List<Long> getSampleSpaceIds(String[] samplePermIds);
- }
-
private Collection<Long> getSampleSpaceIds(final List<String> permIds)
{
- final ISampleToSpaceQuery query =
- QueryTool.getQuery(authorizationDataProvider.getConnection(),
- ISampleToSpaceQuery.class);
if (permIds.size() > ARRAY_SIZE_LIMIT)
{
final Set<Long> spaceIds = new HashSet<Long>(permIds.size());
@@ -127,13 +126,13 @@ public class ScreeningPlateListReadOnlyPredicate extends
{
final List<String> permIdSubList = permIds.subList(startIdx,
Math.min(permIds.size(), startIdx + ARRAY_SIZE_LIMIT));
- spaceIds.addAll(query.getSampleSpaceIds(permIdSubList.toArray(
+ spaceIds.addAll(sampleToSpaceQuery.getSampleSpaceIds(permIdSubList.toArray(
new String[permIdSubList.size()])));
}
return spaceIds;
} else
{
- return query
+ return sampleToSpaceQuery
.getSampleSpaceIds(permIds.toArray(new String[permIds.size()]));
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java
index 62333474dc0..6d8b53533b3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
-import java.sql.Connection;
import java.util.Set;
import net.lemnik.eodsql.QueryTool;
@@ -27,7 +26,6 @@ import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
@@ -71,8 +69,7 @@ abstract class AbstractContentLoader
{
if (screeningDao == null)
{
- Connection connection = DatabaseContextUtils.getConnection(daoFactory);
- screeningDao = QueryTool.getQuery(connection, IScreeningQuery.class);
+ screeningDao = QueryTool.getManagedQuery(IScreeningQuery.class);
}
return screeningDao;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index d3f81de748f..d12829923b5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
-import java.sql.Connection;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
@@ -36,7 +35,6 @@ import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleTypeDAO;
@@ -662,8 +660,7 @@ public class ScreeningApiImpl
private IScreeningQuery createScreeningQuery()
{
- final Connection connection = DatabaseContextUtils.getConnection(daoFactory);
- return QueryTool.getQuery(connection, IScreeningQuery.class);
+ return QueryTool.getManagedQuery(IScreeningQuery.class);
}
private ExperimentPE getExperimentFromDB(ExperimentIdentifier experimentIdentifierFromUser)
--
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