diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java
index e14b13d96a0d9781512a2b5415a9e9bf8e4aade5..f53ebde58f6ae7e9a6228ae3c6f262a559dfba82 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/authorization/PredicateExecutor.java
@@ -16,10 +16,12 @@
package ch.systemsx.cisd.openbis.generic.server.authorization;
-import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import org.hibernate.Query;
import org.hibernate.Session;
@@ -47,7 +49,10 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
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.QueryPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleAccessPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.plugin.generic.server.batch.BatchOperationExecutor;
+import ch.systemsx.cisd.openbis.plugin.generic.server.batch.IBatchOperation;
/**
* A static class to execute {@link IPredicate}.
@@ -255,54 +260,99 @@ public final class PredicateExecutor
}
}
- @SuppressWarnings("unchecked")
public DataSetAccessPE tryGetDatasetAccessData(String dataSetCode)
{
- Session sess = daoFactory.getSessionFactory().getCurrentSession();
- Query query = sess.getNamedQuery(DataSetAccessPE.DATASET_ACCESS_QUERY_NAME);
- query = query.setReadOnly(true);
- String[] codes =
- { dataSetCode };
- List<DataSetAccessPE> results =
- query.setParameterList(DataSetAccessPE.DATA_SET_CODES_PARAMETER_NAME, codes)
- .list();
+ Set<DataSetAccessPE> results =
+ getDatasetCollectionAccessData(Arrays.asList(dataSetCode));
if (results.size() < 1)
return null;
- return results.get(0);
+ return results.iterator().next();
}
- @SuppressWarnings("unchecked")
- public List<DataSetAccessPE> tryGetDatasetCollectionAccessData(List<String> dataSetCodes)
+ public Set<DataSetAccessPE> getDatasetCollectionAccessData(final List<String> dataSetCodes)
{
Session sess = daoFactory.getSessionFactory().getCurrentSession();
- Query query = sess.getNamedQuery(DataSetAccessPE.DATASET_ACCESS_QUERY_NAME);
- query = query.setReadOnly(true);
+ final Query query = sess.getNamedQuery(DataSetAccessPE.DATASET_ACCESS_QUERY_NAME);
+ query.setReadOnly(true);
// WORKAROUND Problem in Hibernate when the number of data set codes > 1000
// Though this query runs quickly within the pgadmin tool, even for large numbers of
// data set codes, Hibernate becomes *very* slow when the size of the data set codes
// exceeds 1000. For that reason, break down the query into smaller sections and
// reassemble the results.
- ArrayList<DataSetAccessPE> fullResults = new ArrayList<DataSetAccessPE>();
+ final Set<DataSetAccessPE> fullResults = new HashSet<DataSetAccessPE>();
- int size = dataSetCodes.size();
- // blockSize is a magic number -- I don't know what the optimal value is, but execution
- // speed slows down if the blockSize > 1999
- int blockSize = 999;
- int start, end;
-
- // Loop over the codes, one block at a time
- for (start = 0, end = Math.min(start + blockSize, size); start < size; start = end, end =
- Math.min(start + blockSize, size))
- {
- List<String> sublist = dataSetCodes.subList(start, end);
- query =
+ BatchOperationExecutor.executeInBatches(new IBatchOperation<String>()
+ {
+ public void execute(List<String> entities)
+ {
query.setParameterList(DataSetAccessPE.DATA_SET_CODES_PARAMETER_NAME,
- sublist);
- List<DataSetAccessPE> results = query.list();
- fullResults.addAll(results);
- }
+ entities);
+ List<DataSetAccessPE> results = cast(query.list());
+ fullResults.addAll(results);
+ }
+
+ public List<String> getAllEntities()
+ {
+ return dataSetCodes;
+ }
+
+ public String getEntityName()
+ {
+ return "dataset";
+ }
+
+ public String getOperationName()
+ {
+ return "authorization";
+ }
+ });
+
+ return fullResults;
+ }
+
+ public Set<SampleAccessPE> getSampleCollectionAccessData(final List<TechId> sampleTechIds)
+ {
+ Session sess = daoFactory.getSessionFactory().getCurrentSession();
+ final Query querySpaceSamples =
+ sess.getNamedQuery(SampleAccessPE.SPACE_SAMPLE_ACCESS_QUERY_NAME);
+ querySpaceSamples.setReadOnly(true);
+ final Query querySharedSamples =
+ sess.getNamedQuery(SampleAccessPE.SHARED_SAMPLE_ACCESS_QUERY_NAME);
+ querySharedSamples.setReadOnly(true);
+
+ final Set<SampleAccessPE> fullResults = new HashSet<SampleAccessPE>();
+
+ BatchOperationExecutor.executeInBatches(new IBatchOperation<TechId>()
+ {
+ public void execute(List<TechId> entities)
+ {
+ querySpaceSamples.setParameterList(
+ SampleAccessPE.SAMPLE_IDS_PARAMETER_NAME, TechId.asLongs(entities));
+ querySharedSamples.setParameterList(
+ SampleAccessPE.SAMPLE_IDS_PARAMETER_NAME, TechId.asLongs(entities));
+ List<SampleAccessPE> spaceSamples = cast(querySpaceSamples.list());
+ List<SampleAccessPE> sharedSamples = cast(querySharedSamples.list());
+ fullResults.addAll(spaceSamples);
+ fullResults.addAll(sharedSamples);
+ }
+
+ public List<TechId> getAllEntities()
+ {
+ return sampleTechIds;
+ }
+
+ public String getEntityName()
+ {
+ return "sample";
+ }
+
+ public String getOperationName()
+ {
+ return "authorization";
+ }
+ });
return fullResults;
}
@@ -352,5 +402,18 @@ public final class PredicateExecutor
return daoFactory.getQueryDAO().getByTechId(techId);
}
+ /**
+ * Casts given <var>list</var> to specified type.
+ * <p>
+ * The purpose of this method is to avoid <code>SuppressWarnings("unchecked")</code> in
+ * calling methods.
+ * </p>
+ */
+ @SuppressWarnings("unchecked")
+ private static final <T> List<T> cast(final List list)
+ {
+ return list;
+ }
+
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
index 3689e98855bf8d7ecddf30d0dd14b22d65a6efec..14b23da2346cdc8e7fe3ac85b6c3b8fecdfe027a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ICommonServer.java
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCo
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ListSampleCriteriaPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.ProjectUpdatesPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleTechIdCollectionPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SpaceIdentifierPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractExpressionPredicate.DeleteGridCustomColumnPredicate;
@@ -643,8 +644,9 @@ public interface ICommonServer extends IServer
@Transactional
@RolesAllowed(RoleSet.POWER_USER)
@DatabaseCreateOrDeleteModification(value = ObjectKind.SAMPLE)
- public void deleteSamples(String sessionToken,
- @AuthorizationGuard(guardClass = SampleTechIdPredicate.class) List<TechId> sampleIds,
+ public void deleteSamples(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = SampleTechIdCollectionPredicate.class) List<TechId> sampleIds,
String reason);
/**
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/IAuthorizationDataProvider.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/IAuthorizationDataProvider.java
index 66de4b37e1b45ce331e97317a4d794227addb66b..f0ca31bd9b4deb2b5d6a47a58ed1bd92aa402669 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/IAuthorizationDataProvider.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/IAuthorizationDataProvider.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.authorization;
import java.util.List;
+import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.IDatabaseInstanceFinder;
import ch.systemsx.cisd.openbis.generic.shared.basic.PermId;
@@ -27,6 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.GridCustomFilterPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.QueryPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleAccessPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
@@ -56,7 +58,12 @@ public interface IAuthorizationDataProvider extends IDatabaseInstanceFinder
/**
* Returns the information necessary to determine if a user is allowed to access the data sets.
*/
- public List<DataSetAccessPE> tryGetDatasetCollectionAccessData(List<String> dataSetCodes);
+ public Set<DataSetAccessPE> getDatasetCollectionAccessData(List<String> dataSetCodes);
+
+ /**
+ * Returns the information necessary to determine if a user is allowed to access the samples.
+ */
+ public Set<SampleAccessPE> getSampleCollectionAccessData(List<TechId> sampleIds);
/**
* Returns the group of an entity with given <var>entityKind</var> and <var>techId</var>
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/DataSetCodeCollectionPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/DataSetCodeCollectionPredicate.java
index a171ef03edbcde5c4305b11b944c443a363e8f6a..28e193c23e5c60f42eaef286b7bf9e9cbe424a45 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/DataSetCodeCollectionPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/DataSetCodeCollectionPredicate.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.authorization.predicate;
import java.util.List;
+import java.util.Set;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.openbis.generic.shared.authorization.RoleWithIdentifier;
@@ -44,13 +45,8 @@ public class DataSetCodeCollectionPredicate extends AbstractGroupPredicate<List<
{
assert initialized : "Predicate has not been initialized";
- List<DataSetAccessPE> accessData =
- authorizationDataProvider.tryGetDatasetCollectionAccessData(dataSetCodes);
-
- if (accessData == null)
- {
- return Status.OK;
- }
+ Set<DataSetAccessPE> accessData =
+ authorizationDataProvider.getDatasetCollectionAccessData(dataSetCodes);
for (DataSetAccessPE accessDatum : accessData)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/DelegatedPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/DelegatedPredicate.java
index 5cb8e4f230add9acfde9417ac101b5b3ab4aee4e..61181f2605084763493daa2be3c9a7cfaef9f8b2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/DelegatedPredicate.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/DelegatedPredicate.java
@@ -39,6 +39,8 @@ public abstract class DelegatedPredicate<P, T> extends AbstractPredicate<T>
{
private final IPredicate<P> delegate;
+ protected IAuthorizationDataProvider authorizationDataProvider;
+
public DelegatedPredicate(final IPredicate<P> delegate)
{
this.delegate = delegate;
@@ -55,6 +57,7 @@ public abstract class DelegatedPredicate<P, T> extends AbstractPredicate<T>
public final void init(IAuthorizationDataProvider provider)
{
+ this.authorizationDataProvider = provider;
delegate.init(provider);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SampleTechIdCollectionPredicate.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SampleTechIdCollectionPredicate.java
new file mode 100644
index 0000000000000000000000000000000000000000..3852ff440af04f6d875ba9420e1c48b322d2e2a6
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/SampleTechIdCollectionPredicate.java
@@ -0,0 +1,77 @@
+/*
+ * Copyright 2009 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.authorization.predicate;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ShouldFlattenCollections;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleAccessPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+
+/**
+ * An <code>IPredicate</code> implementation based on a list of sample {@link TechId}s.
+ *
+ * @author Piotr Buczek
+ */
+@ShouldFlattenCollections(value = false)
+public class SampleTechIdCollectionPredicate extends
+ DelegatedPredicate<List<SampleOwnerIdentifier>, List<TechId>>
+{
+
+ public SampleTechIdCollectionPredicate()
+ {
+ super(new SampleOwnerIdentifierCollectionPredicate(true));
+ }
+
+ @Override
+ public List<SampleOwnerIdentifier> convert(List<TechId> techIds)
+ {
+ ArrayList<SampleOwnerIdentifier> ownerIds = new ArrayList<SampleOwnerIdentifier>();
+
+ Set<SampleAccessPE> accessData =
+ authorizationDataProvider.getSampleCollectionAccessData(techIds);
+
+ for (SampleAccessPE accessDatum : accessData)
+ {
+ String groupCode = accessDatum.getGroupCode();
+ String dbInstanceCode = accessDatum.getDatabaseInstanceCode();
+ if (groupCode != null)
+ {
+ ownerIds.add(new SampleOwnerIdentifier(new SpaceIdentifier(
+ DatabaseInstanceIdentifier.createHome(), groupCode)));
+ } else
+ {
+ ownerIds.add(new SampleOwnerIdentifier(new DatabaseInstanceIdentifier(
+ dbInstanceCode)));
+ }
+ }
+
+ return ownerIds;
+ }
+
+ @Override
+ public final String getCandidateDescription()
+ {
+ return "sample technical ids";
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/TechId.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/TechId.java
index a0a130b4d1e81f3933c57085cdc366abda6f2038..2e174712b2e495f2b66e1828634714205b62a61e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/TechId.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/TechId.java
@@ -88,6 +88,21 @@ public class TechId implements IIdHolder, IsSerializable, Serializable
return results;
}
+ /**
+ * Convenience method for getting a list of long ids from given list of {@link TechId}s.
+ *
+ * @see #create(IIdHolder)
+ */
+ public static List<Long> asLongs(List<TechId> techIds)
+ {
+ List<Long> results = new ArrayList<Long>();
+ for (TechId techId : techIds)
+ {
+ results.add(techId.getId());
+ }
+ return results;
+ }
+
public Long getId()
{
return id;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetAccessPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetAccessPE.java
index 479ca131da1f4ba45c874de2adfc0b7ea6f58444..9b00a972cd40110adf3a1ed0471427af9b7d8694 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetAccessPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataSetAccessPE.java
@@ -22,6 +22,9 @@ import javax.persistence.Id;
import javax.persistence.NamedNativeQuery;
import javax.persistence.SqlResultSetMapping;
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
/**
* A PE for retrieving only the information necessary to determine if a user/person can access a
* data set.
@@ -94,4 +97,37 @@ public class DataSetAccessPE
{
return databaseInstanceCode;
}
+
+ //
+ // Object
+ //
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof DataSetAccessPE == false)
+ {
+ return false;
+ }
+ final DataSetAccessPE that = (DataSetAccessPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getGroupCode(), that.getGroupCode());
+ builder.append(getDatabaseInstanceCode(), that.getDatabaseInstanceCode());
+ builder.append(getDatabaseInstanceUuid(), that.getDatabaseInstanceUuid());
+ return builder.isEquals();
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getGroupCode());
+ builder.append(getDatabaseInstanceCode());
+ builder.append(getDatabaseInstanceUuid());
+ return builder.toHashCode();
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleAccessPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleAccessPE.java
new file mode 100644
index 0000000000000000000000000000000000000000..cde0b2e324c72d973ce75989921ea15406eb71f0
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleAccessPE.java
@@ -0,0 +1,136 @@
+/*
+ * 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 javax.persistence.Entity;
+import javax.persistence.EntityResult;
+import javax.persistence.Id;
+import javax.persistence.NamedNativeQueries;
+import javax.persistence.NamedNativeQuery;
+import javax.persistence.SqlResultSetMapping;
+import javax.persistence.SqlResultSetMappings;
+
+import org.apache.commons.lang.builder.EqualsBuilder;
+import org.apache.commons.lang.builder.HashCodeBuilder;
+
+/**
+ * A PE for retrieving only the information necessary to determine if a user/person can access a
+ * sample.
+ *
+ * @author Piotr Buczek
+ */
+@Entity
+@SqlResultSetMappings(value =
+ {
+ @SqlResultSetMapping(name = "implicit1", entities = @EntityResult(entityClass = SampleAccessPE.class)),
+ @SqlResultSetMapping(name = "implicit2", entities = @EntityResult(entityClass = SampleAccessPE.class))
+
+ })
+@NamedNativeQueries(value =
+ {
+ @NamedNativeQuery(name = "space_sample_access", query = "SELECT DISTINCT g.code as groupCode, null as databaseInstanceCode "
+ + "FROM "
+ + TableNames.SAMPLES_TABLE
+ + " s, "
+ + TableNames.GROUPS_TABLE
+ + " g "
+ + "WHERE s.id in (:ids) and s.grou_id = g.id", resultSetMapping = "implicit1"),
+ @NamedNativeQuery(name = "shared_sample_access", query = "SELECT DISTINCT dbi.code as databaseInstanceCode, null as groupCode "
+ + "FROM "
+ + TableNames.SAMPLES_TABLE
+ + " s, "
+ + TableNames.DATABASE_INSTANCES_TABLE
+ + " dbi "
+ + "WHERE s.id in (:ids) and s.dbin_id = dbi.id", resultSetMapping = "implicit2")
+
+ })
+public class SampleAccessPE
+{
+ private String groupCode;
+
+ private String databaseInstanceCode;
+
+ public final static String SPACE_SAMPLE_ACCESS_QUERY_NAME = "space_sample_access";
+
+ public final static String SHARED_SAMPLE_ACCESS_QUERY_NAME = "shared_sample_access";
+
+ public final static String SAMPLE_IDS_PARAMETER_NAME = "ids";
+
+ /**
+ * A factory method that should only be used for testing.
+ */
+ public static SampleAccessPE createSampleAccessPEForTest(String dataSetId, String dataSetCode,
+ String groupCode, String databaseInstanceCode)
+ {
+ SampleAccessPE newMe = new SampleAccessPE();
+ newMe.setGroupCode(groupCode);
+ newMe.setDatabaseInstanceCode(databaseInstanceCode);
+ return newMe;
+ }
+
+ void setGroupCode(String groupCode)
+ {
+ this.groupCode = groupCode;
+ }
+
+ void setDatabaseInstanceCode(String databaseInstanceCode)
+ {
+ this.databaseInstanceCode = databaseInstanceCode;
+ }
+
+ @Id
+ public String getGroupCode()
+ {
+ return groupCode;
+ }
+
+ public String getDatabaseInstanceCode()
+ {
+ return databaseInstanceCode;
+ }
+
+ //
+ // Object
+ //
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof SampleAccessPE == false)
+ {
+ return false;
+ }
+ final SampleAccessPE that = (SampleAccessPE) obj;
+ final EqualsBuilder builder = new EqualsBuilder();
+ builder.append(getGroupCode(), that.getGroupCode());
+ builder.append(getDatabaseInstanceCode(), that.getDatabaseInstanceCode());
+ return builder.isEquals();
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final HashCodeBuilder builder = new HashCodeBuilder();
+ builder.append(getGroupCode());
+ builder.append(getDatabaseInstanceCode());
+ return builder.toHashCode();
+ }
+}
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 97df9049ff7a94f893c63ef0b5fcb5b81693845d..198be640dc51ab38c7a9ca8e43c5d265f6080d7c 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
@@ -59,8 +59,8 @@ public class GenericDataSetTypeSlaveServerPlugin implements IDataSetTypeSlaveSer
assert session != null : "Unspecified session.";
assert newDataSets != null && newDataSets.size() > 0 : "Unspecified data set or empty data sets.";
- new BatchOperationExecutor<NewDataSet>().executeInBatches(new DataSetBatchUpdate(
- businessObjectFactory.createExternalDataTable(session), newDataSets));
+ BatchOperationExecutor.executeInBatches(new DataSetBatchUpdate(businessObjectFactory
+ .createExternalDataTable(session), newDataSets));
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericSampleTypeSlaveServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericSampleTypeSlaveServerPlugin.java
index ccd7eb52b9df7adb14f76e7bdd27e9f981584a9f..c4967d6d1c9c8ba3f198cd0877c1ef293e081980 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericSampleTypeSlaveServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericSampleTypeSlaveServerPlugin.java
@@ -79,8 +79,8 @@ public final class GenericSampleTypeSlaveServerPlugin implements ISampleTypeSlav
assert session != null : "Unspecified session.";
assert newSamples != null && newSamples.size() > 0 : "Unspecified sample or empty samples.";
- new BatchOperationExecutor<NewSample>().executeInBatches(new SampleBatchRegistration(
- businessObjectFactory.createSampleTable(session), newSamples));
+ BatchOperationExecutor.executeInBatches(new SampleBatchRegistration(businessObjectFactory
+ .createSampleTable(session), newSamples));
}
public void updateSamples(Session session, List<SampleBatchUpdatesDTO> updateSamples)
@@ -88,7 +88,7 @@ public final class GenericSampleTypeSlaveServerPlugin implements ISampleTypeSlav
assert session != null : "Unspecified session.";
assert updateSamples != null && updateSamples.size() > 0 : "Unspecified sample or empty samples.";
- new BatchOperationExecutor<SampleBatchUpdatesDTO>().executeInBatches(new SampleBatchUpdate(
- businessObjectFactory.createSampleTable(session), updateSamples));
+ BatchOperationExecutor.executeInBatches(new SampleBatchUpdate(businessObjectFactory
+ .createSampleTable(session), updateSamples));
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index c20671abbbf0e67ffd1dc22b032c4772fdfa535e..6e6084bc7f6bbde252771305d4e1eaa922c389e1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -274,10 +274,9 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
registerSamples(session, samples);
} else
{
- new BatchOperationExecutor<NewSample>()
- .executeInBatches(new SampleBatchRegisterOrUpdate(businessObjectFactory
- .createSampleLister(session), samples.getNewSamples(), samples
- .getSampleType(), session));
+ BatchOperationExecutor.executeInBatches(new SampleBatchRegisterOrUpdate(
+ businessObjectFactory.createSampleLister(session), samples.getNewSamples(),
+ samples.getSampleType(), session));
}
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/batch/BatchOperationExecutor.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/batch/BatchOperationExecutor.java
index dee516faddee20382b59f5944ab041cbad0de8fa..3d50e443f041f84d864c2d0aeadfddc00a203554 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/batch/BatchOperationExecutor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/batch/BatchOperationExecutor.java
@@ -12,33 +12,34 @@ import ch.systemsx.cisd.common.logging.LogFactory;
*
* @author Izabela Adamczyk
*/
-public class BatchOperationExecutor<S>
+public class BatchOperationExecutor
{
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, BatchOperationExecutor.class);
private static final int DEFAULT_BATCH_SIZE = 1000;
- public void executeInBatches(IBatchOperation<S> strategy)
+ public static <S> void executeInBatches(IBatchOperation<S> strategy)
{
executeInBatches(strategy, DEFAULT_BATCH_SIZE);
}
- public void executeInBatches(IBatchOperation<S> strategy, int batchSize)
+ public static <S> void executeInBatches(IBatchOperation<S> strategy, int batchSize)
{
assert strategy != null : "Unspecified operation.";
final List<S> allEntities = strategy.getAllEntities();
- int startIndex = 0;
int maxIndex = allEntities.size();
- while (startIndex < maxIndex)
+
+ // Loop over the list, one block at a time
+ for (int startIndex = 0, endIndex = Math.min(startIndex + batchSize, maxIndex); startIndex < maxIndex; startIndex =
+ endIndex, endIndex = Math.min(startIndex + batchSize, maxIndex))
{
- final int endIndex = Math.min(startIndex + batchSize, maxIndex);
final List<S> batch = allEntities.subList(startIndex, endIndex);
strategy.execute(batch);
operationLog.info(String.format("%s %s progress: %d/%d", strategy.getEntityName(),
strategy.getOperationName(), endIndex, maxIndex));
- startIndex += batchSize;
}
}
+
}
\ No newline at end of file