diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityWithPropertiesDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityWithPropertiesDAO.java
index e8d48173f1980d28d05400b8279485a985f53de0..75f82c1828207ebeb7f23a4b6769aa811494a647 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityWithPropertiesDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractGenericEntityWithPropertiesDAO.java
@@ -34,8 +34,8 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.IFullTextIndexUpdateScheduler;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.IndexUpdateOperation;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventType;
import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationWithPropertiesHolder;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
@@ -50,21 +50,21 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityInformationWithPropertiesHolder>
extends AbstractGenericEntityDAO<T>
{
- private static final String ATTACHMENT_IDS_PARAM = "attachmentIds";
+ protected static final String ATTACHMENT_CONTENT_IDS_PARAM = "attachmentContentIds";
- private static final String DESCRIPTION_PARAM = "description";
+ protected static final String DESCRIPTION_PARAM = "description";
- private static final String ENTITY_IDS_PARAM = "entityIds";
+ protected static final String ENTITY_IDS_PARAM = "entityIds";
- private static final String ENTITY_TYPE_PARAM = "entityType";
+ protected static final String ENTITY_TYPE_PARAM = "entityType";
- private static final String EVENT_TYPE_PARAM = "eventType";
+ protected static final String EVENT_TYPE_PARAM = "eventType";
- private static final String IDENTIFIERS_PARAM = "identifiers";
+ protected static final String IDENTIFIERS_PARAM = "identifiers";
- private static final String REGISTRATOR_ID_PARAM = "registratorId";
+ protected static final String REGISTRATOR_ID_PARAM = "registratorId";
- private static final String REASON_PARAM = "reason";
+ protected static final String REASON_PARAM = "reason";
private final PersistencyResources persistencyResources;
@@ -111,7 +111,7 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
getEntityClass(), ids);
}
- protected void executePermanentDeleteAction(final EntityKind entityKind,
+ protected void executePermanentDeleteAction(final EntityType entityType,
final List<TechId> entityTechIds, final PersonPE registrator, final String reason,
final String sqlSelectPermIds, final String sqlDeleteProperties,
final String sqlSelectAttachmentContentIds, final String sqlDeleteAttachmentContents,
@@ -120,7 +120,7 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
{
List<Long> entityIds = TechId.asLongs(entityTechIds);
DeletePermanentlyBatchOperation deleteOperation =
- new DeletePermanentlyBatchOperation(entityKind, entityIds, registrator, reason,
+ new DeletePermanentlyBatchOperation(entityType, entityIds, registrator, reason,
sqlSelectPermIds, sqlDeleteProperties, sqlSelectAttachmentContentIds,
sqlDeleteAttachmentContents, sqlDeleteAttachments, sqlDeleteEntities,
sqlInsertEvent, additionalQueries);
@@ -135,7 +135,7 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
protected class DeletePermanentlyBatchOperation implements IBatchOperation<Long>
{
- private final EntityKind entityKind;
+ private final EntityType entityType;
private final List<Long> allEntityIds;
@@ -159,13 +159,13 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
private final String[] additionalQueries;
- DeletePermanentlyBatchOperation(EntityKind entityKind, List<Long> allEntityIds,
+ DeletePermanentlyBatchOperation(EntityType entityType, List<Long> allEntityIds,
PersonPE registrator, String reason, String sqlSelectPermIds,
String sqlDeleteProperties, String sqlSelectAttachmentContentIds,
String sqlDeleteAttachmentContents, String sqlDeleteAttachments,
String sqlDeleteEntities, String sqlInsertEvent, String... additionalQueries)
{
- this.entityKind = entityKind;
+ this.entityType = entityType;
this.allEntityIds = allEntityIds;
this.registrator = registrator;
this.reason = reason;
@@ -186,7 +186,7 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
public String getEntityName()
{
- return entityKind.getDescription();
+ return entityType.name();
}
public String getOperationName()
@@ -264,16 +264,18 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
sqlQueryDeleteProperties.executeUpdate();
}
- private void deleteAttachmentsWithContents(final SQLQuery sqlQueryAttachmentContentIds,
+ private void deleteAttachmentsWithContents(
+ final SQLQuery sqlQuerySelectAttachmentContentIds,
final SQLQuery sqlQueryDeleteAttachments,
final SQLQuery sqlQueryDeleteAttachmentContents, List<Long> entityIds)
{
- sqlQueryAttachmentContentIds.setParameterList(ENTITY_IDS_PARAM, entityIds);
- List<Long> attachmentContentIds = cast(sqlQueryAttachmentContentIds.list());
+ sqlQuerySelectAttachmentContentIds.setParameterList(ENTITY_IDS_PARAM, entityIds);
+ List<Long> attachmentContentIds = cast(sqlQuerySelectAttachmentContentIds.list());
if (attachmentContentIds.size() > 0)
{
- deleteProperties(sqlQueryDeleteAttachments, entityIds);
- sqlQueryDeleteAttachmentContents.setParameterList(ATTACHMENT_IDS_PARAM,
+ sqlQueryDeleteAttachments.setParameterList(ENTITY_IDS_PARAM, entityIds);
+ sqlQueryDeleteAttachments.executeUpdate();
+ sqlQueryDeleteAttachmentContents.setParameterList(ATTACHMENT_CONTENT_IDS_PARAM,
attachmentContentIds);
sqlQueryDeleteAttachmentContents.executeUpdate();
}
@@ -304,7 +306,7 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
sqlQueryInsertEvent.setParameter(EVENT_TYPE_PARAM, EventType.DELETION.name());
sqlQueryInsertEvent.setParameter(REASON_PARAM, reason);
sqlQueryInsertEvent.setParameter(REGISTRATOR_ID_PARAM, registrator.getId());
- sqlQueryInsertEvent.setParameter(ENTITY_TYPE_PARAM, entityKind.name());
+ sqlQueryInsertEvent.setParameter(ENTITY_TYPE_PARAM, entityType.name());
final String allPermIdsAsString =
CollectionUtils.abbreviate(permIds, -1, CollectionStyle.NO_BOUNDARY);
@@ -339,13 +341,13 @@ public abstract class AbstractGenericEntityWithPropertiesDAO<T extends IEntityIn
protected static String createDeleteAttachmentContentsSQL()
{
return "DELETE FROM " + TableNames.ATTACHMENT_CONTENT_TABLE + " WHERE id "
- + in(ATTACHMENT_IDS_PARAM);
+ + in(ATTACHMENT_CONTENT_IDS_PARAM);
}
- protected static String createDeleteAttachmentsSQL()
+ protected static String createDeleteAttachmentsSQL(final String ownerColumnName)
{
- return "DELETE FROM " + TableNames.ATTACHMENTS_TABLE + " WHERE samp_id "
- + inEntityIds();
+ return "DELETE FROM " + TableNames.ATTACHMENTS_TABLE + " WHERE " + ownerColumnName
+ + " " + inEntityIds();
}
protected static String createDeleteEnitiesSQL(final String entitiesTable)
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 6e6dc9ed68d6af455a2273e4cda58e0c6f14d8ab..c1856f122b30e9cb017d1f60e498a0ea2841477b 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
@@ -29,7 +29,9 @@ import org.apache.log4j.Logger;
import org.hibernate.FetchMode;
import org.hibernate.HibernateException;
import org.hibernate.LockMode;
+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;
@@ -38,22 +40,29 @@ import org.springframework.dao.DataAccessException;
import org.springframework.orm.hibernate3.HibernateCallback;
import org.springframework.orm.hibernate3.HibernateTemplate;
+import ch.systemsx.cisd.common.collections.CollectionStyle;
+import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.collections.IToStringConverter;
+import ch.systemsx.cisd.common.collections.ToStringDefaultConverter;
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.common.utilities.MethodUtils;
+import ch.systemsx.cisd.openbis.generic.server.batch.BatchOperationExecutor;
+import ch.systemsx.cisd.openbis.generic.server.batch.IBatchOperation;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
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.IEntityInformationHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.dto.ColumnNames;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DeletedDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EventType;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
@@ -502,51 +511,60 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
// For data sets we load codes, which are logically the same as perm ids.
// We load them ordered by ID because locations need to be loaded in the same order.
final String sqlSelectPermIds = createSelectCodesOrderByIdSQL(dataTable);
+ final String sqlSelectLocations = createSelectLocationsOrderByIdSQL(dataTable);
final String sqlDeleteProperties =
SQLBuilder.createDeletePropertiesSQL(TableNames.DATA_SET_PROPERTIES_TABLE,
ColumnNames.DATA_SET_COLUMN);
- // FIXME
- final String sqlSelectAttachmentContentIds =
- SQLBuilder.createSelectAttachmentContentIdsSQL(ColumnNames.DATA_SET_COLUMN);
- final String sqlDeleteAttachmentContents = SQLBuilder.createDeleteAttachmentContentsSQL();
- final String sqlDeleteAttachments = SQLBuilder.createDeleteAttachmentsSQL();
final String sqlDeleteDataSets = SQLBuilder.createDeleteEnitiesSQL(dataTable);
final String sqlInsertEvent = SQLBuilder.createInsertEventSQL();
// data set specific queries
- // FIXME use locations in events
- // final String sqlSelectLocationsOrderById = createSelectLocationsOrderByIdSQL(dataTable);
+ final String sqlDeleteExternalData = createDeleteExternalDataSQL();
final String sqlDeleteChildrenConnections = createDeleteChildrenConnectionsSQL();
final String sqlDeleteParentConnections = createDeleteParentConnectionsSQL();
final String sqlDeleteComponentConnections = createDeleteComponentConnectionsSQL();
- executePermanentDeleteAction(EntityKind.DATA_SET, dataIds, registrator, reason,
- sqlSelectPermIds, sqlDeleteProperties, sqlSelectAttachmentContentIds,
- sqlDeleteAttachmentContents, sqlDeleteAttachments, sqlDeleteDataSets,
- sqlInsertEvent,
- // sqlSelectLocationsOrderById,
- sqlDeleteChildrenConnections, sqlDeleteParentConnections,
- sqlDeleteComponentConnections);
+ executePermanentDeleteOfDataSets(EntityType.DATASET, dataIds, registrator, reason,
+ sqlSelectPermIds, sqlSelectLocations, sqlDeleteProperties, sqlDeleteDataSets,
+ sqlInsertEvent, sqlDeleteExternalData, sqlDeleteChildrenConnections,
+ sqlDeleteParentConnections, sqlDeleteComponentConnections);
}
- // @Override
- // protected boolean debugDeletion()
- // {
- // return true;
- // }
+ protected void executePermanentDeleteOfDataSets(final EntityType entityType,
+ final List<TechId> entityTechIds, final PersonPE registrator, final String reason,
+ final String sqlSelectPermIds, final String sqlSelectLocations,
+ final String sqlDeleteProperties, final String sqlDeleteEntities,
+ final String sqlInsertEvent, final String... additionalQueries)
+ {
+ List<Long> entityIds = TechId.asLongs(entityTechIds);
+ DeleteDataSetsPermanentlyBatchOperation deleteOperation =
+ new DeleteDataSetsPermanentlyBatchOperation(entityType, entityIds, registrator,
+ reason, sqlSelectPermIds, sqlSelectLocations, sqlDeleteProperties,
+ sqlDeleteEntities, sqlInsertEvent, additionalQueries);
+ BatchOperationExecutor.executeInBatches(deleteOperation);
+
+ // FIXME remove this when we remove the switch to disable trash
+ scheduleRemoveFromFullTextIndex(entityIds);
+ }
- protected static String createSelectCodesOrderByIdSQL(final String dataSetsTable)
+ private static String createSelectCodesOrderByIdSQL(final String dataSetsTable)
{
return "SELECT code FROM " + dataSetsTable + " WHERE id " + SQLBuilder.inEntityIds()
+ " ORDER BY id";
}
- protected static String createSelectLocationsOrderByIdSQL(final String dataSetsTable)
+ private static String createSelectLocationsOrderByIdSQL(final String dataSetsTable)
{
return "SELECT ed.location FROM " + dataSetsTable + " d "
+ "LEFT OUTER JOIN external_data ed ON (d.id = ed.data_id) WHERE id "
+ SQLBuilder.inEntityIds() + " ORDER BY id";
}
+ private static String createDeleteExternalDataSQL()
+ {
+ return "DELETE FROM " + TableNames.EXTERNAL_DATA_TABLE + " WHERE data_id "
+ + SQLBuilder.inEntityIds();
+ }
+
private static String createDeleteChildrenConnectionsSQL()
{
return "DELETE FROM " + TableNames.DATA_SET_RELATIONSHIPS_TABLE + " WHERE data_id_parent "
@@ -565,6 +583,184 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
+ SQLBuilder.inEntityIds();
}
+ // TODO refactor - it is very similar code to the one in AbstractGenericEntityWithPropertiesDAO
+ protected class DeleteDataSetsPermanentlyBatchOperation implements IBatchOperation<Long>
+ {
+
+ private final EntityType entityType;
+
+ private final List<Long> allEntityIds;
+
+ private final PersonPE registrator;
+
+ private final String reason;
+
+ private final String sqlSelectPermIds;
+
+ private final String sqlSelectLocations;
+
+ private final String sqlDeleteProperties;
+
+ private final String sqlDeleteEntities;
+
+ private final String sqlInsertEvent;
+
+ private final String[] additionalQueries;
+
+ public DeleteDataSetsPermanentlyBatchOperation(EntityType entityType,
+ List<Long> allEntityIds, PersonPE registrator, String reason,
+ String sqlSelectPermIds, String sqlSelectLocations, String sqlDeleteProperties,
+ String sqlDeleteEntities, String sqlInsertEvent, String... additionalQueries)
+ {
+ this.entityType = entityType;
+ this.allEntityIds = allEntityIds;
+ this.registrator = registrator;
+ this.reason = reason;
+ this.sqlSelectPermIds = sqlSelectPermIds;
+ this.sqlSelectLocations = sqlSelectLocations;
+ this.sqlDeleteProperties = sqlDeleteProperties;
+ this.sqlDeleteEntities = sqlDeleteEntities;
+ this.sqlInsertEvent = sqlInsertEvent;
+ this.additionalQueries = additionalQueries;
+ }
+
+ public List<Long> getAllEntities()
+ {
+ return allEntityIds;
+ }
+
+ public String getEntityName()
+ {
+ return entityType.name();
+ }
+
+ public String getOperationName()
+ {
+ return "permanently deleting";
+ }
+
+ public void execute(final List<Long> batchEntityIds)
+ {
+ executeStatelessAction(createPermanentDeleteAction(batchEntityIds));
+ }
+
+ private StatelessHibernateCallback createPermanentDeleteAction(
+ final List<Long> entityIdsToDelete)
+ {
+ return new PermanentDeletionAction(entityIdsToDelete);
+ }
+
+ private class PermanentDeletionAction implements StatelessHibernateCallback
+ {
+ private final List<Long> entityIdsToDelete;
+
+ public PermanentDeletionAction(List<Long> entityIdsToDelete)
+ {
+ this.entityIdsToDelete = entityIdsToDelete;
+ }
+
+ public Object doInStatelessSession(StatelessSession session)
+ {
+ final SQLQuery sqlQuerySelectPermIds = session.createSQLQuery(sqlSelectPermIds);
+ final SQLQuery sqlQuerySelectLocations = session.createSQLQuery(sqlSelectLocations);
+ final SQLQuery sqlQueryDeleteProperties =
+ session.createSQLQuery(sqlDeleteProperties);
+ final SQLQuery sqlQueryDeleteEntities = session.createSQLQuery(sqlDeleteEntities);
+ final SQLQuery sqlQueryInsertEvent = session.createSQLQuery(sqlInsertEvent);
+ final List<SQLQuery> additionalSqlQueries = new ArrayList<SQLQuery>();
+ for (String queryString : additionalQueries)
+ {
+ additionalSqlQueries.add(session.createSQLQuery(queryString));
+ }
+
+ final List<String> permIds =
+ selectPermIds(sqlQuerySelectPermIds, entityIdsToDelete);
+ if (permIds.isEmpty())
+ {
+ return null;
+ }
+ final List<String> locations =
+ selectLocations(sqlQuerySelectLocations, entityIdsToDelete);
+ deleteProperties(sqlQueryDeleteProperties, entityIdsToDelete);
+ executeAdditionalQueries(additionalSqlQueries, entityIdsToDelete);
+ deleteMainEntities(sqlQueryDeleteEntities, entityIdsToDelete);
+ insertEvent(sqlQueryInsertEvent, permIds, locations);
+ return null;
+ }
+
+ private List<String> selectPermIds(final SQLQuery sqlQuerySelectPermIds,
+ final List<Long> entityIds)
+ {
+ sqlQuerySelectPermIds.setParameterList(ENTITY_IDS_PARAM, entityIds);
+ final List<String> permIdsOrNull = cast(sqlQuerySelectPermIds.list());
+ return permIdsOrNull == null ? Collections.<String> emptyList() : permIdsOrNull;
+ }
+
+ private List<String> selectLocations(final SQLQuery sqlQuerySelectLocations,
+ final List<Long> entityIds)
+ {
+ sqlQuerySelectLocations.setParameterList(ENTITY_IDS_PARAM, entityIds);
+ return cast(sqlQuerySelectLocations.list());
+ }
+
+ private void deleteProperties(final SQLQuery sqlQueryDeleteProperties,
+ List<Long> entityIds)
+ {
+ sqlQueryDeleteProperties.setParameterList(ENTITY_IDS_PARAM, entityIds);
+ sqlQueryDeleteProperties.executeUpdate();
+ }
+
+ private void executeAdditionalQueries(final List<SQLQuery> additionalSqlQueries,
+ List<Long> entityIds)
+ {
+ for (SQLQuery query : additionalSqlQueries)
+ {
+ query.setParameterList(ENTITY_IDS_PARAM, entityIds);
+ query.executeUpdate();
+ }
+ }
+
+ private void deleteMainEntities(final SQLQuery sqlQueryDeleteEntities,
+ List<Long> entityIds)
+ {
+ sqlQueryDeleteEntities.setParameterList(ENTITY_IDS_PARAM, entityIds);
+ sqlQueryDeleteEntities.executeUpdate();
+ }
+
+ private void insertEvent(final SQLQuery sqlQueryInsertEvent,
+ final List<String> permIds, final List<String> locations)
+ {
+ sqlQueryInsertEvent.setParameter(EVENT_TYPE_PARAM, EventType.DELETION.name());
+ sqlQueryInsertEvent.setParameter(REASON_PARAM, reason);
+ sqlQueryInsertEvent.setParameter(REGISTRATOR_ID_PARAM, registrator.getId());
+ sqlQueryInsertEvent.setParameter(ENTITY_TYPE_PARAM, entityType.name());
+
+ IToStringConverter<Object> toStringConverter = new IToStringConverter<Object>()
+ {
+ IToStringConverter<Object> delegatee = ToStringDefaultConverter
+ .getInstance();
+
+ public String toString(Object value)
+ {
+ return value == null ? "" : delegatee.toString();
+ }
+ };
+ final String allPermIdsAsString =
+ CollectionUtils.abbreviate(permIds, -1, toStringConverter,
+ CollectionStyle.NO_BOUNDARY);
+ sqlQueryInsertEvent.setParameter(IDENTIFIERS_PARAM, allPermIdsAsString);
+ // FIXME handle null locations for containers
+ final String description =
+ CollectionUtils.abbreviate(locations, -1, toStringConverter,
+ CollectionStyle.NO_BOUNDARY);
+ sqlQueryInsertEvent.setParameter(DESCRIPTION_PARAM, description);
+
+ sqlQueryInsertEvent.executeUpdate();
+ }
+ }
+
+ }
+
@SuppressWarnings("unchecked")
public Set<TechId> findParentIds(final Collection<TechId> dataSetIds)
{