diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index 9f2a597ff192c8c177cdd596c34fd2c1a0f7facc..d3097fd6f5871da91515006fee04df9d6101046f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -72,9 +72,9 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.dynamic_property.calc
import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
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.IDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IFileFormatTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IHibernateSearchDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IRoleAssignmentDAO;
@@ -208,7 +208,6 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.DataStoreServiceTransl
import ch.systemsx.cisd.openbis.generic.shared.translator.DataTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.DtoConverters;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.GridCustomExpressionTranslator.GridCustomFilterTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.GroupTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTypeTranslator;
@@ -913,13 +912,13 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
final Session session = getSession(sessionToken);
try
{
- final Set<ExternalDataPE> resultSet = new LinkedHashSet<ExternalDataPE>();
+ final Set<DataPE> resultSet = new LinkedHashSet<DataPE>();
// TODO 2009-08-17, Piotr Buczek: [LMS-1149] optimize performance
addRelatedDataSets(resultSet, relatedEntities.getEntities());
final List<ExternalData> list = new ArrayList<ExternalData>(resultSet.size());
- for (final ExternalDataPE hit : resultSet)
+ for (final DataPE hit : resultSet)
{
- list.add(ExternalDataTranslator.translate(hit, session.getBaseIndexURL(), false));
+ list.add(DataSetTranslator.translate(hit, session.getBaseIndexURL(), false));
}
return list;
} catch (final DataAccessException ex)
@@ -928,16 +927,15 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
}
}
- private void addRelatedDataSets(final Set<ExternalDataPE> resultSet,
+ private void addRelatedDataSets(final Set<DataPE> resultSet,
final List<? extends IEntityInformationHolder> relatedEntities)
{
- final IExternalDataDAO externalDataDAO = getDAOFactory().getExternalDataDAO();
+ final IDataDAO dataDAO = getDAOFactory().getDataDAO();
for (IEntityInformationHolder entity : relatedEntities)
{
if (isEntityKindRelatedWithDataSets(entity.getEntityKind()))
{
- List<ExternalDataPE> relatedDataSets =
- externalDataDAO.listRelatedExternalData(entity);
+ List<DataPE> relatedDataSets = dataDAO.listRelatedDataSets(entity);
resultSet.addAll(relatedDataSets);
}
}
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 b24852f3c9cc71a33c7c2ad508397695cb8ae2d6..30875851f56d58fdbae6744af921d595ed865976 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
@@ -209,6 +209,7 @@ abstract class AbstractBusinessObject implements IDAOFactory
return daoFactory.getDataDAO();
}
+ @Deprecated
public final IExternalDataDAO getExternalDataDAO()
{
return daoFactory.getExternalDataDAO();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
index 8e65530dfebaf211bb1e66e1517b9ac324c937b4..a8a7edfbbcc619a414d358329180629bcf8a36de 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
@@ -29,7 +29,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.bo.util.SampleOwner;
import ch.systemsx.cisd.openbis.generic.server.business.bo.util.SampleUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
@@ -347,11 +347,11 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
return project;
}
- protected void checkAllBusinessRules(SamplePE sample, IExternalDataDAO externalDataDAO,
+ protected void checkAllBusinessRules(SamplePE sample, IDataDAO dataDAO,
Map<EntityTypePE, List<EntityTypePropertyTypePE>> cacheOrNull)
{
checkPropertiesBusinessRules(sample, cacheOrNull);
- checkExperimentBusinessRules(externalDataDAO, sample);
+ checkExperimentBusinessRules(dataDAO, sample);
checkParentBusinessRules(sample);
checkContainerBusinessRules(sample);
}
@@ -370,9 +370,9 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
}
}
- protected void checkExperimentBusinessRules(IExternalDataDAO externalDataDAO, SamplePE sample)
+ protected void checkExperimentBusinessRules(IDataDAO dataDAO, SamplePE sample)
{
- final boolean hasDatasets = hasDatasets(externalDataDAO, sample);
+ final boolean hasDatasets = hasDatasets(dataDAO, sample);
if (hasDatasets && sample.getExperiment() == null)
{
throw UserFailureException.fromTemplate(
@@ -407,11 +407,11 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
SampleGenericBusinessRules.assertValidComponents(sample);
}
- protected boolean hasDatasets(IExternalDataDAO externalDataDAO, SamplePE sample)
+ protected boolean hasDatasets(IDataDAO dataDAO, SamplePE sample)
{
// If we just added new data sets in this BO, they won't have data sets, so no need to
// check.
- return (onlyNewSamples == false) && SampleUtils.hasDatasets(externalDataDAO, sample);
+ return (onlyNewSamples == false) && SampleUtils.hasDatasets(dataDAO, sample);
}
protected void updateSpace(SamplePE sample, SampleIdentifier sampleOwnerIdentifier,
@@ -441,7 +441,7 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
private void removeFromExperiment(SamplePE sample)
{
- if (hasDatasets(getExternalDataDAO(), sample))
+ if (hasDatasets(getDataDAO(), sample))
{
throw UserFailureException.fromTemplate(
"Cannot detach the sample '%s' from the experiment "
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
index cd16c283ad9157c7dd4b775e8dc0d90006350de0..a57e8a46a48456e992605ea6198c99c2a7d06b3a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
@@ -231,7 +231,7 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
{
if (experiment.getDataSets().size() > 0)
{
- getExternalDataDAO().listExternalData(experiment);
+ getDataDAO().listDataSets(experiment);
boolean onlyPlaceholders = true;
for (DataPE data : experiment.getDataSets())
{
@@ -468,7 +468,7 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
{
for (SamplePE sample : samples)
{
- SampleUtils.checkSampleWithoutDatasets(getExternalDataDAO(), sample);
+ SampleUtils.checkSampleWithoutDatasets(getDataDAO(), sample);
experiment.removeSample(sample);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
index 768297549e56f9931e6db2ef72d9a5dde5fc01fd..0919865b01bbe7940275b0dbe0992b1aa1d22a94 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
@@ -65,6 +65,7 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
/**
* @author Franz-Josef Elmer
*/
+@SuppressWarnings("deprecation")
@Friend(toClasses = DataPE.class)
public class ExternalDataBO extends AbstractExternalDataBusinessObject implements IExternalDataBO
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
index e54fa46de24476a2812235d35ef93a02ec6059f6..f4baad2db7b716caa62465a48d8cbef71724e09a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
@@ -80,6 +80,8 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
*
* @author Christian Ribeaud
*/
+@SuppressWarnings("deprecation")
+// FIXME
public final class ExternalDataTable extends AbstractExternalDataBusinessObject implements
IExternalDataTable
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
index aedbe2b3144a1f8ea07042ac11e153420f5a15a6..55237d38a31fa317f839d05632a8fa73f2543af7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
@@ -188,7 +188,7 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
}
attachments.clear();
}
- checkAllBusinessRules(sample, getExternalDataDAO(), null);
+ checkAllBusinessRules(sample, getDataDAO(), null);
onlyNewSamples = false;
}
@@ -223,7 +223,7 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
private final void checkSampleWithoutDatasets()
{
- SampleUtils.checkSampleWithoutDatasets(getExternalDataDAO(), sample);
+ SampleUtils.checkSampleWithoutDatasets(getDataDAO(), sample);
}
private final static void checkSampleUnused(final SamplePE sample)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
index 39e20641d699f746b62ff546e24aee8f82bd24e3..42c245bbe3f9647ba4caa3f46ccf581a380798ea 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
@@ -221,7 +221,7 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
new HashMap<EntityTypePE, List<EntityTypePropertyTypePE>>();
for (SamplePE s : samples)
{
- checkAllBusinessRules(s, getExternalDataDAO(), cache);
+ checkAllBusinessRules(s, getDataDAO(), cache);
}
}
@@ -245,7 +245,7 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
{
updateSpace(sample, updates.getSampleIdentifier(), sampleOwnerCache);
updateExperiment(sample, updates.getExperimentIdentifierOrNull(), experimentCache);
- checkExperimentBusinessRules(getExternalDataDAO(), sample);
+ checkExperimentBusinessRules(getDataDAO(), sample);
}
if (details.isParentsUpdateRequested())
{
@@ -293,14 +293,16 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
final Map<EntityTypePE, List<EntityTypePropertyTypePE>> propertiesCache =
new HashMap<EntityTypePE, List<EntityTypePropertyTypePE>>();
samples = loadSamples(updates, sampleOwnerCache);
- Map<SampleIdentifier, SamplePE> samplesByIdentifiers = new HashMap<SampleIdentifier, SamplePE>();
+ Map<SampleIdentifier, SamplePE> samplesByIdentifiers =
+ new HashMap<SampleIdentifier, SamplePE>();
for (SamplePE sample : samples)
{
samplesByIdentifiers.put(sample.getSampleIdentifier(), sample);
}
for (SampleBatchUpdatesDTO sampleUpdates : updates)
{
- final SamplePE sample = samplesByIdentifiers.get(sampleUpdates.getOldSampleIdentifierOrNull());
+ final SamplePE sample =
+ samplesByIdentifiers.get(sampleUpdates.getOldSampleIdentifierOrNull());
prepareBatchUpdate(sample, sampleUpdates, sampleOwnerCache, experimentCache,
propertiesCache);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/SampleUtils.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/SampleUtils.java
index e371dbf7e6d52836d76d52ae982a01b3b9f9a7ca..24a6c291c4f15cca4578faadab89ebdd27df937f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/SampleUtils.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/util/SampleUtils.java
@@ -17,20 +17,19 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.util;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
/**
* @author Tomasz Pylak
*/
public class SampleUtils
{
- public static final void checkSampleWithoutDatasets(IExternalDataDAO externalDataDAO,
- SamplePE sample)
+ public static final void checkSampleWithoutDatasets(IDataDAO dataDAO, SamplePE sample)
{
- if (hasDatasets(externalDataDAO, sample))
+ if (hasDatasets(dataDAO, sample))
{
throw UserFailureException
.fromTemplate(
@@ -39,11 +38,11 @@ public class SampleUtils
}
}
- public static boolean hasDatasets(IExternalDataDAO externalDataDAO, SamplePE sample)
+ public static boolean hasDatasets(IDataDAO dataDAO, SamplePE sample)
{
assert sample != null;
- return externalDataDAO.hasExternalData(sample);
+ return dataDAO.hasDataSet(sample);
}
/** for all experiment samples which belonged to a group the specified group will be set */
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataDAO.java
index d44effed62e2b78c7dd9a5aacb12ad06e7a94178..36621269586d48cc0957fdc0b54401ad891f6354 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataDAO.java
@@ -58,16 +58,6 @@ public interface IDataDAO extends IGenericDAO<DataPE>
*/
public List<DataPE> listDataSets(final SamplePE sample) throws DataAccessException;
- // /**
- // * List the all {@link ExternalDataPE} for given {@link DataSetArchivingStatus}.
- // *
- // * @param maxResultSize the maximum size of the returned list. Specifying a negative number
- // * (e.g. -1) is equal to no limitation.
- // * @returns list of {@link ExternalDataPE}s with the specified status.
- // */
- // public List<ExternalDataPE> listByArchivingStatus(DataSetArchivingStatus status,
- // int maxResultSize);
-
/**
* List the {@link DataPE} for given <var>experiment</var>.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExternalDataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExternalDataDAO.java
index 921112fe7687977ee569c0fb6e71ee25fc387b56..35f9b3dd03b0f519b6a30f9341e7733c7ce44307 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExternalDataDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExternalDataDAO.java
@@ -22,7 +22,6 @@ import java.util.Set;
import org.springframework.dao.DataAccessException;
-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.dto.DataPE;
@@ -34,8 +33,10 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
/**
* An interface that contains all data access operations on {@link ExternalDataPE}s.
*
+ * @deprecated use {@link IDataDAO}
* @author Christian Ribeaud
*/
+@Deprecated
public interface IExternalDataDAO extends IGenericDAO<ExternalDataPE>
{
/**
@@ -45,15 +46,6 @@ public interface IExternalDataDAO extends IGenericDAO<ExternalDataPE>
*/
public boolean hasExternalData(final SamplePE sample) throws DataAccessException;
- /**
- * List the {@link ExternalDataPE} related to given <var>entity</var>.
- *
- * @returns list of {@link ExternalDataPE}s that are related to given
- * {@link IEntityInformationHolder}.
- */
- public List<ExternalDataPE> listRelatedExternalData(final IEntityInformationHolder entity)
- throws DataAccessException;
-
/**
* List the {@link ExternalDataPE} for given <var>sample</var>.
*
@@ -61,16 +53,6 @@ public interface IExternalDataDAO extends IGenericDAO<ExternalDataPE>
*/
public List<ExternalDataPE> listExternalData(final SamplePE sample) throws DataAccessException;
- // /**
- // * List the all {@link ExternalDataPE} for given {@link DataSetArchivingStatus}.
- // *
- // * @param maxResultSize the maximum size of the returned list. Specifying a negative number
- // * (e.g. -1) is equal to no limitation.
- // * @returns list of {@link ExternalDataPE}s with the specified status.
- // */
- // public List<ExternalDataPE> listByArchivingStatus(DataSetArchivingStatus status,
- // int maxResultSize);
-
/**
* List the {@link ExternalDataPE} for given <var>experiment</var>.
*
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 fbe83c0fc55d0f0cd8fbe8db302fcfc258bf3143..95c57e9a6e49cef44723e5a4adf0cbc2a8ebc31a 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
@@ -44,7 +44,6 @@ 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.dataaccess.IDataDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
@@ -60,7 +59,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.TableNames;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
/**
- * Implementation of {@link IExternalDataDAO} for databases.
+ * Implementation of {@link IDataDAO} for databases.
*
* @author Christian Ribeaud
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java
index 9255dadd9499c5015005ff9720549ed6ca322c0e..02b12b38d576e3fe394e19f46ddd7b46f5c14ff9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java
@@ -63,6 +63,7 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
*
* @author Christian Ribeaud
*/
+@SuppressWarnings("deprecation")
final class ExternalDataDAO extends AbstractGenericEntityWithPropertiesDAO<ExternalDataPE>
implements IExternalDataDAO
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/DataSetGroupLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/DataSetGroupLoader.java
index fa86ddaa30fa8e363854a8c11aa82ee892e856d2..776700cb48e9653e43cabd89e262e1c74ab29fce 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/DataSetGroupLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/DataSetGroupLoader.java
@@ -21,8 +21,8 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
/**
@@ -33,9 +33,9 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
class DataSetGroupLoader implements IGroupLoader
{
- private final IExternalDataDAO dao;
+ private final IDataDAO dao;
- public DataSetGroupLoader(IExternalDataDAO dao)
+ public DataSetGroupLoader(IDataDAO dao)
{
this.dao = dao;
}
@@ -43,8 +43,8 @@ class DataSetGroupLoader implements IGroupLoader
public Map<String, SpacePE> loadGroups(Set<String> keys)
{
Map<String, SpacePE> map = new HashMap<String, SpacePE>();
- List<ExternalDataPE> data = dao.listByCode(keys);
- for (ExternalDataPE d : data)
+ List<DataPE> data = dao.listByCode(keys);
+ for (DataPE d : data)
{
map.put(d.getCode(), d.getExperiment().getProject().getSpace());
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/GroupLoaderFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/GroupLoaderFactory.java
index d07eda0c263f22813005a50c76c63a84d642a220..c8c935cf39abfee420637b3948665aca43e1ee43 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/GroupLoaderFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/GroupLoaderFactory.java
@@ -42,7 +42,7 @@ class GroupLoaderFactory implements IGroupLoaderFactory
case SAMPLE:
return new SampleGroupLoader(factory.getSampleDAO());
case DATA_SET:
- return new DataSetGroupLoader(factory.getExternalDataDAO());
+ return new DataSetGroupLoader(factory.getDataDAO());
case MATERIAL:
throw new UnsupportedOperationException();
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
index 1578ac12e0d4cf574146d4381fe8d1ec53efbcb2..e573125127f44b35dabecc99c157a8de01753d3a 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
@@ -504,7 +504,7 @@ public final class ExperimentBOTest extends AbstractBOTest
context.checking(new Expectations()
{
{
- allowing(externalDataDAO).hasExternalData((with(any(SamplePE.class))));
+ allowing(dataDAO).hasDataSet((with(any(SamplePE.class))));
will(returnValue(false));
}
});
@@ -582,7 +582,7 @@ public final class ExperimentBOTest extends AbstractBOTest
context.checking(new Expectations()
{
{
- allowing(externalDataDAO).hasExternalData(with(assignedSample));
+ allowing(dataDAO).hasDataSet(with(assignedSample));
will(returnValue(true));
}
});
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
index 258862dfd94614d050fa8ebbd3cdd53bb2261312..a0bbd96621a88f3dbf18ae7d48192abf1a830fe2 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
@@ -72,6 +72,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.types.DataSetTypeCode;
* @author Franz-Josef Elmer
*/
// TODO 2009-09-10, Piotr Buczek: write tests with many parents and cycle check
+@SuppressWarnings("deprecation")
public class ExternalDataBOTest extends AbstractBOTest
{
private static final int SPEED_HINT = (Constants.DEFAULT_SPEED_HINT + Constants.MAX_SPEED) / 2;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
index cea27e1e036b2d32f6672b15e58cce0c97599960..cc62493e8e2779585cf1dca8dce78daf03caec20 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
@@ -68,6 +68,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
* @author Christian Ribeaud
*/
@Friend(toClasses = ExternalDataTable.class)
+// FIXME
+@SuppressWarnings("deprecation")
public final class ExternalDataTableTest extends AbstractBOTest
{
private IDataStoreServiceFactory dssFactory;
@@ -308,8 +310,10 @@ public final class ExternalDataTableTest extends AbstractBOTest
prepareFindFullDatasets(new ExternalDataPE[]
{ d1, d2 }, false, false);
- BaseMatcher<List<DatasetDescription>> dataSets = createDatasetDescriptionsMatcher(d2);
- one(dataStoreService2).getKnownDataSets(with(dss2.getSessionToken()), with(dataSets));
+ BaseMatcher<List<DatasetDescription>> dataSets =
+ createDatasetDescriptionsMatcher(d2);
+ one(dataStoreService2).getKnownDataSets(with(dss2.getSessionToken()),
+ with(dataSets));
will(returnValue(Arrays.asList(d2.getLocation())));
PersonPE person = EXAMPLE_SESSION.tryGetPerson();
@@ -318,7 +322,8 @@ public final class ExternalDataTableTest extends AbstractBOTest
one(eventDAO).persist(createDeletionEvent(d2, person, reason));
one(externalDataDAO).delete(d2);
- one(dataStoreService2).deleteDataSets(with(dss2.getSessionToken()), with(dataSets));
+ one(dataStoreService2).deleteDataSets(with(dss2.getSessionToken()),
+ with(dataSets));
}
});
@@ -356,7 +361,8 @@ public final class ExternalDataTableTest extends AbstractBOTest
will(returnValue(Arrays.asList(d2PE.getLocation())));
one(dataStoreService2).uploadDataSetsToCIFEX(
- with(equal(dss2.getSessionToken())), with(new BaseMatcher<List<ExternalData>>()
+ with(equal(dss2.getSessionToken())),
+ with(new BaseMatcher<List<ExternalData>>()
{
public boolean matches(Object item)
@@ -647,7 +653,7 @@ public final class ExternalDataTableTest extends AbstractBOTest
with(equal(ManagerTestTool.EXAMPLE_PERSON.getEmail())),
with(equal(true)));
will(throwException(new RuntimeException()));
-
+
allowing(dataStoreService3).archiveDatasets(
with(equal(dss3.getSessionToken())),
with(createDatasetDescriptionsMatcher(d3Array)),
@@ -719,7 +725,8 @@ public final class ExternalDataTableTest extends AbstractBOTest
}
@SuppressWarnings("unchecked")
- private BaseMatcher<List<DatasetDescription>> createDatasetDescriptionsMatcher(final ExternalDataPE... dataSets)
+ private BaseMatcher<List<DatasetDescription>> createDatasetDescriptionsMatcher(
+ final ExternalDataPE... dataSets)
{
return new BaseMatcher<List<DatasetDescription>>()
{
@@ -730,8 +737,10 @@ public final class ExternalDataTableTest extends AbstractBOTest
assertEquals(dataSets.length, list.size());
for (int i = 0; i < list.size(); i++)
{
- assertEquals("data set " + i, dataSets[i].getCode(), list.get(i).getDataSetCode());
- assertEquals("data set " + i, dataSets[i].getSpeedHint(), list.get(i).getSpeedHint());
+ assertEquals("data set " + i, dataSets[i].getCode(), list.get(i)
+ .getDataSetCode());
+ assertEquals("data set " + i, dataSets[i].getSpeedHint(), list.get(i)
+ .getSpeedHint());
}
return true;
}
@@ -747,7 +756,7 @@ public final class ExternalDataTableTest extends AbstractBOTest
}
};
}
-
+
@SuppressWarnings("unchecked")
private BaseMatcher<List<String>> createUnorderedMarcher(final List<String> list)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
index fd798c1fa46c287f69c4879c1f33317af78c92c0..0c6637d542207574fcb2f3c2922d749620566f02 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
@@ -352,7 +352,7 @@ public final class SampleBOTest extends AbstractBOTest
context.checking(new Expectations()
{
{
- allowing(externalDataDAO).hasExternalData(with(sample));
+ allowing(dataDAO).hasDataSet(with(sample));
will(returnValue(true));
}
});
@@ -445,7 +445,7 @@ public final class SampleBOTest extends AbstractBOTest
allowing(daoFactory).getHomeDatabaseInstance();
will(returnValue(EXAMPLE_DATABASE_INSTANCE));
- allowing(externalDataDAO).hasExternalData(with(sample));
+ allowing(dataDAO).hasDataSet(with(sample));
will(returnValue(false));
}
});
@@ -497,7 +497,7 @@ public final class SampleBOTest extends AbstractBOTest
allowing(sampleDAO).tryFindByCodeAndSpace(parent.getCode(), EXAMPLE_GROUP);
will(returnValue(parent));
- allowing(externalDataDAO).hasExternalData(with(sample));
+ allowing(dataDAO).hasDataSet(with(sample));
will(returnValue(false));
}
});
@@ -564,7 +564,7 @@ public final class SampleBOTest extends AbstractBOTest
EXAMPLE_GROUP2);
will(returnValue(parent3Group2));
- allowing(externalDataDAO).hasExternalData(with(sample));
+ allowing(dataDAO).hasDataSet(with(sample));
will(returnValue(false));
}
});
@@ -621,7 +621,7 @@ public final class SampleBOTest extends AbstractBOTest
allowing(sampleDAO).tryFindByCodeAndSpace(container.getCode(), EXAMPLE_GROUP);
will(returnValue(container));
- allowing(externalDataDAO).hasExternalData(with(sample));
+ allowing(dataDAO).hasDataSet(with(sample));
will(returnValue(false));
}
});
@@ -661,7 +661,7 @@ public final class SampleBOTest extends AbstractBOTest
allowing(sampleDAO).tryFindByCodeAndSpace(container.getCode(), EXAMPLE_GROUP2);
will(returnValue(container));
- allowing(externalDataDAO).hasExternalData(with(sample));
+ allowing(dataDAO).hasDataSet(with(sample));
will(returnValue(false));
one(sampleDAO).createOrUpdateSample(sample);
@@ -692,7 +692,7 @@ public final class SampleBOTest extends AbstractBOTest
{
{
- allowing(externalDataDAO).hasExternalData(with(sample));
+ allowing(dataDAO).hasDataSet(with(sample));
will(returnValue(true));
}
});
@@ -977,7 +977,7 @@ public final class SampleBOTest extends AbstractBOTest
context.checking(new Expectations()
{
{
- allowing(externalDataDAO).hasExternalData(with(sample));
+ allowing(dataDAO).hasDataSet(with(sample));
will(returnValue(false));
}
});
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAOTest.java
index da35a34881111cb8c568eb157a603dc9e7fa6ca5..6c1ac0e4b1317503e6fe9d91520f38b5e930d4e0 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAOTest.java
@@ -65,6 +65,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.types.DataSetTypeCode;
*/
@Test(groups =
{ "db", "externalData" })
+@SuppressWarnings("deprecation")
public final class ExternalDataDAOTest extends AbstractDAOTest
{
@@ -171,7 +172,7 @@ public final class ExternalDataDAOTest extends AbstractDAOTest
{
checkUpdate(4711L);
}
-
+
private void checkUpdate(Long size)
{
IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlUnitMigrationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlUnitMigrationTest.java
index b17e117c6939ab7fc16a09b965a896f4466c4c26..25559dff8b9d388ab0c4241e8262809536d003fd 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlUnitMigrationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SqlUnitMigrationTest.java
@@ -157,15 +157,6 @@ public final class SqlUnitMigrationTest
return "MyDataSource[" + driver + ", " + url + ", " + owner + "]";
}
- public boolean isWrapperFor(Class<?> arg0) throws SQLException
- {
- return false;
- }
-
- public <T> T unwrap(Class<T> arg0) throws SQLException
- {
- return null;
- }
}
private static final IDataSourceFactory DATA_SOURCE_FACTORY = new IDataSourceFactory()
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/scalability/DBCreator.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/scalability/DBCreator.java
index 60db0c64bfb349c2be66f4873e54dbdb1e2330d9..33e140a53acc7ec539f286a7e6e8469fa3dcf11d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/scalability/DBCreator.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/scalability/DBCreator.java
@@ -28,8 +28,8 @@ import org.springframework.test.annotation.Rollback;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IFileFormatTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ILocatorTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.AbstractDAOTest;
@@ -41,11 +41,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermPE;
@@ -73,8 +73,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
* <br>
* IMPORTANT - to make it faster try:
* <ul>
- * <li>commenting out flush() in create methods for in {@link IExternalDataDAO} and
- * {@link SampleDAO}
+ * <li>commenting out flush() in create methods for in {@link IDataDAO} and {@link SampleDAO}
* <li>turning off logging (doesn't make a big difference) - change root logging priority in log.xml
* from "info" to "error".
* </ul>
@@ -305,6 +304,7 @@ public final class DBCreator extends AbstractDAOTest
// DataSets
+ @SuppressWarnings("deprecation")
private void createDataSetsForSample(SamplePE sample)
{
final int size = SizeHelper.getNextDataSetsPerSampleSize();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/DataSetGroupLoaderTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/DataSetGroupLoaderTest.java
index 286e81d776c90c03d4e3e6401550f07b9affd062..3e83f0938aaeaa3ac021665e360931bca8763b32 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/DataSetGroupLoaderTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/DataSetGroupLoaderTest.java
@@ -27,11 +27,11 @@ import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
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.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
/**
* Test cases for {@link DataSetGroupLoader}.
@@ -48,13 +48,13 @@ public class DataSetGroupLoaderTest extends AssertJUnit
private Mockery context;
- private IExternalDataDAO dao;
+ private IDataDAO dao;
@BeforeMethod
public void setUp()
{
context = new Mockery();
- dao = context.mock(IExternalDataDAO.class);
+ dao = context.mock(IDataDAO.class);
}
@AfterMethod
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/GroupLoaderFactoryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/GroupLoaderFactoryTest.java
index d7442f07db15c08c3049e30a075c7d25007bd98a..df17d6597a43841af1b00ec366a039ad499d6132 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/GroupLoaderFactoryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/query/shared/authorization/result_filter/GroupLoaderFactoryTest.java
@@ -89,7 +89,7 @@ public class GroupLoaderFactoryTest extends AssertJUnit
context.checking(new Expectations()
{
{
- one(daoFactory).getExternalDataDAO();
+ one(daoFactory).getDataDAO();
will(returnValue(null));
}
});