diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
index 71734770c1e72fd0e9ee0b44b7677928b9306caf..a6a18fdb75a605542aa812b38e54bb95257b4fbb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
@@ -26,7 +26,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityTypePropertyTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ExperimentTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.GridCustomColumnBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.GridCustomFilterBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.GroupBO;
@@ -39,7 +38,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypePropertyTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGridCustomFilterOrColumnBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGroupBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
@@ -138,11 +136,6 @@ public final class CommonBusinessObjectFactory extends AbstractBusinessObjectFac
return new DataBO(getDaoFactory(), session);
}
- public IExternalDataBO createExternalDataBO(Session session)
- {
- return new ExternalDataBO(getDaoFactory(), session);
- }
-
public final IDataSetTable createDataSetTable(final Session session)
{
return new DataSetTable(getDaoFactory(), getDSSFactory(), session);
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 592523fb9f2162ab95d0514209e9b82b8c017fbc..df2748117442b43c18f47c8e23594e5e4f5c3540 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
@@ -49,7 +49,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypePropertyTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGridCustomFilterOrColumnBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGroupBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
@@ -2254,9 +2253,9 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
switch (entityKind)
{
case DATA_SET:
- IExternalDataBO bo = businessObjectFactory.createExternalDataBO(session);
+ IDataBO bo = businessObjectFactory.createDataBO(session);
bo.loadByCode(entityIdentifier);
- entity = bo.getExternalData();
+ entity = bo.getData();
break;
case EXPERIMENT:
IExperimentBO expBO = businessObjectFactory.createExperimentBO(session);
@@ -2341,13 +2340,12 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
Session session = getSession(sessionToken);
try
{
- IExternalDataBO dataSetBO = businessObjectFactory.createExternalDataBO(session);
+ IDataBO dataSetBO = businessObjectFactory.createDataBO(session);
dataSetBO.loadDataByTechId(experimentId);
// Evaluate the script
dataSetBO.enrichWithProperties();
- Set<? extends EntityPropertyPE> properties =
- dataSetBO.getExternalData().getProperties();
+ Set<? extends EntityPropertyPE> properties = dataSetBO.getData().getProperties();
ManagedPropertyEvaluator evaluator =
tryManagedPropertyEvaluator(managedProperty, properties);
extendWithPerson(updateAction, session.tryGetPerson());
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
index 97cde4b4c38cf8f033aba951b7a3c3eaea9c63e7..4b6832c2363f24c2803b8a4f1fe473b17eae1169 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
@@ -37,7 +37,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObject
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGroupBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IProjectBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IRoleAssignmentTable;
@@ -136,7 +135,6 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.EntityPropertyTranslat
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.LoadableFields;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTypeTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.GroupTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.PersonTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ProjectTranslator;
@@ -693,8 +691,8 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
{
assert sessionToken != null : "Unspecified session token.";
final Session session = getSession(sessionToken);
- final IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
- externalDataBO.addPropertiesToDataSet(dataSetCode, properties);
+ final IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.addPropertiesToDataSet(dataSetCode, properties);
}
public void updateShareIdAndSize(String sessionToken, String dataSetCode, String shareId,
@@ -727,8 +725,8 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
{
assert sessionToken != null : "Unspecified session token.";
final Session session = getSession(sessionToken);
- final IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
- externalDataBO.updateStatuses(dataSetCodes, newStatus, presentInArchive);
+ final IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.updateStatuses(dataSetCodes, newStatus, presentInArchive);
}
public boolean compareAndSetDataSetStatus(String sessionToken, String dataSetCode,
@@ -737,9 +735,9 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
{
assert sessionToken != null : "Unspecified session token.";
final Session session = getSession(sessionToken);
- final IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
- externalDataBO.loadByCode(dataSetCode);
- return externalDataBO.compareAndSetDataSetStatus(oldStatus, newStatus, newPresentInArchive);
+ final IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.loadByCode(dataSetCode);
+ return dataBO.compareAndSetDataSetStatus(oldStatus, newStatus, newPresentInArchive);
}
public ExternalData tryGetDataSet(String sessionToken, String dataSetCode)
@@ -1021,12 +1019,12 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
+ experiment.getIdentifier() + "' is invalid.");
}
- final IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
+ final IDataBO dataBO = businessObjectFactory.createDataBO(session);
SourceType sourceType =
externalData.isMeasured() ? SourceType.MEASUREMENT : SourceType.DERIVED;
- externalDataBO.define(externalData, samplePE, sourceType);
- externalDataBO.save();
- final String dataSetCode = externalDataBO.getExternalData().getCode();
+ dataBO.define(externalData, samplePE, sourceType);
+ dataBO.save();
+ final String dataSetCode = dataBO.getData().getCode();
assert dataSetCode != null : "Data set code not specified.";
}
@@ -1216,24 +1214,24 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
AtomicEntityOperationDetails operationDetails)
{
final Session session = getSession(sessionToken);
- ArrayList<ExternalDataPE> dataSetsCreated = new ArrayList<ExternalDataPE>();
+ ArrayList<DataPE> dataSetsCreated = new ArrayList<DataPE>();
ArrayList<? extends NewExternalData> dataSetRegistrations =
operationDetails.getDataSetRegistrations();
for (NewExternalData dataSet : dataSetRegistrations)
{
SampleIdentifier sampleIdentifier = dataSet.getSampleIdentifierOrNull();
- IExternalDataBO externalData;
+ IDataBO dataBO;
if (sampleIdentifier != null)
{
- externalData = registerDataSetInternal(session, sampleIdentifier, dataSet);
+ dataBO = registerDataSetInternal(session, sampleIdentifier, dataSet);
} else
{
ExperimentIdentifier experimentIdentifier = dataSet.getExperimentIdentifierOrNull();
- externalData = registerDataSetInternal(session, experimentIdentifier, dataSet);
+ dataBO = registerDataSetInternal(session, experimentIdentifier, dataSet);
}
- dataSetsCreated.add(externalData.getExternalData());
+ dataSetsCreated.add(dataBO.getData());
}
- return ExternalDataTranslator.translate(dataSetsCreated, "", session.getBaseIndexURL());
+ return DataSetTranslator.translate(dataSetsCreated, "", session.getBaseIndexURL());
}
private ArrayList<Experiment> createExperiments(String sessionToken,
@@ -1251,7 +1249,7 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
return experimentsCreated;
}
- private IExternalDataBO registerDataSetInternal(final Session session,
+ private IDataBO registerDataSetInternal(final Session session,
SampleIdentifier sampleIdentifier, NewExternalData externalData)
{
ExperimentPE experiment = tryLoadExperimentBySampleIdentifier(session, sampleIdentifier);
@@ -1267,18 +1265,18 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
sampleBO.loadBySampleIdentifier(sampleIdentifier);
final SamplePE cellPlate = sampleBO.getSample();
- final IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
+ final IDataBO dataBO = businessObjectFactory.createDataBO(session);
SourceType sourceType =
externalData.isMeasured() ? SourceType.MEASUREMENT : SourceType.DERIVED;
- externalDataBO.define(externalData, cellPlate, sourceType);
- externalDataBO.save();
- final String dataSetCode = externalDataBO.getExternalData().getCode();
+ dataBO.define(externalData, cellPlate, sourceType);
+ dataBO.save();
+ final String dataSetCode = dataBO.getData().getCode();
assert dataSetCode != null : "Data set code not specified.";
- return externalDataBO;
+ return dataBO;
}
- private IExternalDataBO registerDataSetInternal(final Session session,
+ private IDataBO registerDataSetInternal(final Session session,
ExperimentIdentifier experimentIdentifier, NewExternalData externalData)
{
ExperimentPE experiment = tryToLoadExperimentByIdentifier(session, experimentIdentifier);
@@ -1287,12 +1285,12 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
throw new UserFailureException("Data set can not be registered because experiment '"
+ experiment.getIdentifier() + "' is invalid.");
}
- final IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
+ final IDataBO externalDataBO = businessObjectFactory.createDataBO(session);
SourceType sourceType =
externalData.isMeasured() ? SourceType.MEASUREMENT : SourceType.DERIVED;
externalDataBO.define(externalData, experiment, sourceType);
externalDataBO.save();
- final String dataSetCode = externalDataBO.getExternalData().getCode();
+ final String dataSetCode = externalDataBO.getData().getCode();
assert dataSetCode != null : "Data set code not specified.";
return externalDataBO;
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..7ef236f31c3dd310e16646e4dc64792945a92048 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
@@ -31,7 +31,6 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityPropertyTypeDAO
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEventDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
-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.IGridCustomColumnDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IGridCustomFilterDAO;
@@ -209,11 +208,6 @@ abstract class AbstractBusinessObject implements IDAOFactory
return daoFactory.getDataDAO();
}
- public final IExternalDataDAO getExternalDataDAO()
- {
- return daoFactory.getExternalDataDAO();
- }
-
public final IHibernateSearchDAO getHibernateSearchDAO()
{
return daoFactory.getHibernateSearchDAO();
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
deleted file mode 100644
index 6f2097e129656229ca0fa85bae403d19e220a502..0000000000000000000000000000000000000000
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
+++ /dev/null
@@ -1,722 +0,0 @@
-/*
- * 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.server.business.bo;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.common.collections.CollectionUtils;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-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.IVocabularyDAO;
-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.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SourceType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetPropertyPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
-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.FileFormatTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-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.SamplePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-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;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.types.DataSetTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
-
-/**
- * @author Franz-Josef Elmer
- */
-@SuppressWarnings("deprecation")
-@Friend(toClasses = DataPE.class)
-public class ExternalDataBO extends AbstractDataSetBusinessObject implements IExternalDataBO
-{
- private ExternalDataPE externalData;
-
- public ExternalDataBO(IDAOFactory daoFactory, Session session)
- {
- super(daoFactory, session);
- }
-
- public ExternalDataBO(IDAOFactory daoFactory, Session exampleSession,
- IEntityPropertiesConverter propertiesConverter)
- {
- super(daoFactory, exampleSession, propertiesConverter);
- }
-
- public ExternalDataPE tryExternalData()
- {
- return externalData;
- }
-
- public ExternalDataPE getExternalData()
- {
- // TODO 2010-04-12, CR: This should throw an exception if the external data is null
- // -- will that cause problems with clients?
- return externalData;
- }
-
- public void loadByCode(String dataSetCode)
- {
- loadByCode(dataSetCode, true, false);
- }
-
- private void loadByCode(String dataSetCode, boolean withPropertyTypes, boolean lockForUpdate)
- {
- externalData =
- getExternalDataDAO().tryToFindFullDataSetByCode(dataSetCode, withPropertyTypes,
- lockForUpdate);
- }
-
- static final String DATA_SET_TYPE = "dataSetType";
-
- static final String PROPERTY_TYPES = "dataSetType.dataSetTypePropertyTypesInternal";
-
- public void loadDataByTechId(TechId datasetId)
- {
- String[] connections =
- { PROPERTY_TYPES, DATA_SET_TYPE };
- externalData = getExternalDataDAO().tryGetByTechId(datasetId, connections);
- if (externalData == null)
- {
- throw new UserFailureException(String.format("Data set with ID '%s' does not exist.",
- datasetId));
- }
- }
-
- public void enrichWithParentsAndExperiment()
- {
- if (externalData != null)
- {
- enrichWithParentsAndExperiment(externalData);
- }
- }
-
- public void enrichWithChildren()
- {
- if (externalData != null)
- {
- enrichWithChildren(externalData);
- }
- }
-
- public final void enrichWithProperties()
- {
- if (externalData != null)
- {
- HibernateUtils.initialize(externalData.getProperties());
- }
- }
-
- public void enrichWithContainedDataSets()
- {
- if (externalData != null && externalData.isContainer())
- {
- HibernateUtils.initialize(externalData.getContainedDataSets());
- }
- }
-
- public void define(NewExternalData data, SamplePE sample, SourceType sourceType)
- {
- assert sample != null : "Undefined sample.";
-
- final DataStorePE dataStore = define(data, sourceType);
- final ExperimentPE experiment = sample.getExperiment();
-
- externalData.setSample(sample);
- externalData.setExperiment(experiment);
-
- setParentDataSets(dataStore, experiment, data);
- }
-
- public void define(NewExternalData data, ExperimentPE experiment, SourceType sourceType)
- {
- assert experiment != null : "Undefined experiment.";
-
- final DataStorePE dataStore = define(data, sourceType);
-
- externalData.setExperiment(experiment);
- setParentDataSets(dataStore, experiment, data);
- }
-
- private void setParentDataSets(DataStorePE dataStore, ExperimentPE experiment,
- NewExternalData data)
- {
- final List<String> parentDataSetCodes = data.getParentDataSetCodes();
- if (parentDataSetCodes != null)
- {
- for (String parentCode : parentDataSetCodes)
- {
- final DataPE parent = getOrCreateParentData(parentCode, dataStore, experiment);
- externalData.addParent(parent);
- }
- }
- }
-
- private DataStorePE define(NewExternalData data, SourceType sourceType)
- {
- assert data != null : "Undefined data.";
- final DataSetType dataSetType = data.getDataSetType();
- assert dataSetType != null : "Undefined data set type.";
- final FileFormatType fileFormatType = data.getFileFormatType();
- assert fileFormatType != null : "Undefined file format type.";
- final String location = data.getLocation();
- assert location != null : "Undefined location.";
- final LocatorType locatorType = data.getLocatorType();
- assert locatorType != null : "Undefined location type.";
- assert sourceType != null : "Undefined source type.";
-
- externalData = new ExternalDataPE();
-
- externalData.setDataProducerCode(data.getDataProducerCode());
- externalData.setProductionDate(data.getProductionDate());
- externalData.setCode(data.getCode());
- externalData.setDataSetType(getDataSetType(dataSetType));
- externalData.setFileFormatType(getFileFomatType(fileFormatType));
- externalData.setComplete(data.getComplete());
- externalData.setShareId(data.getShareId());
- externalData.setLocation(location);
- externalData.setSize(data.getSize());
- externalData.setSpeedHint(data.getSpeedHint());
- externalData.setStorageFormatVocabularyTerm(tryToFindStorageFormatTerm(data
- .getStorageFormat()));
- externalData.setLocatorType(getLocatorTypeDAO().tryToFindLocatorTypeByCode(
- locatorType.getCode()));
- externalData.setRegistrator(tryToGetRegistrator(data));
- DataStorePE dataStore = getDataStoreDAO().tryToFindDataStoreByCode(data.getDataStoreCode());
- externalData.setDataStore(dataStore);
- defineDataSetProperties(externalData,
- convertToDataSetProperties(data.getDataSetProperties()));
- externalData.setDerived(sourceType == SourceType.DERIVED);
- return dataStore;
- }
-
- private PersonPE tryToGetRegistrator(NewExternalData data)
- {
- String userId = data.getUserId();
- if (userId != null)
- {
- return getPersonDAO().tryFindPersonByUserId(userId);
- }
- String userEMail = data.getUserEMail();
- if (userEMail == null)
- {
- return null;
- }
- List<PersonPE> persons = getPersonDAO().listPersons();
- for (PersonPE person : persons)
- {
- if (userEMail.equalsIgnoreCase(person.getEmail()))
- {
- return person;
- }
- }
- return null;
- }
-
- private VocabularyTermPE tryToFindStorageFormatTerm(StorageFormat storageFormat)
- {
- IVocabularyDAO vocabularyDAO = getVocabularyDAO();
- VocabularyPE vocabulary =
- vocabularyDAO.tryFindVocabularyByCode(StorageFormat.VOCABULARY_CODE);
- Set<VocabularyTermPE> terms = vocabulary.getTerms();
- for (VocabularyTermPE term : terms)
- {
- if (storageFormat.getCode().equals(term.getCode()))
- {
- return term;
- }
- }
- return null;
- }
-
- private final DataSetTypePE getDataSetType(final DataSetType dataSetType)
- {
- final String dataSetTypeCode = dataSetType.getCode();
- final DataSetTypePE dataSetTypeOrNull =
- getDataSetTypeDAO().tryToFindDataSetTypeByCode(dataSetTypeCode);
- if (dataSetTypeOrNull == null)
- {
- throw UserFailureException.fromTemplate("There is no data set type with code '%s'",
- dataSetTypeCode);
- }
- return dataSetTypeOrNull;
- }
-
- private final FileFormatTypePE getFileFomatType(final FileFormatType fileFormatType)
- {
- final String fileFormatTypeCode = fileFormatType.getCode();
- final FileFormatTypePE fileFormatTypeOrNull =
- getFileFormatTypeDAO().tryToFindFileFormatTypeByCode(fileFormatTypeCode);
- if (fileFormatTypeOrNull == null)
- {
- throw UserFailureException.fromTemplate("There is no file format type with code '%s'",
- fileFormatTypeCode);
- }
- return fileFormatTypeOrNull;
- }
-
- private final DataPE getOrCreateParentData(final String parentDataSetCode,
- DataStorePE dataStore, ExperimentPE experiment)
- {
- assert parentDataSetCode != null : "Unspecified parent data set code.";
-
- final IExternalDataDAO dataDAO = getExternalDataDAO();
- DataPE parent = dataDAO.tryToFindDataSetByCode(parentDataSetCode);
- if (parent == null)
- {
- parent = new DataPE();
- parent.setDataStore(dataStore);
- parent.setCode(parentDataSetCode);
- String code = DataSetTypeCode.UNKNOWN.getCode();
- parent.setDataSetType(getDataSetTypeDAO().tryToFindDataSetTypeByCode(code));
- parent.setExperiment(experiment);
- parent.setPlaceholder(true);
- dataDAO.createDataSet(parent);
- }
- return parent;
- }
-
- public void save() throws UserFailureException
- {
- assert externalData != null : "Undefined external data.";
- IExternalDataDAO externalDataDAO = getExternalDataDAO();
- String dataCode = externalData.getCode();
- DataPE data = externalDataDAO.tryToFindDataSetByCode(dataCode);
- if (data == null)
- {
- externalDataDAO.createDataSet(externalData);
- } else
- {
- if (data.isPlaceholder() == false)
- {
- throw new UserFailureException("Already existing data set for code '" + dataCode
- + "' can not be updated by data set " + externalData);
- }
- // NOTE: If new data set is created and there was no placeholder
- // cycles will not be created because only connections to parents are added
- // and we assume that there were no cycles before. On the other hand placeholders
- // have at least one child so cycles need to be checked when they are updated.
- validateRelationshipGraph(externalData.getParents());
-
- externalData.setPlaceholder(false);
- externalData.setId(HibernateUtils.getId(data));
- externalData.setRegistrationDate(new Date());
- externalData.setModificationDate(data.getModificationDate());
-
- externalDataDAO.updateDataSet(externalData);
- }
- entityPropertiesConverter.checkMandatoryProperties(externalData.getProperties(),
- externalData.getDataSetType());
- }
-
- public void addPropertiesToDataSet(String dataSetCode, List<NewProperty> properties)
- {
- loadByCode(dataSetCode);
- updatePropertiesPreservingExisting(properties);
- entityPropertiesConverter.checkMandatoryProperties(externalData.getProperties(),
- externalData.getDataSetType());
- validateAndSave();
- }
-
- private void updatePropertiesPreservingExisting(List<NewProperty> properties)
- {
- final Set<DataSetPropertyPE> existingProperties = externalData.getProperties();
- Set<String> propertyUpdatesCodes =
- extractPropertyCodesToUpdate(properties, existingProperties);
- List<NewProperty> propertyUpdates =
- extractNewPropertiesToUpdate(properties, propertyUpdatesCodes);
- final DataSetTypePE type = externalData.getDataSetType();
- final PersonPE registrator = findRegistrator();
- externalData.setProperties(entityPropertiesConverter.updateProperties(existingProperties,
- type, Arrays.asList(convertToDataSetProperties(propertyUpdates)), registrator,
- propertyUpdatesCodes));
- }
-
- private List<NewProperty> extractNewPropertiesToUpdate(List<NewProperty> properties,
- Set<String> propertiesToUpdate)
- {
- List<NewProperty> newPropertiesToUpdate = new ArrayList<NewProperty>();
- for (NewProperty np : properties)
- {
- if (propertiesToUpdate.contains(np.getPropertyCode()))
- {
- newPropertiesToUpdate.add(np);
- }
- }
- return newPropertiesToUpdate;
- }
-
- private Set<String> extractPropertyCodesToUpdate(List<NewProperty> properties,
- final Set<DataSetPropertyPE> existingProperties)
- {
- Set<String> propertiesToUpdate = new HashSet<String>();
- for (NewProperty np : properties)
- {
- propertiesToUpdate.add(np.getPropertyCode());
- }
- for (DataSetPropertyPE ep : existingProperties)
- {
- propertiesToUpdate.remove(ep.getEntityTypePropertyType().getPropertyType().getCode());
- }
- return propertiesToUpdate;
- }
-
- public void update(DataSetUpdatesDTO updates)
- {
- loadDataByTechId(updates.getDatasetId());
- if (updates.getVersion().equals(externalData.getModificationDate()) == false)
- {
- throwModifiedEntityException("Data set");
- }
- final SampleIdentifier sampleIdentifierOrNull = updates.getSampleIdentifierOrNull();
- if (sampleIdentifierOrNull != null)
- {
- // update sample and indirectly experiment
- updateSample(updates.getSampleIdentifierOrNull());
- } else
- {
- updateExperiment(updates.getExperimentIdentifierOrNull());
- // remove connection with sample
- externalData.setSample(null);
- }
- updateParents(updates.getModifiedParentDatasetCodesOrNull());
- updateFileFormatType(updates.getFileFormatTypeCode());
- updateProperties(externalData, updates.getProperties());
- entityPropertiesConverter.checkMandatoryProperties(externalData.getProperties(),
- externalData.getDataSetType());
- validateAndSave();
- }
-
- private void validateAndSave()
- {
- getExternalDataDAO().validateAndSaveUpdatedEntity(externalData);
- }
-
- private void updateParents(String[] modifiedParentDatasetCodesOrNull)
- {
- if (modifiedParentDatasetCodesOrNull == null)
- {
- return; // parents were not changed
- } else
- {
- final Set<DataPE> currentParents = externalData.getParents();
- final Set<String> currentParentCodes = extractCodes(currentParents);
- final Set<String> newCodes = asSet(modifiedParentDatasetCodesOrNull);
- newCodes.removeAll(currentParentCodes);
-
- // quick check for direct cycle
- if (newCodes.contains(externalData.getCode()))
- {
- throw new UserFailureException("Data set '" + externalData.getCode()
- + "' can not be its own parent.");
- }
-
- final List<DataPE> parentsToAdd = findDataSetsByCodes(newCodes);
- validateRelationshipGraph(parentsToAdd);
- addParents(parentsToAdd);
-
- final Set<String> removedCodes = currentParentCodes;
- removedCodes.removeAll(asSet(modifiedParentDatasetCodesOrNull));
- removeParents(filterDataSets(currentParents, removedCodes));
- }
- }
-
- /**
- * Throws {@link UserFailureException} if adding specified parents to this data set will create
- * a cycle in data set relationships.
- */
- private void validateRelationshipGraph(Collection<DataPE> parentsToAdd)
- {
- // DFS from new parents that are to be added to this business object going in direction
- // of parent relationship until:
- // - all related ancestors are visited == graph has no cycles
- // - we get to this business object == cycle is found
- // NOTE: The assumption is that there were no cycles in the graph of relationship before.
- // This algorithm will not find cycles that don't include this business object,
- // although such cycles shouldn't cause it to loop forever.
-
- // Algorithm operates only on data set ids to make it perform better
- // - there is no need to join DB tables.
- // To be able to inform user about the exact data set that cannot be connected as a parent
- // we need start seeking cycles starting from each parent to be added separately. Otherwise
- // we would need to get invoke more queries to DB (not going layer by layer of graph depth
- // per query) or use BFS instead (which would also be slower in a general case).
- for (DataPE parentToAdd : parentsToAdd)
- {
- validateRelationshipGraph(parentToAdd);
- }
- }
-
- private void validateRelationshipGraph(DataPE parentToAdd)
- {
- final TechId updatedDataSetId = TechId.create(externalData);
- final Set<TechId> visited = new HashSet<TechId>();
- Set<TechId> toVisit = new HashSet<TechId>();
- toVisit.add(TechId.create(parentToAdd));
- while (toVisit.isEmpty() == false)
- {
- if (toVisit.contains(updatedDataSetId))
- {
- throw UserFailureException.fromTemplate(
- "Data Set '%s' is an ancestor of Data Set '%s' "
- + "and cannot be at the same time set as its child.",
- externalData.getCode(), parentToAdd.getCode());
- } else
- {
- final Set<TechId> nextToVisit = findParentIds(toVisit);
- visited.addAll(toVisit);
- nextToVisit.removeAll(visited);
- toVisit = nextToVisit;
- }
- }
- }
-
- private Set<TechId> findParentIds(Set<TechId> dataSetIds)
- {
- return getExternalDataDAO().findParentIds(dataSetIds);
- }
-
- private Collection<DataPE> filterDataSets(Collection<DataPE> dataSets,
- Collection<String> seekenCodes)
- {
- Collection<DataPE> result = new ArrayList<DataPE>();
- for (DataPE dataSet : dataSets)
- {
- if (seekenCodes.contains(dataSet.getCode()))
- {
- result.add(dataSet);
- }
- }
- return result;
- }
-
- private void addParents(Collection<DataPE> parentsToAdd)
- {
- for (DataPE parent : parentsToAdd)
- {
- externalData.addParent(parent);
- }
- }
-
- private void removeParents(Collection<DataPE> parentsToRemove)
- {
- for (DataPE parent : parentsToRemove)
- {
- externalData.removeParent(parent);
- }
- }
-
- private List<DataPE> findDataSetsByCodes(Set<String> codes)
- {
- final IExternalDataDAO dao = getExternalDataDAO();
- final List<DataPE> dataSets = new ArrayList<DataPE>();
- final List<String> missingDataSetCodes = new ArrayList<String>();
- for (String code : codes)
- {
- DataPE dataSetOrNull = dao.tryToFindDataSetByCode(code);
- if (dataSetOrNull == null)
- {
- missingDataSetCodes.add(code);
- } else
- {
- dataSets.add(dataSetOrNull);
- }
- }
- if (missingDataSetCodes.size() > 0)
- {
- throw UserFailureException.fromTemplate(
- "Data Sets with following codes do not exist: '%s'.",
- CollectionUtils.abbreviate(missingDataSetCodes, 10));
- } else
- {
- return dataSets;
- }
- }
-
- private static Set<String> asSet(String[] objects)
- {
- return new HashSet<String>(Arrays.asList(objects));
- }
-
- private static Set<String> extractCodes(Collection<DataPE> parents)
- {
- Set<String> codes = new HashSet<String>(parents.size());
- for (DataPE parent : parents)
- {
- codes.add(parent.getCode());
- }
- return codes;
- }
-
- //
-
- private void updateSample(SampleIdentifier sampleIdentifierOrNull)
- {
- assert sampleIdentifierOrNull != null;
- SamplePE newSample = getSampleByIdentifier(sampleIdentifierOrNull);
- SamplePE previousSampleOrNull = externalData.tryGetSample();
- if (newSample.equals(previousSampleOrNull))
- {
- return; // nothing to change
- }
- if (newSample.getSpace() == null)
- {
- throw createWrongSampleException(newSample, "the new sample is shared");
- }
- ExperimentPE experiment = newSample.getExperiment();
- if (experiment == null)
- {
- throw createWrongSampleException(newSample,
- "the new sample is not connected to any experiment");
- }
- // move dataset to the experiment if needed
- if (experiment.equals(externalData.getExperiment()) == false)
- {
- externalData.setExperiment(experiment);
- }
- externalData.setSample(newSample);
- }
-
- private void updateExperiment(ExperimentIdentifier experimentIdentifierOrNull)
- {
- assert experimentIdentifierOrNull != null;
- ExperimentPE experiment = getExperimentByIdentifier(experimentIdentifierOrNull);
- externalData.setExperiment(experiment);
- }
-
- private ExperimentPE getExperimentByIdentifier(final ExperimentIdentifier identifier)
- {
- assert identifier != null : "Experiment identifier unspecified.";
- final ProjectPE project =
- getProjectDAO().tryFindProject(identifier.getDatabaseInstanceCode(),
- identifier.getSpaceCode(), identifier.getProjectCode());
- if (project == null)
- {
- throw new UserFailureException("Unkown experiment because of unkown project: "
- + identifier);
- }
- final ExperimentPE exp =
- getExperimentDAO().tryFindByCodeAndProject(project, identifier.getExperimentCode());
- return exp;
- }
-
- private void updateFileFormatType(String fileFormatTypeCode)
- {
- FileFormatTypePE fileFormatTypeOrNull =
- getFileFormatTypeDAO().tryToFindFileFormatTypeByCode(fileFormatTypeCode);
- if (fileFormatTypeOrNull == null)
- {
- throw new UserFailureException(String.format("File type '%s' does not exist.",
- fileFormatTypeCode));
- } else
- {
- externalData.setFileFormatType(fileFormatTypeOrNull);
- }
- }
-
- private UserFailureException createWrongSampleException(SamplePE sample, String reason)
- {
- return UserFailureException.fromTemplate(
- "The dataset '%s' cannot be connected to the sample '%s'" + " because %s.",
- externalData.getCode(), sample.getIdentifier(), reason);
- }
-
- private final void defineDataSetProperties(final ExternalDataPE data,
- final IEntityProperty[] newProperties)
- {
- final String dataSetTypeCode = data.getDataSetType().getCode();
- final List<DataSetPropertyPE> properties =
- entityPropertiesConverter.convertProperties(newProperties, dataSetTypeCode,
- findRegistrator());
- for (final DataSetPropertyPE property : properties)
- {
- data.addProperty(property);
- }
- }
-
- private static IEntityProperty[] convertToDataSetProperties(List<NewProperty> list)
- {
- IEntityProperty[] result = new IEntityProperty[list.size()];
- for (int i = 0; i < list.size(); i++)
- {
- result[i] = convertProperty(list.get(i));
- }
- return result;
- }
-
- private static IEntityProperty convertProperty(NewProperty newProperty)
- {
- IEntityProperty result = new EntityProperty();
- result.setValue(newProperty.getValue());
- PropertyType propertyType = new PropertyType();
- propertyType.setCode(newProperty.getPropertyCode());
- result.setPropertyType(propertyType);
- return result;
- }
-
- public void updateStatuses(List<String> dataSetCodes, DataSetArchivingStatus newStatus,
- boolean newPresentInArchive)
- {
- getExternalDataDAO().updateDataSetStatuses(dataSetCodes, newStatus, newPresentInArchive);
- }
-
- public boolean compareAndSetDataSetStatus(DataSetArchivingStatus oldStatus,
- DataSetArchivingStatus newStatus, boolean newPresentInArchive)
- {
- if (externalData == null || externalData.getStatus() != oldStatus)
- {
- return false;
- }
- updateStatuses(Arrays.asList(externalData.getCode()), newStatus, newPresentInArchive);
- return true;
- }
-
- public void updateManagedProperty(IManagedProperty managedProperty)
- {
- final Set<DataSetPropertyPE> existingProperties = externalData.getProperties();
- final DataSetTypePE type = externalData.getDataSetType();
- final PersonPE registrator = findRegistrator();
- externalData.setProperties(entityPropertiesConverter.updateManagedProperty(
- existingProperties, type, managedProperty, registrator));
- }
-
-}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
index 8f61d8327b97dcc2c3370250c9a49a0a5dd290f3..1b82b956f99fdf64a3a8847786e61e45b78912e1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
@@ -42,8 +42,6 @@ public interface ICommonBusinessObjectFactory
public ISampleBO createSampleBO(final Session session);
- public IExternalDataBO createExternalDataBO(Session session);
-
public IDataBO createDataBO(Session session);
public IDataSetTable createDataSetTable(final Session session);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataBO.java
deleted file mode 100644
index 63bd7b40936b737d8cdefa7ea51bac6e4ffbc227..0000000000000000000000000000000000000000
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataBO.java
+++ /dev/null
@@ -1,127 +0,0 @@
-/*
- * 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.server.business.bo;
-
-import java.util.List;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SourceType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.api.IManagedProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
-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.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-
-/**
- * @deprecated this code will be removed - use IDataBO if possible
- * @author Franz-Josef Elmer
- */
-@Deprecated
-public interface IExternalDataBO extends IEntityBusinessObject
-{
- /**
- * Returns the external data item which has been created by
- * {@link #define(NewExternalData, SamplePE, SourceType)} or null.
- */
- public ExternalDataPE tryExternalData();
-
- /**
- * Returns the external data item which has been created by
- * {@link #define(NewExternalData, SamplePE, SourceType)}.
- */
- public ExternalDataPE getExternalData();
-
- /**
- * Defines a new external data item directly connected to a sample.
- * <p>
- * After invocation of this method {@link IExperimentBO#save()} should be invoked to store the
- * new external data item in the Data Access Layer.
- */
- public void define(NewExternalData externalData, SamplePE sample, SourceType sourceType);
-
- /**
- * Defines a new external data item not directly connected to a sample but with mandatory
- * connection with an experiment.
- * <p>
- * After invocation of this method {@link IExperimentBO#save()} should be invoked to store the
- * new external data item in the Data Access Layer.
- */
- public void define(NewExternalData data, ExperimentPE experiment, SourceType sourceType);
-
- /**
- * Changes given data set. Currently allowed changes: properties, sample.
- */
- public void update(DataSetUpdatesDTO updates);
-
- /**
- * Updates status of given data sets.
- *
- * @throws UserFailureException if a data set does not exist or status couldn't be set.
- */
- public void updateStatuses(List<String> dataSetCodes, DataSetArchivingStatus newStatus,
- boolean newPresentInArchive) throws UserFailureException;
-
- /**
- * Set the status for the loaded dataset to the given new status value if the current status
- * equals an expected value.
- *
- * @return true if the update is successful, false if the current status is different than
- * <code>oldStatus</code>.
- */
- public boolean compareAndSetDataSetStatus(DataSetArchivingStatus oldStatus,
- DataSetArchivingStatus newStatus, boolean newPresentInArchive);
-
- /**
- * Adds chosen properties to given data set. If given property has been already defined, the
- * value is not updated.
- */
- public void addPropertiesToDataSet(String dataSetCode, List<NewProperty> properties);
-
- /**
- * Loads the external data item with specified code.
- */
- public void loadByCode(String dataSetCode);
-
- /**
- * Enrich external data with parents and experiment.
- */
- public void enrichWithParentsAndExperiment();
-
- /**
- * Enrich external data with children and experiment.
- */
- public void enrichWithChildren();
-
- /**
- * Enrich external data with virtual children.
- */
- public void enrichWithContainedDataSets();
-
- /**
- * Enrich external data with properties.
- */
- public void enrichWithProperties();
-
- /**
- * Changes the value of a managed property.
- */
- public void updateManagedProperty(IManagedProperty managedProperty);
-
-}
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 0c3c30881d27549b0de71ee5b2b9c045c77ebda1..2eabc8d6e160796bd55dc1ee6e9d047b0b7ddb09 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
@@ -59,9 +59,6 @@ public interface IAuthorizationDAOFactory
public IDataDAO getDataDAO();
- @Deprecated
- public IExternalDataDAO getExternalDataDAO();
-
public IExperimentDAO getExperimentDAO();
public IProjectDAO getProjectDAO();
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 67ca8690e126144eb453fe70af754dee1bdbe577..70d95ab7e9b4c38223c677c3b068743650a98b81 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
@@ -32,7 +32,6 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDatabaseInstanceDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDynamicPropertyEvaluationScheduler;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IGridCustomColumnDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IGridCustomFilterDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IPersonDAO;
@@ -68,9 +67,6 @@ public class AuthorizationDAOFactory implements IAuthorizationDAOFactory
private final IDataDAO dataDAO;
- // FIXME use IDataDAO
- private final IExternalDataDAO externalDataDAO;
-
private final IExperimentDAO experimentDAO;
private final DatabaseInstancePE homeDatabaseInstance;
@@ -103,7 +99,6 @@ public class AuthorizationDAOFactory implements IAuthorizationDAOFactory
groupDAO = new SpaceDAO(sessionFactory, homeDatabaseInstance);
roleAssignmentDAO = new RoleAssignmentDAO(sessionFactory, homeDatabaseInstance);
dataDAO = new DataDAO(persistencyResources, homeDatabaseInstance);
- externalDataDAO = new ExternalDataDAO(persistencyResources, homeDatabaseInstance);
experimentDAO = new ExperimentDAO(persistencyResources, homeDatabaseInstance);
projectDAO = new ProjectDAO(sessionFactory, homeDatabaseInstance);
sampleDAO = new SampleDAO(persistencyResources, homeDatabaseInstance);
@@ -212,11 +207,6 @@ public class AuthorizationDAOFactory implements IAuthorizationDAOFactory
return dataDAO;
}
- public final IExternalDataDAO getExternalDataDAO()
- {
- return externalDataDAO;
- }
-
public final IExperimentDAO getExperimentDAO()
{
return experimentDAO;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java
index cf285e675e1f6b4e2cd7c4bf2018218e4b0b4c84..b9994f8ffce71c2282b83b8131f6c1529a8e928c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericBusinessObjectFactory.java
@@ -22,7 +22,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IProjectBO;
@@ -83,11 +82,6 @@ public final class GenericBusinessObjectFactory extends AbstractPluginBusinessOb
return getCommonBusinessObjectFactory().createDataBO(session);
}
- public IExternalDataBO createExternalDataBO(Session session)
- {
- return getCommonBusinessObjectFactory().createExternalDataBO(session);
- }
-
public IDataSetTable createDataSetTable(Session session)
{
return getCommonBusinessObjectFactory().createDataSetTable(session);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java
index ce6c7659f90131e70575f52464c72cc435ff9dc5..9cdee5b6fc6f35579e2253449378ae25ba7b26e9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/IGenericBusinessObjectFactory.java
@@ -20,7 +20,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IProjectBO;
@@ -66,11 +65,6 @@ public interface IGenericBusinessObjectFactory
*/
public IDataBO createDataBO(final Session session);
- /**
- * Creates a {@link IExternalDataBO} <i>Business Object</i>.
- */
- public IExternalDataBO createExternalDataBO(final Session session);
-
/**
* Creates a {@link ISampleTable} <i>Business Object</i>.
*/
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
index a784a1e8a896c50600a202cbfb7b4cb8c1d26c72..f8aa3466495fdd32041fa3ce52012f0ca62c969d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceTest.java
@@ -811,12 +811,12 @@ public class ETLServiceTest extends AbstractServerTestCase
one(personDAO).tryFindPersonByUserId(CommonTestUtils.USER_ID);
will(returnValue(new PersonPE()));
- one(boFactory).createExternalDataBO(SESSION);
- will(returnValue(externalDataBO));
+ one(boFactory).createDataBO(SESSION);
+ will(returnValue(dataBO));
- one(externalDataBO).define(externalData, samplePE, SourceType.MEASUREMENT);
- one(externalDataBO).save();
- one(externalDataBO).getExternalData();
+ one(dataBO).define(externalData, samplePE, SourceType.MEASUREMENT);
+ one(dataBO).save();
+ one(dataBO).getData();
ExternalDataPE externalDataPE = new ExternalDataPE();
externalDataPE.setCode(externalData.getCode());
will(returnValue(externalDataPE));
@@ -864,12 +864,12 @@ public class ETLServiceTest extends AbstractServerTestCase
one(sampleBO).getSample();
will(returnValue(samplePE));
- one(boFactory).createExternalDataBO(SESSION);
- will(returnValue(externalDataBO));
+ one(boFactory).createDataBO(SESSION);
+ will(returnValue(dataBO));
- one(externalDataBO).define(externalData, samplePE, SourceType.MEASUREMENT);
- one(externalDataBO).save();
- one(externalDataBO).getExternalData();
+ one(dataBO).define(externalData, samplePE, SourceType.MEASUREMENT);
+ one(dataBO).save();
+ one(dataBO).getData();
ExternalDataPE externalDataPE = new ExternalDataPE();
externalDataPE.setCode(externalData.getCode());
will(returnValue(externalDataPE));
@@ -937,7 +937,7 @@ public class ETLServiceTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- one(externalDataBO).getExternalData();
+ one(dataBO).getData();
ExternalDataPE externalDataPE = new ExternalDataPE();
externalDataPE.setCode(externalData.getCode());
@@ -946,15 +946,15 @@ public class ETLServiceTest extends AbstractServerTestCase
externalDataPE.setDataStore(store);
will(returnValue(externalDataPE));
- // one(boFactory).createExternalDataBO(SESSION);
- // will(returnValue(externalDataBO));
+ // one(boFactory).createDataBO(SESSION);
+ // will(returnValue(dataBO));
//
// exactly(1).of(boFactory).createSampleBO(SESSION);
// will(returnValue(sampleBO));
//
- // one(externalDataBO).define(externalData, samplePE, SourceType.MEASUREMENT);
- // one(externalDataBO).save();
- // one(externalDataBO).getExternalData();
+ // one(dataBO).define(externalData, samplePE, SourceType.MEASUREMENT);
+ // one(dataBO).save();
+ // one(dataBO).getExternalData();
// ExternalDataPE externalDataPE = new ExternalDataPE();
// externalDataPE.setCode(externalData.getCode());
// will(returnValue(externalDataPE));
@@ -1001,12 +1001,12 @@ public class ETLServiceTest extends AbstractServerTestCase
sample.setExperiment(experiment);
will(returnValue(sample));
- one(boFactory).createExternalDataBO(SESSION);
- will(returnValue(externalDataBO));
+ one(boFactory).createDataBO(SESSION);
+ will(returnValue(dataBO));
- one(externalDataBO).define(externalData, sample, sourceType);
- one(externalDataBO).save();
- one(externalDataBO).getExternalData();
+ one(dataBO).define(externalData, sample, sourceType);
+ one(dataBO).save();
+ one(dataBO).getData();
ExternalDataPE externalDataPE = new ExternalDataPE();
externalDataPE.setCode(externalData.getCode());
will(returnValue(externalDataPE));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBOTest.java
index a8c37686a71699835aba44ed74eafc6c0808b6a5..e20989c430624258b586ff784f2b164b6f7484a0 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBOTest.java
@@ -36,7 +36,6 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityPropertyTypeDAO
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEventDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
-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.IGridCustomFilterDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ILocatorTypeDAO;
@@ -84,9 +83,6 @@ public abstract class AbstractBOTest extends AssertJUnit
protected IDataDAO dataDAO;
- // FIXME remove
- protected IExternalDataDAO externalDataDAO;
-
protected IDatabaseInstanceDAO databaseInstanceDAO;
protected ISampleDAO sampleDAO;
@@ -135,7 +131,6 @@ public abstract class AbstractBOTest extends AssertJUnit
sampleDAO = context.mock(ISampleDAO.class);
databaseInstanceDAO = context.mock(IDatabaseInstanceDAO.class);
dataDAO = context.mock(IDataDAO.class);
- externalDataDAO = context.mock(IExternalDataDAO.class);
personDAO = context.mock(IPersonDAO.class);
propertiesConverter = context.mock(IEntityPropertiesConverter.class);
sampleTypeDAO = context.mock(ISampleTypeDAO.class);
@@ -175,8 +170,6 @@ public abstract class AbstractBOTest extends AssertJUnit
will(returnValue(locatorTypeDAO));
allowing(daoFactory).getDataDAO();
will(returnValue(dataDAO));
- allowing(daoFactory).getExternalDataDAO();
- will(returnValue(externalDataDAO));
allowing(daoFactory).getDataStoreDAO();
will(returnValue(dataStoreDAO));
allowing(daoFactory).getVocabularyDAO();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBOTest.java
index a4d631e2330eb2d47584a81620c02828137245db..abc7af21abadb9de71ca128624b05a4b30e6f74f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBOTest.java
@@ -575,8 +575,8 @@ public class DataBOTest extends AbstractBOTest
context.checking(new Expectations()
{
{
- one(dataDAO).tryGetByTechId(TECH_ID, ExternalDataBO.PROPERTY_TYPES,
- ExternalDataBO.DATA_SET_TYPE);
+ one(dataDAO).tryGetByTechId(TECH_ID, DataBO.PROPERTY_TYPES,
+ DataBO.DATA_SET_TYPE);
will(returnValue(dataSet));
one(propertiesConverter).updateProperties(
@@ -605,8 +605,8 @@ public class DataBOTest extends AbstractBOTest
context.checking(new Expectations()
{
{
- one(dataDAO).tryGetByTechId(TECH_ID, ExternalDataBO.PROPERTY_TYPES,
- ExternalDataBO.DATA_SET_TYPE);
+ one(dataDAO).tryGetByTechId(TECH_ID, DataBO.PROPERTY_TYPES,
+ DataBO.DATA_SET_TYPE);
will(returnValue(dataSet));
ExperimentIdentifier identifier = EXPERIMENT_IDENTIFIER;
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
deleted file mode 100644
index a0bbd96621a88f3dbf18ae7d48192abf1a830fe2..0000000000000000000000000000000000000000
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
+++ /dev/null
@@ -1,756 +0,0 @@
-/*
- * 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.server.business.bo;
-
-import static ch.systemsx.cisd.openbis.generic.server.business.ManagerTestTool.EXAMPLE_SESSION;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.jmock.Expectations;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.types.BooleanOrUnknown;
-import ch.systemsx.cisd.openbis.generic.server.business.ManagerTestTool;
-import ch.systemsx.cisd.openbis.generic.shared.Constants;
-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.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SourceType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetPropertyPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePropertyTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
-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.ExperimentPE;
-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.LocatorTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-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.SamplePE;
-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;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-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;
-
- private static final TechId TECH_ID = new TechId(42l);
-
- private static final DatabaseInstanceIdentifier DATABASE_INSTANCE_IDENTIFIER =
- new DatabaseInstanceIdentifier(ManagerTestTool.EXAMPLE_DATABASE_INSTANCE.getCode());
-
- private static final GroupIdentifier GROUP_IDENTIFIER = new GroupIdentifier(
- DATABASE_INSTANCE_IDENTIFIER, ManagerTestTool.EXAMPLE_GROUP.getCode());
-
- private static final SampleIdentifier SAMPLE_IDENTIFIER = new SampleIdentifier(
- GROUP_IDENTIFIER, "EXAMPLE_SAMPLE");
-
- private static final ExperimentIdentifier EXPERIMENT_IDENTIFIER = new ExperimentIdentifier(
- new ProjectIdentifier(GROUP_IDENTIFIER, ManagerTestTool.EXAMPLE_PROJECT.getCode()),
- "EXPERIMENT_CODE");
-
- private static final String DATA_STORE_CODE = "dss1";
-
- private static final String PARENT_CODE = "parent";
-
- private static final Date PRODUCTION_DATE = new Date(1001);
-
- private static final String DATA_PRODUCER_CODE = "DPC";
-
- private static final String DATA_SET_CODE = "DS1";
-
- private static final String LOCATION = "folder/subfolder/file.fft";
-
- private static final LocatorType LOCATOR_TYPE = new LocatorType("LT");
-
- private static final FileFormatType FILE_FORMAT_TYPE = new FileFormatType("FFT");
-
- private static final DataSetType DATA_SET_TYPE = new DataSetType("DST");
-
- private static final class DataMatcher extends BaseMatcher<ExternalDataPE>
- {
- public void describeTo(Description description)
- {
- description.appendText(DATA_SET_CODE);
- }
-
- public boolean matches(Object item)
- {
- if (item instanceof DataPE)
- {
- DataPE data = (DataPE) item;
- return data.getCode().equals(DATA_SET_CODE);
- }
- return false;
- }
- }
-
- @Test
- public void testDefineWithDirectSampleConnection()
- {
- final DataSetTypePE dataSetType = new DataSetTypePE();
- final FileFormatTypePE fileFormatType = new FileFormatTypePE();
- final VocabularyPE vocabulary = new VocabularyPE();
- vocabulary.addTerm(new VocabularyTermPE());
- VocabularyTermPE vocabularyTerm = new VocabularyTermPE();
- vocabularyTerm.setCode(StorageFormat.PROPRIETARY.toString());
- vocabulary.addTerm(vocabularyTerm);
- final LocatorTypePE locatorType = new LocatorTypePE();
- SamplePE sample = new SamplePE();
- ExperimentPE experimentPE = new ExperimentPE();
- sample.setExperiment(experimentPE);
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, new DataStorePE());
-
- IExternalDataBO dataBO = createExternalDataBO();
- dataBO.define(createData(null), sample, SourceType.DERIVED);
- ExternalDataPE externalData = dataBO.getExternalData();
-
- assertEquals(DATA_SET_CODE, externalData.getCode());
- assertEquals(BooleanOrUnknown.U, externalData.getComplete());
- assertEquals(DATA_PRODUCER_CODE, externalData.getDataProducerCode());
- assertSame(dataSetType, externalData.getDataSetType());
- assertSame(fileFormatType, externalData.getFileFormatType());
- assertSame(locatorType, externalData.getLocatorType());
- assertEquals(LOCATION, externalData.getLocation());
- assertEquals(0, externalData.getParents().size());
- assertSame(experimentPE, externalData.getExperiment());
- assertEquals(PRODUCTION_DATE, externalData.getProductionDate());
- assertSame(sample, externalData.tryGetSample());
- assertSame(true, externalData.isDerived());
- assertEquals(StorageFormat.PROPRIETARY, externalData.getStorageFormat());
- assertSame(vocabularyTerm, externalData.getStorageFormatVocabularyTerm());
- assertEquals(null, externalData.getRegistrator());
- assertEquals(SPEED_HINT, externalData.getSpeedHint());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDefineWithUserID()
- {
- final DataSetTypePE dataSetType = new DataSetTypePE();
- final FileFormatTypePE fileFormatType = new FileFormatTypePE();
- final VocabularyPE vocabulary = new VocabularyPE();
- vocabulary.addTerm(new VocabularyTermPE());
- VocabularyTermPE vocabularyTerm = new VocabularyTermPE();
- vocabularyTerm.setCode(StorageFormat.PROPRIETARY.toString());
- vocabulary.addTerm(vocabularyTerm);
- final LocatorTypePE locatorType = new LocatorTypePE();
- SamplePE sample = new SamplePE();
- ExperimentPE experimentPE = new ExperimentPE();
- sample.setExperiment(experimentPE);
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, new DataStorePE());
- final NewExternalData data = createData(null);
- data.setUserId("my-id");
- final PersonPE registrator = new PersonPE();
- context.checking(new Expectations()
- {
- {
- one(personDAO).tryFindPersonByUserId(data.getUserId());
- will(returnValue(registrator));
- }
- });
-
- IExternalDataBO dataBO = createExternalDataBO();
- dataBO.define(data, sample, SourceType.DERIVED);
- ExternalDataPE externalData = dataBO.getExternalData();
-
- assertEquals(DATA_SET_CODE, externalData.getCode());
- assertEquals(BooleanOrUnknown.U, externalData.getComplete());
- assertEquals(DATA_PRODUCER_CODE, externalData.getDataProducerCode());
- assertSame(dataSetType, externalData.getDataSetType());
- assertSame(fileFormatType, externalData.getFileFormatType());
- assertSame(locatorType, externalData.getLocatorType());
- assertEquals(LOCATION, externalData.getLocation());
- assertEquals(0, externalData.getParents().size());
- assertSame(experimentPE, externalData.getExperiment());
- assertEquals(PRODUCTION_DATE, externalData.getProductionDate());
- assertSame(sample, externalData.tryGetSample());
- assertSame(true, externalData.isDerived());
- assertEquals(StorageFormat.PROPRIETARY, externalData.getStorageFormat());
- assertSame(vocabularyTerm, externalData.getStorageFormatVocabularyTerm());
- assertSame(registrator, externalData.getRegistrator());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDefineWithUserEMail()
- {
- final DataSetTypePE dataSetType = new DataSetTypePE();
- final FileFormatTypePE fileFormatType = new FileFormatTypePE();
- final VocabularyPE vocabulary = new VocabularyPE();
- vocabulary.addTerm(new VocabularyTermPE());
- VocabularyTermPE vocabularyTerm = new VocabularyTermPE();
- vocabularyTerm.setCode(StorageFormat.PROPRIETARY.toString());
- vocabulary.addTerm(vocabularyTerm);
- final LocatorTypePE locatorType = new LocatorTypePE();
- SamplePE sample = new SamplePE();
- ExperimentPE experimentPE = new ExperimentPE();
- sample.setExperiment(experimentPE);
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, new DataStorePE());
- final NewExternalData data = createData(null);
- data.setUserEMail("my-email");
- final PersonPE registrator = new PersonPE();
- registrator.setEmail(data.getUserEMail());
- context.checking(new Expectations()
- {
- {
- one(personDAO).listPersons();
- will(returnValue(Arrays.asList(new PersonPE(), registrator)));
- }
- });
-
- IExternalDataBO dataBO = createExternalDataBO();
- dataBO.define(data, sample, SourceType.DERIVED);
- ExternalDataPE externalData = dataBO.getExternalData();
-
- assertEquals(DATA_SET_CODE, externalData.getCode());
- assertEquals(BooleanOrUnknown.U, externalData.getComplete());
- assertEquals(DATA_PRODUCER_CODE, externalData.getDataProducerCode());
- assertSame(dataSetType, externalData.getDataSetType());
- assertSame(fileFormatType, externalData.getFileFormatType());
- assertSame(locatorType, externalData.getLocatorType());
- assertEquals(LOCATION, externalData.getLocation());
- assertEquals(0, externalData.getParents().size());
- assertSame(experimentPE, externalData.getExperiment());
- assertEquals(PRODUCTION_DATE, externalData.getProductionDate());
- assertSame(sample, externalData.tryGetSample());
- assertSame(true, externalData.isDerived());
- assertEquals(StorageFormat.PROPRIETARY, externalData.getStorageFormat());
- assertSame(vocabularyTerm, externalData.getStorageFormatVocabularyTerm());
- assertSame(registrator, externalData.getRegistrator());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDefineWithExistingParentDataSet()
- {
- final DataSetTypePE dataSetType = new DataSetTypePE();
- final FileFormatTypePE fileFormatType = new FileFormatTypePE();
- final VocabularyPE vocabulary = new VocabularyPE();
- vocabulary.addTerm(new VocabularyTermPE());
- VocabularyTermPE vocabularyTerm = new VocabularyTermPE();
- vocabularyTerm.setCode(StorageFormat.PROPRIETARY.toString());
- vocabulary.addTerm(vocabularyTerm);
- final LocatorTypePE locatorType = new LocatorTypePE();
- ExperimentPE experimentPE = new ExperimentPE();
- DataStorePE dataStore = new DataStorePE();
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, dataStore);
- final DataPE data = new DataPE();
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryToFindDataSetByCode(PARENT_CODE);
- will(returnValue(data));
- }
- });
-
- IExternalDataBO dataBO = createExternalDataBO();
- dataBO.define(createData(PARENT_CODE), experimentPE, SourceType.MEASUREMENT);
- ExternalDataPE externalData = dataBO.getExternalData();
-
- assertSame(experimentPE, externalData.getExperiment());
- assertEquals(null, externalData.tryGetSample());
- assertSame(true, externalData.isMeasured());
- assertSame(dataStore, externalData.getDataStore());
- assertEquals(1, externalData.getParents().size());
- assertSame(data, externalData.getParents().iterator().next());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDefineWithNonExistingParentDataSet()
- {
- final DataSetTypePE dataSetType = new DataSetTypePE();
- final FileFormatTypePE fileFormatType = new FileFormatTypePE();
- final VocabularyPE vocabulary = new VocabularyPE();
- vocabulary.addTerm(new VocabularyTermPE());
- VocabularyTermPE vocabularyTerm = new VocabularyTermPE();
- vocabularyTerm.setCode(StorageFormat.PROPRIETARY.toString());
- vocabulary.addTerm(vocabularyTerm);
- final LocatorTypePE locatorType = new LocatorTypePE();
- final ExperimentPE experiment = new ExperimentPE();
- final DataStorePE dataStore = new DataStorePE();
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, dataStore);
- final DataSetTypePE dataSetTypeUnknown = new DataSetTypePE();
- final DataPE parentData = new DataPE();
- parentData.setCode(PARENT_CODE);
- parentData.setDataSetType(dataSetTypeUnknown);
- parentData.setExperiment(createExperiment("EXP1"));
- parentData.setPlaceholder(true);
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryToFindDataSetByCode(PARENT_CODE);
- will(returnValue(null));
-
- one(dataSetTypeDAO).tryToFindDataSetTypeByCode("UNKNOWN");
- will(returnValue(dataSetTypeUnknown));
-
- one(externalDataDAO).createDataSet(parentData);
- }
- });
-
- IExternalDataBO dataBO = createExternalDataBO();
- dataBO.define(createData(PARENT_CODE), experiment, SourceType.MEASUREMENT);
- ExternalDataPE externalData = dataBO.getExternalData();
-
- assertSame(experiment, externalData.getExperiment());
- assertEquals(null, externalData.tryGetSample());
- assertSame(true, externalData.isMeasured());
- assertSame(dataStore, externalData.getDataStore());
- assertEquals(1, externalData.getParents().size());
- assertEquals(parentData, externalData.getParents().iterator().next());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testDefineWithNonExistingParentDataSetAndNonExistingExperiment()
- {
- final DataSetTypePE dataSetType = createDataSetType();
- final FileFormatTypePE fileFormatType = new FileFormatTypePE();
- final VocabularyPE vocabulary = new VocabularyPE();
- vocabulary.addTerm(new VocabularyTermPE());
- VocabularyTermPE vocabularyTerm = new VocabularyTermPE();
- vocabularyTerm.setCode(StorageFormat.PROPRIETARY.toString());
- vocabulary.addTerm(vocabularyTerm);
- final LocatorTypePE locatorType = new LocatorTypePE();
- final DataStorePE dataStore = new DataStorePE();
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, dataStore);
- final DataSetTypePE dataSetTypeUnknown = new DataSetTypePE();
- final DataPE parentData = new DataPE();
- parentData.setCode(PARENT_CODE);
- parentData.setDataSetType(dataSetTypeUnknown);
- ExperimentPE experiment = createExperiment("EXP1");
- parentData.setExperiment(experiment);
- parentData.setPlaceholder(true);
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryToFindDataSetByCode(PARENT_CODE);
- will(returnValue(null));
-
- one(dataSetTypeDAO).tryToFindDataSetTypeByCode(
- DataSetTypeCode.UNKNOWN.getCode());
- will(returnValue(dataSetTypeUnknown));
-
- one(externalDataDAO).createDataSet(parentData);
- }
- });
-
- IExternalDataBO dataBO = createExternalDataBO();
- dataBO.define(createData(PARENT_CODE), experiment, SourceType.MEASUREMENT);
- ExternalDataPE externalData = dataBO.getExternalData();
-
- assertSame(null, externalData.tryGetSample());
- assertSame(true, externalData.isMeasured());
- assertSame(dataStore, externalData.getDataStore());
- assertEquals(1, externalData.getParents().size());
- assertEquals(parentData, externalData.getParents().iterator().next());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testUpdateStatuses()
- {
- final List<String> codes = Arrays.asList(new String[]
- { "CODE-1", "CODE-2" });
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).updateDataSetStatuses(codes,
- DataSetArchivingStatus.ARCHIVED, true);
- }
- });
-
- IExternalDataBO dataBO = createExternalDataBO();
- dataBO.updateStatuses(codes, DataSetArchivingStatus.ARCHIVED, true);
- // TODO 2010-04-26, Piotr Buczek: write a DAO test
- context.assertIsSatisfied();
- }
-
- @Test
- public void testUpdate()
- {
- final SamplePE sample = new SamplePE();
- sample.setCode(SAMPLE_IDENTIFIER.getSampleCode());
- final ExternalDataPE dataSet = createDataSet(sample, null);
- DataSetUpdatesDTO dataSetUpdatesDTO =
- createDataSetUpdates(dataSet, SAMPLE_IDENTIFIER, null);
- prepareForUpdate(dataSet, sample);
- context.checking(new Expectations()
- {
- {
- one(fileFormatTypeDAO)
- .tryToFindFileFormatTypeByCode(FILE_FORMAT_TYPE.getCode());
- FileFormatTypePE fileFormatTypePE = new FileFormatTypePE();
- fileFormatTypePE.setCode(FILE_FORMAT_TYPE.getCode());
- will(returnValue(fileFormatTypePE));
-
- one(propertiesConverter).checkMandatoryProperties(
- Collections.<DataSetPropertyPE> emptySet(), dataSet.getDataSetType());
-
- one(externalDataDAO).validateAndSaveUpdatedEntity(dataSet);
- }
- });
-
- IExternalDataBO dataBO = createExternalDataBO();
- dataBO.update(dataSetUpdatesDTO);
- context.assertIsSatisfied();
- }
-
- @Test
- public void testUpdateWithDataSetAsItsOwnParent()
- {
- final ExperimentPE experiment = new ExperimentPE();
- experiment.setCode(EXPERIMENT_IDENTIFIER.getExperimentCode());
-
- final ExternalDataPE dataSet = createDataSet(null, experiment);
- DataSetUpdatesDTO dataSetUpdatesDTO =
- createDataSetUpdates(dataSet, null, EXPERIMENT_IDENTIFIER);
- String[] parentCodes =
- { dataSet.getCode() };
- dataSetUpdatesDTO.setModifiedParentDatasetCodesOrNull(parentCodes);
- prepareForUpdate(dataSet, experiment);
-
- IExternalDataBO dataBO = createExternalDataBO();
- try
- {
- dataBO.update(dataSetUpdatesDTO);
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals("Data set 'DS1' can not be its own parent.", e.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testUpdateWithNonExistingParentDataSet()
- {
- final ExperimentPE experiment = new ExperimentPE();
- experiment.setCode(EXPERIMENT_IDENTIFIER.getExperimentCode());
-
- final ExternalDataPE dataSet = createDataSet(null, experiment);
- DataSetUpdatesDTO dataSetUpdatesDTO =
- createDataSetUpdates(dataSet, null, EXPERIMENT_IDENTIFIER);
- String[] parentCodes =
- { PARENT_CODE };
- dataSetUpdatesDTO.setModifiedParentDatasetCodesOrNull(parentCodes);
- prepareForUpdate(dataSet, experiment);
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryToFindDataSetByCode(PARENT_CODE);
- will(returnValue(null));
- }
- });
-
- IExternalDataBO dataBO = createExternalDataBO();
- try
- {
- dataBO.update(dataSetUpdatesDTO);
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals("Data Sets with following codes do not exist: '[" + PARENT_CODE + "]'.",
- e.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- private void prepareForUpdate(final ExternalDataPE dataSet, final SamplePE sample)
- {
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryGetByTechId(TECH_ID, ExternalDataBO.PROPERTY_TYPES,
- ExternalDataBO.DATA_SET_TYPE);
- will(returnValue(dataSet));
-
- one(propertiesConverter).updateProperties(
- Collections.<DataSetPropertyPE> emptySet(), dataSet.getDataSetType(),
- null, ManagerTestTool.EXAMPLE_PERSON);
- will(returnValue(Collections.emptySet()));
-
- one(databaseInstanceDAO).tryFindDatabaseInstanceByCode(
- DATABASE_INSTANCE_IDENTIFIER.getDatabaseInstanceCode());
- will(returnValue(ManagerTestTool.EXAMPLE_DATABASE_INSTANCE));
-
- one(groupDAO).tryFindSpaceByCodeAndDatabaseInstance(
- GROUP_IDENTIFIER.getSpaceCode(),
- ManagerTestTool.EXAMPLE_DATABASE_INSTANCE);
- will(returnValue(ManagerTestTool.EXAMPLE_GROUP));
-
- one(sampleDAO).tryFindByCodeAndSpace(SAMPLE_IDENTIFIER.getSampleCode(),
- ManagerTestTool.EXAMPLE_GROUP);
- will(returnValue(sample));
- }
- });
- }
-
- private void prepareForUpdate(final ExternalDataPE dataSet, final ExperimentPE experiment)
- {
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryGetByTechId(TECH_ID, ExternalDataBO.PROPERTY_TYPES,
- ExternalDataBO.DATA_SET_TYPE);
- will(returnValue(dataSet));
-
- ExperimentIdentifier identifier = EXPERIMENT_IDENTIFIER;
-
- one(daoFactory).getProjectDAO();
- will(returnValue(projectDAO));
- one(projectDAO).tryFindProject(identifier.getDatabaseInstanceCode(),
- identifier.getSpaceCode(), identifier.getProjectCode());
- will(returnValue(ManagerTestTool.EXAMPLE_PROJECT));
-
- one(experimentDAO).tryFindByCodeAndProject(ManagerTestTool.EXAMPLE_PROJECT,
- identifier.getExperimentCode());
- will(returnValue(experiment));
- }
- });
- }
-
- private DataSetUpdatesDTO createDataSetUpdates(final ExternalDataPE dataSet,
- final SampleIdentifier sampleIdentifierOrNull,
- final ExperimentIdentifier experimentIdentifierOrNull)
- {
- DataSetUpdatesDTO dataSetUpdatesDTO = new DataSetUpdatesDTO();
- dataSetUpdatesDTO.setDatasetId(TECH_ID);
- dataSetUpdatesDTO.setVersion(dataSet.getModificationDate());
- dataSetUpdatesDTO.setSampleIdentifierOrNull(sampleIdentifierOrNull);
- dataSetUpdatesDTO.setExperimentIdentifierOrNull(experimentIdentifierOrNull);
- dataSetUpdatesDTO.setFileFormatTypeCode(FILE_FORMAT_TYPE.getCode());
- return dataSetUpdatesDTO;
- }
-
- private ExternalDataPE createDataSet(final SamplePE sampleOrNull,
- final ExperimentPE experimentOrNull)
- {
- final ExternalDataPE dataSet = new ExternalDataPE();
- dataSet.setId(TECH_ID.getId());
- dataSet.setCode(DATA_SET_CODE);
- dataSet.setModificationDate(PRODUCTION_DATE);
- dataSet.setSample(sampleOrNull);
- dataSet.setExperiment(experimentOrNull);
- DataSetTypePE dataSetType = new DataSetTypePE();
- dataSetType.setCode(DATA_SET_TYPE.getCode());
- DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
- databaseInstance.setCode("db");
- dataSetType.setDatabaseInstance(databaseInstance);
- dataSetType.setDataSetTypePropertyTypes(new HashSet<DataSetTypePropertyTypePE>());
- dataSet.setDataSetType(dataSetType);
- return dataSet;
- }
-
- @Test
- public void testSaveNewDataSet()
- {
- final DataSetTypePE dataSetType = createDataSetType();
- final FileFormatTypePE fileFormatType = new FileFormatTypePE();
- final VocabularyPE vocabulary = new VocabularyPE();
- vocabulary.addTerm(new VocabularyTermPE());
- VocabularyTermPE vocabularyTerm = new VocabularyTermPE();
- vocabularyTerm.setCode(StorageFormat.PROPRIETARY.toString());
- vocabulary.addTerm(vocabularyTerm);
- final LocatorTypePE locatorType = new LocatorTypePE();
- SamplePE sample = new SamplePE();
- sample.setExperiment(new ExperimentPE());
- final DataStorePE dataStore = new DataStorePE();
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, dataStore);
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryToFindDataSetByCode(DATA_SET_CODE);
- will(returnValue(null));
-
- one(externalDataDAO).createDataSet(with(new DataMatcher()));
-
- expectMandatoryPropertiesCheck(this, dataSetType);
- }
- });
-
- IExternalDataBO dataBO = createExternalDataBO();
- dataBO.define(createData(null), sample, SourceType.DERIVED);
- dataBO.save();
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testUpdatePlaceholderDataSet()
- {
- final DataSetTypePE dataSetType = createDataSetType();
- final FileFormatTypePE fileFormatType = new FileFormatTypePE();
- final VocabularyPE vocabulary = new VocabularyPE();
- vocabulary.addTerm(new VocabularyTermPE());
- VocabularyTermPE vocabularyTerm = new VocabularyTermPE();
- vocabularyTerm.setCode(StorageFormat.PROPRIETARY.toString());
- vocabulary.addTerm(vocabularyTerm);
- final LocatorTypePE locatorType = new LocatorTypePE();
- SamplePE sample = new SamplePE();
- sample.setExperiment(new ExperimentPE());
- final DataStorePE dataStore = new DataStorePE();
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, dataStore);
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryToFindDataSetByCode(DATA_SET_CODE);
- DataPE data = new DataPE();
- data.setId(4711L);
- data.setPlaceholder(true);
- will(returnValue(data));
-
- one(externalDataDAO).updateDataSet(with(new DataMatcher()));
-
- expectMandatoryPropertiesCheck(this, dataSetType);
- }
-
- });
-
- IExternalDataBO dataBO = createExternalDataBO();
- dataBO.define(createData(null), sample, SourceType.DERIVED);
- dataBO.save();
-
- ExternalDataPE externalData = dataBO.getExternalData();
- assertSame(dataStore, externalData.getDataStore());
- assertEquals(false, externalData.isPlaceholder());
- assertEquals(4711, externalData.getId().longValue());
- assertSame(sample, externalData.tryGetSample());
- assertSame(true, externalData.isDerived());
-
- context.assertIsSatisfied();
- }
-
- @SuppressWarnings("unchecked")
- private void expectMandatoryPropertiesCheck(Expectations exp, final DataSetTypePE type)
- {
- exp.one(propertiesConverter).checkMandatoryProperties(
- exp.with(Expectations.any(Collection.class)), exp.with(type));
- }
-
- private DataSetTypePE createDataSetType()
- {
- final DataSetTypePE dataSetType = new DataSetTypePE();
- dataSetType.setCode("data-set-type-code");
- dataSetType.setDatabaseInstance(new DatabaseInstancePE());
- return dataSetType;
- }
-
- private ExperimentPE createExperiment(String experimentCode)
- {
- ExperimentPE experiment = new ExperimentPE();
- experiment.setCode(experimentCode);
- ProjectPE project = new ProjectPE();
- project.setCode("P");
- SpacePE group = new SpacePE();
- group.setCode("G");
- DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
- databaseInstance.setCode("DB");
- group.setDatabaseInstance(databaseInstance);
- project.setSpace(group);
- experiment.setProject(project);
- return experiment;
- }
-
- private void prepareDefine(final DataSetTypePE dataSetType,
- final FileFormatTypePE fileFormatType, final VocabularyPE vocabulary,
- final LocatorTypePE locatorType, final DataStorePE dataStore)
- {
- context.checking(new Expectations()
- {
- {
- one(dataSetTypeDAO).tryToFindDataSetTypeByCode(DATA_SET_TYPE.getCode());
- will(returnValue(dataSetType));
- one(fileFormatTypeDAO)
- .tryToFindFileFormatTypeByCode(FILE_FORMAT_TYPE.getCode());
- will(returnValue(fileFormatType));
- one(vocabularyDAO).tryFindVocabularyByCode(StorageFormat.VOCABULARY_CODE);
- will(returnValue(vocabulary));
- one(locatorTypeDAO).tryToFindLocatorTypeByCode(LOCATOR_TYPE.getCode());
- will(returnValue(locatorType));
-
- one(propertiesConverter).convertProperties(new IEntityProperty[0],
- dataSetType.getCode(), EXAMPLE_SESSION.tryGetPerson());
- ArrayList<DataSetPropertyPE> properties = new ArrayList<DataSetPropertyPE>();
- will(returnValue(properties));
-
- one(dataStoreDAO).tryToFindDataStoreByCode(DATA_STORE_CODE);
- will(returnValue(dataStore));
- }
- });
- }
-
- private NewExternalData createData(String parentDataSetCodeOrNull)
- {
- NewExternalData data = new NewExternalData();
- data.setCode(DATA_SET_CODE);
- if (parentDataSetCodeOrNull != null)
- {
- data.setParentDataSetCodes(Collections.singletonList(parentDataSetCodeOrNull));
- }
- data.setDataProducerCode(DATA_PRODUCER_CODE);
- data.setProductionDate(PRODUCTION_DATE);
- data.setComplete(BooleanOrUnknown.U);
- data.setStorageFormat(StorageFormat.PROPRIETARY);
- data.setDataSetType(DATA_SET_TYPE);
- data.setFileFormatType(FILE_FORMAT_TYPE);
- data.setLocatorType(LOCATOR_TYPE);
- data.setLocation(LOCATION);
- data.setDataStoreCode(DATA_STORE_CODE);
- data.setSpeedHint(SPEED_HINT);
- return data;
- }
-
- private final IExternalDataBO createExternalDataBO()
- {
- return new ExternalDataBO(daoFactory, EXAMPLE_SESSION, propertiesConverter);
- }
-
-}
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
deleted file mode 100644
index 557d0e40763cf8b9c6fb102901716d46a46153ee..0000000000000000000000000000000000000000
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAOTest.java
+++ /dev/null
@@ -1,422 +0,0 @@
-/*
- * Copyright 2008 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.server.dataaccess.db;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertNotNull;
-import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertTrue;
-import static org.testng.AssertJUnit.fail;
-
-import java.util.Date;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.springframework.dao.DataIntegrityViolationException;
-import org.testng.AssertJUnit;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.types.BooleanOrUnknown;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSetTypeDAO;
-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.ISampleDAO;
-import ch.systemsx.cisd.openbis.generic.shared.Constants;
-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;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetPropertyPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
-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.EntityTypePropertyTypePE;
-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.FileFormatTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-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;
-import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.dto.types.DataSetTypeCode;
-
-/**
- * Test cases for corresponding {@link ExternalDataDAO} class.
- *
- * @author Christian Ribeaud
- */
-@Test(groups =
- { "db", "externalData" })
-@SuppressWarnings("deprecation")
-public final class ExternalDataDAOTest extends AbstractDAOTest
-{
-
- private static final int SPEED_HINT = Constants.DEFAULT_SPEED_HINT / 4;
-
- private final String PARENT_CODE = "20081105092158673-1";
-
- private final String CHILD_CODE = "20081105092159188-3";
-
- @Test
- public final void testListExternalData()
- {
- testCreateDataSetWithSample();
- final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
- List<ExternalDataPE> list = externalDataDAO.listExternalData(pickASample());
-
- assertEquals(1, list.size());
- ExternalDataPE dataSet = list.get(0);
- assertEquals("abcd", dataSet.getLocation());
- assertEquals(BooleanOrUnknown.U, dataSet.getComplete());
- }
-
- @Test
- public void testCreateDataSetWithSample()
- {
- IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
- String dataSetCode = daoFactory.getPermIdDAO().createPermId();
- SamplePE sample = pickASample();
- ExternalDataPE externalData = createExternalData(dataSetCode, sample);
- externalData.setShareId("42");
- externalData.setSize(4711L);
- externalData.setSpeedHint(SPEED_HINT);
- externalDataDAO.createDataSet(externalData);
-
- ExternalDataPE dataSet =
- (ExternalDataPE) externalDataDAO.tryToFindDataSetByCode(dataSetCode);
- assertDataEqual(externalData, dataSet);
- assertEquals("42", dataSet.getShareId());
- assertEquals(4711L, dataSet.getSize().longValue());
- assertEquals(SPEED_HINT, dataSet.getSpeedHint());
- }
-
- @Test
- public void testCreateDataSetWithNoSample()
- {
- IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
- String dataSetCode = daoFactory.getPermIdDAO().createPermId();
- ExternalDataPE externalData = createExternalData(dataSetCode, null);
- externalDataDAO.createDataSet(externalData);
-
- ExternalDataPE dataSet =
- (ExternalDataPE) externalDataDAO.tryToFindDataSetByCode(dataSetCode);
- assertDataEqual(externalData, dataSet);
- assertEquals(Constants.DEFAULT_SPEED_HINT, dataSet.getSpeedHint());
- }
-
- private ExternalDataPE createExternalData(String dataSetCode, SamplePE sampleOrNull)
- {
- ExternalDataPE externalData = new ExternalDataPE();
-
- externalData.setCode(dataSetCode);
- externalData.setDataSetType(getDataSetType(DataSetTypeCode.UNKNOWN));
- externalData.setExperiment(pickAnExperiment());
- if (sampleOrNull != null)
- {
- externalData.setSampleAcquiredFrom(sampleOrNull);
- } else
- {
- externalData.setDerived(true);
- }
- externalData.setFileFormatType(pickAFileFormatType());
- externalData.setLocatorType(pickALocatorType());
- externalData.setLocation("abcd");
- externalData.setComplete(BooleanOrUnknown.U);
- externalData.setStorageFormatVocabularyTerm(pickAStorageFormatVocabularyTerm());
- externalData.setPlaceholder(true);
- externalData.setDataStore(pickADataStore());
- return externalData;
- }
-
- private void assertDataEqual(ExternalDataPE externalData, ExternalDataPE dataSet)
- {
- assertEquals(externalData.getCode(), dataSet.getCode());
- assertEquals(externalData.getDataSetType(), dataSet.getDataSetType());
- assertEquals(externalData.getExperiment(), dataSet.getExperiment());
- assertEquals(externalData.getFileFormatType(), dataSet.getFileFormatType());
- assertEquals(externalData.getLocatorType(), dataSet.getLocatorType());
- assertEquals(externalData.getLocation(), dataSet.getLocation());
- assertEquals(externalData.getComplete(), dataSet.getComplete());
- assertEquals(externalData.getStorageFormat(), dataSet.getStorageFormat());
- assertEquals(externalData.isPlaceholder(), dataSet.isPlaceholder());
- assertEquals(externalData.isMeasured(), dataSet.isMeasured());
- assertEquals(externalData.tryGetSample(), dataSet.tryGetSample());
- }
-
- @Test
- public void testUpdateDataSetAquiredFromSampleWithoutDataSetSize()
- {
- checkUpdate(null);
- }
-
- @Test
- public void testUpdateDataSetAquiredFromSampleWithDataSetSize()
- {
- checkUpdate(4711L);
- }
-
- private void checkUpdate(Long size)
- {
- IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
- DataPE data = new DataPE();
- String dataSetCode = daoFactory.getPermIdDAO().createPermId();
- data.setCode(dataSetCode);
- data.setDataSetType(getDataSetType(DataSetTypeCode.UNKNOWN));
- data.setExperiment(pickAnExperiment());
- data.setSampleAcquiredFrom(pickASample());
- data.setPlaceholder(true);
- data.setDataStore(pickADataStore());
- data.setModificationDate(new Date());
- externalDataDAO.createDataSet(data);
-
- ExternalDataPE externalData = new ExternalDataPE();
- externalData.setId(externalDataDAO.tryToFindDataSetByCode(dataSetCode).getId());
- externalData.setCode(dataSetCode);
- externalData.setDataSetType(getDataSetType(DataSetTypeCode.UNKNOWN));
- externalData.setDataStore(pickADataStore());
- externalData.setExperiment(pickAnExperiment());
- externalData.setSampleAcquiredFrom(pickASample());
- externalData.setFileFormatType(pickAFileFormatType());
- externalData.setLocatorType(pickALocatorType());
- externalData.setLocation("abcd");
- externalData.setShareId("share-42");
- externalData.setSize(size);
- externalData.setComplete(BooleanOrUnknown.U);
- externalData.setStorageFormatVocabularyTerm(pickAStorageFormatVocabularyTerm());
- externalData.setPlaceholder(true);
- externalData.setStatus(DataSetArchivingStatus.AVAILABLE);
- final Date modificationTimestamp = data.getModificationDate();
- externalData.setModificationDate(modificationTimestamp);
- externalDataDAO.updateDataSet(externalData);
-
- ExternalDataPE dataSet =
- (ExternalDataPE) externalDataDAO.tryToFindDataSetByCode(dataSetCode);
- assertEquals(externalData.getCode(), dataSet.getCode());
- assertEquals(externalData.getDataSetType(), dataSet.getDataSetType());
- assertEquals(externalData.getExperiment(), dataSet.getExperiment());
- assertEquals(externalData.getFileFormatType(), dataSet.getFileFormatType());
- assertEquals(externalData.getLocatorType(), dataSet.getLocatorType());
- assertEquals(externalData.getShareId(), dataSet.getShareId());
- assertEquals(externalData.getLocation(), dataSet.getLocation());
- assertEquals(externalData.getSize(), dataSet.getSize());
- assertEquals(externalData.getComplete(), dataSet.getComplete());
- assertEquals(externalData.getStorageFormat(), dataSet.getStorageFormat());
- assertEquals(externalData.isPlaceholder(), dataSet.isPlaceholder());
- assertEquals(externalData.isMeasured(), dataSet.isMeasured());
- assertFalse(externalData.getModificationDate().equals(modificationTimestamp));
- }
-
- @Test
- public void testUpdateDataSetWithParent()
- {
- final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
-
- // try to add a parent to a data set that already had one
- final ExternalDataPE dataSetConnectedWithParent = findExternalData(CHILD_CODE);
- assertFalse(dataSetConnectedWithParent.getParents().isEmpty());
- final ExternalDataPE anotherDataSet = findExternalData("20081105092159111-1");
- dataSetConnectedWithParent.addParent(anotherDataSet);
- externalDataDAO.updateDataSet(dataSetConnectedWithParent);
-
- ExternalDataPE dataSet =
- (ExternalDataPE) externalDataDAO.tryToFindDataSetByCode(CHILD_CODE);
- assertEquals(dataSetConnectedWithParent.getParents().size(), dataSet.getParents().size());
- Set<DataPE> extractedParents = dataSet.getParents();
- for (DataPE parent : dataSetConnectedWithParent.getParents())
- {
- assertTrue(extractedParents.contains(parent));
- }
- assertTrue(extractedParents.contains(anotherDataSet));
- }
-
- @Test
- public final void testDeleteWithPropertiesButParentPreserved()
- {
- final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
- final ExternalDataPE deletedData = findExternalData(CHILD_CODE);
-
- // Deleted data set should have all collections which prevent it from deletion empty.
- assertTrue(deletedData.getChildren().isEmpty());
-
- // delete
- externalDataDAO.delete(deletedData);
-
- // test successful deletion of data set
- assertNull(externalDataDAO.tryGetByTechId(TechId.create(deletedData)));
-
- // test successful deletion of data set properties
- assertFalse(deletedData.getProperties().isEmpty());
- List<EntityTypePropertyTypePE> retrievedPropertyTypes =
- daoFactory.getEntityPropertyTypeDAO(EntityKind.DATA_SET).listEntityPropertyTypes(
- deletedData.getEntityType());
- for (DataSetPropertyPE property : deletedData.getProperties())
- {
- int index = retrievedPropertyTypes.indexOf(property.getEntityTypePropertyType());
- EntityTypePropertyTypePE retrievedPropertyType = retrievedPropertyTypes.get(index);
- assertFalse(retrievedPropertyType.getPropertyValues().contains(property));
- }
-
- // deleted sample had parent connected that should not have been deleted
- // NOTE: somehow cannot get parents even though connection is the same as with children
- // DataPE parent = deletedData.tryGetParent();
- // assertNotNull(parent);
- // assertNotNull(externalDataDAO.tryGetByTechId(new TechId(HibernateUtils.getId(parent))));
-
- // FIXME throws ClassCastException, uncomment when fixed, see:
- // http://sysin.wordpress.com/2009/02/27/hibernate-inheritance-classcastexception-part-1/
- // http://docs.jboss.org/hibernate/core/3.3/reference/en/html/performance.html#performance-fetching-proxies
-// findExternalData(PARENT_CODE);
- }
-
- @Test(expectedExceptions = DataIntegrityViolationException.class)
- public final void testDeleteFailWithChildrenDatasets()
- {
- final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
- final ExternalDataPE deletedData = findExternalData(PARENT_CODE);
-
- // Deleted data set should have 'child' data sets which prevent it from deletion.
- assertFalse(deletedData.getChildren().isEmpty());
-
- // delete
- externalDataDAO.delete(deletedData);
- }
-
- protected VocabularyTermPE pickAStorageFormatVocabularyTerm()
- {
- String code = StorageFormat.VOCABULARY_CODE;
- VocabularyPE vocabulary = daoFactory.getVocabularyDAO().tryFindVocabularyByCode(code);
- assertNotNull(vocabulary);
- return vocabulary.getTerms().iterator().next();
- }
-
- protected FileFormatTypePE pickAFileFormatType()
- {
- IFileFormatTypeDAO fileFormatTypeDAO = daoFactory.getFileFormatTypeDAO();
- FileFormatTypePE fileFormatType = fileFormatTypeDAO.tryToFindFileFormatTypeByCode("TIFF");
- assertNotNull(fileFormatType);
- return fileFormatType;
- }
-
- protected LocatorTypePE pickALocatorType()
- {
- ILocatorTypeDAO locatorTypeDAO = daoFactory.getLocatorTypeDAO();
- LocatorTypePE locatorType = locatorTypeDAO.tryToFindLocatorTypeByCode("RELATIVE_LOCATION");
- assertNotNull(locatorType);
- return locatorType;
- }
-
- protected SamplePE pickASample()
- {
- ISampleDAO sampleDAO = daoFactory.getSampleDAO();
- DatabaseInstancePE dbInstance = daoFactory.getHomeDatabaseInstance();
- SamplePE sample = sampleDAO.tryFindByCodeAndDatabaseInstance("MP", dbInstance);
- assertNotNull(sample);
- return sample;
- }
-
- protected DataStorePE pickADataStore()
- {
- return daoFactory.getDataStoreDAO().tryToFindDataStoreByCode("STANDARD");
- }
-
- protected DataSetTypePE getDataSetType(DataSetTypeCode type)
- {
- IDataSetTypeDAO dataSetTypeDAO = daoFactory.getDataSetTypeDAO();
- String code = type.getCode();
- DataSetTypePE dataSetType = dataSetTypeDAO.tryToFindDataSetTypeByCode(code);
- assertNotNull(dataSetType);
- return dataSetType;
- }
-
- protected ExperimentPE pickAnExperiment()
- {
- List<ExperimentPE> experiments = daoFactory.getExperimentDAO().listExperiments();
- for (ExperimentPE experimentPE : experiments)
- {
- if (experimentPE.getInvalidation() == null)
- {
- return experimentPE;
- }
- }
- fail("No valid experiment found.");
- return null; // to make the compiler happy
- }
-
- @Test
- public void testCreateDataSetWithBothSampleAndParent()
- {
- final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
-
- // try to create a dataset connected with a sample and a parent at the same time
- final String dataSetCode = daoFactory.getPermIdDAO().createPermId();
- final SamplePE sample = pickASample();
- ExternalDataPE parentData = findExternalData(PARENT_CODE);
- ExternalDataPE externalData = createExternalData(dataSetCode, sample);
- externalData.addParent(parentData);
- externalDataDAO.createDataSet(externalData);
- }
-
- @Test
- public void testUpdateOfDataSetAddParentWhenThereIsSampleConnected()
- {
- final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
-
- // try to update dataset connected with a sample - adding a parent should succeed
- final ExternalDataPE dataSetConnectedWithSample = findExternalData(PARENT_CODE);
- assertNotNull(dataSetConnectedWithSample.tryGetSample());
- final ExternalDataPE anotherDataSet = findExternalData("20081105092159111-1");
- dataSetConnectedWithSample.addParent(anotherDataSet);
- externalDataDAO.updateDataSet(dataSetConnectedWithSample);
- }
-
- @Test
- public void testUpdateOfDataSetConnectSampleWhenThereIsParent()
- {
- final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
-
- // try to update dataset connected with a parent - connecting with a sample should succeed
- final ExternalDataPE dataSetConnectedWithParent = findExternalData(CHILD_CODE);
- assertFalse(dataSetConnectedWithParent.getParents().isEmpty());
- dataSetConnectedWithParent.setSampleAcquiredFrom(pickASample());
- externalDataDAO.updateDataSet(dataSetConnectedWithParent);
- }
-
- @Test
- public void testLoadByPermId() throws Exception
- {
- ExternalDataPE exp = daoFactory.getExternalDataDAO().listAllEntities().get(0);
- HashSet<String> keys = new HashSet<String>();
- keys.add(exp.getCode());
- keys.add("nonexistent");
- List<ExternalDataPE> result = daoFactory.getExternalDataDAO().listByCode(keys);
- AssertJUnit.assertEquals(1, result.size());
- AssertJUnit.assertEquals(exp, result.get(0));
- }
-
- @Test
- public void testLoadByPermIdNoEntries() throws Exception
- {
- HashSet<String> keys = new HashSet<String>();
- List<ExternalDataPE> result = daoFactory.getExternalDataDAO().listByCode(keys);
- AssertJUnit.assertTrue(result.isEmpty());
- }
-
-}
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 33e140a53acc7ec539f286a7e6e8469fa3dcf11d..2d66ee25a82d81e2e5b356d552b8a86a98eafab7 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
@@ -304,7 +304,6 @@ public final class DBCreator extends AbstractDAOTest
// DataSets
- @SuppressWarnings("deprecation")
private void createDataSetsForSample(SamplePE sample)
{
final int size = SizeHelper.getNextDataSetsPerSampleSize();
@@ -312,7 +311,7 @@ public final class DBCreator extends AbstractDAOTest
{
log("creating dataset: %d/%d", i, size);
ExternalDataPE dataSet = generateDataSetForSample(sample);
- daoFactory.getExternalDataDAO().createDataSet(dataSet);
+ daoFactory.getDataDAO().createDataSet(dataSet);
}
log("created datasets");
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
index f3933d2112fea1a8fcb54e7e539bbfeb573d02ba..073a00327261dea55bff7440825536fb6c36007b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
@@ -33,12 +33,12 @@ import ch.systemsx.cisd.common.logging.BufferedAppender;
import ch.systemsx.cisd.common.logging.LogInitializer;
import ch.systemsx.cisd.openbis.generic.server.CommonServerTest.PersonWithDisplaySettingsMatcher;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypePropertyTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGroupBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialTable;
@@ -57,7 +57,6 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDatabaseInstanceDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
-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.IPersonDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
@@ -114,9 +113,6 @@ public abstract class AbstractServerTestCase extends AssertJUnit
protected ISpaceDAO groupDAO;
- // FIXME use IDataDAO
- protected IExternalDataDAO externalDataDAO;
-
protected IDataDAO dataSetDAO;
protected IPermIdDAO permIdDAO;
@@ -159,7 +155,7 @@ public abstract class AbstractServerTestCase extends AssertJUnit
protected IAttachmentDAO experimentAttachmentDAO;
- protected IExternalDataBO externalDataBO;
+ protected IDataBO dataBO;
protected IEntityTypeBO entityTypeBO;
@@ -197,7 +193,6 @@ public abstract class AbstractServerTestCase extends AssertJUnit
sampleDAO = context.mock(ISampleDAO.class);
roleAssignmentDAO = context.mock(IRoleAssignmentDAO.class);
dataSetDAO = context.mock(IDataDAO.class);
- externalDataDAO = context.mock(IExternalDataDAO.class);
permIdDAO = context.mock(IPermIdDAO.class);
entityTypeDAO = context.mock(IEntityTypeDAO.class);
experimentDAO = context.mock(IExperimentDAO.class);
@@ -219,7 +214,7 @@ public abstract class AbstractServerTestCase extends AssertJUnit
propertyTypeBO = context.mock(IPropertyTypeBO.class);
vocabularyBO = context.mock(IVocabularyBO.class);
entityTypePropertyTypeBO = context.mock(IEntityTypePropertyTypeBO.class);
- externalDataBO = context.mock(IExternalDataBO.class);
+ dataBO = context.mock(IDataBO.class);
// Table
dataSetTable = context.mock(IDataSetTable.class);
sampleLister = context.mock(ISampleLister.class);
@@ -253,8 +248,6 @@ public abstract class AbstractServerTestCase extends AssertJUnit
will(returnValue(sampleTypeDAO));
allowing(daoFactory).getDataDAO();
will(returnValue(dataSetDAO));
- allowing(daoFactory).getExternalDataDAO();
- will(returnValue(externalDataDAO));
allowing(daoFactory).getAttachmentDAO();
will(returnValue(experimentAttachmentDAO));
allowing(daoFactory).getFileFormatTypeDAO();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
index aabc57814459d7865a792f0983a147e01a3a19d8..04b6c0e65cf33a6f7f1b17806fafdeb8d7509119 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
@@ -16,9 +16,9 @@
package ch.systemsx.cisd.openbis.plugin.screening.server;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
@@ -55,7 +55,7 @@ public interface IScreeningBusinessObjectFactory
public IMaterialLister createMaterialLister(Session session);
- public IExternalDataBO createExternalDataBO(Session session);
+ public IDataBO createDataBO(Session session);
public IDatasetLister createDatasetLister(Session session);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
index 2f5c2fcd2db4d5326bcd82a457f66ea3d2473ad2..554e64793c327da82ffbbc0b9d7b85167642ab89 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
@@ -22,9 +22,9 @@ import javax.annotation.Resource;
import org.springframework.stereotype.Component;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataSetTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
@@ -122,9 +122,9 @@ public final class ScreeningBusinessObjectFactory extends AbstractPluginBusiness
return getCommonBusinessObjectFactory().createMaterialBO(session);
}
- public IExternalDataBO createExternalDataBO(Session session)
+ public IDataBO createDataBO(Session session)
{
- return getCommonBusinessObjectFactory().createExternalDataBO(session);
+ return getCommonBusinessObjectFactory().createDataBO(session);
}
public IDatasetLister createDatasetLister(Session session)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/LogicalImageLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/LogicalImageLoader.java
index 2a4fbcda7cc452ceac8b32c88f781a4accd22d0b..44273e6b4bc4eba8c47a39437401537a0e81f6f6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/LogicalImageLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/LogicalImageLoader.java
@@ -20,12 +20,12 @@ import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IDataBO;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
@@ -94,7 +94,7 @@ public class LogicalImageLoader
{
ImageDatasetParameters imageParameters = datasetLoader.getImageParameters();
- ExternalDataPE dataset = loadDatasetWithChildren(datasetCode);
+ DataPE dataset = loadDatasetWithChildren(datasetCode);
DatasetImagesReference datasetImagesReference =
createDatasetImagesReference(translate(dataset), imageParameters);
List<DatasetImagesReference> overlayDatasets = extractImageOverlays(dataset);
@@ -116,7 +116,7 @@ public class LogicalImageLoader
return refs;
}
- private List<DatasetImagesReference> extractImageOverlays(ExternalDataPE imageDataset)
+ private List<DatasetImagesReference> extractImageOverlays(DataPE imageDataset)
{
List<ExternalData> overlayDatasets = fetchOverlayDatasets(imageDataset);
@@ -128,7 +128,7 @@ public class LogicalImageLoader
return overlays;
}
- private List<ExternalData> fetchOverlayDatasets(ExternalDataPE imageDataset)
+ private List<ExternalData> fetchOverlayDatasets(DataPE imageDataset)
{
List<DataPE> overlayPEs =
ScreeningUtils.filterImageOverlayDatasets(imageDataset.getChildren());
@@ -150,18 +150,18 @@ public class LogicalImageLoader
imageParameters);
}
- DatasetImagesReference loadImageDatasetReference(ExternalDataPE imageDataset)
+ DatasetImagesReference loadImageDatasetReference(DataPE imageDataset)
{
return loadImageDatasetReference(translate(imageDataset));
}
- private ExternalDataPE loadDatasetWithChildren(String datasetPermId)
+ private DataPE loadDatasetWithChildren(String datasetPermId)
{
- IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
- externalDataBO.loadByCode(datasetPermId);
- externalDataBO.enrichWithChildren();
- ExternalDataPE externalData = externalDataBO.getExternalData();
- return externalData;
+ IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.loadByCode(datasetPermId);
+ dataBO.enrichWithChildren();
+ DataPE dataSet = dataBO.getData();
+ return dataSet;
}
private static Collection<Long> extractIds(List<DataPE> datasets)
@@ -174,8 +174,8 @@ public class LogicalImageLoader
return ids;
}
- private ExternalData translate(ExternalDataPE externalData)
+ private ExternalData translate(DataPE dataSet)
{
- return ExternalDataTranslator.translate(externalData, session.getBaseIndexURL());
+ return DataSetTranslator.translate(dataSet, session.getBaseIndexURL());
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
index 9fbc2cb96c9da471ec4147cb11c851af776c0d70..749c2dd072267530d4730f3fb891deb28c06cc2b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
@@ -22,8 +22,8 @@ import java.util.Collections;
import java.util.List;
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.IDataSetTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
@@ -35,6 +35,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -128,16 +129,16 @@ public class PlateContentLoader
private PlateImages getPlateContentForDataset(TechId datasetId)
{
- ExternalDataPE externalData = loadDataset(datasetId);
- SamplePE plate = externalData.tryGetSample();
+ DataPE dataSet = loadDataset(datasetId);
+ SamplePE plate = dataSet.tryGetSample();
if (plate == null)
{
throw UserFailureException.fromTemplate("Dataset '%s' has no sample connected.",
- externalData.getCode());
+ dataSet.getCode());
}
List<WellMetadata> wells = loadWells(new TechId(HibernateUtils.getId(plate)));
DatasetImagesReference datasetImagesReference =
- imageLoader.loadImageDatasetReference(externalData);
+ imageLoader.loadImageDatasetReference(dataSet);
Geometry plateGeometry = getPlateGeometry(plate);
PlateMetadata plateMetadata =
new PlateMetadata(translate(plate), wells, plateGeometry.getNumberOfRows(),
@@ -152,12 +153,12 @@ public class PlateContentLoader
return PlateDimensionParser.getPlateGeometry(properties);
}
- private ExternalDataPE loadDataset(TechId datasetId)
+ private DataPE loadDataset(TechId datasetId)
{
- IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
- externalDataBO.loadDataByTechId(datasetId);
- ExternalDataPE externalData = externalDataBO.getExternalData();
- return externalData;
+ IDataBO dataBO = businessObjectFactory.createDataBO(session);
+ dataBO.loadDataByTechId(datasetId);
+ DataPE dataSet = dataBO.getData();
+ return dataSet;
}
private ExternalData translate(ExternalDataPE externalData)
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 8044637a04f1d3ad5117381415f269b64ceca88f..3b8190d5ccee7fa254e719b083ab6d2ba3b74dbf 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
@@ -35,7 +35,7 @@ import org.apache.commons.lang.StringUtils;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.api.v1.Translator;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
+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;
@@ -49,8 +49,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
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.MaterialPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
@@ -282,7 +282,7 @@ public class ScreeningApiImpl
public List<IDatasetIdentifier> getDatasetIdentifiers(List<String> datasetCodes)
{
- IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
+ IDataBO externalDataBO = businessObjectFactory.createDataBO(session);
List<IDatasetIdentifier> identifiers = new ArrayList<IDatasetIdentifier>();
for (String datasetCode : datasetCodes)
{
@@ -291,16 +291,15 @@ public class ScreeningApiImpl
return identifiers;
}
- private IDatasetIdentifier getDatasetIdentifier(IExternalDataBO externalDataBO,
- String datasetCode)
+ private IDatasetIdentifier getDatasetIdentifier(IDataBO dataBO, String datasetCode)
{
- externalDataBO.loadByCode(datasetCode);
- ExternalDataPE externalData = externalDataBO.getExternalData();
- if (externalData == null)
+ dataBO.loadByCode(datasetCode);
+ DataPE dataSet = dataBO.getData();
+ if (dataSet == null)
{
throw UserFailureException.fromTemplate("Dataset '%s' does not exist", datasetCode);
}
- return new DatasetIdentifier(datasetCode, externalData.getDataStore().getDownloadUrl());
+ return new DatasetIdentifier(datasetCode, dataSet.getDataStore().getDownloadUrl());
}
static class DatasetReferenceHolder
@@ -439,7 +438,7 @@ public class ScreeningApiImpl
Sample sample = loadSampleByPermId(wellIdentifier.getPermId(), enrichWithProperties);
return Translator.translate(sample);
}
-
+
public ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample getPlateSample(
PlateIdentifier plateIdentifier)
{