From 1f0948d0550b395c975c86ba0eea41f4209426d0 Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Fri, 27 Jan 2012 16:08:24 +0000
Subject: [PATCH] LMS-2738 DSS robustness - add setStorageConfirmation method
to ExternalData, and expose it through ETLService
SVN: 24298
---
.../openbis/generic/server/ETLService.java | 11 +
.../generic/server/ETLServiceLogger.java | 5 +
.../generic/server/business/bo/DataBO.java | 18 +
.../generic/server/business/bo/IDataBO.java | 8 +
.../server/dataaccess/db/ExternalDataDAO.java | 554 ------------------
.../generic/shared/IETLLIMSService.java | 8 +
.../generic/shared/dto/ExternalDataPE.java | 2 +-
.../generic/server/ETLServiceTest.java | 7 +
.../server/business/bo/DataBOTest.java | 12 +
.../shared/IETLLIMSService.java.expected | 8 +
10 files changed, 78 insertions(+), 555 deletions(-)
delete mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java
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 97f600f372d..536e4538a85 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
@@ -1494,4 +1494,15 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
return trustedOriginDomainProvider.getTrustedDomains();
}
+ public void setStorageConfirmed(String sessionToken, String dataSetCode)
+ {
+ assert sessionToken != null : "Unspecified session token.";
+
+ final Session session = getSession(sessionToken);
+
+ final IDataBO dataBO = businessObjectFactory.createDataBO(session);
+
+ dataBO.loadByCode(dataSetCode);
+ dataBO.setStorageConfirmed();
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
index 663f2578cac..5a660f9548a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceLogger.java
@@ -527,4 +527,9 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLLIMSSe
logAccess(sessionToken, "getTrustedCrossOriginDomains");
return null;
}
+
+ public void setStorageConfirmed(String sessionToken, String dataSetCode)
+ {
+ logAccess(sessionToken, "setStorageConfirmed", "DATA_SET_CODE(%s)", dataSetCode);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBO.java
index 5ce11efde0e..82c4d092b83 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataBO.java
@@ -902,4 +902,22 @@ public class DataBO extends AbstractDataSetBusinessObject implements IDataBO
type, managedProperty, registrator));
}
+ public void setStorageConfirmed()
+ {
+ boolean confirmationSuceeded = false;
+ ExternalDataPE externalData = data.tryAsExternalData();
+ if (null != externalData)
+ {
+ externalData.setStorageConfirmation(true);
+ confirmationSuceeded = true;
+ }
+
+ if (false == confirmationSuceeded)
+ {
+ throw new UserFailureException(
+ String.format(
+ "Couldn't set the storageConfirmation for dataset %s. It is not an external data.",
+ data.getCode()));
+ }
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataBO.java
index 42631ea009d..88b13381402 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IDataBO.java
@@ -128,4 +128,12 @@ public interface IDataBO extends IEntityBusinessObject
*/
public void setContainedDataSets(ExperimentPE experiment, NewContainerDataSet newData);
+ /**
+ * Indicate that the storage of the external data has been confirmed.
+ *
+ * @throws UserFailureException
+ * if the this is not external data
+ */
+ public void setStorageConfirmed();
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java
deleted file mode 100644
index 51281744b2f..00000000000
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java
+++ /dev/null
@@ -1,554 +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 java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-import java.util.Set;
-import java.util.TreeSet;
-
-import org.apache.log4j.Logger;
-import org.hibernate.FetchMode;
-import org.hibernate.HibernateException;
-import org.hibernate.LockMode;
-import org.hibernate.Session;
-import org.hibernate.criterion.Criterion;
-import org.hibernate.criterion.DetachedCriteria;
-import org.hibernate.criterion.Projections;
-import org.hibernate.criterion.Restrictions;
-import org.springframework.dao.DataAccessException;
-import org.springframework.dao.DataIntegrityViolationException;
-import org.springframework.orm.hibernate3.HibernateCallback;
-import org.springframework.orm.hibernate3.HibernateTemplate;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.utilities.MethodUtils;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
-import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
-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.TableNames;
-import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
-
-/**
- * Implementation of IExternalDataDAO for databases.
- *
- * @author Christian Ribeaud
- */
-@SuppressWarnings("deprecation")
-final class ExternalDataDAO extends AbstractGenericEntityWithPropertiesDAO<ExternalDataPE>
- implements IExternalDataDAO
-{
- private final static Class<ExternalDataPE> ENTITY_CLASS = ExternalDataPE.class;
-
- private final static Class<DataPE> ENTITY_SUPER_CLASS = DataPE.class;
-
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- ExternalDataDAO.class);
-
- private static final String TABLE_NAME = ENTITY_CLASS.getSimpleName();
-
- ExternalDataDAO(final PersistencyResources persistencyResources,
- final DatabaseInstancePE databaseInstance)
- {
- super(persistencyResources, databaseInstance, ENTITY_CLASS);
- }
-
- //
- // IExternalDataDAO
- //
-
- public boolean hasExternalData(SamplePE sample) throws DataAccessException
- {
- final DetachedCriteria criteria = DetachedCriteria.forClass(ExternalDataPE.class);
- criteria.add(Restrictions.eq("sampleInternal", sample));
- criteria.setProjection(Projections.rowCount());
- Integer count = (Integer) getHibernateTemplate().findByCriteria(criteria).get(0);
- return count > 0;
- }
-
- public final List<ExternalDataPE> listRelatedExternalData(final IEntityInformationHolder entity)
- throws DataAccessException
- {
- assert entity != null : "Unspecified entity.";
-
- final String entityName = entity.getEntityKind().toString().toLowerCase();
- final String query =
- String.format("from %s e " + "left join fetch e.experimentInternal "
- + "left join fetch e.sampleInternal " + "left join fetch e.parents "
- + "left join fetch e.dataSetProperties " + "where e.%sInternal.id = ?",
- TABLE_NAME, entityName);
- final List<ExternalDataPE> list =
- cast(getHibernateTemplate().find(query, toArray(entity.getId())));
-
- // distinct does not work properly in HQL for left joins
- distinct(list);
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug(String.format("%d external data have been found for [entity=%s].",
- list.size(), entity));
- }
- return list;
- }
-
- public final List<ExternalDataPE> listExternalData(final SamplePE sample)
- throws DataAccessException
- {
- assert sample != null : "Unspecified sample.";
-
- final String query =
- String.format("from %s e " + "left join fetch e.experimentInternal "
- + "left join fetch e.parents " + "left join fetch e.dataSetProperties "
- + "where e.sampleInternal = ?", TABLE_NAME);
- final List<ExternalDataPE> list = cast(getHibernateTemplate().find(query, toArray(sample)));
-
- // distinct does not work properly in HQL for left joins
- distinct(list);
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug(String.format("%d external data have been found for [sample=%s].",
- list.size(), sample));
- }
- return list;
- }
-
- public final List<ExternalDataPE> listExternalData(final DataStorePE dataStore)
- throws DataAccessException
- {
- assert dataStore != null : "Unspecified data store.";
- final DetachedCriteria criteria = DetachedCriteria.forClass(ExternalDataPE.class);
- criteria.add(Restrictions.eq("dataStore", dataStore));
- final List<ExternalDataPE> list = cast(getHibernateTemplate().findByCriteria(criteria));
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug(String.format("%s(%s): %d data set(s) have been found.", MethodUtils
- .getCurrentMethod().getName(), dataStore, list.size()));
- }
- return list;
- }
-
- public final List<ExternalDataPE> listExternalData(final ExperimentPE experiment)
- throws DataAccessException
- {
- assert experiment != null : "Unspecified experiment.";
-
- final String query =
- String.format("from %s e " + "left join fetch e.experimentInternal "
- + "left join fetch e.parents " + "left join fetch e.dataSetProperties "
- + "where e.experimentInternal = ?", TABLE_NAME);
- final List<ExternalDataPE> list =
- cast(getHibernateTemplate().find(query, toArray(experiment)));
-
- // distinct does not work properly in HQL for left joins
- distinct(list);
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug(String.format(
- "%d external data have been found for [experiment=%s].", list.size(),
- experiment));
- }
- return list;
- }
-
- private void distinct(List<ExternalDataPE> list)
- {
- Set<ExternalDataPE> set = new TreeSet<ExternalDataPE>(list);
- list.clear();
- list.addAll(set);
- }
-
- public DataPE tryToFindDataSetByCode(String dataSetCode)
- {
- assert dataSetCode != null : "Unspecified data set code.";
-
- final String mangledCode = CodeConverter.tryToDatabase(dataSetCode);
- final Criterion codeEq = Restrictions.eq("code", mangledCode);
-
- final DetachedCriteria criteria = DetachedCriteria.forClass(ENTITY_SUPER_CLASS);
- criteria.add(codeEq);
- criteria.setFetchMode("dataSetType", FetchMode.JOIN);
- criteria.setFetchMode("dataStore", FetchMode.JOIN);
- criteria.setResultTransformer(DetachedCriteria.DISTINCT_ROOT_ENTITY);
- final List<DataPE> list = cast(getHibernateTemplate().findByCriteria(criteria));
- final DataPE entity = tryFindEntity(list, "data set");
-
- if (operationLog.isDebugEnabled())
- {
- String methodName = MethodUtils.getCurrentMethod().getName();
- operationLog.debug(String.format("%s(%s): '%s'.", methodName, dataSetCode, entity));
- }
- return entity;
- }
-
- public List<ExternalDataPE> tryToFindFullDataSetsByCodes(Collection<String> dataSetCodes,
- boolean withPropertyTypes, boolean lockForUpdate)
- {
- assert dataSetCodes != null : "Unspecified collection";
-
- if (dataSetCodes.size() == 0)
- {
- return Collections.emptyList();
- }
-
- final Criterion codeIn = Restrictions.in("code", dataSetCodes);
-
- final DetachedCriteria criteria = DetachedCriteria.forClass(ENTITY_CLASS);
- criteria.add(codeIn);
- criteria.setFetchMode("dataSetType", FetchMode.SELECT);
- criteria.setFetchMode("dataStore", FetchMode.SELECT);
- criteria.setFetchMode("experimentInternal", FetchMode.SELECT);
- criteria.setFetchMode("sampleInternal", FetchMode.SELECT);
- criteria.setFetchMode("fileFormat", FetchMode.SELECT);
- if (withPropertyTypes)
- {
- criteria.setFetchMode("dataSetType.dataSetTypePropertyTypesInternal", FetchMode.JOIN);
- }
- criteria.setResultTransformer(DetachedCriteria.DISTINCT_ROOT_ENTITY);
- if (lockForUpdate)
- {
- criteria.setLockMode(LockMode.UPGRADE);
- }
- final List<ExternalDataPE> list = cast(getHibernateTemplate().findByCriteria(criteria));
-
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug(String.format("Found '%s' data sets for codes '%s'.", list.size(),
- dataSetCodes));
- }
- return list;
- }
-
- public ExternalDataPE tryToFindFullDataSetByCode(String dataSetCode, boolean withPropertyTypes,
- boolean lockForUpdate)
- {
- assert dataSetCode != null : "Unspecified data set code";
-
- final String mangledCode = CodeConverter.tryToDatabase(dataSetCode);
- final Criterion codeEq = Restrictions.eq("code", mangledCode);
-
- final DetachedCriteria criteria = DetachedCriteria.forClass(ENTITY_CLASS);
- criteria.add(codeEq);
- criteria.setFetchMode("dataSetType", FetchMode.SELECT);
- criteria.setFetchMode("dataStore", FetchMode.SELECT);
- criteria.setFetchMode("experimentInternal", FetchMode.SELECT);
- criteria.setFetchMode("sampleInternal", FetchMode.SELECT);
- criteria.setFetchMode("fileFormat", FetchMode.SELECT);
- if (withPropertyTypes)
- {
- criteria.setFetchMode("dataSetType.dataSetTypePropertyTypesInternal", FetchMode.JOIN);
- }
- criteria.setResultTransformer(DetachedCriteria.DISTINCT_ROOT_ENTITY);
- if (lockForUpdate)
- {
- criteria.setLockMode(LockMode.UPGRADE);
- }
- final List<ExternalDataPE> list = cast(getHibernateTemplate().findByCriteria(criteria));
- final ExternalDataPE entity = tryFindEntity(list, "data set");
-
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug(String.format("External data '%s' found for data set code '%s'.",
- entity, dataSetCode));
- }
- return entity;
- }
-
- public void updateDataSetStatuses(final List<String> dataSetCodes,
- final DataSetArchivingStatus status)
- {
- assert dataSetCodes != null : "Unspecified data set codes";
- assert status != null : "Unspecified code";
-
- if (dataSetCodes.size() == 0)
- {
- return;
- }
-
- final HibernateTemplate hibernateTemplate = getHibernateTemplate();
- int updatedRows = (Integer) hibernateTemplate.execute(new HibernateCallback()
- {
-
- //
- // HibernateCallback
- //
-
- public final Object doInHibernate(final Session session) throws HibernateException,
- SQLException
- {
- // NOTE: 'VERSIONED' makes modification time modified too
- return session
- .createQuery(
- "UPDATE VERSIONED " + TABLE_NAME
- + " SET status = :status WHERE code IN (:codes) ")
- .setParameter("status", status).setParameterList("codes", dataSetCodes)
- .executeUpdate();
- }
- });
- hibernateTemplate.flush();
- if (updatedRows != dataSetCodes.size())
- {
- throw UserFailureException.fromTemplate("Update of %s data set statuses to %s failed.",
- dataSetCodes.size(), status);
- } else if (operationLog.isInfoEnabled())
- {
- operationLog.info(String.format("UPDATED: %s data set statuses to '%s'.",
- dataSetCodes.size(), status));
- }
- }
-
- public void updateDataSetStatuses(final List<String> dataSetCodes,
- final DataSetArchivingStatus status, final boolean presentInArchive)
- {
- assert dataSetCodes != null : "Unspecified data set codes";
- assert status != null : "Unspecified code";
-
- if (dataSetCodes.size() == 0)
- {
- return;
- }
-
- final HibernateTemplate hibernateTemplate = getHibernateTemplate();
- int updatedRows = (Integer) hibernateTemplate.execute(new HibernateCallback()
- {
-
- //
- // HibernateCallback
- //
-
- public final Object doInHibernate(final Session session) throws HibernateException,
- SQLException
- {
- // NOTE: 'VERSIONED' makes modification time modified too
- return session
- .createQuery(
- "UPDATE VERSIONED "
- + TABLE_NAME
- + " SET status = :status, presentInArchive = :presentInArchive"
- + " WHERE code IN (:codes) ")
- .setParameter("status", status)
- .setParameter("presentInArchive", presentInArchive)
- .setParameterList("codes", dataSetCodes).executeUpdate();
- }
- });
- hibernateTemplate.flush();
- if (updatedRows != dataSetCodes.size())
- {
- throw UserFailureException.fromTemplate(
- "Update of %s data set statuses to '%s' and presentInArchive to '%s' failed.",
- dataSetCodes.size(), status, presentInArchive);
- } else if (operationLog.isInfoEnabled())
- {
- operationLog.info(String.format(
- "UPDATED: %s data set statuses to '%s' and presentInArchive flag to '%s'.",
- dataSetCodes.size(), status, presentInArchive));
- }
- }
-
- public void createDataSet(DataPE dataset)
- {
- assert dataset != null : "Unspecified data set.";
-
- dataset.setCode(CodeConverter.tryToDatabase(dataset.getCode()));
- final HibernateTemplate template = getHibernateTemplate();
- if (operationLog.isInfoEnabled())
- {
- operationLog.info(String.format("ADD BEFORE SAVE: data set id '%d'.",
- HibernateUtils.getId(dataset)));
- }
- template.save(dataset);
- if (operationLog.isInfoEnabled())
- {
- operationLog.info(String.format("ADD BEFORE FLUSH: data set id '%d'.",
- HibernateUtils.getId(dataset)));
- }
-
- template.flush();
-
- if (dataset instanceof ExternalDataPE)
- {
- scheduleDynamicPropertiesEvaluation(Collections.singletonList((ExternalDataPE) dataset));
- }
-
- if (operationLog.isInfoEnabled())
- {
- operationLog.info(String.format("ADD: data set '%s'.", dataset));
- }
- }
-
- public void updateDataSet(ExternalDataPE externalData)
- {
- assert externalData != null : "Given external data can not be null.";
- validatePE(externalData);
-
- final HibernateTemplate hibernateTemplate = getHibernateTemplate();
- externalData.setCode(CodeConverter.tryToDatabase(externalData.getCode()));
- Long id = HibernateUtils.getId(externalData);
- final DataPE loaded = (DataPE) hibernateTemplate.load(ENTITY_CLASS, id);
- // This just means that we do not have any entry in 'EXTERNAL_DATA' table for this id. It
- // might happen when we work with placeholder data.
- if (loaded instanceof ExternalDataPE == false)
- {
- String shareId = externalData.getShareId();
- String location = externalData.getLocation();
- Long size = externalData.getSize();
- Long locatorTypeID = externalData.getLocatorType().getId();
- Long fileFormatTypeID = externalData.getFileFormatType().getId();
- char complete = externalData.getComplete().name().charAt(0);
- Long storageFormatTermID = externalData.getStorageFormatVocabularyTerm().getId();
- if (size == null)
- {
- executeUpdate(
- "insert into "
- + TableNames.EXTERNAL_DATA_TABLE
- + " (data_id, share_id, location, loty_id, ffty_id, is_complete, cvte_id_stor_fmt) "
- + "values (?, ?, ?, ?, ?, ?, ?)", id, shareId, location,
- locatorTypeID, fileFormatTypeID, complete, storageFormatTermID);
- } else
- {
- executeUpdate(
- "insert into "
- + TableNames.EXTERNAL_DATA_TABLE
- + " (data_id, share_id, location, size, loty_id, ffty_id, is_complete, cvte_id_stor_fmt) "
- + "values (?, ?, ?, ?, ?, ?, ?, ?)", id, shareId, location, size,
- locatorTypeID, fileFormatTypeID, complete, storageFormatTermID);
- }
- hibernateTemplate.evict(loaded);
- }
- hibernateTemplate.update(externalData);
- hibernateTemplate.flush();
- scheduleDynamicPropertiesEvaluation(Collections.singletonList(externalData));
-
- if (operationLog.isInfoEnabled())
- {
- operationLog.info(String.format("UPDATE: external data '%s'.", externalData));
- }
- }
-
- @Override
- public void delete(ExternalDataPE entity) throws DataAccessException
- {
- assert entity != null : "entity unspecified";
- if (entity.getChildren().size() > 0)
- {
- throw new DataIntegrityViolationException(
- String.format(
- "External Data '%s' cannot be deleted because children datasets are connected.",
- entity.getCode()));
- }
- super.delete(entity);
- }
-
- @SuppressWarnings("unchecked")
- public Set<TechId> findParentIds(final Collection<TechId> dataSetIds)
- {
- // Native SQL query is used to be able to query on 'many-to-many association table -
- // - 'data_set_relationships' without join with 'data' table involved in this association.
- // Drawback of this solution is that instead of list of Long values we get list of
- // BigIntegers and so a transformation is needed.
-
- final String query =
- "select data_id_parent from data_set_relationships where data_id_child in (:ids)";
- final List<? extends Number> results =
- (List<? extends Number>) getHibernateTemplate().execute(new HibernateCallback()
- {
-
- //
- // HibernateCallback
- //
-
- public final Object doInHibernate(final Session session)
- {
- // we could remove this transformation if we choose to pass Long values
- final List<Long> longIds = TechId.asLongs(dataSetIds);
- return session.createSQLQuery(query).setParameterList("ids", longIds)
- .list();
- }
- });
- return transformNumbers2TechIdSet(results);
- }
-
- // data set relationship helper methods
-
- public List<ExternalDataPE> listByCode(Set<String> values)
- {
- if (values == null || values.isEmpty())
- {
- return new ArrayList<ExternalDataPE>();
- }
- final DetachedCriteria criteria = DetachedCriteria.forClass(ExternalDataPE.class);
- criteria.add(Restrictions.in("code", values));
- final List<ExternalDataPE> list = cast(getHibernateTemplate().findByCriteria(criteria));
- if (operationLog.isDebugEnabled())
- {
- operationLog.debug(String.format("%d data set(s) have been found.", list.size()));
- }
- return list;
- }
-
- public void updateDataSets(List<ExternalDataPE> externalData)
- {
- assert externalData != null : "Data sets not defined";
-
- final HibernateTemplate hibernateTemplate = getHibernateTemplate();
- for (ExternalDataPE ed : externalData)
- {
- validatePE(ed);
- ed.setCode(CodeConverter.tryToDatabase(ed.getCode()));
- hibernateTemplate.saveOrUpdate(ed);
- }
-
- if (operationLog.isInfoEnabled())
- {
- operationLog.info(String.format("UPDATE: %d data sets.", externalData.size()));
- }
-
- flushWithSqlExceptionHandling(getHibernateTemplate());
- scheduleDynamicPropertiesEvaluation(externalData);
-
- // if session is not cleared registration of many samples slows down after each batch
- hibernateTemplate.clear();
- }
-
- @Override
- public final void validateAndSaveUpdatedEntity(ExternalDataPE entity)
- throws DataAccessException
- {
- super.validateAndSaveUpdatedEntity(entity);
- scheduleDynamicPropertiesEvaluation(Arrays.asList(entity));
- }
-
- @Override
- Logger getLogger()
- {
- return operationLog;
- }
-
-}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
index 064ab4c86b7..90260a91c69 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
@@ -743,4 +743,12 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public List<String> getTrustedCrossOriginDomains(String sessionToken);
+ /**
+ * Marks the storage of dataset as confirmed.
+ */
+ @Transactional
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ @DatabaseUpdateModification(value =
+ { ObjectKind.DATA_SET })
+ public void setStorageConfirmed(String sessionToken, String dataSetCode);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
index 9b21f342c16..8f8279f6d72 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
@@ -83,7 +83,7 @@ public final class ExternalDataPE extends DataPE
// TODO: Storage confirmation should be set to false.
// At the moment however the logic is not yet implemented, and we want all objects in database
// to have true initialy.
- private boolean storageConfirmation = true;
+ private boolean storageConfirmation = false;
private int speedHint = Constants.DEFAULT_SPEED_HINT;
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 ed009330ba9..7105227aea7 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
@@ -1139,6 +1139,13 @@ public class ETLServiceTest extends AbstractServerTestCase
context.assertIsSatisfied();
}
+ public void testDataSetCofirmation()
+ {
+ // TODO:kuba
+ // call etlservice method setStorageConfirmed
+ // make sure the method setstorageConfirmed was claled on the databo object
+ }
+
private SearchCriteria createSearchCriteriaForSample()
{
SearchCriteria sc = new SearchCriteria();
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 ec508efd4ec..3093d0e7d38 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
@@ -935,6 +935,18 @@ public class DataBOTest extends AbstractBOTest
context.assertIsSatisfied();
}
+ public void testStorageConfirmed()
+ {
+ // TODO:KUBA
+ // create a new data object with external data.
+ // check that externaldataPE has isstorage confirmed set to false
+
+ // call dataBo. setstorageconfirmed on this instance of external data
+
+ // check that the isstorage confirmed is now true on this element
+
+ }
+
@SuppressWarnings("unchecked")
private void expectMandatoryPropertiesCheck(Expectations exp, final DataSetTypePE type)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
index 064ab4c86b7..90260a91c69 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java.expected
@@ -743,4 +743,12 @@ public interface IETLLIMSService extends IServer, ISessionProvider
@RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
public List<String> getTrustedCrossOriginDomains(String sessionToken);
+ /**
+ * Marks the storage of dataset as confirmed.
+ */
+ @Transactional
+ @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
+ @DatabaseUpdateModification(value =
+ { ObjectKind.DATA_SET })
+ public void setStorageConfirmed(String sessionToken, String dataSetCode);
}
--
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