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 fbaea4cd2629722cc57fa5d20bebda84a5f19350..781494c0e1867a05717d5784bd2d17efd1c765de 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
@@ -62,15 +62,12 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
public final class CommonBusinessObjectFactory extends AbstractBusinessObjectFactory implements
ICommonBusinessObjectFactory
{
- public CommonBusinessObjectFactory(final IDAOFactory daoFactory)
+
+ public CommonBusinessObjectFactory(IDAOFactory daoFactory, IDataStoreServiceFactory dssFactory)
{
- super(daoFactory);
+ super(daoFactory, dssFactory);
}
- //
- // IGenericBusinessObjectFactory
- //
-
public final IGroupBO createGroupBO(final Session session)
{
return new GroupBO(getDaoFactory(), session);
@@ -98,7 +95,7 @@ public final class CommonBusinessObjectFactory extends AbstractBusinessObjectFac
public final IExternalDataTable createExternalDataTable(final Session session)
{
- return new ExternalDataTable(getDaoFactory(), session);
+ return new ExternalDataTable(getDaoFactory(), getDSSFactory(), session);
}
public IExperimentTable createExperimentTable(final Session 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 6d655aa1ab9cfcb981e2579f5f1ec8673881dcf6..79a611a3a2de2d058dfe4691fbdd669f98c421ac 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
@@ -31,7 +31,6 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.authentication.Principal;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.DataStoreServerSessionManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypePropertyTypeBO;
@@ -113,19 +112,15 @@ public final class CommonServer extends AbstractServer<ICommonServer> implements
private final ICommonBusinessObjectFactory businessObjectFactory;
- private final DataStoreServerSessionManager dssSessionManager;
-
private final LastModificationState lastModificationState;
public CommonServer(final IAuthenticationService authenticationService,
- final ISessionManager<Session> sessionManager,
- DataStoreServerSessionManager dssSessionManager, final IDAOFactory daoFactory,
+ final ISessionManager<Session> sessionManager, final IDAOFactory daoFactory,
final ICommonBusinessObjectFactory businessObjectFactory,
LastModificationState lastModificationState)
{
super(sessionManager, daoFactory);
this.authenticationService = authenticationService;
- this.dssSessionManager = dssSessionManager;
this.businessObjectFactory = businessObjectFactory;
this.lastModificationState = lastModificationState;
}
@@ -646,7 +641,7 @@ public final class CommonServer extends AbstractServer<ICommonServer> implements
{
DataSetTypePE dataSetType = entry.getKey();
IDataSetTypeSlaveServerPlugin plugin = getDataSetTypeSlaveServerPlugin(dataSetType);
- plugin.deleteDataSets(session, dssSessionManager, entry.getValue(), reason);
+ plugin.deleteDataSets(session, entry.getValue(), reason);
}
} catch (final DataAccessException ex)
{
@@ -663,7 +658,7 @@ public final class CommonServer extends AbstractServer<ICommonServer> implements
IExternalDataTable externalDataTable =
businessObjectFactory.createExternalDataTable(session);
externalDataTable.loadByDataSetCodes(dataSetCodes);
- externalDataTable.uploadLoadedDataSetsToCIFEX(dssSessionManager, uploadContext);
+ externalDataTable.uploadLoadedDataSetsToCIFEX(uploadContext);
} catch (final DataAccessException ex)
{
throw createUserFailureException(ex);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ComponentNames.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ComponentNames.java
index adf1e4c8c61e2d89ef86412567385f0d8919299e..e54907126cbc3c26692880626b6feae2d20d1a8c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ComponentNames.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ComponentNames.java
@@ -36,6 +36,8 @@ public final class ComponentNames
public static final String LOG_INTERCEPTOR = "log-interceptor";
public static final String DAO_FACTORY = "dao-factory";
+
+ public static final String DSS_FACTORY = "dss-factory";
public static final String COMMON_BUSINESS_OBJECT_FACTORY = "common-business-object-factory";
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/DataStoreServiceFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/DataStoreServiceFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..0087c4223b9749fd1bc160f048ccdda5ac40f081
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/DataStoreServiceFactory.java
@@ -0,0 +1,48 @@
+/*
+ * 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;
+
+import static ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants.DATA_STORE_SERVER_SERVICE_NAME;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
+import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
+
+/**
+ * Factory of cached {@link IDataStoreService} instances.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataStoreServiceFactory implements IDataStoreServiceFactory
+{
+ private final Map<String, IDataStoreService> services = new HashMap<String, IDataStoreService>();
+
+ public IDataStoreService create(String serverURL)
+ {
+ IDataStoreService service = services.get(serverURL);
+ if (service == null)
+ {
+ service = HttpInvokerUtils.createServiceStub(IDataStoreService.class, serverURL + "/"
+ + DATA_STORE_SERVER_SERVICE_NAME, 5);
+ services.put(serverURL, service);
+ }
+ return service;
+ }
+
+}
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 e75e88a6e376c87a3998f5ec61a62f993049b43f..f1deabd587ba42cc956e31ce6e4dd2ac087da9d2 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
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.openbis.generic.server;
-import static ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants.DATA_STORE_SERVER_SERVICE_NAME;
-
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.List;
@@ -27,18 +25,18 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
import ch.systemsx.cisd.common.utilities.BeanUtils;
-import ch.systemsx.cisd.openbis.generic.server.business.DataStoreServerSessionManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
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.dataaccess.IAttachmentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.IWebService;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
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.ExternalData;
@@ -72,36 +70,17 @@ public class ETLService extends AbstractServer<IETLService> implements IETLServi
private final ISessionManager<Session> sessionManager;
- private final DataStoreServerSessionManager dssSessionManager;
-
private final IDAOFactory daoFactory;
private final ICommonBusinessObjectFactory boFactory;
private final IDataStoreServiceFactory dssFactory;
- public ETLService(ISessionManager<Session> sessionManager,
- DataStoreServerSessionManager dssSessionManager, IDAOFactory daoFactory,
- ICommonBusinessObjectFactory boFactory)
- {
- this(sessionManager, dssSessionManager, daoFactory, boFactory,
- new IDataStoreServiceFactory()
- {
- public IDataStoreService create(String serverURL)
- {
- return HttpInvokerUtils.createServiceStub(IDataStoreService.class,
- serverURL + "/" + DATA_STORE_SERVER_SERVICE_NAME, 5);
- }
- });
- }
-
- ETLService(ISessionManager<Session> sessionManager,
- DataStoreServerSessionManager dssSessionManager, IDAOFactory daoFactory,
+ public ETLService(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
ICommonBusinessObjectFactory boFactory, IDataStoreServiceFactory dssFactory)
{
super(sessionManager, daoFactory);
this.sessionManager = sessionManager;
- this.dssSessionManager = dssSessionManager;
this.daoFactory = daoFactory;
this.boFactory = boFactory;
this.dssFactory = dssFactory;
@@ -129,13 +108,17 @@ public class ETLService extends AbstractServer<IETLService> implements IETLServi
return daoFactory.getHomeDatabaseInstance();
}
- public void registerDataStoreServer(String sessionToken, int port, final String dssSessionToken)
+ public void registerDataStoreServer(String sessionToken, DataStoreServerInfo info)
{
Session session = sessionManager.getSession(sessionToken);
+
+ String dssSessionToken = info.getSessionToken();
String remoteHost = session.getRemoteHost();
+ int port = info.getPort();
final String dssURL = "https://" + remoteHost + ":" + port;
- DataStoreServerSession dssSession = dssSessionManager.tryToGetSession(dssURL);
- if (dssSession == null)
+ IDataStoreDAO dataStoreDAO = daoFactory.getDataStoreDAO();
+ DataStorePE dataStore = dataStoreDAO.tryToFindDataStoreByCode(info.getDataStoreCode());
+ if (dataStore == null)
{
final IDataStoreService service = dssFactory.create(dssURL);
if (operationLog.isInfoEnabled())
@@ -146,8 +129,8 @@ public class ETLService extends AbstractServer<IETLService> implements IETLServi
if (IDataStoreService.VERSION != dssVersion)
{
String msg =
- "Data Store Server version is " + dssVersion + " instead of "
- + IDataStoreService.VERSION;
+ "Data Store Server version is " + dssVersion + " instead of "
+ + IDataStoreService.VERSION;
notificationLog.error(msg);
throw new ConfigurationFailureException(msg);
}
@@ -156,10 +139,14 @@ public class ETLService extends AbstractServer<IETLService> implements IETLServi
operationLog.info("Data Store Server (version " + dssVersion + ") registered for "
+ dssURL);
}
- dssSession = new DataStoreServerSession(dssURL, service);
- dssSessionManager.registerDataStoreServer(dssSession);
+ dataStore = new DataStorePE();
+ dataStore.setDatabaseInstance(getHomeDatabaseInstance(sessionToken));
}
- dssSession.setSessionToken(dssSessionToken);
+ dataStore.setCode(info.getDataStoreCode());
+ dataStore.setDownloadUrl(info.getDownloadUrl());
+ dataStore.setRemoteUrl(dssURL);
+ dataStore.setSessionToken(dssSessionToken);
+ dataStoreDAO.createOrUpdateDataStore(dataStore);
}
public String authenticate(String user, String password) throws UserFailureException
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 d556cc0df852908e2de64664dd32ddcad706a5f8..ef606f9a8be9b252e0138ee15e2223d1cb176257 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
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.generic.server;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
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.ExternalData;
@@ -50,10 +51,15 @@ public class ETLServiceLogger extends AbstractServerLogger implements IETLServic
return null;
}
- public void registerDataStoreServer(String sessionToken, int port, String dssSessionToken)
+ public void registerDataStoreServer(String sessionToken, DataStoreServerInfo info)
{
- logTracking(sessionToken, "register_data_store_server_session_token", "PORT(%s) DSS-TOKEN(%s)",
- port, dssSessionToken);
+ String code = info.getDataStoreCode();
+ String downloadUrl = info.getDownloadUrl();
+ int port = info.getPort();
+ String dssSessionToken = info.getSessionToken();
+ logTracking(sessionToken, "register_data_store_server_session_token",
+ "CODE(%s) DOWNLOAD-URL(%s) PORT(%s) DSS-TOKEN(%s)", code, downloadUrl, port,
+ dssSessionToken);
}
public void registerDataSet(String sessionToken, SampleIdentifier sampleIdentifier,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/DataStoreServerSessionManager.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/DataStoreServerSessionManager.java
deleted file mode 100644
index 6dc593f3256501900a34ba3d1a8191ca19a72f85..0000000000000000000000000000000000000000
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/DataStoreServerSessionManager.java
+++ /dev/null
@@ -1,70 +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;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
-
-/**
- * Class managing Data Store Server (DSS) sessions. It is assumed that the URL of the DSS is unique
- * in order to allow more than one DSS.
- *
- * @author Franz-Josef Elmer
- */
-public class DataStoreServerSessionManager
-{
- private final Map<String, DataStoreServerSession> sessions = new HashMap<String, DataStoreServerSession>();
-
- /**
- * Registers the specified DSS session.
- */
- public void registerDataStoreServer(DataStoreServerSession session)
- {
- synchronized (sessions)
- {
- sessions.put(session.getDataStoreServerURL(), session);
- }
- }
-
- /**
- * Tries to get the DSS session identified by the specified Data Store Server URL.
- *
- * @return <code>null</code> if no session has been registered for the specified URL.
- */
- public DataStoreServerSession tryToGetSession(String dssURL)
- {
- synchronized (sessions)
- {
- return sessions.get(dssURL);
- }
- }
-
- /**
- * Returns all registered DSS sessions.
- */
- public Collection<DataStoreServerSession> getSessions()
- {
- synchronized (sessions)
- {
- return new ArrayList<DataStoreServerSession>(sessions.values());
- }
- }
-}
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 2742676ee63fc925baa9f66e975f3fd7d786e8f5..0f0ea0de0f83e9a700772ab15900f8ea979eb22d 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
@@ -21,6 +21,7 @@ import org.springframework.dao.DataAccessException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSetTypeDAO;
+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.IEntityPropertyTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
@@ -197,4 +198,9 @@ abstract class AbstractBusinessObject implements IDAOFactory
{
return daoFactory.getCodeSequenceDAO();
}
+
+ public IDataStoreDAO getDataStoreDAO()
+ {
+ return daoFactory.getDataStoreDAO();
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObjectFactory.java
index 2ba222d2d596aa9630b5ccf00981d7affd607749..d7413f838d52273028cd7e36fc4e3a7b7fe36994 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractBusinessObjectFactory.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo;
import javax.annotation.Resource;
import ch.systemsx.cisd.openbis.generic.server.ComponentNames;
+import ch.systemsx.cisd.openbis.generic.server.IDataStoreServiceFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
/**
@@ -30,18 +31,27 @@ public abstract class AbstractBusinessObjectFactory
{
@Resource(name = ComponentNames.DAO_FACTORY)
private IDAOFactory daoFactory;
+
+ @Resource(name = ComponentNames.DSS_FACTORY)
+ private IDataStoreServiceFactory dssFactory;
protected AbstractBusinessObjectFactory()
{
}
- protected AbstractBusinessObjectFactory(final IDAOFactory daoFactory)
+ protected AbstractBusinessObjectFactory(final IDAOFactory daoFactory, IDataStoreServiceFactory dssFactory)
{
this.daoFactory = daoFactory;
+ this.dssFactory = dssFactory;
}
protected final IDAOFactory getDaoFactory()
{
return daoFactory;
}
+
+ protected final IDataStoreServiceFactory getDSSFactory()
+ {
+ return dssFactory;
+ }
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
index f954a03f56126158cff8db8d9d64300af97c82a1..8ab996f977bcab55af0bd88afbdf88b724b05a13 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
@@ -115,6 +115,7 @@ public class ExternalDataBO extends AbstractExternalDataBusinessObject implement
.getStorageFormat()));
externalData.setLocatorType(getLocatorTypeDAO().tryToFindLocatorTypeByCode(
locatorType.getCode()));
+ externalData.setDataStore(getDataStoreDAO().tryToFindDataStoreByCode(data.getDataStoreCode()));
defineDataSetProperties(externalData, convertToDataSetProperties(data
.getDataSetProperties()));
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
index c3854676661ed1cdfb4411204b56296f5c745670..1010523250504d32a32de2bd1f28c0a3d12cc305 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTable.java
@@ -17,23 +17,24 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.ArrayList;
-import java.util.Collection;
+import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
+import java.util.Map;
import java.util.Set;
import org.apache.commons.lang.StringUtils;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.DataStoreServerSessionManager;
+import ch.systemsx.cisd.openbis.generic.server.IDataStoreServiceFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
+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.ProjectPE;
@@ -84,12 +85,15 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
return builder.toString();
}
+ private final IDataStoreServiceFactory dssFactory;
private List<ExternalDataPE> externalData;
- public ExternalDataTable(final IDAOFactory daoFactory, final Session session)
+ public ExternalDataTable(final IDAOFactory daoFactory, IDataStoreServiceFactory dssFactory,
+ final Session session)
{
super(daoFactory, session);
+ this.dssFactory = dssFactory;
}
//
@@ -157,63 +161,62 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
}
}
- public void deleteLoadedDataSets(DataStoreServerSessionManager dssSessionManager, String reason)
+ public void deleteLoadedDataSets(String reason)
{
- assertDataSetsAreKnown(dssSessionManager);
- for (ExternalDataPE dataSet : externalData)
- {
- IExternalDataDAO externalDataDAO = getExternalDataDAO();
- externalDataDAO.markAsDeleted(dataSet, session.tryGetPerson(), DELETION_DESCRIPTION, reason);
- }
- Collection<DataStoreServerSession> sessions = dssSessionManager.getSessions();
- List<String> locations = getLocations();
- for (DataStoreServerSession dssSession : sessions)
+ Map<DataStorePE, List<ExternalDataPE>> map = groupDataSetsByDataStores();
+ assertDataSetsAreKnown(map);
+ IExternalDataDAO externalDataDAO = getExternalDataDAO();
+ for (Map.Entry<DataStorePE, List<ExternalDataPE>> entry : map.entrySet())
{
- dssSession.getService().deleteDataSets(dssSession.getSessionToken(), locations);
+ DataStorePE dataStore = entry.getKey();
+ List<ExternalDataPE> dataSets = entry.getValue();
+ for (ExternalDataPE dataSet : dataSets)
+ {
+ externalDataDAO.markAsDeleted(dataSet, session.tryGetPerson(), DELETION_DESCRIPTION, reason);
+ }
+ deleteDataSets(dataStore, getLocations(dataSets));
}
}
- public void uploadLoadedDataSetsToCIFEX(DataStoreServerSessionManager dssSessionManager,
- DataSetUploadContext uploadContext)
+ public void uploadLoadedDataSetsToCIFEX(DataSetUploadContext uploadContext)
{
- assertDataSetsAreKnown(dssSessionManager);
- Collection<DataStoreServerSession> sessions = dssSessionManager.getSessions();
+ Map<DataStorePE, List<ExternalDataPE>> map = groupDataSetsByDataStores();
+ assertDataSetsAreKnown(map);
uploadContext.setUserEMail(session.getPrincipal().getEmail());
if (StringUtils.isBlank(uploadContext.getComment()))
{
uploadContext.setComment(createUploadComment(externalData));
}
- for (ExternalDataPE dataSet : externalData)
+ for (Map.Entry<DataStorePE, List<ExternalDataPE>> entry : map.entrySet())
{
- HibernateUtils.initialize(dataSet.getParents());
- SamplePE sample = dataSet.getAssociatedSample();
- ExperimentPE experiment;
- if (sample != null)
+ DataStorePE dataStore = entry.getKey();
+ List<ExternalDataPE> dataSets = entry.getValue();
+ for (ExternalDataPE dataSet : dataSets)
{
- experiment = sample.getExperiment();
- } else
- {
- experiment = dataSet.getExperiment();
+ HibernateUtils.initialize(dataSet.getParents());
+ SamplePE sample = dataSet.getAssociatedSample();
+ ExperimentPE experiment;
+ if (sample != null)
+ {
+ experiment = sample.getExperiment();
+ } else
+ {
+ experiment = dataSet.getExperiment();
+ }
+ HibernateUtils.initialize(experiment.getProject().getGroup());
}
- HibernateUtils.initialize(experiment.getProject().getGroup());
- }
- for (DataStoreServerSession dssSession : sessions)
- {
- dssSession.getService().uploadDataSetsToCIFEX(dssSession.getSessionToken(), externalData,
- uploadContext);
+ uploadDataSetsToCIFEX(dataStore, dataSets, uploadContext);
}
}
- private void assertDataSetsAreKnown(DataStoreServerSessionManager dssSessionManager)
+ private void assertDataSetsAreKnown(Map<DataStorePE, List<ExternalDataPE>> map)
{
- List<String> locations = getLocations();
Set<String> knownLocations = new LinkedHashSet<String>();
- Collection<DataStoreServerSession> sessions = dssSessionManager.getSessions();
- for (DataStoreServerSession dssSession : sessions)
+ for (Map.Entry<DataStorePE, List<ExternalDataPE>> entry : map.entrySet())
{
- IDataStoreService service = dssSession.getService();
- String dssSessionToken = dssSession.getSessionToken();
- knownLocations.addAll(service.getKnownDataSets(dssSessionToken, locations));
+ DataStorePE dataStore = entry.getKey();
+ List<String> locations = getLocations(entry.getValue());
+ knownLocations.addAll(getKnownDataSets(dataStore, locations));
}
List<String> unknownDataSets = new ArrayList<String>();
for (ExternalDataPE dataSet : externalData)
@@ -232,13 +235,52 @@ public final class ExternalDataTable extends AbstractExternalDataBusinessObject
}
}
- private List<String> getLocations()
+ private Map<DataStorePE, List<ExternalDataPE>> groupDataSetsByDataStores()
{
- List<String> locations = new ArrayList<String>();
+ Map<DataStorePE, List<ExternalDataPE>> map = new LinkedHashMap<DataStorePE, List<ExternalDataPE>>();
for (ExternalDataPE dataSet : externalData)
+ {
+ DataStorePE dataStore = dataSet.getDataStore();
+ List<ExternalDataPE> list = map.get(dataStore);
+ if (list == null)
+ {
+ list = new ArrayList<ExternalDataPE>();
+ map.put(dataStore, list);
+ }
+ list.add(dataSet);
+ }
+ return map;
+ }
+
+ private List<String> getLocations(List<ExternalDataPE> dataSets)
+ {
+ List<String> locations = new ArrayList<String>();
+ for (ExternalDataPE dataSet : dataSets)
{
locations.add(dataSet.getLocation());
}
return locations;
}
+
+ private void uploadDataSetsToCIFEX(DataStorePE dataStore, List<ExternalDataPE> dataSets,
+ DataSetUploadContext context)
+ {
+ IDataStoreService service = dssFactory.create(dataStore.getRemoteUrl());
+ String sessionToken = dataStore.getSessionToken();
+ service.uploadDataSetsToCIFEX(sessionToken, dataSets, context);
+ }
+
+ private void deleteDataSets(DataStorePE dataStore, List<String> locations)
+ {
+ IDataStoreService service = dssFactory.create(dataStore.getRemoteUrl());
+ String sessionToken = dataStore.getSessionToken();
+ service.deleteDataSets(sessionToken, locations);
+ }
+
+ private List<String> getKnownDataSets(DataStorePE dataStore, List<String> locations)
+ {
+ IDataStoreService service = dssFactory.create(dataStore.getRemoteUrl());
+ String sessionToken = dataStore.getSessionToken();
+ return service.getKnownDataSets(sessionToken, locations);
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java
index d9d1a91dc82e6d4d6889f1217776506bd5e7b774..14796d990b23c3f0a537d859fa25fb253c97d84e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataTable.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.List;
-import ch.systemsx.cisd.openbis.generic.server.business.DataStoreServerSessionManager;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
@@ -58,16 +57,13 @@ public interface IExternalDataTable
void setExternalData(List<ExternalDataPE> externalData);
/**
- * Deletes loaded data sets for specified reason on all Data Store Servers registered
- * at specified manager.
+ * Deletes loaded data sets for specified reason.
*/
- void deleteLoadedDataSets(DataStoreServerSessionManager dssSessionManager, String reason);
+ void deleteLoadedDataSets(String reason);
/**
- * Uploads loaded data sets to CIFEX server of specified URL using specified upload
- * context.
+ * Uploads loaded data sets to CIFEX server as specified in the upload context.
*/
- void uploadLoadedDataSetsToCIFEX(DataStoreServerSessionManager dssSessionManager,
- DataSetUploadContext uploadContext);
+ void uploadLoadedDataSetsToCIFEX(DataSetUploadContext uploadContext);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDAOFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDAOFactory.java
index a9afc29f50e27a213b273675f50607d0bc8f9080..ca0672a77d7b85c25ce826dcfa28d2262508a682 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDAOFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDAOFactory.java
@@ -91,5 +91,8 @@ public interface IDAOFactory extends IAuthorizationDAOFactory
/** Returns an implementation of {@link ICodeSequenceDAO} */
public ICodeSequenceDAO getCodeSequenceDAO();
+
+ /** Returns an implementation of {@link IDataStoreDAO}. */
+ public IDataStoreDAO getDataStoreDAO();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataStoreDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataStoreDAO.java
new file mode 100644
index 0000000000000000000000000000000000000000..8463e7abf8274289e0738416591c05259d249e46
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataStoreDAO.java
@@ -0,0 +1,37 @@
+/*
+ * 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.dataaccess;
+
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+
+/**
+ * <i>Data Access Object</i> for {@link DataStorePE}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IDataStoreDAO
+{
+ /**
+ * Creates or updates specified data store.
+ */
+ public void createOrUpdateDataStore(DataStorePE dataStore);
+
+ /**
+ * Tries to returns specified data store or <code>null</code> if not found.
+ */
+ public DataStorePE tryToFindDataStoreByCode(String dataStoreCode);
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java
index 459058f29b8f6e8b096c5a2ec9cbdd2d21ef2464..73d4c8b3bbf6cfe448351caaee45cd7a2b98a79b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DAOFactory.java
@@ -24,6 +24,7 @@ import org.hibernate.SessionFactory;
import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSetTypeDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
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.IAttachmentDAO;
@@ -79,6 +80,8 @@ public final class DAOFactory extends AuthorizationDAOFactory implements IDAOFac
private final IMaterialDAO materialDAO;
private final ICodeSequenceDAO codeSequenceDAO;
+
+ private final IDataStoreDAO dataStoreDAO;
public DAOFactory(final DatabaseConfigurationContext context,
final SessionFactory sessionFactory)
@@ -98,6 +101,7 @@ public final class DAOFactory extends AuthorizationDAOFactory implements IDAOFac
locatorTypeDAO = new LocatorTypeDAO(sessionFactory, databaseInstance);
materialDAO = new MaterialDAO(sessionFactory, databaseInstance);
codeSequenceDAO = new CodeSequenceDAO(sessionFactory, databaseInstance);
+ dataStoreDAO = new DataStoreDAO(sessionFactory, databaseInstance);
final EntityKind[] entityKinds = EntityKind.values();
for (final EntityKind entityKind : entityKinds)
{
@@ -187,4 +191,9 @@ public final class DAOFactory extends AuthorizationDAOFactory implements IDAOFac
{
return codeSequenceDAO;
}
+
+ public IDataStoreDAO getDataStoreDAO()
+ {
+ return dataStoreDAO;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataStoreDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataStoreDAO.java
new file mode 100644
index 0000000000000000000000000000000000000000..c868b2c5a9a013664a9c44a7008a831b660d4ca5
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataStoreDAO.java
@@ -0,0 +1,69 @@
+/*
+ * 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.dataaccess.db;
+
+import org.apache.log4j.Logger;
+import org.hibernate.Criteria;
+import org.hibernate.SessionFactory;
+import org.hibernate.criterion.Restrictions;
+import org.springframework.orm.hibernate3.HibernateTemplate;
+
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.CodeConverter;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+
+/**
+ * Hibernate-based implementation of {@link IDataStoreDAO}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataStoreDAO extends AbstractDAO implements IDataStoreDAO
+{
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, DataStoreDAO.class);
+
+ public DataStoreDAO(SessionFactory sessionFactory, DatabaseInstancePE databaseInstance)
+ {
+ super(sessionFactory, databaseInstance);
+ }
+
+ public void createOrUpdateDataStore(DataStorePE dataStore)
+ {
+ assert dataStore != null : "Unspecified data store";
+
+ HibernateTemplate template = getHibernateTemplate();
+ template.saveOrUpdate(dataStore);
+ template.flush();
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info(String.format("SAVE/UPDATE: data store '%s'.", dataStore));
+ }
+ }
+
+ public DataStorePE tryToFindDataStoreByCode(String dataStoreCode)
+ {
+ assert dataStoreCode != null : "Unspecified data store code.";
+
+ final Criteria criteria = getSession().createCriteria(DataStorePE.class);
+ criteria.add(Restrictions.eq("code", CodeConverter.tryToDatabase(dataStoreCode)));
+ return (DataStorePE) criteria.uniqueResult();
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetTypeSlaveServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetTypeSlaveServerPlugin.java
index 7f8bf05d36f1ebecd73c4966d1830c9da712af15..491aef5de97d9a6bb4d0e7888ab94b029fbab711 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetTypeSlaveServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/plugin/IDataSetTypeSlaveServerPlugin.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.generic.server.plugin;
import java.util.List;
-import ch.systemsx.cisd.openbis.generic.server.business.DataStoreServerSessionManager;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.DAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -36,10 +35,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
public interface IDataSetTypeSlaveServerPlugin
{
/**
- * Deletes the specified data sets for the specified reason on all Data Store Servers
- * managed by the specifed DSS manager.
+ * Deletes the specified data sets for the specified reason.
*/
- public void deleteDataSets(Session session, DataStoreServerSessionManager dssSessionManager,
- List<ExternalDataPE> dataSets, String reason);
+ public void deleteDataSets(Session session, List<ExternalDataPE> dataSets, String reason);
}
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 168f9c59fcceaf557541d62bdde55264cc9c72fa..b71514b52150fdc2c85a8791b4bf7d5f637ba6c5 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
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared;
-import javax.servlet.http.HttpServletRequest;
-
import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -26,6 +24,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.Authoriz
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleOwnerIdentifierPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
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.ExternalData;
@@ -49,13 +48,11 @@ public interface IETLLIMSService extends IWebService, ISessionProvider
public DatabaseInstancePE getHomeDatabaseInstance(final String sessionToken);
/**
- * Registers a Data Store Server for the specified port and DSS session token.
- * It should be reachable via this port and the DSS session token should be used when invoking
- * methods. Note, that the host can be inferred by the asking {@link HttpServletRequest}.
+ * Registers a Data Store Server for the specified info.
*/
@Transactional
@RolesAllowed(RoleSet.ETL_SERVER)
- public void registerDataStoreServer(String sessionToken, int port, String dssSessionToken);
+ public void registerDataStoreServer(String sessionToken, DataStoreServerInfo dataStoreServerInfo);
/**
* Gets an {@link ExperimentPE} object specified by experiment ID and sample code.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStorePE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStorePE.java
index 83b53229095d10aa0b1937ed0d68050413590c8f..53008088c819ce7238483e001b1a48d7847f65e9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStorePE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStorePE.java
@@ -20,11 +20,15 @@ import java.util.Date;
import javax.persistence.Column;
import javax.persistence.Entity;
+import javax.persistence.FetchType;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
+import javax.persistence.Version;
import org.hibernate.annotations.Generated;
import org.hibernate.annotations.GenerationTime;
@@ -61,6 +65,10 @@ public final class DataStorePE extends AbstractIdAndCodeHolder<DataStorePE>
private String sessionToken;
+ private DatabaseInstancePE databaseInstance;
+
+ private Date modificationDate;
+
public final void setId(final Long id)
{
this.id = id;
@@ -119,6 +127,31 @@ public final class DataStorePE extends AbstractIdAndCodeHolder<DataStorePE>
this.registrationDate = registrationDate;
}
+ @Version
+ @Column(name = ColumnNames.MODIFICATION_TIMESTAMP_COLUMN, nullable = false)
+ public Date getModificationDate()
+ {
+ return modificationDate;
+ }
+
+ public void setModificationDate(Date versionDate)
+ {
+ this.modificationDate = versionDate;
+ }
+
+ @ManyToOne(fetch = FetchType.EAGER)
+ @NotNull(message = ValidationMessages.DATABASE_INSTANCE_NOT_NULL_MESSAGE)
+ @JoinColumn(name = ColumnNames.DATABASE_INSTANCE_COLUMN, updatable = false)
+ public DatabaseInstancePE getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public void setDatabaseInstance(final DatabaseInstancePE databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
//
// AbstractIdAndCodeHolder
//
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStoreServerInfo.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStoreServerInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..1dd0584d7e0ea0203903ab5a57f37f65afffd9d8
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStoreServerInfo.java
@@ -0,0 +1,92 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.dto;
+
+import java.io.Serializable;
+
+import javax.servlet.http.HttpServletRequest;
+
+import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
+
+/**
+ * Information about a data store server (DSS) needed by openBIS server.
+ * <p>
+ * It contains
+ * <ul>
+ * <li>the port on which the DSS is reachable. Note, that the host can be inferred by the asking
+ * {@link HttpServletRequest}.
+ * <li>the DSS session token which has to used when invoking methods on the DSS.
+ * <li>the download URL which is the URL at which the DSS Web server can be accessed from a Web
+ * browser.
+ * <li>the unique code of the DSS.
+ * </ul>
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataStoreServerInfo implements Serializable
+{
+ private static final long serialVersionUID = GenericSharedConstants.VERSION;
+
+ private int port;
+
+ private String dataStoreCode;
+
+ private String downloadUrl;
+
+ private String sessionToken;
+
+ public final int getPort()
+ {
+ return port;
+ }
+
+ public final void setPort(int port)
+ {
+ this.port = port;
+ }
+
+ public final String getDataStoreCode()
+ {
+ return dataStoreCode;
+ }
+
+ public final void setDataStoreCode(String dataStoreCode)
+ {
+ this.dataStoreCode = dataStoreCode;
+ }
+
+ public final String getDownloadUrl()
+ {
+ return downloadUrl;
+ }
+
+ public final void setDownloadUrl(String downloadUrl)
+ {
+ this.downloadUrl = downloadUrl;
+ }
+
+ public final String getSessionToken()
+ {
+ return sessionToken;
+ }
+
+ public final void setSessionToken(String sessionToken)
+ {
+ this.sessionToken = sessionToken;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStoreServerSession.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStoreServerSession.java
deleted file mode 100644
index a1be4426d5a649153089540d7a6d677d84b5f32c..0000000000000000000000000000000000000000
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataStoreServerSession.java
+++ /dev/null
@@ -1,63 +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.shared.dto;
-
-import java.io.Serializable;
-
-import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
-
-/**
- * Class for session on a Data Store Server.
- *
- * @author Franz-Josef Elmer
- */
-public class DataStoreServerSession implements Serializable
-{
- private static final long serialVersionUID = 1L;
-
- private final String dataStoreServerURL;
- private final IDataStoreService service;
-
- private String sessionToken;
-
- public DataStoreServerSession(String dataStoreServerURL, IDataStoreService service)
- {
- this.dataStoreServerURL = dataStoreServerURL;
- this.service = service;
- }
-
- public final String getDataStoreServerURL()
- {
- return dataStoreServerURL;
- }
-
- public final String getSessionToken()
- {
- return sessionToken;
- }
-
- public final void setSessionToken(String sessionToken)
- {
- this.sessionToken = sessionToken;
- }
-
- public final IDataStoreService getService()
- {
- return service;
- }
-
-}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalData.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalData.java
index 780f052840b2d258c4ae1a873037bb56c23454c8..9f3c426555e3693dbb9f5436998991b74666f84c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalData.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalData.java
@@ -50,6 +50,8 @@ public final class ExternalData extends ExtractableData
private String associatedSampleCode;
+ private String dataStoreCode;
+
private boolean measured;
/** Returns <code>dataSetType</code>. */
@@ -159,6 +161,16 @@ public final class ExternalData extends ExtractableData
this.associatedSampleCode = sampleCode;
}
+ public final String getDataStoreCode()
+ {
+ return dataStoreCode;
+ }
+
+ public final void setDataStoreCode(String dataStoreCode)
+ {
+ this.dataStoreCode = dataStoreCode;
+ }
+
public final boolean isMeasured()
{
return measured;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetTypeSlaveServerPlugin.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetTypeSlaveServerPlugin.java
index b1d5a8267f2499d9d66f198fe6506ff8c82bb396..04e948808a44428a3803956af2c67b1609e76a4e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetTypeSlaveServerPlugin.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericDataSetTypeSlaveServerPlugin.java
@@ -23,7 +23,6 @@ import javax.annotation.Resource;
import org.springframework.stereotype.Component;
import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.openbis.generic.server.business.DataStoreServerSessionManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
@@ -47,12 +46,11 @@ public class GenericDataSetTypeSlaveServerPlugin implements IDataSetTypeSlaveSer
{
}
- public void deleteDataSets(Session session, DataStoreServerSessionManager dssSessionManager,
- List<ExternalDataPE> dataSets, String reason)
+ public void deleteDataSets(Session session, List<ExternalDataPE> dataSets, String reason)
{
IExternalDataTable externalDataTable = businessObjectFactory.createExternalDataTable(session);
externalDataTable.setExternalData(dataSets);
- externalDataTable.deleteLoadedDataSets(dssSessionManager, reason);
+ externalDataTable.deleteLoadedDataSets(reason);
}
diff --git a/openbis/source/java/genericApplicationContext.xml b/openbis/source/java/genericApplicationContext.xml
index 7f12f487957afe1c68772f1f2e53bf68ac56ba49..e11302dc5bdb9c5a3245c8ee59bc33741db97b74 100644
--- a/openbis/source/java/genericApplicationContext.xml
+++ b/openbis/source/java/genericApplicationContext.xml
@@ -36,6 +36,8 @@
<constructor-arg ref="db-configuration-context" />
<constructor-arg ref="hibernate-session-factory" />
</bean>
+
+ <bean id="dss-factory" class="ch.systemsx.cisd.openbis.generic.server.DataStoreServiceFactory"/>
<bean id="authentication-service"
class="ch.systemsx.cisd.openbis.generic.server.AuthenticationServiceHolder">
@@ -62,6 +64,7 @@
<bean id="common-business-object-factory"
class="ch.systemsx.cisd.openbis.generic.server.CommonBusinessObjectFactory">
<constructor-arg ref="dao-factory" />
+ <constructor-arg ref="dss-factory" />
</bean>
<bean id="last-modification-state"
@@ -74,7 +77,6 @@
<bean id="common-server" class="ch.systemsx.cisd.openbis.generic.server.CommonServer">
<constructor-arg ref="authentication-service" />
<constructor-arg ref="session-manager" />
- <constructor-arg ref="dss-session-manager" />
<constructor-arg ref="dao-factory" />
<constructor-arg ref="common-business-object-factory" />
<constructor-arg ref="last-modification-state" />
@@ -100,9 +102,9 @@
<property name="target">
<bean class="ch.systemsx.cisd.openbis.generic.server.ETLService">
<constructor-arg ref="session-manager" />
- <constructor-arg ref="dss-session-manager" />
<constructor-arg ref="dao-factory" />
<constructor-arg ref="common-business-object-factory" />
+ <constructor-arg ref="dss-factory" />
</bean>
</property>
<property name="interceptorNames">
@@ -113,8 +115,6 @@
</property>
</bean>
- <bean id="dss-session-manager" class="ch.systemsx.cisd.openbis.generic.server.business.DataStoreServerSessionManager"/>
-
<bean id="exception-translator"
class="ch.systemsx.cisd.common.spring.ServiceExceptionTranslator">
<property name="packagesNotMasqueraded">
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
index d3125f8aa33b3fd5cf4db8f42646f64cc48f3d04..f01e822c63c7c3c32f11cb2fd474d977aadce478 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
@@ -27,7 +27,6 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.DataStoreServerSessionManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlugin;
@@ -91,15 +90,13 @@ public final class CommonServerTest extends AbstractServerTestCase
private ICommonBusinessObjectFactory commonBusinessObjectFactory;
- private DataStoreServerSessionManager dssSessionManager;
-
private ISampleTypeSlaveServerPlugin sampleTypeSlaveServerPlugin;
private IDataSetTypeSlaveServerPlugin dataSetTypeSlaveServerPlugin;
private final ICommonServer createServer()
{
- CommonServer server = new CommonServer(authenticationService, sessionManager, dssSessionManager,
+ CommonServer server = new CommonServer(authenticationService, sessionManager,
daoFactory, commonBusinessObjectFactory, new LastModificationState());
server.setSampleTypeSlaveServerPlugin(sampleTypeSlaveServerPlugin);
server.setDataSetTypeSlaveServerPlugin(dataSetTypeSlaveServerPlugin);
@@ -122,7 +119,6 @@ public final class CommonServerTest extends AbstractServerTestCase
public final void setUp()
{
super.setUp();
- dssSessionManager = new DataStoreServerSessionManager();
commonBusinessObjectFactory = context.mock(ICommonBusinessObjectFactory.class);
sampleTypeSlaveServerPlugin = context.mock(ISampleTypeSlaveServerPlugin.class);
dataSetTypeSlaveServerPlugin = context.mock(IDataSetTypeSlaveServerPlugin.class);
@@ -871,10 +867,10 @@ public final class CommonServerTest extends AbstractServerTestCase
ExternalDataPE ds3 = createDataSet("ds3", "type2");
will(returnValue(Arrays.asList(ds1, ds2, ds3)));
- one(dataSetTypeSlaveServerPlugin).deleteDataSets(SESSION, dssSessionManager,
- Arrays.asList(ds1, ds2), "reason");
- one(dataSetTypeSlaveServerPlugin).deleteDataSets(SESSION, dssSessionManager,
- Arrays.asList(ds3), "reason");
+ one(dataSetTypeSlaveServerPlugin).deleteDataSets(SESSION, Arrays.asList(ds1, ds2),
+ "reason");
+ one(dataSetTypeSlaveServerPlugin).deleteDataSets(SESSION, Arrays.asList(ds3),
+ "reason");
}
});
@@ -907,8 +903,7 @@ public final class CommonServerTest extends AbstractServerTestCase
will(returnValue(externalDataTable));
one(externalDataTable).loadByDataSetCodes(dataSetCodes);
- one(externalDataTable).uploadLoadedDataSetsToCIFEX(dssSessionManager,
- uploadContext);
+ one(externalDataTable).uploadLoadedDataSetsToCIFEX(uploadContext);
}
});
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 95a178b81587150ed1fcdb99b6129703c06e8eab..6e38458396d5d959f9dbb92755dffdac29ac4a8f 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
@@ -22,6 +22,8 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.LinkedHashSet;
+import org.hamcrest.BaseMatcher;
+import org.hamcrest.Description;
import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@@ -29,14 +31,15 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.DataStoreServerSessionManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentContentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
@@ -56,67 +59,139 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@Friend(toClasses=ETLService.class)
public class ETLServiceTest extends AbstractServerTestCase
{
+ private static final String DOWNLOAD_URL = "download-url";
+ private static final String DSS_CODE = "my-dss";
+ private static final String DSS_SESSION_TOKEN = "dss42";
+ private static final int PORT = 443;
+ private static final String URL = "https://" + SESSION.getRemoteHost() + ":" + PORT;
private ICommonBusinessObjectFactory boFactory;
- private DataStoreServerSessionManager dssSessionManager;
private IDataStoreServiceFactory dssfactory;
private IDataStoreService dataStoreService;
+ private IDataStoreDAO dataStoreDAO;
@Override
@BeforeMethod
public final void setUp()
{
super.setUp();
- dssSessionManager = new DataStoreServerSessionManager();
boFactory = context.mock(ICommonBusinessObjectFactory.class);
dssfactory = context.mock(IDataStoreServiceFactory.class);
dataStoreService = context.mock(IDataStoreService.class);
+ dataStoreDAO = context.mock(IDataStoreDAO.class);
}
@Test
public void testRegisterDataStoreServer()
{
- final String url = "https://" + SESSION.getRemoteHost() + ":443";
- final String dssToken = "dss42";
prepareGetSession();
context.checking(new Expectations()
{
{
- one(dssfactory).create(url);
+ one(daoFactory).getDataStoreDAO();
+ will(returnValue(dataStoreDAO));
+
+ one(dataStoreDAO).tryToFindDataStoreByCode(DSS_CODE);
+ will(returnValue(null));
+
+ one(dssfactory).create(URL);
will(returnValue(dataStoreService));
- one(dataStoreService).getVersion(dssToken);
+ one(dataStoreService).getVersion(DSS_SESSION_TOKEN);
will(returnValue(IDataStoreService.VERSION));
+
+ one(dataStoreDAO).createOrUpdateDataStore(with(new BaseMatcher<DataStorePE>()
+ {
+ public void describeTo(Description description)
+ {
+ }
+
+ public boolean matches(Object item)
+ {
+ if (item instanceof DataStorePE)
+ {
+ DataStorePE store = (DataStorePE) item;
+ return DSS_CODE.equals(store.getCode())
+ && URL.equals(store.getRemoteUrl())
+ && DOWNLOAD_URL.equals(store.getDownloadUrl())
+ && DSS_SESSION_TOKEN.equals(store.getSessionToken());
+ }
+ return false;
+ }
+
+ }));
}
});
- createService().registerDataStoreServer(SESSION_TOKEN, 443, dssToken);
-
- DataStoreServerSession session = dssSessionManager.tryToGetSession(url);
- assertEquals(dssToken, session.getSessionToken());
+ createService().registerDataStoreServer(SESSION_TOKEN, createDSSInfo());
context.assertIsSatisfied();
}
+ @Test
+ public void testRegisterDataStoreServerAgain()
+ {
+ prepareGetSession();
+ context.checking(new Expectations()
+ {
+ {
+ one(daoFactory).getDataStoreDAO();
+ will(returnValue(dataStoreDAO));
+
+ one(dataStoreDAO).tryToFindDataStoreByCode(DSS_CODE);
+ will(returnValue(new DataStorePE()));
+
+ one(dataStoreDAO).createOrUpdateDataStore(with(new BaseMatcher<DataStorePE>()
+ {
+ public void describeTo(Description description)
+ {
+ }
+
+ public boolean matches(Object item)
+ {
+ if (item instanceof DataStorePE)
+ {
+ DataStorePE store = (DataStorePE) item;
+ return DSS_CODE.equals(store.getCode())
+ && URL.equals(store.getRemoteUrl())
+ && DOWNLOAD_URL.equals(store.getDownloadUrl())
+ && DSS_SESSION_TOKEN.equals(store.getSessionToken());
+ }
+ return false;
+ }
+
+ }));
+ }
+ });
+
+ createService().registerDataStoreServer(SESSION_TOKEN, createDSSInfo());
+
+ context.assertIsSatisfied();
+ }
+
@Test
public void testRegisterDataStoreServerWithWrongVersion()
{
- final String url = "https://" + SESSION.getRemoteHost() + ":443";
- final String dssToken = "dss42";
prepareGetSession();
context.checking(new Expectations()
{
{
- one(dssfactory).create(url);
+ one(daoFactory).getDataStoreDAO();
+ will(returnValue(dataStoreDAO));
+
+ one(dataStoreDAO).tryToFindDataStoreByCode(DSS_CODE);
+ will(returnValue(null));
+
+ one(dssfactory).create(URL);
will(returnValue(dataStoreService));
- one(dataStoreService).getVersion(dssToken);
+ one(dataStoreService).getVersion(DSS_SESSION_TOKEN);
will(returnValue(VERSION + 1));
}
});
try
{
- createService().registerDataStoreServer(SESSION_TOKEN, 443, dssToken);
+ createService().registerDataStoreServer(SESSION_TOKEN, createDSSInfo());
fail("ConfigurationFailureException expected");
} catch (ConfigurationFailureException e)
{
@@ -462,6 +537,16 @@ public class ETLServiceTest extends AbstractServerTestCase
private IETLLIMSService createService()
{
- return new ETLService(sessionManager, dssSessionManager, daoFactory, boFactory, dssfactory);
+ return new ETLService(sessionManager, daoFactory, boFactory, dssfactory);
+ }
+
+ private DataStoreServerInfo createDSSInfo()
+ {
+ DataStoreServerInfo info = new DataStoreServerInfo();
+ info.setPort(PORT);
+ info.setSessionToken(DSS_SESSION_TOKEN);
+ info.setDataStoreCode(DSS_CODE);
+ info.setDownloadUrl(DOWNLOAD_URL);
+ return info;
}
}
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 51627fb72f44e2fe51b756317b9d2a8a88586d61..2ebbc10779c89b6b9e825ef66b4bb6a66aeaf7fa 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
@@ -24,6 +24,7 @@ import org.testng.annotations.BeforeMethod;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSetTypeDAO;
+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.IEntityPropertyTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
@@ -85,6 +86,8 @@ public abstract class AbstractBOTest extends AssertJUnit
ILocatorTypeDAO locatorTypeDAO;
+ IDataStoreDAO dataStoreDAO;
+
@BeforeMethod
public void beforeMethod()
{
@@ -107,6 +110,7 @@ public abstract class AbstractBOTest extends AssertJUnit
dataSetTypeDAO = context.mock(IDataSetTypeDAO.class);
fileFormatTypeDAO = context.mock(IFileFormatTypeDAO.class);
locatorTypeDAO = context.mock(ILocatorTypeDAO.class);
+ dataStoreDAO = context.mock(IDataStoreDAO.class);
context.checking(new Expectations()
{
{
@@ -128,6 +132,8 @@ public abstract class AbstractBOTest extends AssertJUnit
will(returnValue(locatorTypeDAO));
allowing(daoFactory).getExternalDataDAO();
will(returnValue(externalDataDAO));
+ allowing(daoFactory).getDataStoreDAO();
+ will(returnValue(dataStoreDAO));
}
});
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
index 397941b759a6999da324ae14a8db0e252513dd73..af6f67b256de59112c097ad8368a087189c17391 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
@@ -33,6 +33,7 @@ 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.DataSetType;
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.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalData;
@@ -56,6 +57,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.types.ProcedureTypeCode;
*/
public class ExternalDataBOTest extends AbstractBOTest
{
+ private static final String DATA_STORE_CODE = "dss1";
+
private static final String PARENT_CODE = "parent";
private static final Date PRODUCTION_DATE = new Date(1001);
@@ -104,7 +107,7 @@ public class ExternalDataBOTest extends AbstractBOTest
SamplePE sample = new SamplePE();
ExperimentPE experimentPE = new ExperimentPE();
sample.setExperiment(experimentPE);
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType);
+ prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, new DataStorePE());
IExternalDataBO sampleBO = createExternalDataBO();
sampleBO.define(createData(null), sample, SourceType.DERIVED);
@@ -141,7 +144,8 @@ public class ExternalDataBOTest extends AbstractBOTest
SamplePE sample = new SamplePE();
ExperimentPE experimentPE = new ExperimentPE();
sample.setExperiment(experimentPE);
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType);
+ DataStorePE dataStore = new DataStorePE();
+ prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, dataStore);
final DataPE data = new DataPE();
context.checking(new Expectations()
{
@@ -157,6 +161,7 @@ public class ExternalDataBOTest extends AbstractBOTest
assertSame(sample, externalData.getSampleAcquiredFrom());
assertSame(null, externalData.getSampleDerivedFrom());
+ assertSame(dataStore, externalData.getDataStore());
assertEquals(1, externalData.getParents().size());
assertSame(data, externalData.getParents().iterator().next());
context.assertIsSatisfied();
@@ -174,7 +179,8 @@ public class ExternalDataBOTest extends AbstractBOTest
vocabulary.addTerm(vocabularyTerm);
final LocatorTypePE locatorType = new LocatorTypePE();
final SamplePE sample = new SamplePE();
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType);
+ 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);
@@ -202,6 +208,7 @@ public class ExternalDataBOTest extends AbstractBOTest
assertSame(sample, externalData.getSampleAcquiredFrom());
assertSame(null, externalData.getSampleDerivedFrom());
+ assertSame(dataStore, externalData.getDataStore());
assertEquals(1, externalData.getParents().size());
assertEquals(parentData, externalData.getParents().iterator().next());
context.assertIsSatisfied();
@@ -219,7 +226,8 @@ public class ExternalDataBOTest extends AbstractBOTest
vocabulary.addTerm(vocabularyTerm);
final LocatorTypePE locatorType = new LocatorTypePE();
final SamplePE data = new SamplePE();
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType);
+ 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);
@@ -236,7 +244,7 @@ public class ExternalDataBOTest extends AbstractBOTest
one(dataSetTypeDAO).tryToFindDataSetTypeByCode(
DataSetTypeCode.UNKNOWN.getCode());
will(returnValue(dataSetTypeUnknown));
-
+
one(externalDataDAO).createDataSet(parentData);
}
});
@@ -247,6 +255,7 @@ public class ExternalDataBOTest extends AbstractBOTest
assertSame(data, externalData.getSampleAcquiredFrom());
assertSame(null, externalData.getSampleDerivedFrom());
+ assertSame(dataStore, externalData.getDataStore());
assertEquals(1, externalData.getParents().size());
assertEquals(parentData, externalData.getParents().iterator().next());
context.assertIsSatisfied();
@@ -265,7 +274,8 @@ public class ExternalDataBOTest extends AbstractBOTest
final LocatorTypePE locatorType = new LocatorTypePE();
SamplePE sample = new SamplePE();
sample.setExperiment(new ExperimentPE());
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType);
+ final DataStorePE dataStore = new DataStorePE();
+ prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, dataStore);
context.checking(new Expectations()
{
{
@@ -298,7 +308,8 @@ public class ExternalDataBOTest extends AbstractBOTest
final LocatorTypePE locatorType = new LocatorTypePE();
SamplePE sample = new SamplePE();
sample.setExperiment(new ExperimentPE());
- prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType);
+ final DataStorePE dataStore = new DataStorePE();
+ prepareDefine(dataSetType, fileFormatType, vocabulary, locatorType, dataStore);
context.checking(new Expectations()
{
{
@@ -320,6 +331,7 @@ public class ExternalDataBOTest extends AbstractBOTest
sampleBO.save();
ExternalDataPE externalData = sampleBO.getExternalData();
+ assertSame(dataStore, externalData.getDataStore());
assertEquals(false, externalData.isPlaceholder());
assertEquals(4711, externalData.getId().longValue());
assertEquals(null, externalData.getSampleDerivedFrom());
@@ -359,7 +371,7 @@ public class ExternalDataBOTest extends AbstractBOTest
private void prepareDefine(final DataSetTypePE dataSetType,
final FileFormatTypePE fileFormatType, final VocabularyPE vocabulary,
- final LocatorTypePE locatorType)
+ final LocatorTypePE locatorType, final DataStorePE dataStore)
{
context.checking(new Expectations()
{
@@ -378,6 +390,9 @@ public class ExternalDataBOTest extends AbstractBOTest
dataSetType.getCode(), EXAMPLE_SESSION.tryGetPerson());
ArrayList<DataSetPropertyPE> properties = new ArrayList<DataSetPropertyPE>();
will(returnValue(properties));
+
+ one(dataStoreDAO).tryToFindDataStoreByCode(DATA_STORE_CODE);
+ will(returnValue(dataStore));
}
});
}
@@ -395,6 +410,7 @@ public class ExternalDataBOTest extends AbstractBOTest
data.setFileFormatType(FILE_FORMAT_TYPE);
data.setLocatorType(LOCATOR_TYPE);
data.setLocation(LOCATION);
+ data.setDataStoreCode(DATA_STORE_CODE);
return data;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
index 2a8079a03da72e5a30bfa20130be0670626afb0f..b0a4bb9b3f900c2342ce5a303593f95c7fa42fdd 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataTableTest.java
@@ -30,13 +30,13 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.DataStoreServerSessionManager;
+import ch.systemsx.cisd.openbis.generic.server.IDataStoreServiceFactory;
import ch.systemsx.cisd.openbis.generic.server.business.ManagerTestTool;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUploadContext;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
+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;
@@ -59,12 +59,15 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@Friend(toClasses=ExternalDataTable.class)
public final class ExternalDataTableTest extends AbstractBOTest
{
- private DataStoreServerSessionManager dssSessionManager;
- private IDataStoreService dataStoreService;
+ private IDataStoreServiceFactory dssFactory;
+ private DataStorePE dss1;
+ private DataStorePE dss2;
+ private IDataStoreService dataStoreService1;
+ private IDataStoreService dataStoreService2;
private final ExternalDataTable createExternalDataTable()
{
- return new ExternalDataTable(daoFactory, ManagerTestTool.EXAMPLE_SESSION);
+ return new ExternalDataTable(daoFactory, dssFactory, ManagerTestTool.EXAMPLE_SESSION);
}
@BeforeMethod
@@ -72,8 +75,21 @@ public final class ExternalDataTableTest extends AbstractBOTest
public void beforeMethod()
{
super.beforeMethod();
- dssSessionManager = new DataStoreServerSessionManager();
- dataStoreService = context.mock(IDataStoreService.class);
+ dssFactory = context.mock(IDataStoreServiceFactory.class);
+ dss1 = createDataStore("dss1");
+ dss2 = createDataStore("dss2");
+ dataStoreService1 = context.mock(IDataStoreService.class, "dataStoreService1");
+ dataStoreService2 = context.mock(IDataStoreService.class, "dataStoreService2");
+ context.checking(new Expectations()
+ {
+ {
+ allowing(dssFactory).create(dss1.getRemoteUrl());
+ will(returnValue(dataStoreService1));
+
+ allowing(dssFactory).create(dss2.getRemoteUrl());
+ will(returnValue(dataStoreService2));
+ }
+ });
}
@Test
@@ -215,40 +231,11 @@ public final class ExternalDataTableTest extends AbstractBOTest
context.assertIsSatisfied();
}
- @Test
- public void testDeleteLoadedDataSetsButDataStoreServerIsDown()
- {
- final ExternalDataPE d1 = createDataSet("d1");
- context.checking(new Expectations()
- {
- {
- one(externalDataDAO).tryToFindFullDataSetByCode(d1.getCode());
- will(returnValue(d1));
- }
- });
-
- ExternalDataTable externalDataTable = createExternalDataTable();
- externalDataTable.loadByDataSetCodes(Arrays.asList(d1.getCode()));
- try
- {
- externalDataTable.deleteLoadedDataSets(dssSessionManager, "");
- fail("UserFailureException expected");
- } catch (UserFailureException e)
- {
- assertEquals(
- "The following data sets are unknown by any registered Data Store Server. "
- + "May be the responsible Data Store Server is not running.\n[d1]", e
- .getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
@Test
public void testLoadByDataSetCodes()
{
- final ExternalDataPE d1 = createDataSet("d1");
- final ExternalDataPE d2 = createDataSet("d2");
+ final ExternalDataPE d1 = createDataSet("d1", dss1);
+ final ExternalDataPE d2 = createDataSet("d2", dss2);
context.checking(new Expectations()
{
{
@@ -272,32 +259,32 @@ public final class ExternalDataTableTest extends AbstractBOTest
@Test
public void testDeleteLoadedDataSetsButOneDataSetIsUnknown()
{
- dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url",
- dataStoreService));
- final ExternalDataPE d1 = createDataSet("d1");
- final ExternalDataPE d2 = createDataSet("d2");
+ final ExternalDataPE d1 = createDataSet("d1", dss1);
+ final ExternalDataPE d2 = createDataSet("d2", dss2);
context.checking(new Expectations()
- {
{
- one(externalDataDAO).tryToFindFullDataSetByCode(d1.getCode());
- will(returnValue(d1));
-
- one(externalDataDAO).tryToFindFullDataSetByCode(d2.getCode());
- will(returnValue(d2));
-
- List<String> locations = Arrays.asList(d1.getLocation(), d2.getLocation());
- one(dataStoreService).getKnownDataSets(with(any(String.class)),
- with(equal(locations)));
- will(returnValue(Arrays.asList(d1.getLocation())));
-
- }
- });
+ {
+ one(externalDataDAO).tryToFindFullDataSetByCode(d1.getCode());
+ will(returnValue(d1));
+
+ one(externalDataDAO).tryToFindFullDataSetByCode(d2.getCode());
+ will(returnValue(d2));
+
+ one(dataStoreService1).getKnownDataSets(dss1.getSessionToken(),
+ Arrays.asList(d1.getLocation()));
+ will(returnValue(Arrays.asList(d1.getLocation())));
+
+ one(dataStoreService2).getKnownDataSets(dss2.getSessionToken(),
+ Arrays.asList(d2.getLocation()));
+ will(returnValue(Arrays.asList()));
+ }
+ });
ExternalDataTable externalDataTable = createExternalDataTable();
externalDataTable.loadByDataSetCodes(Arrays.asList(d1.getCode(), d2.getCode()));
try
{
- externalDataTable.deleteLoadedDataSets(dssSessionManager, "");
+ externalDataTable.deleteLoadedDataSets("");
fail("UserFailureException expected");
} catch (UserFailureException e)
{
@@ -313,10 +300,8 @@ public final class ExternalDataTableTest extends AbstractBOTest
@Test
public void testDeleteLoadedDataSets()
{
- dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url",
- dataStoreService));
- final ExternalDataPE d1 = createDataSet("d1");
- final ExternalDataPE d2 = createDataSet("d2");
+ final ExternalDataPE d1 = createDataSet("d1", dss1);
+ final ExternalDataPE d2 = createDataSet("d2", dss2);
context.checking(new Expectations()
{
{
@@ -325,23 +310,27 @@ public final class ExternalDataTableTest extends AbstractBOTest
one(externalDataDAO).tryToFindFullDataSetByCode(d2.getCode());
will(returnValue(d2));
+
+ List<String> d1Locations = Arrays.asList(d1.getLocation());
+ one(dataStoreService1).getKnownDataSets(dss1.getSessionToken(), d1Locations);
+ will(returnValue(d1Locations));
- List<String> locations = Arrays.asList(d1.getLocation(), d2.getLocation());
- one(dataStoreService).getKnownDataSets(with(any(String.class)),
- with(equal(locations)));
- will(returnValue(locations));
+ List<String> d2Locations = Arrays.asList(d2.getLocation());
+ one(dataStoreService2).getKnownDataSets(dss2.getSessionToken(), d2Locations);
+ will(returnValue(d2Locations));
PersonPE person = EXAMPLE_SESSION.tryGetPerson();
one(externalDataDAO).markAsDeleted(d1, person, DELETION_DESCRIPTION, "reason");
one(externalDataDAO).markAsDeleted(d2, person, DELETION_DESCRIPTION, "reason");
- one(dataStoreService).deleteDataSets(with(any(String.class)),
- with(equal(locations)));
+
+ one(dataStoreService1).deleteDataSets(dss1.getSessionToken(), d1Locations);
+ one(dataStoreService2).deleteDataSets(dss2.getSessionToken(), d2Locations);
}
});
ExternalDataTable externalDataTable = createExternalDataTable();
externalDataTable.loadByDataSetCodes(Arrays.asList(d1.getCode(), d2.getCode()));
- externalDataTable.deleteLoadedDataSets(dssSessionManager, "reason");
+ externalDataTable.deleteLoadedDataSets("reason");
context.assertIsSatisfied();
}
@@ -349,10 +338,8 @@ public final class ExternalDataTableTest extends AbstractBOTest
@Test
public void testUploadDataSets()
{
- dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url",
- dataStoreService));
- final ExternalDataPE d1 = createDataSet("d1");
- final ExternalDataPE d2 = createDataSet("d2");
+ final ExternalDataPE d1 = createDataSet("d1", dss1);
+ final ExternalDataPE d2 = createDataSet("d2", dss2);
final DataSetUploadContext uploadContext = new DataSetUploadContext();
uploadContext.setCifexURL("cifexURL");
uploadContext.setUserID(EXAMPLE_SESSION.getUserName());
@@ -367,20 +354,25 @@ public final class ExternalDataTableTest extends AbstractBOTest
one(externalDataDAO).tryToFindFullDataSetByCode(d2.getCode());
will(returnValue(d2));
-
- List<String> locations = Arrays.asList(d1.getLocation(), d2.getLocation());
- one(dataStoreService).getKnownDataSets(with(any(String.class)),
- with(equal(locations)));
- will(returnValue(locations));
-
- one(dataStoreService).uploadDataSetsToCIFEX(with(any(String.class)),
- with(equal(Arrays.asList(d1, d2))), with(equal(uploadContext)));
+
+ List<String> d1Locations = Arrays.asList(d1.getLocation());
+ one(dataStoreService1).getKnownDataSets(dss1.getSessionToken(), d1Locations);
+ will(returnValue(d1Locations));
+
+ List<String> d2Locations = Arrays.asList(d2.getLocation());
+ one(dataStoreService2).getKnownDataSets(dss2.getSessionToken(), d2Locations);
+ will(returnValue(d2Locations));
+
+ one(dataStoreService1).uploadDataSetsToCIFEX(dss1.getSessionToken(),
+ Arrays.asList(d1), uploadContext);
+ one(dataStoreService2).uploadDataSetsToCIFEX(dss2.getSessionToken(),
+ Arrays.asList(d2), uploadContext);
}
});
ExternalDataTable externalDataTable = createExternalDataTable();
externalDataTable.loadByDataSetCodes(Arrays.asList(d1.getCode(), d2.getCode()));
- externalDataTable.uploadLoadedDataSetsToCIFEX(dssSessionManager, uploadContext);
+ externalDataTable.uploadLoadedDataSetsToCIFEX(uploadContext);
context.assertIsSatisfied();
}
@@ -433,10 +425,11 @@ public final class ExternalDataTableTest extends AbstractBOTest
return sequence.substring(0, codeLength - result.length()) + result;
}
- private ExternalDataPE createDataSet(String code)
+ private ExternalDataPE createDataSet(String code, DataStorePE dataStore)
{
ExternalDataPE data = new ExternalDataPE();
data.setCode(code);
+ data.setDataStore(dataStore);
data.setLocation("here/" + code);
ExperimentPE experiment = new ExperimentPE();
experiment.setCode("exp1");
@@ -449,4 +442,13 @@ public final class ExternalDataTableTest extends AbstractBOTest
data.setExperiment(experiment);
return data;
}
+
+ private DataStorePE createDataStore(String code)
+ {
+ DataStorePE dataStore = new DataStorePE();
+ dataStore.setCode(code);
+ dataStore.setRemoteUrl("http://" + code);
+ dataStore.setSessionToken("session-" + code);
+ return dataStore;
+ }
}
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 65cfa59590bde5318103fc5f53a1c95b58377681..75d8808a69397cbe60c667188a810435f7884dca 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
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.openbis.generic.shared;
-import javax.servlet.http.HttpServletRequest;
-
import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -26,6 +24,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.Authoriz
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleOwnerIdentifierPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerInfo;
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.ExternalData;
@@ -33,41 +32,85 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+/**
+ * <b>LIMS</b> <i>Web Service</i> interface for the <b>ETL</b> (<i>Extract, Transform, Load</i>)
+ * server.
+ *
+ * @author Christian Ribeaud
+ */
public interface IETLLIMSService extends IWebService, ISessionProvider
{
-
+ /**
+ * Returns the home database instance.
+ */
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.ETL_SERVER)
public DatabaseInstancePE getHomeDatabaseInstance(final String sessionToken);
-
+
+ /**
+ * Registers a Data Store Server for the specified info.
+ */
@Transactional
@RolesAllowed(RoleSet.ETL_SERVER)
- public void registerDataStoreServer(String sessionToken, int port, String dssSessionToken);
-
+ public void registerDataStoreServer(String sessionToken, DataStoreServerInfo dataStoreServerInfo);
+
+ /**
+ * Gets an {@link ExperimentPE} object specified by experiment ID and sample code.
+ *
+ * @param sessionToken the user authentication token. Must not be <code>null</code>.
+ * @param sampleIdentifier an identifier which uniquely identifies the sample.
+ * @return <code>null</code> if no experiment could be found for given <var>sampleIdentifier</var>.
+ */
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.ETL_SERVER)
public ExperimentPE tryToGetBaseExperiment(final String sessionToken,
@AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
final SampleIdentifier sampleIdentifier) throws UserFailureException;
+ /**
+ * Tries to return the properties of the top sample (e.g. master plate) registered for the
+ * specified sample code.
+ *
+ * @param sessionToken the user authentication token. Must not be <code>null</code>.
+ * @param sampleIdentifier an identifier which uniquely identifies the sample.
+ * @return <code>null</code> if no appropriated sample found. Returns an empty array if a a
+ * sample found with no properties.
+ */
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.ETL_SERVER)
public SamplePropertyPE[] tryToGetPropertiesOfTopSampleRegisteredFor(final String sessionToken,
@AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
final SampleIdentifier sampleIdentifier) throws UserFailureException;
+ /**
+ * Registers the specified data.
+ *
+ * @param sessionToken The user authentication token. Must not be <code>null</code>.
+ * @param sampleIdentifier an identifier which uniquely identifies the sample.
+ * @param externalData Data set to be registered. It is assumed that the attributes
+ * <code>location</code>, <code>fileFormatType</code>, <code>dataSetType</code>,
+ * and <code>locatorType</code> are not-<code>null</code>.
+ * @throws UserFailureException if given data set code could not be found in the persistence
+ * layer.
+ */
@Transactional
@RolesAllowed(RoleSet.ETL_SERVER)
public void registerDataSet(final String sessionToken,
@AuthorizationGuard(guardClass = SampleOwnerIdentifierPredicate.class)
final SampleIdentifier sampleIdentifier, final ExternalData externalData)
throws UserFailureException;
-
+
+ /**
+ * Tries to return the data set specified by its code.
+ */
@Transactional
@RolesAllowed(RoleSet.OBSERVER)
public ExternalDataPE tryGetDataSet(String sessionToken, String dataSetCode)
throws UserFailureException;
+ /**
+ * Creates and returns a unique code for a new data set.
+ */
@Transactional
@RolesAllowed(RoleSet.ETL_SERVER)
public String createDataSetCode(final String sessionToken) throws UserFailureException;