From 193506f5ebfa546369b4cf214296ce9c3859e56a Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 10 Feb 2009 08:07:42 +0000
Subject: [PATCH] LMS-740 IETLLIMSService implemented but not yet tested in no
respect
SVN: 9754
---
.../server/CommonBusinessObjectFactory.java | 7 +
.../openbis/generic/server/CommonServer.java | 5 +
.../openbis/generic/server/ETLService.java | 342 ++++++++++++++++++
.../business/bo/AbstractBusinessObject.java | 18 +
.../server/business/bo/ExternalDataBO.java | 226 ++++++++++++
.../bo/ICommonBusinessObjectFactory.java | 6 +
.../server/business/bo/IExternalDataBO.java | 45 +++
.../server/dataaccess/IDAOFactory.java | 9 +
.../server/dataaccess/IDataSetTypeDAO.java | 33 ++
.../server/dataaccess/IExternalDataDAO.java | 20 +
.../server/dataaccess/IFileFormatTypeDAO.java | 33 ++
.../server/dataaccess/ILocatorTypeDAO.java | 33 ++
.../server/dataaccess/db/DAOFactory.java | 33 +-
.../server/dataaccess/db/DataSetTypeDAO.java | 48 +++
.../server/dataaccess/db/ExternalDataDAO.java | 63 ++++
.../dataaccess/db/FileFormatTypeDAO.java | 48 +++
.../server/dataaccess/db/LocatorTypeDAO.java | 48 +++
.../generic/shared/IETLLIMSService.java | 6 +-
18 files changed, 1017 insertions(+), 6 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataBO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataSetTypeDAO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IFileFormatTypeDAO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ILocatorTypeDAO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataSetTypeDAO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/FileFormatTypeDAO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/LocatorTypeDAO.java
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 ab7c6570dc9..af372714f8a 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
@@ -20,12 +20,14 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.AbstractBusinessObjec
import ch.systemsx.cisd.openbis.generic.server.business.bo.EntityTypePropertyTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ExperimentTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.GroupBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IEntityTypePropertyTypeBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGroupBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IProcedureBO;
@@ -85,6 +87,11 @@ public final class CommonBusinessObjectFactory extends AbstractBusinessObjectFac
return new SampleBO(getDaoFactory(), session);
}
+ public IExternalDataBO createExternalDataBO(Session session)
+ {
+ return new ExternalDataBO(getDaoFactory(), session);
+ }
+
public final IExternalDataTable createExternalDataTable(final Session session)
{
return new ExternalDataTable(getDaoFactory(), 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 61e476f7b0e..0b25d6acd18 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
@@ -93,6 +93,11 @@ public final class CommonServer extends AbstractServer<ICommonServer> implements
this.authenticationService = authenticationService;
this.businessObjectFactory = businessObjectFactory;
}
+
+ ICommonBusinessObjectFactory getBusinessObjectFactory()
+ {
+ return businessObjectFactory;
+ }
//
// AbstractServer
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
new file mode 100644
index 00000000000..498e00b95fa
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
@@ -0,0 +1,342 @@
+/*
+ * 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.dto.types.ProcedureTypeCode.DATA_ACQUISITION;
+
+import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.utilities.BeanUtils;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IProcedureBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentAttachmentDAO;
+import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
+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.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;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProcedurePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProcessingInstructionDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SourceType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.exception.UndefinedGroupException;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ETLService implements IETLLIMSService
+{
+ private static final String PROCESSING_PATH = "$processing-path-for-";
+ private static final String PROCESSING_PATH_TEMPLATE = PROCESSING_PATH + "%s";
+ private static final String PROCESSING_PARAMETERS_TEMPLATE = "$processing-parameters-for-%s";
+ private static final String PROCESSING_DESCRIPTION_TEMPLATE = "$processing-description-for-%s";
+ private static final String ENCODING = "utf-8";
+
+ private final CommonServer commonServer;
+ private final IDAOFactory daoFactory;
+ private final ICommonBusinessObjectFactory boFactory;
+
+ public ETLService(CommonServer commonServer)
+ {
+ this.commonServer = commonServer;
+ this.daoFactory = commonServer.getDAOFactory();
+ boFactory = commonServer.getBusinessObjectFactory();
+ }
+
+ public int getVersion()
+ {
+ return IWebService.VERSION;
+ }
+
+ public DatabaseInstancePE getHomeDatabaseInstance()
+ {
+ return daoFactory.getHomeDatabaseInstance();
+ }
+
+ public String authenticate(String user, String password) throws UserFailureException
+ {
+ Session session = commonServer.tryToAuthenticate(user, password);
+ return session == null ? null : session.getSessionToken();
+ }
+
+ public void closeSession(String sessionToken) throws UserFailureException
+ {
+ commonServer.logout(sessionToken);
+ }
+
+ public String createDataSetCode(String sessionToken) throws UserFailureException
+ {
+ return daoFactory.getExternalDataDAO().createDataSetCode();
+ }
+
+ public ExperimentPE tryToGetBaseExperiment(String sessionToken, SampleIdentifier sampleIdentifier)
+ throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert sampleIdentifier != null : "Unspecified sample identifier.";
+
+ final Session session = commonServer.getSessionManager().getSession(sessionToken);
+ ExperimentPE experiment = tryToLoadExperimentBySampleIdentifier(session, sampleIdentifier);
+ enrichWithProcessingInstructions(experiment);
+ return experiment;
+
+ }
+
+ private ExperimentPE tryToLoadExperimentBySampleIdentifier(final Session session,
+ SampleIdentifier sampleIdentifier)
+ {
+ final ISampleBO sampleBO = boFactory.createSampleBO(session);
+ sampleBO.loadBySampleIdentifier(sampleIdentifier);
+ sampleBO.enrichWithValidProcedure();
+ final SamplePE sample = sampleBO.getSample();
+ if (sample == null)
+ {
+ return null;
+ }
+ ProcedurePE procedure = sample.getValidProcedure();
+ return procedure == null ? null : procedure.getExperiment();
+ }
+
+ private void enrichWithProcessingInstructions(ExperimentPE experiment)
+ {
+ if (experiment == null)
+ {
+ return;
+ }
+ final List<ProcessingInstructionDTO> instructions =
+ new ArrayList<ProcessingInstructionDTO>();
+ final IExperimentAttachmentDAO experimentAttachmentDAO =
+ daoFactory.getExperimentAttachmentDAO();
+ final List<AttachmentPE> attachments =
+ experimentAttachmentDAO.listExperimentAttachments(experiment);
+ for (final AttachmentPE attachment : attachments)
+ {
+ final String fileName = attachment.getFileName();
+ if (fileName.startsWith(PROCESSING_PATH))
+ {
+ final ProcessingInstructionDTO processingInstruction =
+ new ProcessingInstructionDTO();
+ BeanUtils.fillBean(ProcessingInstructionDTO.class, processingInstruction,
+ attachment);
+ processingInstruction.setProcedureTypeCode(fileName.substring(PROCESSING_PATH
+ .length()));
+ instructions.add(processingInstruction);
+ }
+ }
+ for (final ProcessingInstructionDTO instruction : instructions)
+ {
+ final String procedureType = instruction.getProcedureTypeCode();
+ instruction.setPath(loadText(experiment, PROCESSING_PATH_TEMPLATE, procedureType));
+ instruction.setDescription(loadText(experiment, PROCESSING_DESCRIPTION_TEMPLATE,
+ procedureType));
+ instruction.setParameters(load(experiment, PROCESSING_PARAMETERS_TEMPLATE,
+ procedureType));
+ }
+ experiment.setProcessingInstructions(instructions.toArray(new ProcessingInstructionDTO[0]));
+ }
+
+ private final String createKey(final String template, final String procedureTypeCode)
+ {
+ return String.format(template, procedureTypeCode);
+ }
+
+ private final String createText(final byte[] textBytes)
+ {
+ try
+ {
+ return textBytes == null ? null : new String(textBytes, ENCODING);
+ } catch (UnsupportedEncodingException ex)
+ {
+ throw new EnvironmentFailureException("Unsupported character encoding: " + ENCODING);
+ }
+ }
+
+ private final String loadText(final ExperimentPE experiment, final String template,
+ final String procedureTypeCode)
+ {
+ final byte[] value = load(experiment, template, procedureTypeCode);
+ return createText(value);
+ }
+
+ private final byte[] load(final ExperimentPE experiment, final String template,
+ final String procedureTypeCode)
+ {
+ final String key = createKey(template, procedureTypeCode);
+ final IExperimentAttachmentDAO experimentAttachmentDAO = daoFactory.getExperimentAttachmentDAO();
+ final AttachmentPE attachment =
+ experimentAttachmentDAO.tryFindExpAttachmentByExpAndFileName(experiment, key);
+ if (attachment != null)
+ {
+ return attachment.getAttachmentContent().getValue();
+ }
+ return null;
+ }
+
+ public SamplePropertyPE[] tryToGetPropertiesOfTopSampleRegisteredFor(String sessionToken,
+ SampleIdentifier sampleIdentifier) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert sampleIdentifier != null : "Unspecified sample identifier.";
+
+ final Session session = commonServer.getSessionManager().getSession(sessionToken);
+ final ISampleBO sampleBO = boFactory.createSampleBO(session);
+ sampleBO.loadBySampleIdentifier(sampleIdentifier);
+ SamplePE sample = sampleBO.getSample();
+ throwExceptionIfSampleEqualsNull(sample, sampleIdentifier);
+ SamplePE top = sample.getTop();
+ if (top == sample)
+ {
+ throw new UserFailureException("Missing top of sample " + sampleIdentifier);
+ }
+ HibernateUtils.initialize(top.getProperties());
+ return top.getProperties().toArray(new SamplePropertyPE[0]);
+ }
+
+ private void throwExceptionIfSampleEqualsNull(SamplePE sample, SampleIdentifier sampleIdentifier)
+ {
+ if (sample == null)
+ {
+ throw new UserFailureException("Couldn't find sample " + sampleIdentifier);
+ }
+ }
+
+ public DataStorePE getDataStore(String sessionToken, ExperimentIdentifier experimentIdentifier,
+ String dataSetTypeCode) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert experimentIdentifier != null : "Unspecified experiment identifier.";
+
+ final Session session = commonServer.getSessionManager().getSession(sessionToken);
+ makeSureGroupCodeIsFilled(session, experimentIdentifier);
+ final IExperimentBO experimentBO = boFactory.createExperimentBO(session);
+ experimentBO.loadByExperimentIdentifier(experimentIdentifier);
+ ExperimentPE experiment = experimentBO.getExperiment();
+ DataStorePE result;
+ DataStorePE experimentDataStore = experiment.getDataStore();
+ if (experimentDataStore != null)
+ {
+ result = experimentDataStore;
+ } else
+ {
+ DataStorePE projectDataStore = experiment.getProject().getDataStore();
+ if (projectDataStore != null)
+ {
+ result = projectDataStore;
+ } else
+ {
+ DataStorePE groupDataStore = experiment.getProject().getGroup().getDataStore();
+ if (groupDataStore != null)
+ {
+ result = groupDataStore;
+ } else
+ {
+ DataStorePE databaseDataStore =
+ experiment.getProject().getGroup().getDatabaseInstance().getDataStore();
+ result = databaseDataStore;
+ }
+ }
+ }
+ return result;
+ }
+
+ private void makeSureGroupCodeIsFilled(final Session session,
+ ExperimentIdentifier experimentIdentifier)
+ {
+ if (experimentIdentifier.getGroupCode() == null)
+ {
+ final String homeGroupCode = session.tryGetHomeGroupCode();
+ if (StringUtils.isBlank(homeGroupCode))
+ {
+ throw new UndefinedGroupException();
+ } else
+ {
+ experimentIdentifier.setGroupCode(homeGroupCode);
+ }
+ }
+ }
+
+ public void registerDataSet(String sessionToken, SampleIdentifier sampleIdentifier,
+ String procedureTypeCode, ExternalData externalData) throws UserFailureException
+ {
+ assert sessionToken != null : "Unspecified session token.";
+ assert sampleIdentifier != null : "Unspecified sample identifier.";
+
+ final Session session = commonServer.getSessionManager().getSession(sessionToken);
+ ExperimentPE experiment = tryToLoadExperimentBySampleIdentifier(session, sampleIdentifier);
+ if (experiment == null)
+ {
+ throw new UserFailureException("No experiment found for sample " + sampleIdentifier);
+ }
+ if (experiment.getInvalidation() != null)
+ {
+ throw new UserFailureException("Data set can not be registered because experiment '"
+ + experiment.getCode() + "' is invalid.");
+ }
+ List<ProcedurePE> procedures = experiment.getProcedures();
+ ProcedurePE procedure = tryToFindProcedureByType(procedures, procedureTypeCode);
+ if (procedure == null)
+ {
+ final IProcedureBO procedureBO = boFactory.createProcedureBO(session);
+ procedureBO.define(experiment, procedureTypeCode);
+ procedureBO.save();
+ procedure = procedureBO.getProcedure();
+ }
+ final ISampleBO sampleBO = boFactory.createSampleBO(session);
+ sampleBO.loadBySampleIdentifier(sampleIdentifier);
+ sampleBO.enrichWithValidProcedure();
+ final SamplePE cellPlate = sampleBO.getSample();
+ assert cellPlate.getValidProcedure() != null : "Any cell plate should have been connected to one procedure.";
+ final IExternalDataBO externalDataBO = boFactory.createExternalDataBO(session);
+ final boolean dataAcquisition = procedureTypeCode.equals(DATA_ACQUISITION.getCode());
+ final SourceType type = dataAcquisition ? SourceType.MEASUREMENT : SourceType.DERIVED;
+ externalDataBO.define(externalData, procedure, cellPlate, type);
+ externalDataBO.save();
+ final String dataSetCode = externalDataBO.getExternalData().getCode();
+ assert dataSetCode != null : "Data set code not specified.";
+ }
+
+ private ProcedurePE tryToFindProcedureByType(List<ProcedurePE> procedures, String procedureTypeCode)
+ {
+ for (ProcedurePE procedure : procedures)
+ {
+ if (procedure.getProcedureType().getCode().equals(procedureTypeCode))
+ {
+ return procedure;
+ }
+ }
+ return null;
+ }
+}
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 85676789aa0..e662624364a 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
@@ -20,14 +20,17 @@ 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.IDatabaseInstanceDAO;
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.IExperimentAttachmentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IFileFormatTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IGroupDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IHibernateSearchDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ILocatorTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IPersonDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProcedureDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProcedureTypeDAO;
@@ -168,4 +171,19 @@ abstract class AbstractBusinessObject implements IDAOFactory
{
return daoFactory.getExperimentAttachmentDAO();
}
+
+ public IDataSetTypeDAO getDataSetTypeDAO()
+ {
+ return daoFactory.getDataSetTypeDAO();
+ }
+
+ public IFileFormatTypeDAO getFileFormatTypeDAO()
+ {
+ return daoFactory.getFileFormatTypeDAO();
+ }
+
+ public ILocatorTypeDAO getLocatorTypeDAO()
+ {
+ return daoFactory.getLocatorTypeDAO();
+ }
}
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
new file mode 100644
index 00000000000..e206150d377
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
@@ -0,0 +1,226 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server.business.bo;
+
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProcedureTypeDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IVocabularyDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+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.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProcedurePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProcedureTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SourceType;
+import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
+import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyTermPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.types.DataSetTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.dto.types.ProcedureTypeCode;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ExternalDataBO extends AbstractBusinessObject implements IExternalDataBO
+{
+ private ExternalDataPE externalData;
+ private SourceType sourceType;
+
+ public ExternalDataBO(IDAOFactory daoFactory, Session session)
+ {
+ super(daoFactory, session);
+ }
+
+ public ExternalDataPE getExternalData()
+ {
+ return externalData;
+ }
+
+ public void define(ExternalData data, ProcedurePE procedure, SamplePE sample,
+ SourceType type)
+ {
+ assert data != null : "Undefined data.";
+ final DataSetType dataSetType = data.getDataSetType();
+ assert dataSetType != null : "Undefined data set type.";
+ final FileFormatType fileFormatType = data.getFileFormatType();
+ assert fileFormatType != null : "Undefined file format type.";
+ final String location = data.getLocation();
+ assert location != null : "Undefined location.";
+ final LocatorType locatorType = data.getLocatorType();
+ assert locatorType != null : "Undefined location type.";
+ assert sourceType != null : "Undefined source type.";
+ assert procedure != null : "Unspecified procedure";
+
+ sourceType = type;
+ externalData = new ExternalDataPE();
+ externalData.setProcedure(procedure);
+ externalData.setDataProducerCode(data.getDataProducerCode());
+ externalData.setProductionDate(data.getProductionDate());
+ externalData.setCode(data.getCode());
+ externalData.setDataSetType(getDataSetType(dataSetType));
+ externalData.setFileFormatType(getFileFomatType(fileFormatType));
+ externalData.setComplete(data.getComplete());
+ externalData.setLocation(location);
+ externalData.setStorageFormatVocabularyTerm(tryToFindStorageFormatTerm(data.getStorageFormat()));
+ externalData.setLocatorType(getLocatorTypeDAO().tryToFindLocatorTypeByCode(
+ locatorType.getCode()));
+ final String parentDataSetCode = data.getParentDataSetCode();
+ if (parentDataSetCode != null)
+ {
+ final Set<DataPE> parents = new HashSet<DataPE>();
+ ExperimentPE experiment = procedure.getExperiment();
+ parents.add(getOrCreateParentData(parentDataSetCode, experiment, sample));
+ externalData.setParents(parents);
+ }
+ sourceType.setSample(externalData, sample);
+ }
+
+ private VocabularyTermPE tryToFindStorageFormatTerm(StorageFormat storageFormat)
+ {
+ IVocabularyDAO vocabularyDAO = getVocabularyDAO();
+ VocabularyPE vocabulary = vocabularyDAO.tryFindVocabularyByCode(StorageFormat.VOCABULARY_CODE);
+ Set<VocabularyTermPE> terms = vocabulary.getTerms();
+ for (VocabularyTermPE term : terms)
+ {
+ if (storageFormat.getCode().equals(term.getCode()))
+ {
+ return term;
+ }
+ }
+ return null;
+ }
+
+ private final DataSetTypePE getDataSetType(final DataSetType dataSetType)
+ {
+ final String dataSetTypeCode = dataSetType.getCode();
+ final DataSetTypePE dataSetTypeOrNull =
+ getDataSetTypeDAO().tryToFindDataSetTypeByCode(dataSetTypeCode);
+ if (dataSetTypeOrNull == null)
+ {
+ throw UserFailureException.fromTemplate("There is no data set type with code '%s'",
+ dataSetTypeCode);
+ }
+ return dataSetTypeOrNull;
+ }
+
+ private final FileFormatTypePE getFileFomatType(final FileFormatType fileFormatType)
+ {
+ final String fileFormatTypeCode = fileFormatType.getCode();
+ final FileFormatTypePE fileFormatTypeOrNull =
+ getFileFormatTypeDAO().tryToFindFileFormatTypeByCode(fileFormatTypeCode);
+ if (fileFormatTypeOrNull == null)
+ {
+ throw UserFailureException.fromTemplate("There is no file format type with code '%s'",
+ fileFormatTypeCode);
+ }
+ return fileFormatTypeOrNull;
+ }
+
+ private final ExternalDataPE getOrCreateParentData(final String parentDataSetCode,
+ ExperimentPE experiment, SamplePE sample)
+ {
+ assert parentDataSetCode != null : "Unspecified parent data set code.";
+
+ final IExternalDataDAO dataDAO = getExternalDataDAO();
+ ExternalDataPE parent = dataDAO.tryToFindDataSetByCode(parentDataSetCode);
+ if (parent == null)
+ {
+ final ProcedurePE procedure = getOrCreateUnknownProcedure(experiment);
+ parent = new ExternalDataPE();
+ parent.setCode(parentDataSetCode);
+ DataSetTypePE dataSetType = new DataSetTypePE();
+ dataSetType.setCode(DataSetTypeCode.UNKNOWN.getCode());
+ parent.setDataSetType(dataSetType);
+ parent.setProcedure(procedure);
+ parent.setSampleDerivedFrom(sample);
+ parent.setPlaceholder(true);
+ dataDAO.createDataSet(parent);
+ }
+ return parent;
+ }
+
+ private final ProcedurePE getOrCreateUnknownProcedure(ExperimentPE experiment)
+ {
+ List<ProcedurePE> procedures = experiment.getProcedures();
+ for (ProcedurePE procedure : procedures)
+ {
+ if (procedure.getProcedureType().getCode().equals(ProcedureTypeCode.UNKNOWN.getCode()))
+ {
+ return procedure;
+ }
+ }
+ ProcedurePE procedure = new ProcedurePE();
+ procedure.setExperiment(experiment);
+ final IProcedureTypeDAO procedureTypeDAO = getProcedureTypeDAO();
+ final String code = ProcedureTypeCode.UNKNOWN.getCode();
+ final ProcedureTypePE procedureTypeDTO = procedureTypeDAO.tryFindProcedureTypeByCode(code);
+ procedure.setProcedureType(procedureTypeDTO);
+ getProcedureDAO().createProcedure(procedure);
+ return procedure;
+ }
+
+ public void save() throws UserFailureException
+ {
+ assert externalData != null : "Undefined external data.";
+ IExternalDataDAO externalDataDAO = getExternalDataDAO();
+ String dataCode = externalData.getCode();
+ ExternalDataPE data = externalDataDAO.tryToFindDataSetByCode(dataCode);
+ if (data == null)
+ {
+ externalDataDAO.createDataSet(externalData);
+ } else
+ {
+ if (data.isPlaceholder() == false)
+ {
+ throw new UserFailureException("Already existing data set for code '"
+ + dataCode + "' can not be updated by data set " + externalData);
+ }
+ data.setPlaceholder(false);
+ data.setComplete(externalData.getComplete());
+ data.setDataProducerCode(externalData.getDataProducerCode());
+ data.setDataSetType(externalData.getDataSetType());
+ data.setFileFormatType(externalData.getFileFormatType());
+ data.setLocatorType(externalData.getLocatorType());
+ data.setLocation(externalData.getLocation());
+ data.setProcedure(externalData.getProcedure());
+ data.setParents(externalData.getParents());
+ data.setProductionDate(externalData.getProductionDate());
+ data.setRegistrationDate(new Date());
+ data.setSampleAcquiredFrom(externalData.getSampleAcquiredFrom());
+ data.setSampleDerivedFrom(externalData.getSampleDerivedFrom());
+ data.setStorageFormatVocabularyTerm(externalData.getStorageFormatVocabularyTerm());
+ externalDataDAO.updateDataSet(externalData);
+ }
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
index e4e8ad2d4bb..897693f39e4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ICommonBusinessObjectFactory.java
@@ -37,6 +37,11 @@ public interface ICommonBusinessObjectFactory
*/
public ISampleBO createSampleBO(final Session session);
+ /**
+ * Creates a {@link IExternalDataBO} <i>Business Object</i>.
+ */
+ public IExternalDataBO createExternalDataBO(Session session);
+
/**
* Creates a {@link IExternalDataTable} <i>Business Object</i>.
*/
@@ -82,4 +87,5 @@ public interface ICommonBusinessObjectFactory
* Creates a {@link IProjectBO} <i>Business Object</i>.
*/
public IProjectBO createProjectBO(final Session session);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataBO.java
new file mode 100644
index 00000000000..7e17dd55504
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExternalDataBO.java
@@ -0,0 +1,45 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server.business.bo;
+
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProcedurePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SourceType;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IExternalDataBO extends IBusinessObject
+{
+ /**
+ * Returns the external data item which has been created by
+ * {@link #define(ExternalData, ProcedurePE, SamplePE, SourceType)}.
+ */
+ public ExternalDataPE getExternalData();
+
+ /**
+ * Defines a new external data item. After invocation of this method {@link IExperimentBO#save()} should
+ * be invoked to store the new external data item in the Data Access Layer.
+ */
+ public void define(ExternalData externalData, ProcedurePE procedure, SamplePE sample,
+ SourceType sourceType);
+
+}
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 af5414e030b..0bc83b2aa8c 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
@@ -88,4 +88,13 @@ public interface IDAOFactory extends IAuthorizationDAOFactory
/** Returns an implementation of {@link IExperimentAttachmentDAO}. */
public IExperimentAttachmentDAO getExperimentAttachmentDAO();
+
+ /** Returns an implementation of {@link IDataSetTypeDAO}. */
+ public IDataSetTypeDAO getDataSetTypeDAO();
+
+ /** Returns an implementation of {@link IFileFormatTypeDAO}. */
+ public IFileFormatTypeDAO getFileFormatTypeDAO();
+
+ /** Returns an implementation of {@link ILocatorTypeDAO}. */
+ public ILocatorTypeDAO getLocatorTypeDAO();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataSetTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataSetTypeDAO.java
new file mode 100644
index 00000000000..c912e19bac7
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IDataSetTypeDAO.java
@@ -0,0 +1,33 @@
+/*
+ * 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.DataSetTypePE;
+
+/**
+ * Interface to the data access layer for retrieving instances of {@link DataSetTypePE}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IDataSetTypeDAO
+{
+ /**
+ * Tries to find the {@link DataSetTypePE} for the specified code.
+ */
+ public DataSetTypePE tryToFindDataSetTypeByCode(String code);
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExternalDataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExternalDataDAO.java
index bf5c2eaa415..a2d5f8267a7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExternalDataDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExternalDataDAO.java
@@ -39,5 +39,25 @@ public interface IExternalDataDAO
*/
public List<ExternalDataPE> listExternalData(final SamplePE sample, final SourceType sourceType)
throws DataAccessException;
+
+ /**
+ * Tries to get the data set for the specified code.
+ */
+ public ExternalDataPE tryToFindDataSetByCode(String dataSetCode);
+
+ /**
+ * Creates a unique data set code.
+ */
+ public String createDataSetCode();
+ /**
+ * Persists the specified data set.
+ */
+ public void createDataSet(ExternalDataPE dataset);
+
+ /**
+ * Updates the specified data set.
+ */
+ public void updateDataSet(ExternalDataPE dataset);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IFileFormatTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IFileFormatTypeDAO.java
new file mode 100644
index 00000000000..e14d47f9ef6
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IFileFormatTypeDAO.java
@@ -0,0 +1,33 @@
+/*
+ * 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.FileFormatTypePE;
+
+/**
+ * Interface to the data access layer for retrieving instances of {@link FileFormatTypePE}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IFileFormatTypeDAO
+{
+ /**
+ * Tries to find the {@link FileFormatTypePE} for the specified code.
+ */
+ public FileFormatTypePE tryToFindFileFormatTypeByCode(String code);
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ILocatorTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ILocatorTypeDAO.java
new file mode 100644
index 00000000000..d3ff1e204e4
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/ILocatorTypeDAO.java
@@ -0,0 +1,33 @@
+/*
+ * 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.LocatorTypePE;
+
+/**
+ * Interface to the data access layer for retrieving instances of {@link LocatorTypePE}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface ILocatorTypeDAO
+{
+ /**
+ * Tries to find the {@link LocatorTypePE} for the specified code.
+ */
+ public LocatorTypePE tryToFindLocatorTypeByCode(String code);
+
+}
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 c0d1616505b..356259b1125 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
@@ -23,12 +23,15 @@ 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.IEntityPropertyTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentAttachmentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IFileFormatTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IHibernateSearchDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ILocatorTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProcedureDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProcedureTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
@@ -69,11 +72,17 @@ public final class DAOFactory extends AuthorizationDAOFactory implements IDAOFac
private final IVocabularyDAO vocabularyDAO;
- private IProcedureTypeDAO procedureTypeDAO;
+ private final IProcedureTypeDAO procedureTypeDAO;
- private IProcedureDAO procedureDAO;
+ private final IProcedureDAO procedureDAO;
- private IExperimentAttachmentDAO experimentAttachmentDAO;
+ private final IExperimentAttachmentDAO experimentAttachmentDAO;
+
+ private final DataSetTypeDAO dataSetTypeDAO;
+
+ private final FileFormatTypeDAO fileFormatTypeDAO;
+
+ private final LocatorTypeDAO locatorTypeDAO;
public DAOFactory(final DatabaseConfigurationContext context,
final SessionFactory sessionFactory)
@@ -91,6 +100,9 @@ public final class DAOFactory extends AuthorizationDAOFactory implements IDAOFac
procedureTypeDAO = new ProcedureTypeDAO(sessionFactory, databaseInstance);
procedureDAO = new ProcedureDAO(sessionFactory, databaseInstance);
experimentAttachmentDAO = new ExperimentAttachmentDAO(sessionFactory, databaseInstance);
+ dataSetTypeDAO = new DataSetTypeDAO(sessionFactory, databaseInstance);
+ fileFormatTypeDAO = new FileFormatTypeDAO(sessionFactory, databaseInstance);
+ locatorTypeDAO = new LocatorTypeDAO(sessionFactory, databaseInstance);
final EntityKind[] entityKinds = EntityKind.values();
for (final EntityKind entityKind : entityKinds)
{
@@ -170,4 +182,19 @@ public final class DAOFactory extends AuthorizationDAOFactory implements IDAOFac
{
return experimentAttachmentDAO;
}
+
+ public IDataSetTypeDAO getDataSetTypeDAO()
+ {
+ return dataSetTypeDAO;
+ }
+
+ public IFileFormatTypeDAO getFileFormatTypeDAO()
+ {
+ return fileFormatTypeDAO;
+ }
+
+ public ILocatorTypeDAO getLocatorTypeDAO()
+ {
+ return locatorTypeDAO;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataSetTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataSetTypeDAO.java
new file mode 100644
index 00000000000..cb5a6b21152
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataSetTypeDAO.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.dataaccess.db;
+
+import org.hibernate.SessionFactory;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataSetTypeDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+
+/**
+ * Data access object for {@link DataSetTypePE}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataSetTypeDAO extends AbstractTypeDAO<DataSetTypePE> implements IDataSetTypeDAO
+{
+ public DataSetTypeDAO(SessionFactory sessionFactory, DatabaseInstancePE databaseInstance)
+ {
+ super(sessionFactory, databaseInstance);
+ }
+
+ @Override
+ Class<?> getEntityClass()
+ {
+ return DataSetTypePE.class;
+ }
+
+ public DataSetTypePE tryToFindDataSetTypeByCode(String code)
+ {
+ return tryFindTypeByCode(code);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java
index 735af0434f0..9f6cad195d4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExternalDataDAO.java
@@ -16,18 +16,26 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.db;
+import java.util.Date;
import java.util.List;
+import net.sf.beanlib.hibernate3.Hibernate3SequenceGenerator;
+
+import org.apache.commons.lang.time.DateFormatUtils;
import org.apache.log4j.Logger;
import org.hibernate.SessionFactory;
import org.springframework.dao.DataAccessException;
+import org.springframework.orm.hibernate3.HibernateTemplate;
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.shared.dto.CodeConverter;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
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.SequenceNames;
import ch.systemsx.cisd.openbis.generic.shared.dto.SourceType;
/**
@@ -37,6 +45,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SourceType;
*/
final class ExternalDataDAO extends AbstractDAO implements IExternalDataDAO
{
+ private final static String DATA_CODE_DATE_FORMAT_PATTERN = "yyyyMMddHHmmssSSS";
+
private final static Class<ExternalDataPE> ENTITY_CLASS = ExternalDataPE.class;
private static final Logger operationLog =
@@ -71,4 +81,57 @@ final class ExternalDataDAO extends AbstractDAO implements IExternalDataDAO
}
return list;
}
+
+ public ExternalDataPE tryToFindDataSetByCode(String dataSetCode)
+ {
+ assert dataSetCode != null : "Unspecified data set code.";
+
+ final List<ExternalDataPE> list =
+ cast(getHibernateTemplate().find(
+ String.format("select e from %s e where e.code = ?", ENTITY_CLASS.getSimpleName()),
+ toArray(dataSetCode)));
+ final ExternalDataPE 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 String createDataSetCode()
+ {
+ long id =
+ Hibernate3SequenceGenerator.nextval(SequenceNames.DATA_SEQUENCE, getSession(true));
+ return DateFormatUtils.format(new Date(), DATA_CODE_DATE_FORMAT_PATTERN) + "-"
+ + Long.toString(id);
+ }
+
+ public void createDataSet(ExternalDataPE dataset)
+ {
+ assert dataset != null : "Unspecified data set.";
+
+ dataset.setCode(CodeConverter.tryToDatabase(dataset.getCode()));
+ final HibernateTemplate template = getHibernateTemplate();
+ template.save(dataset);
+ template.flush();
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info(String.format("ADD: data set '%s'.", dataset));
+ }
+ }
+
+ public void updateDataSet(ExternalDataPE dataset)
+ {
+ assert dataset != null : "Given data set can not be null.";
+ validatePE(dataset);
+
+ final HibernateTemplate template = getHibernateTemplate();
+ template.update(dataset);
+ template.flush();
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info(String.format("UPDATE: data set '%s'.", dataset));
+ }
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/FileFormatTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/FileFormatTypeDAO.java
new file mode 100644
index 00000000000..3322a453a5c
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/FileFormatTypeDAO.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.dataaccess.db;
+
+import org.hibernate.SessionFactory;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IFileFormatTypeDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+
+/**
+ * Data access object for {@link FileFormatTypePE}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FileFormatTypeDAO extends AbstractTypeDAO<FileFormatTypePE> implements IFileFormatTypeDAO
+{
+ public FileFormatTypeDAO(SessionFactory sessionFactory, DatabaseInstancePE databaseInstance)
+ {
+ super(sessionFactory, databaseInstance);
+ }
+
+ @Override
+ Class<?> getEntityClass()
+ {
+ return FileFormatTypePE.class;
+ }
+
+ public FileFormatTypePE tryToFindFileFormatTypeByCode(String code)
+ {
+ return tryFindTypeByCode(code);
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/LocatorTypeDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/LocatorTypeDAO.java
new file mode 100644
index 00000000000..b63087725b0
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/LocatorTypeDAO.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.dataaccess.db;
+
+import org.hibernate.SessionFactory;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ILocatorTypeDAO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+
+/**
+ * Data access object for {@link LocatorTypePE}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class LocatorTypeDAO extends AbstractTypeDAO<LocatorTypePE> implements ILocatorTypeDAO
+{
+ public LocatorTypeDAO(SessionFactory sessionFactory, DatabaseInstancePE databaseInstance)
+ {
+ super(sessionFactory, databaseInstance);
+ }
+
+ @Override
+ Class<?> getEntityClass()
+ {
+ return LocatorTypePE.class;
+ }
+
+ public LocatorTypePE tryToFindLocatorTypeByCode(String code)
+ {
+ return tryFindTypeByCode(code);
+ }
+
+}
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 053fd0e2a36..52403090843 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
@@ -41,9 +41,9 @@ public interface IETLLIMSService extends IWebService, IDataStoreInfoProvider
*
* @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>dataSetInfo</var>.
+ * @return <code>null</code> if no experiment could be found for given <var>sampleIdentifier</var>.
*/
- public ExperimentPE getBaseExperiment(final String sessionToken,
+ public ExperimentPE tryToGetBaseExperiment(final String sessionToken,
final SampleIdentifier sampleIdentifier) throws UserFailureException;
/**
@@ -55,7 +55,7 @@ public interface IETLLIMSService extends IWebService, IDataStoreInfoProvider
* @return <code>null</code> if no appropriated sample found. Returns an empty array if a a
* sample found with no properties.
*/
- public SamplePropertyPE[] getPropertiesOfTopSampleRegisteredFor(final String sessionToken,
+ public SamplePropertyPE[] tryToGetPropertiesOfTopSampleRegisteredFor(final String sessionToken,
final SampleIdentifier sampleIdentifier) throws UserFailureException;
/**
--
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