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Commit b5d3e441 authored by cramakri's avatar cramakri
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LMS-1503 Added server-side support for data set registration using the api. 

SVN: 16252
parent b21ab898
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datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetRegistrationHelper.java deleted 100644 → 0
+ 0
− 167
View file @ b21ab898
/*
* Copyright 2010 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.etlserver.api.v1;
import java.io.File;
import java.util.concurrent.locks.Lock;
import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.filesystem.FileOperations;
import ch.systemsx.cisd.common.filesystem.IFileOperations;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
import ch.systemsx.cisd.etlserver.IDataStrategyStore;
import ch.systemsx.cisd.etlserver.IETLServerPlugin;
import ch.systemsx.cisd.etlserver.IStorageProcessor;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
/**
* @author Chandrasekhar Ramakrishnan
*/
class DataSetRegistrationHelper extends DataSetRegistrationAlgorithm
{
private final PutDataSetService service;
private final IETLServerPlugin plugin;
/**
* @param incomingDataSetFile
* @param cleanAftrewardsAction
*/
public DataSetRegistrationHelper(PutDataSetService service, IETLServerPlugin plugin,
File incomingDataSetFile, IDelegatedActionWithResult<Boolean> cleanAftrewardsAction)
{
super(incomingDataSetFile, cleanAftrewardsAction);
this.service = service;
this.plugin = plugin;
}
@Override
protected IDataSetInfoExtractor getDataSetInfoExtractor()
{
return plugin.getDataSetInfoExtractor();
}
@Override
protected IDataSetValidator getDataSetValidator()
{
// TODO Auto-generated method stub
return null;
}
@Override
protected String getDataStoreCode()
{
// TODO Auto-generated method stub
return null;
}
@Override
protected IDataStrategyStore getDataStrategyStore()
{
// TODO Auto-generated method stub
return null;
}
@Override
protected String getEmailSubjectTemplate()
{
// TODO Auto-generated method stub
return null;
}
@Override
protected IFileOperations getFileOperations()
{
return FileOperations.getMonitoredInstanceForCurrentThread();
}
@Override
protected DatabaseInstance getHomeDatabaseInstance()
{
// TODO Auto-generated method stub
return null;
}
@Override
protected IMailClient getMailClient()
{
return service.getMailClient();
}
@Override
protected Logger getNotificationLog()
{
return service.getOperationLog();
}
@Override
protected IEncapsulatedOpenBISService getOpenBisService()
{
return service.getOpenBisService();
}
@Override
protected Logger getOperationLog()
{
return service.getOperationLog();
}
@Override
protected Lock getRegistrationLock()
{
return service.getRegistrationLock();
}
@Override
protected IStorageProcessor getStorageProcessor()
{
return plugin.getStorageProcessor();
}
@Override
protected ITypeExtractor getTypeExtractor()
{
return plugin.getTypeExtractor();
}
@Override
protected void rollback(Throwable ex)
{
rollbackStorageProcessor(ex);
}
@Override
protected boolean shouldDeleteUnidentified()
{
return true;
}
@Override
protected boolean shouldNotifySuccessfulRegistration()
{
return false;
}
}
datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
+ 264
− 23
View file @ b5d3e441
......@@ -23,19 +23,33 @@ import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.concurrent.locks.Lock;
import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.FileOperations;
import ch.systemsx.cisd.common.filesystem.IFileOperations;
import ch.systemsx.cisd.common.io.ConcatenatedFileOutputStreamWriter;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
import ch.systemsx.cisd.etlserver.IDataStrategyStore;
import ch.systemsx.cisd.etlserver.IETLServerPlugin;
import ch.systemsx.cisd.etlserver.IStorageProcessor;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.etlserver.TransferredDataSetHandler;
import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwner;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
......@@ -72,6 +86,10 @@ class PutDataSetExecutor
this.newDataSet = newDataSet;
this.inputStream = inputStream;
this.dataSetDir = new File(service.getIncomingDir(), newDataSet.getDataSetFolderName());
if (dataSetDir.exists())
{
deleteDataSetDir();
}
if (false == this.dataSetDir.mkdir())
{
throw new EnvironmentFailureException("Could not create directory for data set "
......@@ -94,16 +112,25 @@ class PutDataSetExecutor
writeDataSetToTempDirectory();
// TODO: When registering, set the registrator to the session owner; only an admin on
// the space or an ETL server can override.
// Register data set
DataSetRegistrationHelper helper =
new DataSetRegistrationHelper(service, plugin, dataSetDir, null);
helper.prepare();
helper.registerDataSet();
deleteDataSetDir();
// Register the data set
try
{
DataSetRegistrationHelper helper =
new DataSetRegistrationHelper(service, plugin, dataSetDir);
helper.prepare();
if (helper.hasDataSetBeenIdentified())
{
helper.registerDataSet();
} else
{
helper.dealWithUnidentifiedDataSet();
throw new UserFailureException("Could not find owner:\n\t"
+ newDataSet.getDataSetOwner() + "\nfor data set:\n\t" + newDataSet);
}
} finally
{
deleteDataSetDir();
}
}
private void writeDataSetToTempDirectory() throws IOException
......@@ -114,6 +141,8 @@ class PutDataSetExecutor
{
OutputStream output = getOutputStream(fileInfo);
imagesWriter.writeNextBlock(output);
output.flush();
output.close();
}
}
......@@ -148,24 +177,65 @@ class PutDataSetExecutor
private SpaceIdentifier getSpaceIdentifierForNewDataSet()
{
SpaceIdentifier spaceId;
SpaceIdentifier spaceId = null;
DataSetOwner owner = newDataSet.getDataSetOwner();
if (DataSetOwnerType.EXPERIMENT == owner.getType())
{
ExperimentIdentifier experimentId =
new ExperimentIdentifierFactory(owner.getIdentifier()).createIdentifier();
spaceId =
new SpaceIdentifier(experimentId.getDatabaseInstanceCode(), experimentId
.getSpaceCode());
} else
switch (owner.getType())
{
SampleIdentifier sampleId =
new SampleIdentifierFactory(owner.getIdentifier()).createIdentifier();
spaceId = sampleId.getSpaceLevel();
case EXPERIMENT:
{
ExperimentIdentifier experimentId = tryExperimentIdentifier();
spaceId =
new SpaceIdentifier(experimentId.getDatabaseInstanceCode(), experimentId
.getSpaceCode());
break;
}
case SAMPLE:
{
SampleIdentifier sampleId = trySampleIdentifier();
spaceId = sampleId.getSpaceLevel();
break;
}
}
return spaceId;
}
private ExperimentIdentifier tryExperimentIdentifier()
{
DataSetOwner owner = newDataSet.getDataSetOwner();
switch (owner.getType())
{
case EXPERIMENT:
{
return new ExperimentIdentifierFactory(owner.getIdentifier()).createIdentifier();
}
case SAMPLE:
{
return null;
}
}
return null;
}
private SampleIdentifier trySampleIdentifier()
{
DataSetOwner owner = newDataSet.getDataSetOwner();
switch (owner.getType())
{
case EXPERIMENT:
{
return null;
}
case SAMPLE:
{
return new SampleIdentifierFactory(owner.getIdentifier()).createIdentifier();
}
}
return null;
}
private IEncapsulatedOpenBISService getOpenBisService()
{
return service.getOpenBisService();
......@@ -175,4 +245,175 @@ class PutDataSetExecutor
{
return service.getOperationLog();
}
private static class CleanAfterwardsAction implements IDelegatedActionWithResult<Boolean>
{
public Boolean execute()
{
return true; // do nothing
}
}
/**
* An implementation of the registration algorithm that gets its state from the executor.
*
* @author Chandrasekhar Ramakrishnan
*/
private class DataSetRegistrationHelper extends DataSetRegistrationAlgorithm
{
/**
* @param service The provider of global state for the data set registration algorithm
* @param plugin The provider of the storage processor
* @param incomingDataSetFile The data set to register
*/
public DataSetRegistrationHelper(PutDataSetService service, IETLServerPlugin plugin,
File incomingDataSetFile)
{
super(incomingDataSetFile, new CleanAfterwardsAction());
}
@Override
protected IDataSetInfoExtractor getDataSetInfoExtractor()
{
return plugin.getDataSetInfoExtractor();
}
@Override
protected IDataSetValidator getDataSetValidator()
{
return service.getDataSetValidator();
}
@Override
protected String getDataStoreCode()
{
return service.getDataStoreCode();
}
@Override
protected IDataStrategyStore getDataStrategyStore()
{
return service.getDataStrategyStore();
}
@Override
protected String getEmailSubjectTemplate()
{
return TransferredDataSetHandler.EMAIL_SUBJECT_TEMPLATE;
}
@Override
protected IFileOperations getFileOperations()
{
return FileOperations.getMonitoredInstanceForCurrentThread();
}
@Override
protected DatabaseInstance getHomeDatabaseInstance()
{
return service.getHomeDatabaseInstance();
}
@Override
protected IMailClient getMailClient()
{
return service.getMailClient();
}
@Override
protected Logger getNotificationLog()
{
return service.getOperationLog();
}
@Override
protected IEncapsulatedOpenBISService getOpenBisService()
{
return service.getOpenBisService();
}
@Override
protected Logger getOperationLog()
{
return service.getOperationLog();
}
@Override
protected Lock getRegistrationLock()
{
return service.getRegistrationLock();
}
@Override
protected IStorageProcessor getStorageProcessor()
{
return plugin.getStorageProcessor();
}
@Override
protected ITypeExtractor getTypeExtractor()
{
return plugin.getTypeExtractor();
}
@Override
protected void rollback(Throwable ex)
{
rollbackStorageProcessor(ex);
if (ex instanceof UserFailureException)
{
throw (UserFailureException) ex;
}
throw new EnvironmentFailureException("Could not register data set " + newDataSet, ex);
}
@Override
protected boolean shouldDeleteUnidentified()
{
return true;
}
@Override
protected boolean shouldNotifySuccessfulRegistration()
{
return false;
}
@Override
protected DataSetInformation extractDataSetInformation(final File incomingDataSetPath)
{
DataSetInformation dataSetInfo = super.extractDataSetInformation(incomingDataSetPath);
if (null == dataSetInfo)
{
return dataSetInfo;
}
DataSetOwner owner = newDataSet.getDataSetOwner();
switch (owner.getType())
{
case EXPERIMENT:
dataSetInfo.setExperimentIdentifier(tryExperimentIdentifier());
break;
case SAMPLE:
SampleIdentifier sampleId = trySampleIdentifier();
dataSetInfo.setSampleCode(sampleId.getSampleCode());
dataSetInfo.setSpaceCode(sampleId.getSpaceLevel().getSpaceCode());
dataSetInfo.setInstanceCode(sampleId.getSpaceLevel().getDatabaseInstanceCode());
break;
}
// TODO: Get the session owner's email address from OpenBIS
// dataSetInfo.setUploadingUserEmail()
// TODO: When registering, set the registrator to the session owner; only an admin on
// the space or an ETL server can override.
return dataSetInfo;
}
@Override
protected DataSetType extractDataSetType()
{
return new DataSetType(newDataSet.getDataSetType());
}
}
}
datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
+ 57
− 3
View file @ b5d3e441
......@@ -32,8 +32,12 @@ import ch.systemsx.cisd.etlserver.DataStrategyStore;
import ch.systemsx.cisd.etlserver.IETLServerPlugin;
import ch.systemsx.cisd.etlserver.Parameters;
import ch.systemsx.cisd.etlserver.ThreadParameters;
import ch.systemsx.cisd.etlserver.validation.DataSetValidator;
import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
/**
* Helper class that maintains the state for handling put requests. The requests themselves are
......@@ -51,6 +55,12 @@ public class PutDataSetService
private final DataStrategyStore dataStrategyStore;
// These are all initialized only once, but it is not possible to initialize them at
// construction time, since this causes a dependency loop that causes problems in Spring.
private File storeDirectory;
private String dataStoreCode;
private boolean isInitialized = false;
private MailClient mailClient;
......@@ -59,6 +69,10 @@ public class PutDataSetService
private File incomingDir;
private IDataSetValidator dataSetValidator;
private DatabaseInstance homeDatabaseInstance;
public PutDataSetService(IEncapsulatedOpenBISService openBisService, Logger operationLog)
{
this.openBisService = openBisService;
......@@ -80,7 +94,6 @@ public class PutDataSetService
try
{
new PutDataSetExecutor(this, plugin, sessionToken, newDataSet, inputStream).execute();
} catch (UserFailureException e)
{
throw new IllegalArgumentException(e);
......@@ -108,9 +121,16 @@ public class PutDataSetService
incomingDir.mkdir();
plugin = initializer.getPlugin();
plugin.getStorageProcessor().setStoreRootDirectory(storeDirectory);
mailClient = new MailClient(initializer.getMailProperties());
this.dataStoreCode = initializer.getDataStoreCode();
homeDatabaseInstance = openBisService.getHomeDatabaseInstance();
dataSetValidator = initializer.getDataSetValidator();
isInitialized = true;
}
......@@ -134,16 +154,41 @@ public class PutDataSetService
return operationLog;
}
public Lock getRegistrationLock()
Lock getRegistrationLock()
{
return registrationLock;
}
public DataStrategyStore getDataStrategyStore()
DataStrategyStore getDataStrategyStore()
{
return dataStrategyStore;
}
String getDataStoreCode()
{
return dataStoreCode;
}
IDataSetValidator getDataSetValidator()
{
return dataSetValidator;
}
DatabaseInstance getHomeDatabaseInstance()
{
return homeDatabaseInstance;
}
public File getStoreRootDirectory()
{
return storeDirectory;
}
public void setStoreDirectory(File storeDirectory)
{
this.storeDirectory = storeDirectory;
}
}
/**
......@@ -176,4 +221,13 @@ class PutDataSetServiceInitializer
return threadParams[0].getPlugin();
}
String getDataStoreCode()
{
return DssPropertyParametersUtil.getDataStoreCode(params.getProperties());
}
DataSetValidator getDataSetValidator()
{
return new DataSetValidator(params.getProperties());
}
}
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