net.sf.basedb.ws.client
Class BioAssaySetClient

java.lang.Object
  net.sf.basedb.ws.client.AbstractRPCClient
      net.sf.basedb.ws.client.BioAssaySetClient

public class BioAssaySetClient
extends AbstractRPCClient

Web service client for BioAssaySetService in BASE. BioAssaySetService

Version:

2.5

Author:

Martin

Field Summary

private SessionClient

session

Constructor Summary

BioAssaySetClient(SessionClient session)
Creates new BioAssayClient for a session.

Method Summary

InputStream	downloadBioAssaySet(int bioAssaySetId, String format, String[] reporterFields, String[] spotFields, boolean mergeReporters) Deprecated. In 2.12. See BioAssaySetService.downloadBioAssaySet(String, int, String, String[], String[], Boolean) for more information. Use downloadDataFile(int, String) instead.
InputStream	downloadDataFile(int bioAssaySetId, String dataFileType) Gets spot data as a file for a bioassay set if it is stored in a file in BASE.
DataFileTypeInfo[]	getDataFileTypes(int bioAssaySetId, QueryOptions qOpt) Returns information about data file types that are used storing spot data for a bioassay set.
String[]	getExportFormats() Deprecated. In 2.12. Use getDataFileTypes(int, QueryOptions) instead.
Boolean	hasDownloadableData(int bioAssaySetId) Returns if a bioassay set has spot data in the form of files that can be downloaded or not.

Methods inherited from class net.sf.basedb.ws.client.AbstractRPCClient

getOperation, getService, getServiceFactory, invokeBlocking, invokeBlocking, invokeBlocking, invokeFileBlocking, setServiceFactory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

session

private final SessionClient session

Constructor Detail

BioAssaySetClient

public BioAssaySetClient(SessionClient session)

Creates new BioAssayClient for a session.

Parameters:

session - Active session.

Method Detail

getExportFormats

public String[] getExportFormats()
                          throws org.apache.axis2.AxisFault

Deprecated. In 2.12. Use getDataFileTypes(int, QueryOptions) instead.

Calls the BioAssaySetService and gets the available formats to export a BioAssaySet from BASE in.

Returns:

An array with the formats.

Throws:

org.apache.axis2.AxisFault - If communication with the service fails.

downloadBioAssaySet

public InputStream downloadBioAssaySet(int bioAssaySetId,
                                       String format,
                                       String[] reporterFields,
                                       String[] spotFields,
                                       boolean mergeReporters)
                                throws org.apache.axis2.AxisFault,
                                       IOException

Deprecated. In 2.12. See BioAssaySetService.downloadBioAssaySet(String, int, String, String[], String[], Boolean) for more information. Use downloadDataFile(int, String) instead.

Call the service in BioAssaySetService that exports a bioassay set and then sends it as a file.

Parameters:

bioAssaySetId - Id of the bioAssay set to export

format - Export format to use when exporting the bioassay set

reporterFields - Reporter fields to include in the export

spotFields - Spot fields to include in the export

mergeReporters - If the reporters should be merged or not.

Returns:

An InputStream to read the file data from

Throws:

org.apache.axis2.AxisFault - If communication with services fails.

IOException - If accessing the file files.

hasDownloadableData

public Boolean hasDownloadableData(int bioAssaySetId)
                            throws org.apache.axis2.AxisFault

Returns if a bioassay set has spot data in the form of files that can be downloaded or not.

Parameters:

bioAssaySetId - Id of the bioassay set it concerns.

Returns:

TRUE if there are data to be downloaded, FALSE otherwise.

Throws:

org.apache.axis2.AxisFault - If the communication with the webservice fails.

Since:

2.12

getDataFileTypes

public DataFileTypeInfo[] getDataFileTypes(int bioAssaySetId,
                                           QueryOptions qOpt)
                                    throws org.apache.axis2.AxisFault

Returns information about data file types that are used storing spot data for a bioassay set.

Parameters:

bioAssaySetId - Id of the bioassay set to get the information about.

qOpt - Restrictions and includes to put on the query when getting the information.

Returns:

An array of DataFileTypeInfo, one for each data file type used in the raw bioassay.

Throws:

org.apache.axis2.AxisFault - If communication with webservice fails.

Since:

2.12

downloadDataFile

public InputStream downloadDataFile(int bioAssaySetId,
                                    String dataFileType)
                             throws org.apache.axis2.AxisFault,
                                    IOException

Gets spot data as a file for a bioassay set if it is stored in a file in BASE.

Parameters:

bioAssaySetId - Id of bioassay set to get the file from

dataFileType - The external ID of the data file type to download

Returns:

An InputStream to read the file data from, or null if no file of the specified type exists

Throws:

org.apache.axis2.AxisFault - If communication with webservices fails.

IOException - If writing to the target file fails.

Since:

2.12