net.sf.basedb.ws.client
Class RawBioAssayClient

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

public class RawBioAssayClient
extends AbstractRPCClient

Webservice client for RawBioAssay. This class covers all services provided in RawBioAssayService

Version:

2.5

Author:

Martin

Field Summary

private SessionClient

session

Constructor Summary

RawBioAssayClient(SessionClient session)
Creates a new object for a session.

Method Summary

InputStream	downloadRawDataByType(int rawBioAssayId, String dataFileType) Gets RawData as a file for a rawbioassay if it is stored in a file in BASE.
AnnotationInfo[]	getAnnotationValues(int rawBioAssayId, Integer[] annotationTypes, boolean findInherited) Get annotation values for one or more annotation types.
ArrayDesignInfo	getArrayDesign(int rawBioAssayId) Returns information about the array design used in a rawbioassay
RawBioAssayInfo	getById(int itemId) Get info about a raw bioassay when you know the ID.
DataFileTypeInfo[]	getDataFileTypes(int rawBioAssayId, QueryOptions qOpt) Returns information about data file types that are used storing raw data for a raw bioassay.
RawBioAssayInfo[]	getRawBioAssays(QueryOptions qOpt) Gets info about raw bioassays that are available in the logged in session.
Boolean	hasDownloadableData(int rawBioAssayId) Returns if a rawbioassay has raw data 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 SessionClient session

Constructor Detail

RawBioAssayClient

public RawBioAssayClient(SessionClient session)

Creates a new object for a session.

Parameters:

session -

Method Detail

getById

public RawBioAssayInfo getById(int itemId)
                        throws org.apache.axis2.AxisFault

Get info about a raw bioassay when you know the ID.

Parameters:

itemId - The ID of the raw bioassay

Returns:

An RawBioAssayInfo object

Throws:

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

getRawBioAssays

public RawBioAssayInfo[] getRawBioAssays(QueryOptions qOpt)
                                  throws org.apache.axis2.AxisFault

Gets info about raw bioassays that are available in the logged in session.

Parameters:

qOpt - Options to put on the query

Returns:

An array with info object for each raw bioassay that was found.

Throws:

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

getArrayDesign

public ArrayDesignInfo getArrayDesign(int rawBioAssayId)
                               throws org.apache.axis2.AxisFault

Returns information about the array design used in a rawbioassay

Parameters:

rawBioAssayId - RawBioAssay to get the array design for.

Returns:

ArrayDesignInfo object.

Throws:

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

downloadRawDataByType

public InputStream downloadRawDataByType(int rawBioAssayId,
                                         String dataFileType)
                                  throws org.apache.axis2.AxisFault,
                                         IOException

Gets RawData as a file for a rawbioassay if it is stored in a file in BASE.

Parameters:

rawBioAssayId - Id of rawbioassay to get raw data 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.

hasDownloadableData

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

Returns if a rawbioassay has raw data that can be downloaded or not.

Parameters:

rawBioAssayId - Id of the RawBioAssay 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.

getDataFileTypes

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

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

Parameters:

rawBioAssayId - Id of the raw bioassay 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.

getAnnotationValues

public AnnotationInfo[] getAnnotationValues(int rawBioAssayId,
                                            Integer[] annotationTypes,
                                            boolean findInherited)
                                     throws org.apache.axis2.AxisFault

Get annotation values for one or more annotation types.

Parameters:

rawBioAssayId - Id of the raw bioassay to load the annotations from

annotationTypes - Array with the ID:s of the annotation types

findInherited - TRUE to look among inherited annotations, FALSE to only look among primary annotations

Returns:

An array with annotation information, each element corresponds to the annotation type at the same position in the annotationTypes array

Throws:

org.apache.axis2.AxisFault