net.sf.basedb.ws.server
Class RawBioAssayService

java.lang.Object
  net.sf.basedb.ws.server.AbstractRPCService
      net.sf.basedb.ws.server.RawBioAssayService

public class RawBioAssayService
extends AbstractRPCService

Web service class for RawBioAssay

Version:

2.5

Author:

Martin

Field Summary

Fields inherited from class net.sf.basedb.ws.server.AbstractRPCService

util

Constructor Summary

RawBioAssayService()

Method Summary

org.apache.axiom.om.OMElement	downloadRawDataByType(String ID, int rawBioAssayId, String dataFileType) Returns a rawdata file of a certain type attached to an OMElement.
AnnotationInfo[]	getAnnotations(String ID, int rawBioAssayId, Integer[] annotationTypes, boolean findInherited) Get the annotation values for one or more annotation types.
ArrayDesignInfo	getArrayDesign(String ID, int rawBioAssayId) Gets information about the array design used in a rawbioassay.
RawBioAssayInfo	getById(String ID, int itemId) Get information about a raw bioassay that you know the ID of.
DataFileTypeInfo[]	getDataFileTypes(String ID, int rawBioAssayId, QueryOptions qOpt) Returns information objects for each DataFileType represented in the FileSet of a RawBioAssay.
RawBioAssayInfo[]	getRawBioAssays(String ID, QueryOptions qOpt) Gets an array with info about raw bioassays available for the active session.
Boolean	hasDownloadableData(String ID, int rawBioAssayId) Gets if the rawdata files can be downloaded or not.

Methods inherited from class net.sf.basedb.ws.server.AbstractRPCService

attachFile, getRemoteId, getSessionControl

Methods inherited from class java.lang.Object

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

Constructor Detail

RawBioAssayService

public RawBioAssayService()

Method Detail

getById

public RawBioAssayInfo getById(String ID,
                               int itemId)

Get information about a raw bioassay that you know the ID of.

Parameters:

ID - Id to identify the session.

itemId - The ID of the raw bioassay

Returns:

The raw bioassay information

getRawBioAssays

public RawBioAssayInfo[] getRawBioAssays(String ID,
                                         QueryOptions qOpt)

Gets an array with info about raw bioassays available for the active session.

Parameters:

ID - Id for the session to use.

qOpt - QueryOptions to put on the query

Returns:

An RawBioAssayInfo array.

getArrayDesign

public ArrayDesignInfo getArrayDesign(String ID,
                                      int rawBioAssayId)

Gets information about the array design used in a rawbioassay.

Parameters:

ID - To identify the active session with

rawBioAssayId - ArrayDesign from RawBioAssay with this id.

Returns:

ArrayDesignInfo object containing information about the used arraydesign.

downloadRawDataByType

public org.apache.axiom.om.OMElement downloadRawDataByType(String ID,
                                                           int rawBioAssayId,
                                                           String dataFileType)

Returns a rawdata file of a certain type attached to an OMElement.

Parameters:

ID - Used to identify an active session with.

rawBioAssayId - Id of the rawbio assay the file belongs to.

dataFileType - The external ID of the file type.

Returns:

OMElement with the file attached, or NULL if no file was found.

See Also:

DataFileType

hasDownloadableData

public Boolean hasDownloadableData(String ID,
                                   int rawBioAssayId)

Gets if the rawdata files can be downloaded or not.

Parameters:

ID - Used to identify an active session with

rawBioAssayId - Id of the rawbio assay it concerns

Returns:

TRUE if there are files to download, FALSE otherwise.

getDataFileTypes

public DataFileTypeInfo[] getDataFileTypes(String ID,
                                           int rawBioAssayId,
                                           QueryOptions qOpt)

Returns information objects for each DataFileType represented in the FileSet of a RawBioAssay.

Parameters:

ID - Id of the active session.

rawBioAssayId - Id of the rawbioassay it concerns

qOpt - Restrictions and includes to put on the query

Returns:

An array with DataFileTypeInfo:s.

getAnnotations

public AnnotationInfo[] getAnnotations(String ID,
                                       int rawBioAssayId,
                                       Integer[] annotationTypes,
                                       boolean findInherited)

Get the annotation values for one or more annotation types.

Parameters:

ID - Id of the active session.

rawBioAssayId - Id of the rawbioassay it concerns

annotationTypes - Array with the ID of the annotation types

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

Returns:

An array with AnnotationInfo object, each element in the array corresponds to the annotation type with the same index in the annotationTypes array