net.sf.basedb.ws.server
Class BioAssaySetService

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

public class BioAssaySetService
extends AbstractRPCService

Web service for BioAssaySet BioAssaySet. This class provides services to get information and data from BioAssaySet.

Version:

2.5

Author:

Martin

Field Summary

private static String	MATRIX_BASEFILE
private static String	MEV
private static String	SERIAL_BASEFILE

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

util

Constructor Summary

BioAssaySetService()

Method Summary

org.apache.axiom.om.OMElement	downloadBioAssaySet(String ID, int bioAssaySetId, String format, String[] reporterFieldArray, String[] spotFieldArray, Boolean mergeReporters) Deprecated. In 2.12. Spot data should not be exported dynamically. Instead, plug-ins should be used and attach the result to the bioassay set and the files can then be downloaded when needed. Use downloadDataFile(String, int, String) instead.
org.apache.axiom.om.OMElement	downloadDataFile(String ID, int bioAssaySetId, String dataFileType) Returns a data file of a certain type attached to an OMElement.
AnnotationInfo[]	getAnnotations(String ID, int bioAssaySetId, Integer[] annotationTypes, boolean findInherited) Get the annotation values for one or more annotation types.
DataFileTypeInfo[]	getDataFileTypes(String ID, int bioAssaySetId, QueryOptions qOpt) Returns information objects for each DataFileType represented in the FileSet of a BioAssaySet.
String[]	getExportFormats(String ID) Deprecated. In 2.12. Use getDataFileTypes(String, int, QueryOptions) instead
Boolean	hasDownloadableData(String ID, int bioAssaySetId) Checks if the files has been attached to bioassay set.

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

Field Detail

SERIAL_BASEFILE

private static final String SERIAL_BASEFILE

See Also:

Constant Field Values

MATRIX_BASEFILE

private static final String MATRIX_BASEFILE

See Also:

Constant Field Values

MEV

private static final String MEV

See Also:

Constant Field Values

Constructor Detail

BioAssaySetService

public BioAssaySetService()

Method Detail

getExportFormats

public String[] getExportFormats(String ID)

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

Gets the available file formats a bioassay set can be exported in through webservices.

Parameters:

ID - A string that identify the active session

Returns:

A string-array with the available formats or null if there is no active session.

downloadBioAssaySet

public org.apache.axiom.om.OMElement downloadBioAssaySet(String ID,
                                                         int bioAssaySetId,
                                                         String format,
                                                         String[] reporterFieldArray,
                                                         String[] spotFieldArray,
                                                         Boolean mergeReporters)
                                                  throws Exception

Deprecated. In 2.12. Spot data should not be exported dynamically. Instead, plug-ins should be used and attach the result to the bioassay set and the files can then be downloaded when needed. Use downloadDataFile(String, int, String) instead.

Returns an OMElement with an attached file that contains the exported bioassay set. Different file formats to export the bioassay set is available There may be some parameters that needs to be configured depending on the selected file format.

Parameters:

ID - An id to identify the active session with

bioAssaySetId - The id of the bioassay-set, which should be exported.

format - File format of which the bioassay set should be exported in. Available formats are:

• "Mev file" (deprecated in BASE 2.12). MeV support has been completely moved to the MeV extension (http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev) This web service will continue to
• "Serial BASEfile"
• "Matrix BASEfile"

reporterFieldArray - The reporter fields to include in the export

spotFieldArray - The spot fields to include in the export

mergeReporters - TRUE to merge spot data having the same reporter. see BioAssaySetExporter

Returns:

An OMElement containing the exported file or NULL if there an exception is thrown.

Throws:

Exception - If the data could not be exported to the file.

downloadDataFile

public org.apache.axiom.om.OMElement downloadDataFile(String ID,
                                                      int bioAssaySetId,
                                                      String dataFileType)

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

Parameters:

ID - Used to identify an active session with.

bioAssaySetId - Id of the bioassay set 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.

Since:

2.12

See Also:

DataFileType

hasDownloadableData

public Boolean hasDownloadableData(String ID,
                                   int bioAssaySetId)

Checks if the files has been attached to bioassay set.

Parameters:

ID - Used to identify an active session with

bioAssaySetId - Id of the bioassay set it concerns

Returns:

TRUE if there are files to download, FALSE otherwise.

Since:

2.12

getDataFileTypes

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

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

Parameters:

ID - Id of the active session.

bioAssaySetId - Id of the bioassay set it concerns

qOpt - Restrictions and includes to put on the query

Returns:

An array with DataFileTypeInfo:s.

Since:

2.12

getAnnotations

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

Get the annotation values for one or more annotation types.

Parameters:

ID - Id of the active session.

bioAssaySetId - Id of the bioassay set 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