2.8.2: 2008-09-18

net.sf.basedb.clients.migrate
Class RawBioAssayTransfer

java.lang.Object
  extended by net.sf.basedb.clients.migrate.Manager
      extended by net.sf.basedb.clients.migrate.Transfer
          extended by net.sf.basedb.clients.migrate.SharedItemTransfer
              extended by net.sf.basedb.clients.migrate.CommonItemTransfer
                  extended by net.sf.basedb.clients.migrate.RawBioAssayTransfer

public class RawBioAssayTransfer
extends CommonItemTransfer

This class provides methods for transferring RawBioAssay and RawBioAssayData from base 1 to BASE 2. Base 1 files are located in /userfiles/rawdata/

Version:
2.0
Author:
Gregory, Martin
Last modified
$Date: 2008-09-05 17:15:54 +0200 (Fri, 05 Sep 2008) $

Field Summary
private  ArrayTypeTransfer arrayTypeT
           
private  Platform generic
           
private static Logger log
          Logger for this class
private  DataFileType rawDataFileType
           
private  SampleTransfer sampleT
           
private  ScanTransfer scanT
           
private  SoftwareTransfer softwareT
           
private  UploadFileTransfer uploadFT
           
 
Fields inherited from class net.sf.basedb.clients.migrate.CommonItemTransfer
DESCRIPTION, NAME, REMOVED
 
Fields inherited from class net.sf.basedb.clients.migrate.SharedItemTransfer
GID, GROUP_ACCESS, groupT, ID, OWNER, userT, WORLD_ACCESS
 
Fields inherited from class net.sf.basedb.clients.migrate.Transfer
BASE2, FROM, itemList, LIMIT, LOCAL_MYSQL_TRANSFER, mapIds, progress, properties, QUICK_TRANSFER, selectOffset, sessionControl, TO
 
Constructor Summary
RawBioAssayTransfer()
           
RawBioAssayTransfer(UserTransfer userT, GroupTransfer groupT, ScanTransfer scanT, ArrayTypeTransfer arrayTypeT, UploadFileTransfer uploadFT, SoftwareTransfer softwareT, SampleTransfer sampleT)
          Constructs a new RawBioAssayTransfer.
 
Method Summary
protected  RawBioAssay createItem(DbControl dc, ResultSet rs)
          Creates a RawBioAssay from the current position in ResultSet.
 RawBioAssay getRawBioAssayById(DbControl dc, int base1Id)
           
 void parseFileHeader(RawBioAssay rba, String fileHeader)
          Fileheaders containing parameters on the form 'parameter=value' are set on the RawBioAssay.
 void start()
          Starts the actual transfer.
 
Methods inherited from class net.sf.basedb.clients.migrate.CommonItemTransfer
setCommonItemData
 
Methods inherited from class net.sf.basedb.clients.migrate.SharedItemTransfer
chmod, chown, getOwner, setSharedItemData
 
Methods inherited from class net.sf.basedb.clients.migrate.Transfer
cleanUpMemory, commit, createItem, dependencyFailure, done, getBase2Id, getBatchSize, getCount, getDependencyStatus, getIdMap, getInt, getProperty, initIdMap, isDone, mapId, newDbControl, readRestorePointData, run, run, runUnBatched, saveItem, setup, startProgress, writeRestorePointData
 
Methods inherited from class net.sf.basedb.clients.migrate.Manager
getPreparedStatements, prepareStatementFromFile, print, printDate, setPreparedStatements, stop
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

log

private static final Logger log
Logger for this class


scanT

private ScanTransfer scanT

arrayTypeT

private ArrayTypeTransfer arrayTypeT

uploadFT

private UploadFileTransfer uploadFT

softwareT

private SoftwareTransfer softwareT

sampleT

private SampleTransfer sampleT

generic

private Platform generic

rawDataFileType

private DataFileType rawDataFileType
Constructor Detail

RawBioAssayTransfer

RawBioAssayTransfer()

RawBioAssayTransfer

RawBioAssayTransfer(UserTransfer userT,
                    GroupTransfer groupT,
                    ScanTransfer scanT,
                    ArrayTypeTransfer arrayTypeT,
                    UploadFileTransfer uploadFT,
                    SoftwareTransfer softwareT,
                    SampleTransfer sampleT)
Constructs a new RawBioAssayTransfer.

Parameters:
userT - A finished UserTransfer
groupT - A finished GroupTransfer
Method Detail

start

public void start()
Description copied from class: Transfer
Starts the actual transfer.

Specified by:
start in class Transfer

createItem

protected RawBioAssay createItem(DbControl dc,
                                 ResultSet rs)
                          throws BaseException,
                                 SQLException
Creates a RawBioAssay from the current position in ResultSet.

Overrides:
createItem in class Transfer
Parameters:
dc - DbControl used to transfer this item
rs - ResultSet containing the data for this item.
Returns:
RawBioAssay
Throws:
BaseException - If a new RawBioAssay cannot be created.
SQLException - If current ResultSet position is invalid or number of columns in the select statement is to low.

parseFileHeader

public void parseFileHeader(RawBioAssay rba,
                            String fileHeader)
Fileheaders containing parameters on the form 'parameter=value' are set on the RawBioAssay.


getRawBioAssayById

public RawBioAssay getRawBioAssayById(DbControl dc,
                                      int base1Id)
Returns:
RawBioAssay from the given base 1 id or null if no such RawBioAssay has been transferrend.

2.8.2: 2008-09-18