2.12.0: 2009-05-27

net.sf.basedb.clients.migrate
Class WellTransfer

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.WellTransfer

public class WellTransfer
extends Transfer

Transfers well annotations for all previously transferred plates.

Base 1 tables
Well
Unused columns
Well: reporter_id

Version:
2.0
Author:
gregory
Last modified
$Date: 2009-04-06 14:52:39 +0200 (Mon, 06 Apr 2009) $

Field Summary
private  AnnotationType bacterialGrowthAT
           
private  AnnotationType bandsAT
           
private  AnnotationType commentAT
           
private static Logger log
          The logger for this class
private  AnnotationType seqVerifiedAT
           
private  UnmappedPlateTransfer unmappedPlateT
           
 
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
WellTransfer(UnmappedPlateTransfer unmappedPlateT)
           
 
Method Summary
private  void annotateWells(DbControl dc, Plate plate, ResultSet rs)
          Annotate wells for a given plate.
private  void annotateWellsForEachPlate()
           
private  int countPlates()
           
private  AnnotationType getAnnotationTypeByName(DbControl dc, String name)
           
private  String matchEnumeratedValue(AnnotationType at, String inValue)
           
(package private)  void start()
          Starts the actual transfer.
 
Methods inherited from class net.sf.basedb.clients.migrate.Transfer
cleanUpMemory, commit, createItem, 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

unmappedPlateT

private UnmappedPlateTransfer unmappedPlateT

seqVerifiedAT

private AnnotationType seqVerifiedAT

bandsAT

private AnnotationType bandsAT

bacterialGrowthAT

private AnnotationType bacterialGrowthAT

commentAT

private AnnotationType commentAT

log

private static final Logger log
The logger for this class

Constructor Detail

WellTransfer

public WellTransfer(UnmappedPlateTransfer unmappedPlateT)
Method Detail

start

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

Specified by:
start in class Transfer

annotateWellsForEachPlate

private void annotateWellsForEachPlate()

annotateWells

private void annotateWells(DbControl dc,
                           Plate plate,
                           ResultSet rs)
Annotate wells for a given plate.

Parameters:
dc - DbControl
plate - Wells from this plate will be connected

matchEnumeratedValue

private String matchEnumeratedValue(AnnotationType at,
                                    String inValue)

getAnnotationTypeByName

private AnnotationType getAnnotationTypeByName(DbControl dc,
                                               String name)
                                        throws ItemNotFoundException,
                                               BaseException
Parameters:
dc -
name - AnnotationType name too look for
Returns:
AnnotationType
Throws:
ItemNotFoundException - if AnnotationType by that name doesn't exsist
BaseException - if the query fails

countPlates

private int countPlates()

2.12.0: 2009-05-27