2.14.1: 2009-11-05

net.sf.basedb.clients.migrate
Class SampleTransfer

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.MeasuredBioMaterialTransfer
                      extended by net.sf.basedb.clients.migrate.SampleTransfer

public class SampleTransfer
extends MeasuredBioMaterialTransfer

This class provides methods for transferring Sample data from base 1 to BASE 2. The original quantity of a sample is unknown in base 1. A minimum quantity could be calculated from the sum over extract quantities but. sampleDate is mapped to a BioMaterialEvent indicating when the sample was taken.

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

Field Summary
private static Logger log
          Logger for this class
private  Map<Integer,Float> sampleQuantities
          base 1 sample id's are mapped to totalQuantity amount
private  SampleTissueTransfer sampleTissueT
           
 
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
SampleTransfer(UserTransfer userT, GroupTransfer groupT, ProtocolTransfer protocolFT, SampleTissueTransfer sampleTissueT)
          Constructs a new SampleTransfer.
 
Method Summary
protected  Sample createItem(DbControl b2c, ResultSet rs)
          Creates a Sample from the current position in ResultSet.
 Sample getSampleById(DbControl dbc, int base1SampleId)
          Returns a Sample from a base1 sample id.
 void start()
          Starts the actual transfer.
 
Methods inherited from class net.sf.basedb.clients.migrate.MeasuredBioMaterialTransfer
setMeasuredBioMaterialData
 
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


sampleQuantities

private Map<Integer,Float> sampleQuantities
base 1 sample id's are mapped to totalQuantity amount


sampleTissueT

private SampleTissueTransfer sampleTissueT
Constructor Detail

SampleTransfer

SampleTransfer(UserTransfer userT,
               GroupTransfer groupT,
               ProtocolTransfer protocolFT,
               SampleTissueTransfer sampleTissueT)
Constructs a new SampleTransfer.

Parameters:
userT - A finished UserTransfer
groupT - A finished GroupTransfer
protocolFT - A finished ProtocolTransfer
sampleTissueT - A finished SampleTissueTransfer
Method Detail

start

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

Specified by:
start in class Transfer

createItem

protected Sample createItem(DbControl b2c,
                            ResultSet rs)
                     throws BaseException,
                            SQLException
Creates a Sample from the current position in ResultSet.

Overrides:
createItem in class Transfer
Parameters:
b2c - DbControl used to transfer this item
rs - ResultSet containing the data for this item.
Returns:
Sample
Throws:
BaseException - If SampleTissue is missing.
SQLException - If current ResultSet position is invalid or number of columns in the select statement is to low.

getSampleById

public Sample getSampleById(DbControl dbc,
                            int base1SampleId)
Returns a Sample from a base1 sample id.

Parameters:
dbc - DbControl used to get the sample
base1SampleId - Base1 sample id

2.14.1: 2009-11-05