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2.9.2: 2009-01-08 | ||||||||
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java.lang.Objectnet.sf.basedb.clients.migrate.Manager
net.sf.basedb.clients.migrate.Transfer
net.sf.basedb.clients.migrate.RawBioAssayDataTransfer
public class RawBioAssayDataTransfer
This class provides methods for transferring RawBioAssay and RawBioAssayData from base 1 to BASE 2. Base 1 files are located in /userfiles/rawdata/
Field Summary | |
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private String[] |
floatProperties
Set string and text properties, order must match the select statement except for the id and reporterId in the beginning Extended properties are defined in the extended-properties.xml file for class ReporterData Why do it this way and not using the column name for lookup? |
private String[] |
intProperties
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private static Logger |
log
Logger for this class |
private RawBioAssayTransfer |
rbaT
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private ReporterTransfer |
reporterT
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Fields inherited from class net.sf.basedb.clients.migrate.Transfer |
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BASE2, FROM, itemList, LIMIT, LOCAL_MYSQL_TRANSFER, mapIds, progress, properties, QUICK_TRANSFER, selectOffset, sessionControl, TO |
Constructor Summary | |
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RawBioAssayDataTransfer(RawBioAssayTransfer rbaT,
ReporterTransfer reporterT)
Constructs a new RawBioAssayTransfer. |
Method Summary | |
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protected void |
createItem(ResultSet rs)
Transfers associated RawBioAssayData for each RawBioAssay and creates spotImages if necessary. |
protected void |
runRawBioAssay(RawBioAssay rawBioAssay,
RawDataBatcher batcher,
boolean hasArrayDesign,
int base1RawBioAssayId)
Recursive run over a SQL query defined by a prepared statement and LIMIT values from and size. |
void |
start()
Starts the actual transfer. |
private void |
transferRawBioAssayData(RawBioAssay rawBioAssay,
int rawBioAssayId,
boolean hasArrayDesign)
This method starts the data transfer. |
Methods inherited from class net.sf.basedb.clients.migrate.Transfer |
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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 |
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getPreparedStatements, prepareStatementFromFile, print, printDate, setPreparedStatements, stop |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private static final Logger log
private String[] floatProperties
private String[] intProperties
private RawBioAssayTransfer rbaT
private ReporterTransfer reporterT
Constructor Detail |
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RawBioAssayDataTransfer(RawBioAssayTransfer rbaT, ReporterTransfer reporterT)
rbaT
- A finished RawBioAssayTransfer
reporterT
- A finished ReporterTransfer
Method Detail |
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public void start()
Transfer
start
in class Transfer
protected void createItem(ResultSet rs) throws SQLException
createItem
in class Transfer
rs
- ResultSet
containing the data for this item.
SQLException
- If current ResultSet position is invalid or number
of columns in the select statement is to low.private void transferRawBioAssayData(RawBioAssay rawBioAssay, int rawBioAssayId, boolean hasArrayDesign)
rawBioAssay
- Existing rawBioAssay for which data will be
transfered.rawBioAssayId
- Base 1 id of the rawBioAssay.protected void runRawBioAssay(RawBioAssay rawBioAssay, RawDataBatcher batcher, boolean hasArrayDesign, int base1RawBioAssayId)
rawBioAssay
- The raw bio assay to transfer data tobatcher
- RawDataBatcher used in this transferhasArrayDesign
- (Currently not used)base1RawBioAssayId
- The ID of the raw bioassay in the BASE 1.2 installationManager.prepareStatementFromFile(String)
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2.9.2: 2009-01-08 | ||||||||
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