Package net.sf.basedb.core

Class MigrateRbaToDba.Rba

java.lang.Object

net.sf.basedb.core.MigrateRbaToDba.Rba

All Implemented Interfaces:

LoggableData

Enclosing class:

MigrateRbaToDba

public static class MigrateRbaToDba.Rba
extends Object
implements LoggableData

Hold information a raw bioassay.

Field Summary

Fields

Modifier and Type	Field	Description
(package private) final Integer	annotationSetId
(package private) final Integer	arrayDesignId
(package private) Integer	arrayDesignLinkId
(package private) final Integer	bioAssayId
(package private) int	dbaId
(package private) final String	description
(package private) final Date	entryDate
(package private) final Integer	extractId
(package private) final Integer	fileSetId
(package private) Map<Integer,Integer>	fileTypes
(package private) final Integer	itemKeyId
(package private) final Integer	jobId
(package private) final String	name
(package private) final Integer	ownerId
(package private) final Integer	platformId
(package private) final Integer	projectKeyId
(package private) final Integer	protocolId
(package private) final String	rawDataType
(package private) final Integer	rbaId
(package private) final Integer	removedBy
(package private) final Integer	softwareId
(package private) Integer	subtypeId
(package private) final Integer	variantId
(package private) final Integer	version

Constructor Summary

Constructors

Constructor	Description
Rba(Object[] data)

Method Summary

Modifier and Type	Method	Description
(package private) void	clean(AnnotationBatcher.UpdateBatcher batcher)	Remove links to from the raw bioassay to annotations, files, etc.
(package private) void	createDerivedBioAssay(AnnotationBatcher.InsertBatcher batcher)	Create the new derived bioassay.
(package private) void	linkAnnotations(AnnotationBatcher.UpdateBatcher batcher)	Link the annotation set to the new derived bioassay.
(package private) void	linkAnyToAny(AnnotationBatcher.UpdateBatcher from, AnnotationBatcher.UpdateBatcher to)	Link any-to-any links with the new derived bioassay.
(package private) void	linkArrayDesign(AnnotationBatcher.InsertBatcher batcher)
(package private) void	linkChangeHistory(AnnotationBatcher.UpdateBatcher batcher)	Link change history entries with the new derived bioassay.
(package private) void	linkFiles(AnnotationBatcher.UpdateBatcher batcher, AnnotationBatcher.UpdateBatcher updateMember)	Link the file set to the new derived bioassay and update file types on members.
(package private) void	linkParentBioAssays(AnnotationBatcher.UpdateBatcher batcherDba, AnnotationBatcher.UpdateBatcher batcherPba)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

rbaId

final Integer rbaId

version

final Integer version

entryDate

final Date entryDate

fileSetId

final Integer fileSetId

jobId

final Integer jobId

softwareId

final Integer softwareId

protocolId

final Integer protocolId

arrayDesignId

final Integer arrayDesignId

bioAssayId

final Integer bioAssayId

extractId

final Integer extractId

annotationSetId

final Integer annotationSetId

name

final String name

description

final String description

removedBy

final Integer removedBy

itemKeyId

final Integer itemKeyId

projectKeyId

final Integer projectKeyId

ownerId

final Integer ownerId

platformId

final Integer platformId

variantId

final Integer variantId

rawDataType

final String rawDataType

dbaId

int dbaId

subtypeId

Integer subtypeId

arrayDesignLinkId

Integer arrayDesignLinkId

fileTypes

Map<Integer,Integer> fileTypes

Constructor Details

Rba

Rba(Object[] data)

Method Details

toString

public String toString()

Overrides:

toString in class Object

createDerivedBioAssay

void createDerivedBioAssay(AnnotationBatcher.InsertBatcher batcher)
                    throws SQLException

Create the new derived bioassay.

Throws:

SQLException

linkParentBioAssays

void linkParentBioAssays(AnnotationBatcher.UpdateBatcher batcherDba,
 AnnotationBatcher.UpdateBatcher batcherPba)
                  throws SQLException

Throws:

SQLException

linkArrayDesign

void linkArrayDesign(AnnotationBatcher.InsertBatcher batcher)
              throws SQLException

Throws:

SQLException

clean

void clean(AnnotationBatcher.UpdateBatcher batcher)
    throws SQLException

Remove links to from the raw bioassay to annotations, files, etc.

Throws:

SQLException

linkAnnotations

void linkAnnotations(AnnotationBatcher.UpdateBatcher batcher)
              throws SQLException

Link the annotation set to the new derived bioassay.

Throws:

SQLException

linkFiles

void linkFiles(AnnotationBatcher.UpdateBatcher batcher,
 AnnotationBatcher.UpdateBatcher updateMember)
        throws SQLException

Link the file set to the new derived bioassay and update file types on members.

Throws:

SQLException

linkAnyToAny

void linkAnyToAny(AnnotationBatcher.UpdateBatcher from,
 AnnotationBatcher.UpdateBatcher to)
           throws SQLException

Link any-to-any links with the new derived bioassay.

Throws:

SQLException

linkChangeHistory

void linkChangeHistory(AnnotationBatcher.UpdateBatcher batcher)
                throws SQLException

Link change history entries with the new derived bioassay. We need to the session id to avoid moving the newly inserted entries about the migration.

Throws:

SQLException