Package net.sf.basedb.core

Class ArrayBatch

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.OwnedItem

net.sf.basedb.core.SharedItem

net.sf.basedb.core.CommonItem

net.sf.basedb.core.AnnotatedItem

net.sf.basedb.core.ArrayBatch

All Implemented Interfaces:

AccessControlled, Annotatable, Identifiable, Nameable, Ownable, Registered, Removable, Shareable

public class ArrayBatch
extends AnnotatedItem
implements Registered

This class represents the making of a new batch of microarray slides of a particular design.

Version:

2.0

Author:

Enell

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	protocolHasBeenSet
private boolean	robotHasBeenSet
static final Item	TYPE	The type of item represented by this class.

Fields inherited from interface net.sf.basedb.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

Constructors

Constructor	Description
ArrayBatch(ArrayBatchData annotatedData)

Method Summary

Modifier and Type	Method	Description
Set<Annotatable>	getAnnotatableParents()	Get the array design.
ArrayDesign	getArrayDesign()	Get the ArrayDesign item that was used for this batch.
ItemQuery<ArraySlide>	getArraySlides()	Get a query that returns the slides in this batch.
static ArrayBatch	getById(DbControl dc, int id)	Get a ArrayBatch object when you know the ID.
(package private) ArrayBatchData	getData()	Get the BasicData object that holds all data for this item.
Date	getEntryDate()	Get the date that the item was registered in the database.
static ArrayBatch	getNew(DbControl dc, ArrayDesign arrayDesign)	Create a new ArrayBatch item.
Hardware	getPrintRobot()	Get the print robot used for printing the arrays.
Protocol	getProtocol()	Get the Protocol used for printing the arrays.
static ItemQuery<ArrayBatch>	getQuery()	Get a ItemQuery that returns array batches.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: ArraySlide:s in this batch
boolean	isUsed()	Check if this item is used by some other item.
ArraySlide	newArraySlide()	Create a new ArraySlide item for this batch.
private void	setArrayDesign(ArrayDesign arrayDesign)	Set the ArrayDesign used in this ArrayBatch.
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setPrintRobot(Hardware printRobot)	Set the print robot used for this array batch.
(package private) void	setProjectDefaults(Project activeProject)	Set print robot and protocol from project default settings.
void	setProtocol(Protocol protocol)	Set the Protocol used for printing the arrays.

Methods inherited from class net.sf.basedb.core.AnnotatedItem

getAnnotationSet, isAnnotated, removeAnnotations

Methods inherited from class net.sf.basedb.core.CommonItem

getDescription, getName, getRemovedBy, isRemoved, setDescription, setName, setRemoved

Methods inherited from class net.sf.basedb.core.SharedItem

getItemKey, getProjectKey, initPermissions, isShared, onBeforeCommit, setItemKey, setProjectKey

Methods inherited from class net.sf.basedb.core.OwnedItem

getOwner, isOwner, setOwner, takeOwnership

Methods inherited from class net.sf.basedb.core.BasicItem

addAnnotatableParents, addUsingItems, addUsingItems, breakCircularReferences, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onRollback, setDbControl, toString, validate

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.AccessControlled

checkPermission, getPermissions, hasPermission

Methods inherited from interface net.sf.basedb.core.Identifiable

getId, getVersion

Methods inherited from interface net.sf.basedb.core.Ownable

getOwner, isOwner, setOwner, takeOwnership

Field Details

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

• Item.ARRAYBATCH
• getType()

protocolHasBeenSet

private boolean protocolHasBeenSet

robotHasBeenSet

private boolean robotHasBeenSet

Constructor Details

ArrayBatch

ArrayBatch(ArrayBatchData annotatedData)

Method Details

getNew

public static ArrayBatch getNew(DbControl dc,
 ArrayDesign arrayDesign)
                         throws BaseException

Create a new ArrayBatch item.

Parameters:

dc - The DbControl which will be used for permission checking and database access

arrayDesign - The ArrayDesign used for the batch

Returns:

The new ArrayBatch item

Throws:

PermissionDeniedException - If the logged in user doesn't have create permission for this type of item, or use permission for the design

BaseException - If there is another error

getById

public static ArrayBatch getById(DbControl dc,
 int id)
                          throws ItemNotFoundException,
PermissionDeniedException,
BaseException

Get a ArrayBatch object when you know the ID.

Parameters:

dc - The DbControl which will be used for permission checking and database access.

id - The ID of the item to load

Returns:

The ArrayBatch item

Throws:

ItemNotFoundException - If an item with the specified ID is not found

PermissionDeniedException - If the logged in user doesn't have read permission to the item

BaseException - If there is another error

getQuery

public static ItemQuery<ArrayBatch> getQuery()

Get a ItemQuery that returns array batches.

Returns:

An ItemQuery object

getData

ArrayBatchData getData()

Description copied from class: BasicItem

Get the BasicData object that holds all data for this item.

Overrides:

getData in class AnnotatedItem

getType

public Item getType()

Description copied from interface: Identifiable

Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.

Specified by:

getType in interface Identifiable

Returns:

A value indicating the type of item

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the array design.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

getEntryDate

public Date getEntryDate()

Description copied from interface: Registered

Get the date that the item was registered in the database.

Specified by:

getEntryDate in interface Registered

Returns:

A date or null if this is not known

setEntryDate

public void setEntryDate(Date entryDate)

Description copied from interface: Registered

Set the date the entry was registered in the database. Implementations should only allow this property to be set before the item is first stored in the database. The intention of this method is to facilitate export/import of data between server.

Specified by:

setEntryDate in interface Registered

Parameters:

entryDate - A date or null to use today's date

isUsed

public boolean isUsed()
               throws BaseException

Description copied from class: BasicItem

Check if this item is used by some other item. With used we mean that another item is linking to this item in way that prevents this item from beeing deleted. Ie. if we tried to delete an item that is used, we would get a foreign key violation error from the database. If the subclass overrides this method it should propagate the call to the superclass, ie. super.isUsed(), unless it has decided that the item is used by some other means.

Overrides:

isUsed in class BasicItem

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException - If not able to tell if item is used or not.

See Also:

• BasicItem.getUsingItems()

getUsingItems

public Set<ItemProxy> getUsingItems()

Get all:

• ArraySlide:s in this batch

Overrides:

getUsingItems in class BasicItem

Returns:

A set containing proxies for the items, or an empty set if no items are using this item

Since:

2.2

See Also:

• BasicItem.addUsingItems(Set, Item, org.hibernate.query.Query)

setProjectDefaults

void setProjectDefaults(Project activeProject)
                 throws BaseException

Set print robot and protocol from project default settings.

Overrides:

setProjectDefaults in class BasicItem

Parameters:

activeProject - The currently active project

Throws:

BaseException

Since:

2.9

getArrayDesign

public ArrayDesign getArrayDesign()
                           throws PermissionDeniedException,
BaseException

Get the ArrayDesign item that was used for this batch.

Returns:

The ArrayDesign item

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission to the item

BaseException - If there is an error

setArrayDesign

private void setArrayDesign(ArrayDesign arrayDesign)
                     throws InvalidDataException,
PermissionDeniedException

Set the ArrayDesign used in this ArrayBatch.

Parameters:

arrayDesign - the arrayDesign to be set. Cannot be null.

Throws:

InvalidDataException - if arrayDesign is null.

PermissionDeniedException - If the logged in user doesn't have use permission for the array design.

getProtocol

public Protocol getProtocol()
                     throws PermissionDeniedException,
BaseException

Get the Protocol used for printing the arrays.

Specified by:

getProtocol in interface Annotatable

Overrides:

getProtocol in class AnnotatedItem

Returns:

The Protocol item

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission to the item

BaseException - If there is an error

setProtocol

public void setProtocol(Protocol protocol)
                 throws PermissionDeniedException

Set the Protocol used for printing the arrays.

Parameters:

protocol - A Protocol item of the Protocol.PRINTING protocol type

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission on this array batch or use permission for the protocol

getPrintRobot

public Hardware getPrintRobot()
                       throws PermissionDeniedException,
BaseException

Get the print robot used for printing the arrays.

Returns:

A Hardware item of type Hardware.PRINT_ROBOT

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission to the item

BaseException - If there is an error

setPrintRobot

public void setPrintRobot(Hardware printRobot)
                   throws PermissionDeniedException

Set the print robot used for this array batch.

Parameters:

printRobot - A Hardware item of type Hardware.PRINT_ROBOT

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission on this array batch or use permission for the hardware

newArraySlide

public ArraySlide newArraySlide()
                         throws PermissionDeniedException,
BaseException

Create a new ArraySlide item for this batch.

Returns:

The new ArraySlide item

Throws:

PermissionDeniedException - If the logged in user doesn't have use permission for this batch

BaseException - If there is another error

getArraySlides

public ItemQuery<ArraySlide> getArraySlides()

Get a query that returns the slides in this batch.

Returns:

An ItemQuery object