Package net.sf.basedb.core

Class RootRawBioAssay

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.ChildItem

net.sf.basedb.core.RootRawBioAssay

All Implemented Interfaces:

AccessControlled, Annotatable, Identifiable, Nameable

public class RootRawBioAssay
extends ChildItem
implements Annotatable, Nameable

Represents the use of a raw bioassay in an experiment. Except for keeping the link between the experiment and raw bioassay the main purpose of this class is to make it possible to store experimental factor values as annotations (primary or inherited) without "contaminating" the raw bioassay and without problems with access permissions. Access permissions for this item is follows that of the experiment it belongs to.

Since:

3.6

Author:

nicklas

Field Summary

Fields

Modifier and Type	Field	Description
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
RootRawBioAssay(RootRawBioAssayData data)	Creates a new root raw bioassay item from the given data.

Method Summary

Modifier and Type	Method	Description
Set<Annotatable>	getAnnotatableParents()	Get the raw bioassay.
AnnotationSet	getAnnotationSet()	Get the annotation set containing the annotations for this item.
static RootRawBioAssay	getById(DbControl dc, int id)	Get a RootRawBioAssay item when you know the id.
(package private) RootRawBioAssayData	getData()	Get the BasicData object that holds all data for this item.
String	getDescription()	Get the description for the item.
Experiment	getExperiment()	Get the experiment this root raw bioassay belongs to.
String	getName()	Get the name of the item.
(package private) Permission	getPermissionForWriteDeleteAndCreate()	WRITE permission is required to be able to manage root raw bioassays.
Protocol	getProtocol()	A protcol used in the creation of an item that is used to attach annotations for the protocol parameters.
(package private) static ItemQuery<RootRawBioAssay>	getQuery()	Get a query configured to retrieve raw bioassays.
RawBioAssay	getRawBioAssay()	Get the raw bioassay this root raw bioassay is representing.
(package private) SharedData	getSharedParent()	Get the experiment.
Item	getType()	Get the type of item represented by the object.
(package private) void	initPermissions(int granted, int denied)	Deny DELETE permission.
boolean	isAnnotated()	Check if this item has an annotation set.
void	removeAnnotations()	Remove all annotations from this item, by deleting the annotation set.
void	setDescription(String description)	Set the description for the item.
void	setName(String name)	Set the name of the item.

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

getPermissionForUse, getPluginPermissions

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

addAnnotatableParents, addUsingItems, addUsingItems, breakCircularReferences, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, getSessionControl, getUsingItems, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, onAfterCommit, onAfterInsert, onBeforeCommit, onRollback, setDbControl, setProjectDefaults, 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

Field Details

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

• Item.ROOTRAWBIOASSAY
• getType()

Constructor Details

RootRawBioAssay

RootRawBioAssay(RootRawBioAssayData data)

Creates a new root raw bioassay item from the given data.

Parameters:

data - the data

Method Details

getById

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

Get a RootRawBioAssay item 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 RootRawBioAssay item

Throws:

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

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission to the item

BaseException - If there is another error

getQuery

static ItemQuery<RootRawBioAssay> getQuery()

Get a query configured to retrieve raw bioassays.

Returns:

An ItemQuery object

getData

RootRawBioAssayData getData()

Description copied from class: BasicItem

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

Specified by:

getData in class BasicItem

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

getAnnotationSet

public AnnotationSet getAnnotationSet()
                               throws PermissionDeniedException,
BaseException

Description copied from interface: Annotatable

Get the annotation set containing the annotations for this item. If the item doesn't have any annotations a new annotation set is created and automatically saved to the database when DbControl.commit() is called. To check if an item has annotations without creating a new annotation set use the Annotatable.isAnnotated() method.

Specified by:

getAnnotationSet in interface Annotatable

Returns:

An AnnotationSet

Throws:

PermissionDeniedException - If the logged in user doesn't have enough permissions

BaseException - If there is another error

isAnnotated

public boolean isAnnotated()

Description copied from interface: Annotatable

Check if this item has an annotation set. The annotation set may be empty.

Specified by:

isAnnotated in interface Annotatable

Returns:

TRUE if an annotation set exists, FALSE otherwise

removeAnnotations

public void removeAnnotations()
                       throws PermissionDeniedException,
BaseException

Description copied from interface: Annotatable

Remove all annotations from this item, by deleting the annotation set.

Specified by:

removeAnnotations in interface Annotatable

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

BaseException - If there is another error

getProtocol

public Protocol getProtocol()

Description copied from interface: Annotatable

A protcol used in the creation of an item that is used to attach annotations for the protocol parameters.

Specified by:

getProtocol in interface Annotatable

Returns:

A protocol or null if the protocol is unknown

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the raw bioassay.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

initPermissions

void initPermissions(int granted,
 int denied)
              throws BaseException

Deny DELETE permission. Root raw bioAssays are automatically deleted when the parent experiment is deleted or by calling Experiment.removeRawBioAssay(RawBioAssay)

Overrides:

initPermissions in class ChildItem

Parameters:

granted - Permissions that have been granted by the subclass

denied - Permissions that have been denied by the subclass

Throws:

BaseException - If the permissions couldn't be initialised

getSharedParent

SharedData getSharedParent()

Get the experiment.

Specified by:

getSharedParent in class ChildItem

Returns:

The parent item

getPermissionForWriteDeleteAndCreate

Permission getPermissionForWriteDeleteAndCreate()

WRITE permission is required to be able to manage root raw bioassays.

Overrides:

getPermissionForWriteDeleteAndCreate in class ChildItem

getName

public String getName()

Description copied from interface: Nameable

Get the name of the item.

Specified by:

getName in interface Nameable

Returns:

A String with the name of the item

setName

public void setName(String name)
             throws PermissionDeniedException,
InvalidDataException

Description copied from interface: Nameable

Set the name of the item. The name cannot be null and mustn't be longer than the value specified by the Nameable.MAX_NAME_LENGTH constant.

Specified by:

setName in interface Nameable

Parameters:

name - The new name for the item

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the name is null or longer than specified by the Nameable.MAX_NAME_LENGTH constant

getDescription

public String getDescription()

Description copied from interface: Nameable

Get the description for the item.

Specified by:

getDescription in interface Nameable

Returns:

A String with a description of the item

setDescription

public void setDescription(String description)
                    throws PermissionDeniedException,
InvalidDataException

Description copied from interface: Nameable

Set the description for the item. The description can be null but mustn't be longer than the value specified by the Nameable.MAX_DESCRIPTION_LENGTH constant.

Specified by:

setDescription in interface Nameable

Parameters:

description - The new description for the item

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

InvalidDataException - If the description longer than specified by the Nameable.MAX_DESCRIPTION_LENGTH constant

getExperiment

public Experiment getExperiment()
                         throws PermissionDeniedException,
BaseException

Get the experiment this root raw bioassay belongs to.

Returns:

An Experiment object

Throws:

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

BaseException - If there is another error

getRawBioAssay

public RawBioAssay getRawBioAssay()
                           throws PermissionDeniedException,
BaseException

Get the raw bioassay this root raw bioassay is representing.

Returns:

A RawBioAssay object

Throws:

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

BaseException - If there is another error