Package net.sf.basedb.core

Class ExtraValueType

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.ExtraValueType

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Registered, Removable

public class ExtraValueType
extends BasicItem
implements Nameable, Removable, Registered

Defines extra values that can be calculated by plugins or some other application and inserted as part of a BioAssaySet. All extra value types must have a unique external id that is used for identification.

Currently only extra values of Type.INT, Type.FLOAT and Type.STRING are supported.

Version:

2.0

Author:

Nicklas

See Also:

• ExtraValue
• BioAssaySet.getSpotExtraValueBatcher(Class, ExtraValueType, Job)
• BioAssaySet.getPositionExtraValueBatcher(Class, ExtraValueType, Job)

Last modified

$Date: 2017-05-22 14:35:27 +0200 (må, 22 maj 2017) $

Field Summary

Fields

Modifier and Type	Field	Description
private Coloring	coloring
static final int	MAX_EXTERNAL_ID_LENGTH	The maximum length of the external id variable that can be stored in the database.
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
ExtraValueType(ExtraValueTypeData data)	Creates a new extra value type item.

Method Summary

Modifier and Type	Method	Description
Formula.AverageMethod	getAverageMethod()	Get the average method for this extra value type.
static ExtraValueType	getByExternalId(DbControl dc, String externalId)	Get a ExtraValueType when you know the external id.
static ExtraValueType	getById(DbControl dc, int id)	Get an ExtraValueType object when you know the id.
Coloring	getColoring()	Get coloring information for this extra value.
(package private) ExtraValueTypeData	getData()	Get the BasicData object that holds all data for this item.
String	getDescription()	Get the description for the item.
Date	getEntryDate()	Get the date that the item was registered in the database.
String	getExternalId()	Get the external id for this ExtraValueType item.
String	getName()	Get the name of the item.
static ExtraValueType	getNew(DbControl dc, String externalId, Type valueType)	Create a new ExtraValue item.
static ItemQuery<ExtraValueType>	getQuery()	Get a query configured to retrieve extra value types.
User	getRemovedBy()	Get the user that flagged this item for removal.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: ExtraValue:s of this type
Type	getValueType()	Get the value type for this extra value type.
boolean	isRemoved()	Check if the removed flag is set for this item.
boolean	isUsed()	Check if: Any ExtraValue:s of this type exists
void	setAverageMethod(Formula.AverageMethod averageMethod)	Set the average method of the extra value type..
void	setDescription(String description)	Set the description for the item.
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setExternalId(String externalId)	Set the external id for this Client item.
void	setName(String name)	Set the name of the item.
void	setRemoved(boolean removed)	Set the removed flag for this item.
private void	setValueType(Type valueType)	Set the value type for this extra value type.

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, initPermissions, isDetached, isInDatabase, 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.EXTRAVALUETYPE
• getType()

MAX_EXTERNAL_ID_LENGTH

public static final int MAX_EXTERNAL_ID_LENGTH

The maximum length of the external id variable that can be stored in the database. Check the length against this value before calling the setExternalId(String) method to avoid exceptions.

See Also:

• Constant Field Values

coloring

private Coloring coloring

Constructor Details

ExtraValueType

ExtraValueType(ExtraValueTypeData data)

Creates a new extra value type item.

Parameters:

data - The data

Method Details

getNew

public static ExtraValueType getNew(DbControl dc,
 String externalId,
 Type valueType)
                             throws BaseException

Create a new ExtraValue item. Currently only extra values of Type.INT, Type.FLOAT and Type.STRING are supported.

Parameters:

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

externalId - A unique string identifying the extra value type

valueType - The Type of the extra value

Returns:

The new ExtraValue item

Throws:

BaseException - If there is an error

getById

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

Get an ExtraValueType 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 ExtraValueType 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 items

BaseException - If there is an error

getByExternalId

public static ExtraValueType getByExternalId(DbControl dc,
 String externalId)
                                      throws ItemNotFoundException,
PermissionDeniedException,
BaseException

Get a ExtraValueType when you know the external id.

Parameters:

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

externalId - The external id of the extra value type to load

Returns:

The ExtraValueType 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<ExtraValueType> getQuery()

Get a query configured to retrieve extra value types.

Returns:

An ItemQuery object

getData

ExtraValueTypeData 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

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

isRemoved

public boolean isRemoved()

Description copied from interface: Removable

Check if the removed flag is set for this item.

Specified by:

isRemoved in interface Removable

Returns:

TRUE if the item is flagged as removed, FALSE otherwise

setRemoved

public void setRemoved(boolean removed)
                throws PermissionDeniedException

Description copied from interface: Removable

Set the removed flag for this item.

Specified by:

setRemoved in interface Removable

Parameters:

removed - TRUE if the item should be flagged as removed, FALSE otherwise

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.DELETE permission for setting the flag to TRUE or Permission.WRITE permission for setting the flag to FALSE

getRemovedBy

public User getRemovedBy()
                  throws PermissionDeniedException,
ItemNotFoundException

Description copied from interface: Removable

Get the user that flagged this item for removal.

Specified by:

getRemovedBy in interface Removable

Returns:

A User object, or null if this item has not been flagged

Throws:

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

ItemNotFoundException - If the user that removed this item can't be found

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

Check if:

• Any ExtraValue:s of this type exists

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:

• ExtraValue:s of this type

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)

getValueType

public Type getValueType()

Get the value type for this extra value type. It can't be change once the object has been created.

setValueType

private void setValueType(Type valueType)
                   throws InvalidDataException

Set the value type for this extra value type. Null is not allowed and it must be one of the supported value types.

Throws:

InvalidDataException

See Also:

• VirtualColumn.extraValue(Type)

getExternalId

public String getExternalId()

Get the external id for this ExtraValueType item.

Returns:

A string with the external id of this item

setExternalId

public void setExternalId(String externalId)
                   throws PermissionDeniedException,
InvalidDataException

Set the external id for this Client item. The value cannot be null and must not be longer than the value specified by the MAX_EXTERNAL_ID_LENGTH constant.

Parameters:

externalId - The new external id for this item

Throws:

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

InvalidDataException - If the new value is null or longer than MAX_EXTERNAL_ID_LENGTH

getColoring

public Coloring getColoring()

Get coloring information for this extra value.

Returns:

A Coloring object

getAverageMethod

public Formula.AverageMethod getAverageMethod()

Get the average method for this extra value type.

Returns:

A Formula.AverageMethod object

Since:

2.4

setAverageMethod

public void setAverageMethod(Formula.AverageMethod averageMethod)
                      throws PermissionDeniedException,
InvalidDataException

Set the average method of the extra value type..

Parameters:

averageMethod - A Formula.AverageMethod object, null is not allowed

Throws:

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

InvalidDataException - If the averageMethod is null

Since:

2.4