Package net.sf.basedb.core

Class Tag

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.Tag

All Implemented Interfaces:

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

public class Tag
extends AnnotatedItem
implements Registered, Subtypable

This class represents a tag. Tags are used on extracts so that they can be tracked on physical bioassays.

Since:

3.0

Author:

Nicklas

Last modified

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

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BARCODE	The ID for the BARCODE tag type.
static final String	LABEL	The ID for the LABEL tag type.
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
Tag(TagData data)

Method Summary

Modifier and Type	Method	Description
Set<Annotatable>	getAnnotatableParents()	Get all parents objects which are annotatable and the logged in user has read permission to.
static Tag	getById(DbControl dc, int id)	Get a Tag item when you know the id.
(package private) TagData	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.
ItemSubtype	getItemSubtype()	Get the subtype of the item.
static Tag	getNew(DbControl dc)	Create a new Tag item.
static ItemQuery<Tag>	getQuery()	Get a query that returns tags.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: Extract:s marked with this tag
boolean	isUsed()	Check if: Some Extract:s are marked with this tag
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setItemSubtype(ItemSubtype subtype)	Set the subtype on the item.

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

getAnnotationSet, getProtocol, 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, 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

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.TAG
• getType()

LABEL

public static final String LABEL

The ID for the LABEL tag type.

See Also:

• Constant Field Values

BARCODE

public static final String BARCODE

The ID for the BARCODE tag type.

See Also:

• Constant Field Values

Constructor Details

Tag

Tag(TagData data)

Method Details

getNew

public static Tag getNew(DbControl dc)
                  throws BaseException

Create a new Tag item.

Parameters:

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

Returns:

The new Label item

Throws:

BaseException - If there is an error

getById

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

Get a Tag 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 Tag 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

public static ItemQuery<Tag> getQuery()

Get a query that returns tags.

Returns:

An ItemQuery object

getData

TagData 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

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

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()

Description copied from interface: Annotatable

Get all parents objects which are annotatable and the logged in user has read permission to. If the item doesn't have any annotatable parents, it may return null or an empty set. The method should only return the immediate parent(s), not parents to parents, etc. As of BASE 3.1 this method may also return child items if the child item is a Subtypable item that has a subtype with the ItemSubtype.getPushAnnotations() flag set.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

Always null

Since:

3.3

getItemSubtype

public ItemSubtype getItemSubtype()

Description copied from interface: Subtypable

Get the subtype of the item.

Specified by:

getItemSubtype in interface Subtypable

Returns:

A subtype of null if not set

See Also:

• SubtypableRelatedItems

setItemSubtype

public void setItemSubtype(ItemSubtype subtype)

Description copied from interface: Subtypable

Set the subtype on the item.

Specified by:

setItemSubtype in interface Subtypable

Parameters:

subtype - A subtype or null

See Also:

• ItemSubtype.setOnItem(Subtypable)

isUsed

public boolean isUsed()
               throws BaseException

Check if:

• Some Extract:s are marked with this tag

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:

• Extract:s marked with this tag

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)