Package net.sf.basedb.core

Class Kit

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.Kit

All Implemented Interfaces:

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

public class Kit
extends AnnotatedItem
implements Registered, Subtypable

This class is used to represent a kit of reagents and other stuff used in the lab process.

Since:

3.7

Author:

Nicklas

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CLUSTER_GENERATION	The ID for the cluster generation (in a flow cell) kit type, for example a protocol used when creating a PhysicalBioAssay.
static final String	EXTRACTION	The ID for the extraction kit type, for example a kit used when creating an Extract from a Sample.
static final String	HYBRIDIZATION	The ID for the hybridization kit type, for example a kit used when creating a PhysicalBioAssay from a set of (labeled) Extract:s.
static final String	LABELING	The ID for the labeling kit type, for example a kit used when creating a labeled extract from an Extract.
static final String	LIBRARY_PREPARATION	The ID for the library preparation kit type, for example a kit used when creating a library extract from an Extract.
static final String	SAMPLING	The ID for the sampling kit type, for example a kit used when creating a Sample from a BioSource.
static final String	SEQUENCING	The ID for the sequencing kit type, for example a kit used when creating a DerivedBioAssay from a PhysicalBioAssay.
private 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
Kit(KitData data)	Creates a new kit item.

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 Kit	getById(DbControl dc, int id)	Get a Kit item when you know the ID.
(package private) KitData	getData()	Get the BasicData object that holds all data for this item.
static String	getDefaultSystemId(Item itemType)	Get the system id for the kit subtype that should be used on an item that doesn't have a subtype.
Date	getEntryDate()	Get the date that the item was registered in the database.
Date	getExpirationDate()	Get the expiration date of the kit.
ItemSubtype	getItemSubtype()	Get the subtype of the item.
static Kit	getNew(DbControl dc)	Create a new Kit item.
static ItemQuery<Kit>	getQuery()	Get a query configured to retrieve kits.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: BioMaterial:s and PhysicalBioAssay:s using this kit BioPlateEvent:s with this kit DerivedBioAssay: with this kit
boolean	isInactive()	Check if the kit is inactive.
boolean	isUsed()	Check if: a BioMaterialEvent is linked to this kit a BioPlateEvent is linked to this kit
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setExpirationDate(Date expirationDate)	Set the expiration date.
void	setInactive(boolean inactive)	Set the inactive flag.
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

private static final Item TYPE

The type of item represented by this class.

See Also:

• Item.KIT
• getType()

SAMPLING

public static final String SAMPLING

The ID for the sampling kit type, for example a kit used when creating a Sample from a BioSource.

See Also:

• Constant Field Values

EXTRACTION

public static final String EXTRACTION

The ID for the extraction kit type, for example a kit used when creating an Extract from a Sample.

See Also:

• Constant Field Values

LABELING

public static final String LABELING

The ID for the labeling kit type, for example a kit used when creating a labeled extract from an Extract.

See Also:

• Constant Field Values

LIBRARY_PREPARATION

public static final String LIBRARY_PREPARATION

The ID for the library preparation kit type, for example a kit used when creating a library extract from an Extract.

See Also:

• Constant Field Values

HYBRIDIZATION

public static final String HYBRIDIZATION

The ID for the hybridization kit type, for example a kit used when creating a PhysicalBioAssay from a set of (labeled) Extract:s.

See Also:

• Constant Field Values

CLUSTER_GENERATION

public static final String CLUSTER_GENERATION

The ID for the cluster generation (in a flow cell) kit type, for example a protocol used when creating a PhysicalBioAssay.

See Also:

• Constant Field Values

SEQUENCING

public static final String SEQUENCING

The ID for the sequencing kit type, for example a kit used when creating a DerivedBioAssay from a PhysicalBioAssay.

See Also:

• Constant Field Values

Constructor Details

Kit

Kit(KitData data)

Creates a new kit item.

Parameters:

data - the data

Method Details

getDefaultSystemId

public static String getDefaultSystemId(Item itemType)

Get the system id for the kit subtype that should be used on an item that doesn't have a subtype. This includes Subtypable items with a null ItemSubtype and all other non-subtypable items which can be linked to a kit.

Parameters:

itemType - The item type

Returns:

The system id of the default kit type or null

getNew

public static Kit getNew(DbControl dc)
                  throws BaseException

Create a new Kit item.

Parameters:

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

Returns:

The new Kit item

Throws:

BaseException - This exception is thrown if there is another error

getById

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

Get a Kit 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 Kit 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<Kit> getQuery()
                               throws BaseException

Get a query configured to retrieve kits.

Returns:

An ItemQuery object

Throws:

BaseException - If getting the query fails.

getData

KitData 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

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:

• a BioMaterialEvent is linked to this kit
• a BioPlateEvent is linked to this kit

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:

• BioMaterial:s and PhysicalBioAssay:s using this kit
• BioPlateEvent:s with this kit
• DerivedBioAssay: with this kit

Overrides:

getUsingItems in class BasicItem

Returns:

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

See Also:

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

isInactive

public boolean isInactive()

Check if the kit is inactive. An inactive kit should not be used when creating new biomaterial. This is a recommendation only and is not enforced by the core API.

setInactive

public void setInactive(boolean inactive)
                 throws PermissionDeniedException

Set the inactive flag.

Parameters:

inactive - TRUE if the kit is inactive, FALSE otherwise.

Throws:

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

getExpirationDate

public Date getExpirationDate()

Get the expiration date of the kit. A kit should not be used after it's expiration date. This is a recommendation only and is not enforced by the core API.

setExpirationDate

public void setExpirationDate(Date expirationDate)

Set the expiration date.

Parameters:

expirationDate - A date or null

Throws:

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