Package net.sf.basedb.core

Class Extract

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.BioMaterial

net.sf.basedb.core.MeasuredBioMaterial

net.sf.basedb.core.Extract

All Implemented Interfaces:

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

public class Extract
extends MeasuredBioMaterial

This class is used to represent extract items. An extract is created from a Sample or by combining other extracts (pooling). It is also possible to create standalone extracts, with no reference to a sample or to other extracts.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2019-02-06 10:41:56 +0100 (ons, 06 feb. 2019) $

Nested Class Summary

Nested classes/interfaces inherited from class net.sf.basedb.core.MeasuredBioMaterial

MeasuredBioMaterial.RemainingQuantityAction

Field Summary

Fields

Modifier and Type	Field	Description
static final String	LABELED	The id for the ExtractType item representing a labeled extract.
static final String	LIBRARY	The id for the ExtractType item representing a library.
static final Item	TYPE	The type of item represented by this class.

Fields inherited from class net.sf.basedb.core.BioMaterial

MAX_EXTERNAL_ID_LENGTH

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

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

Constructors

Constructor	Description
Extract(ExtractData extractData)

Method Summary

Modifier and Type	Method	Description
long	countChildren(boolean extractsOnly)	Count the number of child extracts.
long	countExtracts()	Counts all extracts that have been created from this extract.
Set<Annotatable>	getAnnotatableParents()	Get the tag and parent extracts.
static Extract	getById(DbControl dc, int id)	Get an Extract item when you know the id.
ItemQuery<Extract>	getChildExtracts()	Creates a query that returns all child (pooled) extracts that has this extracts as one of it's sources.
(package private) ExtractData	getData()	Get the BasicData object that holds all data for this item.
ItemQuery<DerivedBioAssay>	getDerivedBioAssays()	Get a query that returns all derived bioassays created from this extract.
ItemSubtype	getItemSubtype()	Get the subtype of the item.
static Extract	getNew(DbControl dc)	Create a new Extract item.
static Extract	getNew(DbControl dc, BioPlateEventParticipant master)	Create a new Extract item as part of a master bioplate event.
ItemQuery<PhysicalBioAssay>	getPhysicalBioAssays()	Get a query that returns all bioassays created from this extract.
static ItemQuery<Extract>	getQuery()	Get a query that returns extracts.
ItemQuery<RawBioAssay>	getRawBioAssays()	Get a query that returns all raw bioassays created from this extract.
Tag	getTag()	Get the tag that has been applied to this extract in order to be able to distinguish it from other extracts on a physical bioassay.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: Child extracts created from the extract PhysicalBioAssay:s created from this extract DerivedBioAssay:s referencing the extract RawBioAssay:s referencing the extract
boolean	isUsed()	Check that: no PhysicalBioAssay:s has been created from this item no Extract:s has been created from this item no DerivedBioAssay is referencing this item no RawBioAssay is referencing this item
void	setTag(Tag tag)	Set the tag that was applied to this extract in order to be able to distinguish it from other extracts on a physical bioassay.

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

breakCircularReferences, getAnnotatableParents, getBioWell, getCreationEvent, getEntryDate, getEvents, getOriginalQuantity, getParent, getParentType, getProtocol, getRemainingQuantity, hasSingleParent, isInWell, isLockedInWell, newEvent, newEvent, onBeforeCommit, setBioPlateEventParticipant, setBioWell, setEntryDate, setOriginalQuantity, updateRemainingQuantity

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

getChildCreationEvents, getExternalId, setExternalId, setItemSubtype

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, 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, 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.Nameable

getDescription, getName, setDescription, setName

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.EXTRACT
• getType()

LABELED

public static final String LABELED

The id for the ExtractType item representing a labeled extract.

Since:

3.0

See Also:

• Constant Field Values

LIBRARY

public static final String LIBRARY

The id for the ExtractType item representing a library.

Since:

3.0

See Also:

• Constant Field Values

Constructor Details

Extract

Extract(ExtractData extractData)

Method Details

getNew

public static Extract getNew(DbControl dc)
                      throws BaseException

Create a new Extract item.

Parameters:

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

Returns:

The new Extract item

Throws:

BaseException - If there is an error

getNew

public static Extract getNew(DbControl dc,
 BioPlateEventParticipant master)
                      throws BaseException

Create a new Extract item as part of a master bioplate event.

Parameters:

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

master - The master bioplate event participant or null

Returns:

The new Extract item

Throws:

BaseException - If there is an error

Since:

2.17

getById

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

Get an Extract 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 Extract 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<Extract> getQuery()

Get a query that returns extracts.

Returns:

An ItemQuery object.

getData

ExtractData getData()

Description copied from class: BasicItem

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

Overrides:

getData in class MeasuredBioMaterial

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.

Returns:

A value indicating the type of item

getItemSubtype

@SupportsPushAnnotations
@SubtypableRelatedItems({PROTOCOL,KIT,HARDWARE,TAG,SAMPLE,EXTRACT})
public ItemSubtype getItemSubtype()

Description copied from interface: Subtypable

Get the subtype of the item.

Specified by:

getItemSubtype in interface Subtypable

Overrides:

getItemSubtype in class MeasuredBioMaterial

Returns:

A subtype of null if not set

See Also:

• SubtypableRelatedItems

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• no PhysicalBioAssay:s has been created from this item
• no Extract:s has been created from this item
• no DerivedBioAssay is referencing this item
• no RawBioAssay is referencing this item

Overrides:

isUsed in class MeasuredBioMaterial

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:

• Child extracts created from the extract
• PhysicalBioAssay:s created from this extract
• DerivedBioAssay:s referencing the extract
• RawBioAssay:s referencing the extract

Overrides:

getUsingItems in class MeasuredBioMaterial

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)

getTag

public Tag getTag()

Get the tag that has been applied to this extract in order to be able to distinguish it from other extracts on a physical bioassay.

Returns:

A tag or null if the extract is not tagged

Since:

3.0

setTag

public void setTag(Tag tag)

Set the tag that was applied to this extract in order to be able to distinguish it from other extracts on a physical bioassay.

Parameters:

tag - The tag, or null if the extract is not tagged

Since:

3.0

getChildExtracts

public ItemQuery<Extract> getChildExtracts()

Creates a query that returns all child (pooled) extracts that has this extracts as one of it's sources.

Returns:

A query

Since:

2.10

countExtracts

public long countExtracts()
                   throws BaseException

Counts all extracts that have been created from this extract. The count includes extracts that the logged in user doesn't have access to.

Returns:

The number of extracts

Throws:

BaseException - If there is some kind of error.

Since:

2.16

countChildren

public long countChildren(boolean extractsOnly)

Count the number of child extracts. Since an extract can only have other extracts as children, this method always return 0 if extractsOnly = false.

Specified by:

countChildren in class BioMaterial

Parameters:

extractsOnly - If TRUE, the count is for biomaterials of the same type, if FALSE the count is for biomaterials of the child type

Since:

2.16

getPhysicalBioAssays

public ItemQuery<PhysicalBioAssay> getPhysicalBioAssays()

Get a query that returns all bioassays created from this extract.

Returns:

An ItemQuery object

getDerivedBioAssays

public ItemQuery<DerivedBioAssay> getDerivedBioAssays()

Get a query that returns all derived bioassays created from this extract.

Returns:

An ItemQuery object

Since:

3.14.1

getRawBioAssays

public ItemQuery<RawBioAssay> getRawBioAssays()

Get a query that returns all raw bioassays created from this extract.

Returns:

An ItemQuery object

Since:

3.14.1

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the tag and parent extracts.

Specified by:

getAnnotatableParents in interface Annotatable

Overrides:

getAnnotatableParents in class MeasuredBioMaterial

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error