Package net.sf.basedb.core

Class PhysicalBioAssay

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.PhysicalBioAssay

All Implemented Interfaces:

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

public class PhysicalBioAssay
extends AnnotatedItem
implements Registered, Subtypable, Listable

A physical bioassay is a representation of the process of performing an experiment one or more Extract:s.

Since:

3.0

Author:

Nicklas

Last modified

$Date$

Field Summary

Fields

Modifier and Type	Field	Description
private BioPlateEventParticipant	bioPlateEventParticipant
static final String	CLONAL_AMPLIFICATION	The id for the PhysicalBioAssayType item representing a flow cell.
private BioMaterialEvent	creationEvent
static final String	HYBRIDIZATION	The id for the PhysicalBioAssayType item representing a hybridization.
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
PhysicalBioAssay(PhysicalBioAssayData physicalBioAssayData)

Method Summary

Modifier and Type	Method	Description
long	countRootDerivedBioAssays()	Counts all root derived bioassays that have been created from this physical bioassay.
Set<Annotatable>	getAnnotatableParents()	Get the extracts and array slide.
Set<Annotatable>	getAnnotatableParents(int position, Collection<Extract> extracts)	Get the extracts, possible on a specific assay position or only a given set of specific extracts, and the array slide.
Set<Annotatable>	getAnnotatableParents(int position, Extract extract)	Get the extracts, possible on a specific assay position or only a specific extract, and the array slide.
ArraySlide	getArraySlide()	Get the ArraySlide this hyridization is using.
static PhysicalBioAssay	getById(DbControl dc, int id)	Get a Hybridization item when you know the id.
BioMaterialEvent	getCreationEvent()	Get the event that represents the creation of this hybridization.
(package private) PhysicalBioAssayData	getData()	Get the BasicData object that holds all data for this item.
ItemQuery<DerivedBioAssay>	getDerivedBioAssays()	Get a query that returns all derived bioassay created from this physical bioassay.
Date	getEntryDate()	Get the date that the item was registered in the database.
ItemQuery<Extract>	getExtracts(int position)	Get a query that returns extracts connected to this bioassay.
ItemSubtype	getItemSubtype()	Get the subtype of the item.
static PhysicalBioAssay	getNew(DbControl dc)	Create a new PhysicalBioAssay item.
static PhysicalBioAssay	getNew(DbControl dc, BioPlateEventParticipant master)	Create a new PhysicalBioAssay item as part of a master bioplate event.
Protocol	getProtocol()	Get the protocol from the creation event.
static ItemQuery<PhysicalBioAssay>	getQuery()	Get a query that returns physical bioassays.
ItemQuery<DerivedBioAssay>	getRootDerivedBioAssays()	Get a query that returns all root derived bioassay created from this physical bioassay.
int	getSize()	Get the size of the bioassay.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: (root) DerivedBioAssay:s created from this physical bioassay
boolean	isUsed()	Check that: No DerivedBioAssay:s use the physical bioassay
(package private) void	onBeforeCommit(Transactional.Action action)	Make sure the creation event is created at the same time this item is created and that source biomaterials get their used quantities back if this item is deleted.
void	setArraySlide(ArraySlide arraySlide)	Set the ArraySlide this hybridization is using.
(package private) void	setBioPlateEventParticipant(BioPlateEventParticipant bioPlateEventParticipant)
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setItemSubtype(ItemSubtype subtype)	Set the subtype on the item.
void	setSize(int size)	Set the size of the bioassay.

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, 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.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.PHYSICALBIOASSAY
• getType()

HYBRIDIZATION

public static final String HYBRIDIZATION

The id for the PhysicalBioAssayType item representing a hybridization.

See Also:

• Constant Field Values

CLONAL_AMPLIFICATION

public static final String CLONAL_AMPLIFICATION

The id for the PhysicalBioAssayType item representing a flow cell.

See Also:

• Constant Field Values

creationEvent

private BioMaterialEvent creationEvent

bioPlateEventParticipant

private BioPlateEventParticipant bioPlateEventParticipant

Constructor Details

PhysicalBioAssay

PhysicalBioAssay(PhysicalBioAssayData physicalBioAssayData)

Method Details

getNew

public static PhysicalBioAssay getNew(DbControl dc)
                               throws BaseException

Create a new PhysicalBioAssay item.

Parameters:

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

Returns:

The new PhysicalBioAssay item

Throws:

BaseException - If there is an error

getNew

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

Create a new PhysicalBioAssay 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 PhysicalBioAssay item

Throws:

BaseException - If there is an error

Since:

2.17

getById

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

Get a Hybridization 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 Hybridization 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<PhysicalBioAssay> getQuery()

Get a query that returns physical bioassays.

Returns:

An ItemQuery object

getData

PhysicalBioAssayData 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

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the extracts and array slide. Note that this method will include all extracts, even on bioassays with multiple positions.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

See Also:

• getAnnotatableParents(int, Extract)

getProtocol

public Protocol getProtocol()

Get the protocol from the creation event.

Specified by:

getProtocol in interface Annotatable

Overrides:

getProtocol in class AnnotatedItem

Returns:

Always null

Since:

2.2

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

getItemSubtype

@SupportsPushAnnotations
@SubtypableRelatedItems({HARDWARE,PROTOCOL,KIT,EXTRACT})
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 that:

• No DerivedBioAssay:s use the physical bioassay

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:

• (root) DerivedBioAssay:s created from this physical bioassay

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)

onBeforeCommit

void onBeforeCommit(Transactional.Action action)
             throws BaseException

Make sure the creation event is created at the same time this item is created and that source biomaterials get their used quantities back if this item is deleted. All events are deleted by cascade mapping in Hibernate.

Overrides:

onBeforeCommit in class SharedItem

Throws:

BaseException - If there is another error

See Also:

• Transactional
• Developer documentation: Transactions
• Developer documentation: Coding rules and guidelines for item classes

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents(int position,
 Extract extract)
                                       throws BaseException

Get the extracts, possible on a specific assay position or only a specific extract, and the array slide.

Parameters:

position - If > 0 only include the extracts on that position in the bioassay (see BioMaterialEventSource.getPosition(). If <= 0 include all extracts.

extract - If not null, only include that extract (if present on the bioassay)

Throws:

BaseException

Since:

3.0

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents(int position,
 Collection<Extract> extracts)
                                       throws BaseException

Get the extracts, possible on a specific assay position or only a given set of specific extracts, and the array slide.

Parameters:

position - If > 0 only include the extracts on that position in the bioassay (see BioMaterialEventSource.getPosition(). If <= 0 include all extracts.

extracts - If not null or empty, only include the given extracts (if present on the bioassay)

Throws:

BaseException

Since:

3.2

getCreationEvent

public BioMaterialEvent getCreationEvent()
                                  throws PermissionDeniedException,
BaseException

Get the event that represents the creation of this hybridization. Use this event to add source labeled extracts, a protocol, etc.

Returns:

A BioMaterialEvent data.

Throws:

PermissionDeniedException - If the logged in user don't have read permissions

BaseException - If there is another error.

setBioPlateEventParticipant

void setBioPlateEventParticipant(BioPlateEventParticipant bioPlateEventParticipant)

getArraySlide

public ArraySlide getArraySlide()
                         throws PermissionDeniedException,
BaseException

Get the ArraySlide this hyridization is using. A single slide can only be used on one hybridization.

Returns:

The ArraySlide item

Throws:

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

BaseException - If there is another error.

setArraySlide

public void setArraySlide(ArraySlide arraySlide)
                   throws PermissionDeniedException

Set the ArraySlide this hybridization is using.

Parameters:

arraySlide - The array slide, or null

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the hybridization or use permission for the array slide

BaseException - If there is another error.

getSize

public int getSize()

Get the size of the bioassay. The size is the number of independent positions for biomaterial. The default value is 1.

setSize

public void setSize(int size)

Set the size of the bioassay.

Parameters:

size - A value > 0

Throws:

NumberOutOfRangeException - If the value is <=0

getExtracts

public ItemQuery<Extract> getExtracts(int position)

Get a query that returns extracts connected to this bioassay.

Parameters:

position - If > 0 only extracts on the specific position are returned by the query, if <= 0, all extracts are returned

Returns:

An ItemQuery object

getDerivedBioAssays

public ItemQuery<DerivedBioAssay> getDerivedBioAssays()

Get a query that returns all derived bioassay created from this physical bioassay.

Returns:

An ItemQuery object

getRootDerivedBioAssays

public ItemQuery<DerivedBioAssay> getRootDerivedBioAssays()

Get a query that returns all root derived bioassay created from this physical bioassay.

Returns:

An ItemQuery object

countRootDerivedBioAssays

public long countRootDerivedBioAssays()
                               throws BaseException

Counts all root derived bioassays that have been created from this physical bioassay. The count includes bioassays that the logged in user doesn't have access to.

Returns:

The number of root bioassay

Throws:

BaseException - If the bioassay could not be counted.