Package net.sf.basedb.core

Class MeasuredBioMaterial

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

All Implemented Interfaces:

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

Direct Known Subclasses:

Extract, Sample

public abstract class MeasuredBioMaterial
extends BioMaterial
implements Registered

This class is the base class for measured biomaterial items. A measured item is an item which can have original and remaining quantities associated with them.

The core keeps track of the remaining quantity whenever an item is used to create other items. As it is, an item can be used when creating another item of the same type (pooling) or when creating an item of the appropriate subtype, ie. Sample -> Extract -> LabeledExtract.

It is also possible to add a note using a BioMaterialEvent saying that the quantity has been changed and why.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2017-06-07 13:28:31 +0200 (on, 07 jun 2017) $

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) static class	MeasuredBioMaterial.RemainingQuantityAction	Transaction handler for updating the remaining quantity of a biomaterial based on the sum of the used quantity in this transaction.

Field Summary

Fields

Modifier and Type	Field	Description
private BioPlateEventParticipant	bioPlateEventParticipant
private BioMaterialEvent	creationEvent

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
MeasuredBioMaterial(MeasuredBioMaterialData measuredBioMaterialData)

Method Summary

Modifier and Type	Method	Description
(package private) int	breakCircularReferences(Set<ItemProxy> items)	Any parent items found among the given items are removed from the creation event of this item.
Set<Annotatable>	getAnnotatableParents()	Get the biosource or pooled samples and the bioplate the biomaterial is located on.
Set<Annotatable>	getAnnotatableParents(Collection<? extends MeasuredBioMaterial> parents)	Get the annotable parents, possible only a given set of specific parents items.
BioWell	getBioWell()	Get the well this biomaterial is located in.
BioMaterialEvent	getCreationEvent()	Get the event that represents the creation of this biomaterial.
(package private) MeasuredBioMaterialData	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.
ItemQuery<BioMaterialEvent>	getEvents()	Get a query that returns all events for this biomaterial.
ItemSubtype	getItemSubtype()	Get the subtype of the item.
Float	getOriginalQuantity()	Get the original quantity of the biomaterial.
BioMaterial	getParent()	Get the parent biomaterial if there is a single parent item only.
Item	getParentType()	Get the item type of the parent biomaterial.
Protocol	getProtocol()	Get the protocol from the creation event.
Float	getRemainingQuantity()	Get the remaining quantity of the biomaterial.
Set<ItemProxy>	getUsingItems()	Get all: BioMaterial:s where this item has been used as a source
boolean	hasSingleParent()	Checks if this biomaterial has a single parent item or not.
boolean	isInWell()	Check if this biomaterial is located in a well on a bioplate or not.
boolean	isLockedInWell()	Check if this biomaterial is placed in a well that it can't be removed from.
boolean	isUsed()	Check that: no pooled biomaterial has been created from this item
BioMaterialEvent	newEvent()	Create a new event for this biomaterial.
BioMaterialEvent	newEvent(BioPlateEventParticipant master)	Create a new event for this biomaterial that is part of a master bioplate event.
(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.
(package private) void	setBioPlateEventParticipant(BioPlateEventParticipant bioPlateEventParticipant)
void	setBioWell(BioWell well)	Sets the BioWell where this biomaterial is located.
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setOriginalQuantity(Float originalQuantity)	Set the original quantity of the biomaterial.
private void	updateFreeWells(BioPlateData plate, int delta)
(package private) static void	updateRemainingQuantity(DbControl dc, MeasuredBioMaterialData bioMaterial, Float usedQuantity)	Update the remaining quantity of a biomaterial.

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

countChildren, getById, 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, getType, 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

bioPlateEventParticipant

private BioPlateEventParticipant bioPlateEventParticipant

creationEvent

private BioMaterialEvent creationEvent

Constructor Details

MeasuredBioMaterial

MeasuredBioMaterial(MeasuredBioMaterialData measuredBioMaterialData)

Method Details

getData

MeasuredBioMaterialData getData()

Description copied from class: BasicItem

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

Overrides:

getData in class BioMaterial

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• no pooled biomaterial has been created from this item

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 where this item has been used as a source

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)

breakCircularReferences

int breakCircularReferences(Set<ItemProxy> items)

Any parent items found among the given items are removed from the creation event of this item.

Overrides:

breakCircularReferences in class BasicItem

Since:

3.8

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

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

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the biosource or pooled samples and the bioplate the biomaterial is located on.

Specified by:

getAnnotatableParents in interface Annotatable

Overrides:

getAnnotatableParents in class BioMaterial

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents(Collection<? extends MeasuredBioMaterial> parents)
                                       throws BaseException

Get the annotable parents, possible only a given set of specific parents items.

Parameters:

parents - If not null or empty, only include the given parent items (for pooled items only)

Throws:

BaseException

Since:

3.3

getItemSubtype

@SubtypableRelatedItems({PROTOCOL,HARDWARE})
public ItemSubtype getItemSubtype()

Description copied from interface: Subtypable

Get the subtype of the item.

Specified by:

getItemSubtype in interface Subtypable

Overrides:

getItemSubtype in class BioMaterial

Returns:

A subtype of null if not set

See Also:

• SubtypableRelatedItems

getCreationEvent

public BioMaterialEvent getCreationEvent()
                                  throws PermissionDeniedException,
BaseException

Get the event that represents the creation of this biomaterial.

Returns:

A BioMaterialEvent data.

Throws:

PermissionDeniedException - If logged in user doesn't have read permission on the biomaterial.

BaseException - If there is some other error.

setBioPlateEventParticipant

void setBioPlateEventParticipant(BioPlateEventParticipant bioPlateEventParticipant)

getOriginalQuantity

public Float getOriginalQuantity()

Get the original quantity of the biomaterial.

Returns:

A Float holding the original quantity, or null if not known

setOriginalQuantity

public void setOriginalQuantity(Float originalQuantity)
                         throws PermissionDeniedException,
InvalidDataException,
BaseException

Set the original quantity of the biomaterial. If the remaining quantity is null, it's value is also set to the same as the original value.

Parameters:

originalQuantity - The new value for the original quantity, or null if not known

Throws:

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

InvalidDataException - If the original quantity is below zero

BaseException - If there is some other kind of error.

getRemainingQuantity

public Float getRemainingQuantity()

Get the remaining quantity of the biomaterial. The remaining quantity cannot be modified directly. It is calculated based on the events for this biomaterial. Use the newEvent() method to get an event object where you can specify the used quantity.

Returns:

A Float holding the remaining quantity or null if not known

updateRemainingQuantity

static void updateRemainingQuantity(DbControl dc,
 MeasuredBioMaterialData bioMaterial,
 Float usedQuantity)

Update the remaining quantity of a biomaterial. This method does nothing if the usedQuantity parameter is null or if the remaining quantity is null.

getParentType

public Item getParentType()

Get the item type of the parent biomaterial. The parent type must be either the same type as the current biomaterial or "one step up" in the Extract -- Sample -- BioSource chain.

Returns:

The parent type, or null if the biomaterial doesn't have any parents

Since:

3.0

getParent

public BioMaterial getParent()

Get the parent biomaterial if there is a single parent item only.

Returns:

The parent biomaterial or null if there is not exactly one parent

Since:

3.0

See Also:

• hasSingleParent()

hasSingleParent

public boolean hasSingleParent()

Checks if this biomaterial has a single parent item or not.

Returns:

TRUE if there is exactly one parent, FALSE if there are 0 or 2 or more parents

Since:

3.0

See Also:

• getParentType()

newEvent

public BioMaterialEvent newEvent()
                          throws PermissionDeniedException,
BaseException

Create a new event for this biomaterial.

Returns:

a BioMaterialEvent object.

Throws:

PermissionDeniedException - If the logged in user doesn't have use permission for this biomaterial

BaseException - If there is another error

newEvent

public BioMaterialEvent newEvent(BioPlateEventParticipant master)
                          throws PermissionDeniedException,
BaseException

Create a new event for this biomaterial that is part of a master bioplate event.

Returns:

a BioMaterialEvent object.

Throws:

PermissionDeniedException - If the logged in user doesn't have use permission for this biomaterial

BaseException - If there is another error

Since:

2.17

getEvents

public ItemQuery<BioMaterialEvent> getEvents()

Get a query that returns all events for this biomaterial.

Returns:

An ItemQuery object

setBioWell

public void setBioWell(BioWell well)
                throws PermissionDeniedException,
BaseException

Sets the BioWell where this biomaterial is located.

Parameters:

well - The BioWell to set.

Throws:

ItemInUseException - If the well is already used by another biomaterial

PermissionDeniedException - If logged in user doesn't have Permission.WRITE for this MeasuredBioMaterial or Permission.USE for the BioWell.

BaseException - If there is another error.

Since:

2.10

getBioWell

public BioWell getBioWell()

Get the well this biomaterial is located in.

Returns:

A BioWell object or null if this biomaterial is not located on a plate

Since:

2.10

updateFreeWells

private void updateFreeWells(BioPlateData plate,
 int delta)

isInWell

public boolean isInWell()

Check if this biomaterial is located in a well on a bioplate or not.

Returns:

TRUE if the biomaterial is in a well, FALSE if not

Since:

2.17

isLockedInWell

public boolean isLockedInWell()

Check if this biomaterial is placed in a well that it can't be removed from.

Returns:

TRUE if the biomaterial is locked, FALSE if is not in a well or in a well that allows moving it

Since:

2.16