net.sf.basedb.core
Class BioMaterialEvent

java.lang.Object
  net.sf.basedb.core.BasicItem<D>
      net.sf.basedb.core.ChildItem<BioMaterialEventData>
          net.sf.basedb.core.BioMaterialEvent

All Implemented Interfaces:

AccessControlled, Identifiable, Registered

public class BioMaterialEvent
extends ChildItem<BioMaterialEventData>
implements Registered

This class represents an event in the life of a MeasuredBioMaterial. There are three main types of events: creation events, hybridization events and other events. A creation event is an event that produces a measured biomaterial from other biomaterials. A hybridization event is an event that produces a hybridization from labeled extracts. Other events are used to leave a note about something that affected an already existing biomaterial.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2011-01-31 10:51:00 +0100 (Mon, 31 Jan 2011) $

Nested Class Summary

static class

BioMaterialEvent.Type The type of the event.

Field Summary

private boolean	hardwareHasBeenSet
static int	MAX_COMMENT_LENGTH The maximum length of the comment about this event.
private boolean	protocolHasBeenSet
static Item	TYPE The type of item represented by this class.

Constructor Summary

BioMaterialEvent(BioMaterialEventData bioMaterialEventData)

Method Summary

void	addSource(MeasuredBioMaterial bioMaterial, Float usedQuantity) Add a source biomaterial to this event or update the used quantity of an existing source.
private void	checkAllowedSource(MeasuredBioMaterial bioMaterial) Check if the biomaterial is allowed as a source.
(package private) void	clearSources() Clear the sources collection and return the used quantities to the source biomaterials.
MeasuredBioMaterial	getBioMaterial() Get the MeasuredBioMaterial that was affected or created by this event.
BioPlateEventParticipant	getBioPlateEventParticipant() Get the bioplate event participant that is the master of this event.
static BioMaterialEvent	getById(DbControl dc, int id) Get a BioMaterialEvent item when you know the id.
String	getComment() Get the comment about this event.
Date	getEntryDate() Get the date this event was added to the database.
Date	getEventDate() Get the date this event was done in the lab.
BioMaterialEvent.Type	getEventType() Get the type of event.
Hardware	getHardware() Get the Hardware that was used in this event.
Hybridization	getHybridization() Get the Hybridization that was created by this event.
static BioMaterialEvent	getNew(DbControl dc, MeasuredBioMaterial bioMaterial) Create a new BioMaterialEvent of the BioMaterialEvent.Type.OTHER type.
static BioMaterialEvent	getNew(DbControl dc, MeasuredBioMaterial bioMaterial, BioPlateEventParticipant master) Create a new BioMaterialEvent of the BioMaterialEvent.Type.OTHER type that is linked with a master BioPlateEventParticipant.
(package private) static BioMaterialEvent	getNewCreationEvent(DbControl dc, MeasuredBioMaterial bioMaterial, BioPlateEventParticipant master) Create a new BioMaterialEvent of the BioMaterialEvent.Type.CREATION type (creation event).
(package private) static BioMaterialEvent	getNewHybridizationEvent(DbControl dc, Hybridization hybridization, BioPlateEventParticipant master) Create a new BioMaterialEvent of the BioMaterialEvent.Type.HYBRIDIZATION type.
Protocol	getProtocol() Get the Protocol describing the procedure used in this event.
static ItemQuery<BioMaterialEvent>	getQuery(MeasuredBioMaterial bioMaterial) Get a query that returns events for a biomaterial.
(package private) SharedData	getSharedParent() Get the shareable parent item of this child item.
int	getSourceGroup(MeasuredBioMaterial bioMaterial) Get the source group of the biomaterial
ItemQuery<? extends MeasuredBioMaterial>	getSources() Get a query that return all biomaterials used as sources for this event.
Item	getType() Get the type of item represented by the object.
Float	getUsedQuantity() Get the quantity that was used from the biomaterial by this event.
Float	getUsedQuantity(MeasuredBioMaterial bioMaterial) Get the quantity that was used by this event for the specified biomaterial.
User	getUser() Get the User that is responsible for this event.
(package private) void	initPermissions(int granted, int denied) READ permission is granted and DELETE permissions is denied to evereyone for creation events.
boolean	isPlateEvent() Check if this event is related with a bioplate event.
(package private) void	onBeforeCommit(Transactional.Action action) Return used guantity to biomaterials on delete action.
void	removeSource(MeasuredBioMaterial bioMaterial) Remove a biomaterial used as a source.
private void	setBioMaterial(MeasuredBioMaterial bioMaterial) Set the biomaterial that was affected or created by this event.
void	setComment(String comment) Set the comment about this event.
void	setEventDate(Date eventDate) Set the date this event was done in the lab.
void	setHardware(Hardware hardware) Get the Hardware that was used in this event.
private void	setHybridization(Hybridization hybridization) Set the hybidization that was created by this event.
(package private) void	setProjectDefaults(Project activeProject) Set protocol and hardware from project default settings.
void	setProtocol(Protocol protocol) Set the Protocol that describes the procedure used in this event.
(package private) void	setSource(MeasuredBioMaterial bioMaterial, Float usedQuantity) Set a single source.
void	setSourceGroup(MeasuredBioMaterial bioMaterial, int sourceGroup) Set the source group for a biomaterial that was used as a source in this event.
void	setUsedQuantity(Float usedQuantity) Set the used quantity.

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

getPermissionForWriteDeleteAndCreate, getPluginPermissions

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

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getSessionControl, getUsingItems, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, onAfterCommit, onAfterInsert, onRollback, setDbControl, toString, toTransferable, validate

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.Identifiable

getId, getVersion

Methods inherited from interface net.sf.basedb.core.AccessControlled

checkPermission, getPermissions, hasPermission

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.BIOMATERIALEVENT, getType()

protocolHasBeenSet

private boolean protocolHasBeenSet

hardwareHasBeenSet

private boolean hardwareHasBeenSet

MAX_COMMENT_LENGTH

public static final int MAX_COMMENT_LENGTH

The maximum length of the comment about this event. Check the length against this value before calling the setComment(String) method to avoid exceptions.

See Also:

Constant Field Values

Constructor Detail

BioMaterialEvent

BioMaterialEvent(BioMaterialEventData bioMaterialEventData)

Method Detail

getNew

public static BioMaterialEvent getNew(DbControl dc,
                                      MeasuredBioMaterial bioMaterial)
                               throws BaseException

Create a new BioMaterialEvent of the BioMaterialEvent.Type.OTHER type.

Parameters:

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

bioMaterial - The affected biomaterial

Returns:

The new BioMaterialEvent item

Throws:

BaseException - If there is an error

getNew

public static BioMaterialEvent getNew(DbControl dc,
                                      MeasuredBioMaterial bioMaterial,
                                      BioPlateEventParticipant master)
                               throws BaseException

Create a new BioMaterialEvent of the BioMaterialEvent.Type.OTHER type that is linked with a master BioPlateEventParticipant. If a master bioplate event is used it must be a new event that has not yet been saved to the database.

Parameters:

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

bioMaterial - The affected biomaterial

master - The master bioplate event or null

Returns:

The new BioMaterialEvent item

Throws:

BaseException - If there is an error

Since:

2.17

getNewCreationEvent

static BioMaterialEvent getNewCreationEvent(DbControl dc,
                                            MeasuredBioMaterial bioMaterial,
                                            BioPlateEventParticipant master)
                                     throws BaseException

Create a new BioMaterialEvent of the BioMaterialEvent.Type.CREATION type (creation event).

Parameters:

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

bioMaterial - The biomaterial that was created.

master - The master bioplate event or null

Returns:

The new BioMaterialEvent item

Throws:

BaseException - If there is an error

Since:

2.17

getNewHybridizationEvent

static BioMaterialEvent getNewHybridizationEvent(DbControl dc,
                                                 Hybridization hybridization,
                                                 BioPlateEventParticipant master)
                                          throws BaseException

Create a new BioMaterialEvent of the BioMaterialEvent.Type.HYBRIDIZATION type.

Parameters:

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

hybridization - The hybridization that was created.

master - The master bioplate event or null

Returns:

The new BioMaterialEvent item

Throws:

BaseException - If there is an error

Since:

2.17

getById

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

Get a BioMaterialEvent 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 BioMaterialEvent 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<BioMaterialEvent> getQuery(MeasuredBioMaterial bioMaterial)
                                            throws InvalidDataException

Get a query that returns events for a biomaterial. All events where the given biomaterial is either a source or a product are returned.

Parameters:

bioMaterial - The biomaterial to retreive events for, null is not allowed

Returns:

An ItemQuery object

Throws:

InvalidDataException - If the bioMaterial is null

See Also:

MeasuredBioMaterial.getEvents()

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

onBeforeCommit

void onBeforeCommit(Transactional.Action action)
              throws BaseException

Return used guantity to biomaterials on delete action.

Overrides:

onBeforeCommit in class BasicItem<BioMaterialEventData>

Throws:

BaseException - If there is an error

See Also:

Transactional, Core API overview - Transaction handling, Coding rules and guidelines for item classes

initPermissions

void initPermissions(int granted,
                     int denied)
               throws BaseException

READ permission is granted and DELETE permissions is denied to evereyone for creation events. WRITE permission is denied if this event is associated with a plate event. Other permissions are always checked on the parent biomaterial or hybridization.

Overrides:

initPermissions in class ChildItem<BioMaterialEventData>

Parameters:

granted - Permissions that have been granted by the subclass

denied - Permissions that have been denied by the subclass

Throws:

BaseException - If the permissions couldn't be initialised

setProjectDefaults

void setProjectDefaults(Project activeProject)
                  throws BaseException

Set protocol and hardware from project default settings.

Overrides:

setProjectDefaults in class BasicItem<BioMaterialEventData>

Parameters:

activeProject - The currently active project

Throws:

BaseException

Since:

2.9

getSharedParent

SharedData getSharedParent()

Description copied from class: ChildItem

Get the shareable parent item of this child item. This is used by the ChildItem.initPermissions(int, int) method to calculate the logged in user's permissions for the child item.

Specified by:

getSharedParent in class ChildItem<BioMaterialEventData>

Returns:

The parent item

getEventType

public BioMaterialEvent.Type getEventType()

Get the type of event.

See Also:

BioMaterialEvent.Type

getBioMaterial

public MeasuredBioMaterial getBioMaterial()
                                   throws PermissionDeniedException,
                                          BaseException

Get the MeasuredBioMaterial that was affected or created by this event.

Returns:

A MeasuredBioMaterial item or null if this is hybridization event

Throws:

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

BaseException - If there is another error

setBioMaterial

private void setBioMaterial(MeasuredBioMaterial bioMaterial)
                     throws PermissionDeniedException,
                            InvalidDataException

Set the biomaterial that was affected or created by this event.

Throws:

PermissionDeniedException

InvalidDataException

getHybridization

public Hybridization getHybridization()
                               throws PermissionDeniedException,
                                      BaseException

Get the Hybridization that was created by this event.

Returns:

A Hybridization item or null if this isn't a hybridization event

Throws:

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

BaseException - If there is another error

setHybridization

private void setHybridization(Hybridization hybridization)
                       throws PermissionDeniedException,
                              InvalidDataException

Set the hybidization that was created by this event.

Throws:

PermissionDeniedException

InvalidDataException

isPlateEvent

public boolean isPlateEvent()

Check if this event is related with a bioplate event.

Since:

2.17

getBioPlateEventParticipant

public BioPlateEventParticipant getBioPlateEventParticipant()

Get the bioplate event participant that is the master of this event. If this event has a master event, many properties such as event date, protocol, etc. must be set on the master event.

Returns:

A bioplate event participant or null

Since:

2.17

getUser

public User getUser()
             throws PermissionDeniedException,
                    BaseException

Get the User that is responsible for this event.

Returns:

A User item

Throws:

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

BaseException - If there is another error

getProtocol

public Protocol getProtocol()
                     throws PermissionDeniedException,
                            BaseException

Get the Protocol describing the procedure used in this event.

Returns:

A Protocol item, or null if not known

Throws:

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

BaseException - If there is another error

setProtocol

public void setProtocol(Protocol protocol)
                 throws PermissionDeniedException

Set the Protocol that describes the procedure used in this event.

Parameters:

protocol - A Protocol item, or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission on this event or use permission for the protocol

getHardware

public Hardware getHardware()
                     throws PermissionDeniedException,
                            BaseException

Get the Hardware that was used in this event.

Returns:

A Hardware item, or null if not known

Throws:

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

BaseException - If there is another error

setHardware

public void setHardware(Hardware hardware)
                 throws PermissionDeniedException

Get the Hardware that was used in this event.

Parameters:

hardware - A Hardware item, or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission on this event or use permission for the hardware

getUsedQuantity

public Float getUsedQuantity()

Get the quantity that was used from the biomaterial by this event. If this is a creation event this value is the negative value of the original quantity of the created biomaterial.

setUsedQuantity

public void setUsedQuantity(Float usedQuantity)
                     throws PermissionDeniedException

Set the used quantity.

Parameters:

usedQuantity - The quantity to set.

Throws:

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

getUsedQuantity

public Float getUsedQuantity(MeasuredBioMaterial bioMaterial)

Get the quantity that was used by this event for the specified biomaterial.

Parameters:

bioMaterial - A biomaterial object

getSourceGroup

public int getSourceGroup(MeasuredBioMaterial bioMaterial)

Get the source group of the biomaterial

Parameters:

bioMaterial - The source biomaterial

Returns:

The source group index or 0 if the biomaterial is not a source of this event

Since:

2.6

See Also:

setSourceGroup(MeasuredBioMaterial, int)

addSource

public void addSource(MeasuredBioMaterial bioMaterial,
                      Float usedQuantity)
               throws PermissionDeniedException,
                      InvalidDataException,
                      BaseException

Add a source biomaterial to this event or update the used quantity of an existing source. Sources can only be specified if the produced biomaterial is a pooled biomaterial and this is a creation event.

Parameters:

bioMaterial - The biomaterial used as a source

usedQuantity - The quantity that was used from the source biomaterial

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for this event of use permission for the source

InvalidDataException - If this is not a creation event or if the produced biomaterial is not pooled or if the source biomaterial is of another type

BaseException - If there is another error

setSourceGroup

public void setSourceGroup(MeasuredBioMaterial bioMaterial,
                           int sourceGroup)
                    throws PermissionDeniedException,
                           InvalidDataException,
                           BaseException

Set the source group for a biomaterial that was used as a source in this event. The source group value is used to group sources that are related. The only example and use case is when using multi-array hybridizations where it is essential to know which array a labeled extract goes on. The source group is then simply the number of the array on the hybridization and should be a value between 1 and Hybridization.getNumArrays().

A single labeled extract can only be used in a single group. Experiments using a n-channel platform and a common reference must first split the reference labeled extract into individual labeled extracts. This can be done with the 'pooling' functionality.

If the source biomaterial has not been added with addSource(MeasuredBioMaterial, Float) this method will automatically add it with usedQuantity = null.

Parameters:

bioMaterial - The source biomaterial

sourceGroup - The source group

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for this event of use permission for the source

InvalidDataException - If this is not a creation event or if the produced biomaterial is not pooled or if the source biomaterial is of another type

BaseException

Since:

2.6

removeSource

public void removeSource(MeasuredBioMaterial bioMaterial)
                  throws PermissionDeniedException,
                         InvalidDataException,
                         BaseException

Remove a biomaterial used as a source. Sources can only be specified if the produced biomaterial is a pooled biomaterial and this is a creation event.

Parameters:

bioMaterial - The biomaterial used as a source

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for this event of use permission for the source

InvalidDataException - If this is not a creation event or if the produced biomaterial is not pooled or if the source biomaterial is of another type

BaseException - If there is another error

checkAllowedSource

private void checkAllowedSource(MeasuredBioMaterial bioMaterial)
                         throws PermissionDeniedException,
                                InvalidDataException,
                                BaseException

Check if the biomaterial is allowed as a source. It is allowed if:

• This is a creation event
• The created biomaterial is pooled
• It is of the same type as the created biomaterial
• It is not the same item as the created biomaterial

Throws:

PermissionDeniedException

InvalidDataException

BaseException

setSource

void setSource(MeasuredBioMaterial bioMaterial,
               Float usedQuantity)
         throws PermissionDeniedException,
                InvalidDataException

Set a single source. This method is used for non-pooled biomaterial to specify the parent.

Throws:

PermissionDeniedException

InvalidDataException

See Also:

Extract.setSample(Sample, Float), LabeledExtract.setExtract(Extract, Float)

clearSources

void clearSources()

Clear the sources collection and return the used quantities to the source biomaterials.

getSources

public ItemQuery<? extends MeasuredBioMaterial> getSources()

Get a query that return all biomaterials used as sources for this event. To filter or sort on the used quantity or source group columns use 'srcevt' as alias. For example to only return sources in source group 2 and to order the result by used quantity:

query = event.getSources();
query.restrict(Expressions.gteq(
  Hql.property("srcevt", "sourceGroup"), Expressions.integer(2))
);
query.order(Orders.asc(Hql.property("srcevt", "usedQuantity")));

NOTE! The filtering and ordering on the "srcevt" columns is only available in BASE 2.6 and later.

Returns:

An ItemQuery object

getComment

public String getComment()

Get the comment about this event.

Returns:

The comment

setComment

public void setComment(String comment)
                throws PermissionDeniedException,
                       InvalidDataException

Set the comment about this event. The value may be null, but mustn't be longer than the value specified by the MAX_COMMENT_LENGTH constant.

Parameters:

comment - The new comment

Throws:

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

InvalidDataException - If the comment is too long

getEntryDate

public Date getEntryDate()

Get the date this event was added to the database.

Specified by:

getEntryDate in interface Registered

Returns:

A Date object

getEventDate

public Date getEventDate()

Get the date this event was done in the lab.

Returns:

A Date object, or null if not known

setEventDate

public void setEventDate(Date eventDate)
                  throws PermissionDeniedException

Set the date this event was done in the lab.

Parameters:

eventDate - The date, or null if not known

Throws:

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