Package net.sf.basedb.core

Class BioMaterialEvent

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.ChildItem

net.sf.basedb.core.BioMaterialEvent

All Implemented Interfaces:

AccessControlled, Identifiable, Registered

public class BioMaterialEvent
extends ChildItem
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: 2019-02-26 11:10:15 +0100 (tis, 26 feb. 2019) $

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	BioMaterialEvent.Type	The type of the event.

Field Summary

Fields

Modifier and Type	Field	Description
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

Constructors

Constructor	Description
BioMaterialEvent(BioMaterialEventData bioMaterialEventData)

Method Summary

Modifier and Type	Method	Description
private BioMaterialEventSource	addCheckedSource(BioMaterial bioMaterial)
BioMaterialEventSource	addSource(BioMaterial bioMaterial)	Add a biomaterial as a source to this event.
private void	checkAllowedSource(BioMaterial source, boolean forAdd)	Check if the biomaterial is allowed as a source.
void	clearSources()	Clear the sources collection and return the used quantities to the source biomaterials.
private void	clearSourcesExcept(BioMaterial parent)	Clear the sources collection and return the used quantities to the source biomaterials, except for the given biomaterial.
(package private) static void	ensureProductParentCorrectness(BioMaterialEventData event)	Ensure that the MeasuredBioMaterial.getParent() and MeasuredBioMaterial.getParentType() reflect the current sources collection.
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.
(package private) BioMaterialEventData	getData()	Get the BasicData object that holds all data for this item.
Date	getEntryDate()	Get the date this event was added to the database.
Date	getEventDate()	Get the date this event was done in the lab.
BioMaterialEventSource	getEventSource(BioMaterial bioMaterial)	Get information about a biomaterial used as a source to this event.
SpecialQuery<BioMaterialEventSource>	getEventSources()	Create a special query that return BioMaterialEventSource objects.
List<BioMaterialEventSource>	getEventSources(DbControl dc, int position)	Utility method for finding all sources on a given bioassay position.
BioMaterialEvent.Type	getEventType()	Get the type of event.
Hardware	getHardware()	Get the Hardware that was used in this event.
Kit	getKit()	Get the Kit that was used in 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	getNewBioAssayEvent(DbControl dc, PhysicalBioAssay physicalBioAssay, BioPlateEventParticipant master)	Create a new BioMaterialEvent of the BioMaterialEvent.Type.BIOASSAY type.
(package private) static BioMaterialEvent	getNewCreationEvent(DbControl dc, MeasuredBioMaterial bioMaterial, BioPlateEventParticipant master)	Create a new BioMaterialEvent of the BioMaterialEvent.Type.CREATION type (creation event).
PhysicalBioAssay	getPhysicalBioAssay()	Get the PhysicalBioAssay that was created by this event.
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.
<T extends BioMaterial> ItemQuery<T>	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.
boolean	isSource(BioMaterial bioMaterial)	Check if the given biomaterial has been used as a source in this event.
(package private) void	onBeforeCommit(Transactional.Action action)	Return used guantity to biomaterials on delete action.
void	removeSource(BioMaterial 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	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
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.
void	setKit(Kit kit)	Set the Kit that was used in this event.
private void	setPhysicalBioAssay(PhysicalBioAssay physicalBioAssay)	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.
BioMaterialEventSource	setSource(BioMaterial parent)	Set a single parent item for this event.
void	setUsedQuantity(Float usedQuantity)	Set the used quantity.

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

getPermissionForUse, getPermissionForWriteDeleteAndCreate, getPluginPermissions

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

addAnnotatableParents, addUsingItems, addUsingItems, breakCircularReferences, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, getSessionControl, getUsingItems, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, onAfterCommit, onAfterInsert, onRollback, setDbControl, 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

Field Details

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 Details

BioMaterialEvent

BioMaterialEvent(BioMaterialEventData bioMaterialEventData)

Method Details

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

getNewBioAssayEvent

static BioMaterialEvent getNewBioAssayEvent(DbControl dc,
PhysicalBioAssay physicalBioAssay,
BioPlateEventParticipant master)
                                     throws BaseException

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

Parameters:

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

physicalBioAssay - 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()

getData

BioMaterialEventData getData()

Description copied from class: BasicItem

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

Specified by:

getData in class BasicItem

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

Throws:

BaseException - If there is an error

See Also:

Transactional, Developer documentation: Transactions, Developer documentation: 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

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

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

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

getPhysicalBioAssay

public PhysicalBioAssay getPhysicalBioAssay()
                                     throws PermissionDeniedException,
BaseException

Get the PhysicalBioAssay that was created by this event.

Returns:

A PhysicalBioAssay item or null if this isn't a bioassay event

Throws:

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

BaseException - If there is another error

setPhysicalBioAssay

private void setPhysicalBioAssay(PhysicalBioAssay physicalBioAssay)
                          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

getKit

public Kit getKit()
           throws PermissionDeniedException,
BaseException

Get the Kit that was used in this event.

Returns:

A Kit item, or null if not known

Throws:

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

BaseException - If there is another error

Since:

3.7

setKit

public void setKit(Kit kit)
            throws PermissionDeniedException

Set the Kit that was used in this event.

Parameters:

kit - A Kit 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 kit

Since:

3.7

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

getEventSource

public BioMaterialEventSource getEventSource(BioMaterial bioMaterial)

Get information about a biomaterial used as a source to this event.

Parameters:

bioMaterial - The biomaterial

Returns:

A BioMaterialEventSource object or null if the given biomaterial is not a source to the event

Since:

3.0

See Also:

addSource(BioMaterial)

isSource

public boolean isSource(BioMaterial bioMaterial)

Check if the given biomaterial has been used as a source in this event.

Parameters:

bioMaterial - The biomaterial to check

setSource

public BioMaterialEventSource setSource(BioMaterial parent)

Set a single parent item for this event. Any sources that are currently associated with it are removed and the used quantity is returned.

Parameters:

parent - The parent biomaterial, or null to remove all parents

Since:

3.0

addSource

public BioMaterialEventSource addSource(BioMaterial bioMaterial)

Add a biomaterial as a source to this event. If the given biomaterial already is a source, the existing information is returned. If this event already has sources the new source must be of the same type as the existing sources and the produced biomaterial.

Parameters:

bioMaterial - The biomaterial (null is not allowed)

Returns:

A BioMaterialEventSource object

Since:

3.0

addCheckedSource

private BioMaterialEventSource addCheckedSource(BioMaterial bioMaterial)

removeSource

public void removeSource(BioMaterial 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

Since:

3.0

ensureProductParentCorrectness

static void ensureProductParentCorrectness(BioMaterialEventData event)

Ensure that the MeasuredBioMaterial.getParent() and MeasuredBioMaterial.getParentType() reflect the current sources collection.

checkAllowedSource

private void checkAllowedSource(BioMaterial source,
boolean forAdd)
                         throws PermissionDeniedException,
InvalidDataException,
BaseException

Check if the biomaterial is allowed as a source.

Throws:

PermissionDeniedException

InvalidDataException

BaseException

clearSources

public void clearSources()

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

Since:

3.0

clearSourcesExcept

private void clearSourcesExcept(BioMaterial parent)

Clear the sources collection and return the used quantities to the source biomaterials, except for the given biomaterial.

Parameters:

parent - A biomaterial that should already be a parent biomaterial or null to clear all sources

Since:

3.0.4

getSources

public <T extends BioMaterial> ItemQuery<T> getSources()

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

query = event.getSources();
query.restrict(Expressions.gteq(
  Hql.property("srcevt", "position"), 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

getEventSources

public SpecialQuery<BioMaterialEventSource> getEventSources()

Create a special query that return BioMaterialEventSource objects. The objects are not BasicItem:s but can be used to get information about and modify the source biomaterials used in the event. Note that the query may return objects that link to biomaterial that the logged in used doesn't have read access to.

Returns:

A special query

Since:

3.0

getEventSources

public List<BioMaterialEventSource> getEventSources(DbControl dc,
int position)

Utility method for finding all sources on a given bioassay position.

Parameters:

position - The position number (between 1 and PhysicalBioAssay.getSize().

Returns:

A list (empty if no sources are found)

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

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

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