Package net.sf.basedb.core

Class BioPlate

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.BioPlate

All Implemented Interfaces:

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

public class BioPlate
extends AnnotatedItem
implements Registered

This class is represents physical bio-plates. A bio-plate must have a PlateGeometry

A bio-plate consists of BioWell:s which are organised into rows and columns as specified by the plate geometry.

Version:

2.10

Author:

martin

Last modified

$Date: 2017-05-22 14:35:27 +0200 (må, 22 maj 2017) $

Field Summary

Fields

Modifier and Type	Field	Description
static final int	MAX_BARCODE_LENGTH	The maximum length of the barcode that can be stored in the database.
static final int	MAX_POSITION_LENGTH	The maximum length of the position coordinate that can be stored in the database.
static final int	MAX_SECTION_LENGTH	The maximum length of the section coordinate that can be stored in the database.
static final int	MAX_TRAY_LENGTH	The maximum length of the tray coordinate that can be stored in the database.
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
BioPlate(BioPlateData annotatedData)

Method Summary

Modifier and Type	Method	Description
Set<Annotatable>	getAnnotatableParents()	Get the freezer.
String	getBarcode()	Gets the barcode of this bio plate.
MeasuredBioMaterial	getBioMaterial(PlateCoordinate wellC)	Get the biomaterial in the well at the given location.
BioPlateType	getBioPlateType()	Get the BioPlateType of this bioplate.
BioWell	getBioWell(int row, int column)	Gets bio well for specific location.
BioWell	getBioWell(PlateCoordinate wellC)	Gets bio well for specific location.
ItemQuery<BioWell>	getBioWells()	Gets a query that returns all BioWells on this plate.
static BioPlate	getById(DbControl dc, int id)	Gets a BioPlate when knowing the item's id
int	getColumns()	Get the number of rows on this plate.
(package private) BioPlateData	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.
Date	getEventDate()	Get the date this plate was created.
ItemQuery<BioPlateEvent>	getEvents()	Get a query returning events that this plate has been a part of.
String	getExternalId()	Gets the external id of this bio plate
int	getFreeWells()	Get the number of free wells on this plate.
Hardware	getFreezer()	Gets the storage location of this bio plate
static BioPlate	getNew(DbControl dc, PlateGeometry geometry, BioPlateType plateType)	Creates a new bioplate with a specific plate geometry and type.
PlateGeometry	getPlateGeometry()	Get the PlateGeometry of this bioplate.
String	getPosition()	Get the position within the "storage location" for this bioplate.
static ItemQuery<BioPlate>	getQuery()	Gets query that selects all available bioplates
int	getRows()	Get the number of rows on this plate.
String	getSection()	Get the section within the "storage location" for this bioplate.
int	getTotalWells()	Get the total number of wells on this plate.
String	getTray()	Get the tray within the "storage location" for this bioplate.
Item	getType()	Get the type of item represented by the object.
int	getUsedWells()	Get the number of used wells on this plate.
Set<ItemProxy>	getUsingItems()	Gets all MeasuredBioMaterial located on this plate and all child plates created from this plate.
boolean	isDestroyed()	Check if the plate has been destroyed.
boolean	isUsed()	Check if there are any MeasuredBioMaterial on this plate.
(package private) void	onBeforeCommit(Transactional.Action action)	If a project is active, automatically share the new item according to the settings of that project, unless a project or item key has been explicitely set (including null).
void	setBarcode(String barcode)	Sets the bio plates barcode
private void	setBioPlateType(BioPlateType plateType)
void	setDestroyed(boolean destroyed)	Set the destroyed flag.
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setEventDate(Date eventDate)	Set the date this plate was created.
void	setExternalId(String externalId)	Sets the external id of this bio plate
void	setFreezer(Hardware freezer)	Sets the freezer where this bio plate is stored
private void	setPlateGeometry(PlateGeometry plateGeometry)
void	setPosition(String position)	Set the position within the "storage location" for this bioplate.
void	setSection(String section)	Set the section within the "storage location" for this bioplate.
void	setTray(String tray)	Set the tray within the "storage location" for this bioplate.

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

getAnnotationSet, getProtocol, 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.Ownable

getOwner, isOwner, setOwner, takeOwnership

Field Details

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

• Item.BIOPLATE
• getType()

MAX_BARCODE_LENGTH

public static final int MAX_BARCODE_LENGTH

The maximum length of the barcode that can be stored in the database. Check the length against this value before calling the setBarcode(String) method to avoid exceptions.

See Also:

• Constant Field Values

MAX_SECTION_LENGTH

public static final int MAX_SECTION_LENGTH

The maximum length of the section coordinate that can be stored in the database. Check the length against this value before calling the setSection(String) method to avoid exceptions.

Since:

3.2

See Also:

• Constant Field Values

MAX_TRAY_LENGTH

public static final int MAX_TRAY_LENGTH

The maximum length of the tray coordinate that can be stored in the database. Check the length against this value before calling the setTray(String) method to avoid exceptions.

Since:

3.2

See Also:

• Constant Field Values

MAX_POSITION_LENGTH

public static final int MAX_POSITION_LENGTH

The maximum length of the position coordinate that can be stored in the database. Check the length against this value before calling the setPosition(String) method to avoid exceptions.

Since:

3.2

See Also:

• Constant Field Values

Constructor Details

BioPlate

BioPlate(BioPlateData annotatedData)

Method Details

getNew

public static BioPlate getNew(DbControl dc,
 PlateGeometry geometry,
 BioPlateType plateType)
                       throws BaseException,
InvalidDataException

Creates a new bioplate with a specific plate geometry and type.

Parameters:

dc - DbControl used for database access

geometry - The geometry the new plate should have

plateType - The type of the new plate

Returns:

A new BioPlate object

Throws:

BaseException - If anything goes wrong when creating.

InvalidDataException - If gemoetry or type is null

Since:

2.16

getById

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

Gets a BioPlate when knowing the item's id

Parameters:

dc - DbControl used for database access

id - The item's id.

Returns:

BioPlate object

Throws:

ItemNotFoundException - If no item with the given id was found

PermissionDeniedException - If logged in user doesn't have enough permission to the requested item

BaseException - If there is another error.

getQuery

public static ItemQuery<BioPlate> getQuery()

Gets query that selects all available bioplates

Returns:

ItemQuery object

getData

BioPlateData getData()

Description copied from class: BasicItem

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

Overrides:

getData in class AnnotatedItem

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the freezer.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

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

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

Since:

3.1

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

isUsed

public boolean isUsed()

Check if there are any MeasuredBioMaterial on this plate.

Overrides:

isUsed in class BasicItem

Returns:

TRUE if this item is used, FALSE otherwise

See Also:

• BasicItem.getUsingItems()

getUsingItems

public Set<ItemProxy> getUsingItems()

Gets all MeasuredBioMaterial located on this plate and all child plates created from this plate.

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 NotLoggedInException,
BaseException

Description copied from class: SharedItem

If a project is active, automatically share the new item according to the settings of that project, unless a project or item key has been explicitely set (including null).

Overrides:

onBeforeCommit in class SharedItem

Throws:

NotLoggedInException - If no user is logged in

BaseException - If there is another error

See Also:

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

getPlateGeometry

public PlateGeometry getPlateGeometry()
                               throws PermissionDeniedException,
BaseException

Get the PlateGeometry of this bioplate.

Returns:

The PlateGeometry item

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission for the plate geometry

BaseException - If there is another error

setPlateGeometry

private void setPlateGeometry(PlateGeometry plateGeometry)
                       throws PermissionDeniedException,
InvalidDataException

Throws:

PermissionDeniedException

InvalidDataException

getBioPlateType

public BioPlateType getBioPlateType()
                             throws PermissionDeniedException,
BaseException

Get the BioPlateType of this bioplate.

Returns:

The BioPlateType item

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission for the plate type

BaseException - If there is another error

Since:

2.16

setBioPlateType

private void setBioPlateType(BioPlateType plateType)
                      throws PermissionDeniedException,
InvalidDataException

Throws:

PermissionDeniedException

InvalidDataException

setExternalId

public void setExternalId(String externalId)
                   throws PermissionDeniedException,
InvalidDataException

Sets the external id of this bio plate

Parameters:

externalId - The external id to set. Null is allowed. Maximum length BioPlateData.MAX_EXTERNAL_ID_LENGTH characters.

Throws:

PermissionDeniedException - If logged in user doesn't have Permission.WRITE on the plate

InvalidDataException - If maximum length of externalId is exceeded.

getExternalId

public String getExternalId()

Gets the external id of this bio plate

Returns:

A String object or null

setBarcode

public void setBarcode(String barcode)
                throws PermissionDeniedException,
InvalidDataException

Sets the bio plates barcode

Parameters:

barcode - The barcode to set. Null is allowed. Maximum length BioPlateData.MAX_BARCODE_LENGTH characters.

Throws:

PermissionDeniedException - If logged in user doesn't have Permission.WRITE on the plate.

InvalidDataException - If maximum length of barcode is exceeded.

getBarcode

public String getBarcode()

Gets the barcode of this bio plate.

Returns:

A String object or null.

isDestroyed

public boolean isDestroyed()

Check if the plate has been destroyed. This is currently only a flag. It doesn't limit what can be done with the plate through the API.

Since:

2.16

setDestroyed

public void setDestroyed(boolean destroyed)
                  throws PermissionDeniedException

Set the destroyed flag.

Parameters:

destroyed - TRUE if the plate is destroyed, FALSE otherwise.

Throws:

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

Since:

2.16

getEventDate

public Date getEventDate()

Get the date this plate was created.

Returns:

A Date object, or null if not known

Since:

3.1

setEventDate

public void setEventDate(Date eventDate)
                  throws PermissionDeniedException

Set the date this plate was created.

Parameters:

eventDate - The date, or null if not known

Throws:

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

Since:

3.1

setFreezer

public void setFreezer(Hardware freezer)
                throws PermissionDeniedException

Sets the freezer where this bio plate is stored

Parameters:

freezer - The freezer to set. Null is allowed.

Throws:

PermissionDeniedException - If logged in user doesn't have Permission.WRITE on this bio plate or Permission.USE on the freezer.

getFreezer

public Hardware getFreezer()

Gets the storage location of this bio plate

Returns:

A Hardware item or null

See Also:

• getSection()

getSection

public String getSection()

Get the section within the "storage location" for this bioplate.

Returns:

A string or null

Since:

3.2

setSection

public void setSection(String section)

Set the section within the "storage location" for this bioplate.

Since:

3.2

getTray

public String getTray()

Get the tray within the "storage location" for this bioplate.

Returns:

A string or null

Since:

3.2

setTray

public void setTray(String tray)

Set the tray within the "storage location" for this bioplate.

Since:

3.2

getPosition

public String getPosition()

Get the position within the "storage location" for this bioplate.

Returns:

A string or null

Since:

3.2

setPosition

public void setPosition(String position)

Set the position within the "storage location" for this bioplate.

Since:

3.2

getBioWells

public ItemQuery<BioWell> getBioWells()

Gets a query that returns all BioWells on this plate.

Returns:

an ItemQuery object.

getRows

public int getRows()

Get the number of rows on this plate. This is a shortcut for getPlateGeometry().getRows()

Since:

2.17

getColumns

public int getColumns()

Get the number of rows on this plate. This is a shortcut for getPlateGeometry().getColumns()

Since:

2.17

getFreeWells

public int getFreeWells()

Get the number of free wells on this plate.

Since:

2.17

getUsedWells

public int getUsedWells()

Get the number of used wells on this plate.

Since:

2.17

getTotalWells

public int getTotalWells()

Get the total number of wells on this plate.

Since:

2.17

getBioWell

public BioWell getBioWell(int row,
 int column)

Gets bio well for specific location.

Parameters:

row - Row index where the bio well is located.

column - Column index where the bio well is located

Returns:

A BioWell object or null if no bio well can be found

getBioWell

public BioWell getBioWell(PlateCoordinate wellC)

Gets bio well for specific location.

Parameters:

wellC - The coordinate of the well

Returns:

A BioWell object or null if no bio well can be found

Since:

2.16

getBioMaterial

public MeasuredBioMaterial getBioMaterial(PlateCoordinate wellC)

Get the biomaterial in the well at the given location. This method is a shortcut for BioPlate.getBioWell().getBioMaterial().

Parameters:

wellC - The coordinate of the well

Returns:

A MeasuredBioMaterial or null if the well doesn't exists or is empty

Since:

2.16

getEvents

public ItemQuery<BioPlateEvent> getEvents()

Get a query returning events that this plate has been a part of.