Package net.sf.basedb.core

Class Hardware

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.Hardware

All Implemented Interfaces:

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

public class Hardware
extends AnnotatedItem
implements Registered, Subtypable

This class is used to represent individual hardware items and information about them. In the current version of BASE the only type of hardware we keep information about is scanners.

Version:

2.0

Author:

enell

Last modified

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

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CABINET	The id for the HardwareType object representing a cabinet.
static final String	CLUSTER_GENERATOR	The id for the HardwareType object representing a cluster generator station.
static final String	FREEZER	The id for the HardwareType object representing a freezer.
static final String	HYBRIDIZATION_STATION	The id for the HardwareType object representing a hybridization station.
static final int	MAX_VERSIONSTRING_LENGTH	The maximum length of the version variable that can be stored in the database.
static final String	OTHER	The id for the HardwareType object representing something else.
static final String	PRINT_ROBOT	The id for the HardwareType object representing a print robot.
static final String	SCANNER	The id for the HardwareType object representing a scanner.
static final String	SEQUENCER	The id for the HardwareType object representing a sequencer.
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
Hardware(HardwareData data)	Creates a new hardware item.

Method Summary

Modifier and Type	Method	Description
Set<Annotatable>	getAnnotatableParents()	Get all parents objects which are annotatable and the logged in user has read permission to.
static Hardware	getById(DbControl dc, int id)	Get a Hardware item when you know the ID.
(package private) HardwareData	getData()	Get the BasicData object that holds all data for this item.
static String	getDefaultSystemId(Item itemType)	Get the system id for the hardware subtype that should be used on an item that doesn't have a subtype.
Date	getEntryDate()	Get the date that the item was registered in the database.
ItemSubtype	getItemSubtype()	Get the subtype of the item.
static Hardware	getNew(DbControl dc)	Create a new Hardware item.
static ItemQuery<Hardware>	getQuery()	Get a query configured to retrieve hardware.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: DerivedBioAssay:s with this hardware ArrayBatch:s with this hardware BioMaterial:s and PhysicalBioAssay:s with this hardware Plate:s with this hardware
String	getVersionString()	Get the versionstring of this Hardware item.
boolean	isUsed()	Check if: a DerivedBioAssay is linked to this hardware an ArrayBatch is linked to this hardware a BioMaterialEvent is linked to this hardware a PlateEvent is linked to this hardware
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	setVersionString(String versionString)	Set the versionstring for this Hardware item.

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, onBeforeCommit, 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.HARDWARE
• getType()

SCANNER

public static final String SCANNER

The id for the HardwareType object representing a scanner.

Since:

3.0

See Also:

• Constant Field Values

PRINT_ROBOT

public static final String PRINT_ROBOT

The id for the HardwareType object representing a print robot.

Since:

3.0

See Also:

• Constant Field Values

HYBRIDIZATION_STATION

public static final String HYBRIDIZATION_STATION

The id for the HardwareType object representing a hybridization station.

Since:

3.0

See Also:

• Constant Field Values

CLUSTER_GENERATOR

public static final String CLUSTER_GENERATOR

The id for the HardwareType object representing a cluster generator station. Used when creating a PhysicalBioAssay.

Since:

3.0

See Also:

• Constant Field Values

SEQUENCER

public static final String SEQUENCER

The id for the HardwareType object representing a sequencer.

Since:

3.0

See Also:

• Constant Field Values

FREEZER

public static final String FREEZER

The id for the HardwareType object representing a freezer.

Since:

3.0

See Also:

• Constant Field Values

CABINET

public static final String CABINET

The id for the HardwareType object representing a cabinet.

Since:

3.2

See Also:

• Constant Field Values

OTHER

public static final String OTHER

The id for the HardwareType object representing something else.

Since:

3.0

See Also:

• Constant Field Values

MAX_VERSIONSTRING_LENGTH

public static final int MAX_VERSIONSTRING_LENGTH

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

See Also:

• Constant Field Values

Constructor Details

Hardware

Hardware(HardwareData data)

Creates a new hardware item.

Parameters:

data - the data

Method Details

getDefaultSystemId

public static String getDefaultSystemId(Item itemType)

Get the system id for the hardware subtype that should be used on an item that doesn't have a subtype. This includes Subtypable items with a null ItemSubtype and all other non-subtypable items which can be linked to a hardware.

Parameters:

itemType - The item type

Returns:

The system id of the default hardware type or null

Since:

3.0

getNew

public static Hardware getNew(DbControl dc)
                       throws BaseException

Create a new Hardware item.

Parameters:

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

Returns:

The new Hardware item

Throws:

BaseException - If there is an error

getById

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

Get a Hardware 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 Hardware item

Throws:

ItemNotFoundException - If an item with the specified ID is not found

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission to the item

BaseException - If there is another error

getQuery

public static ItemQuery<Hardware> getQuery()
                                    throws BaseException

Get a query configured to retrieve hardware.

Returns:

An ItemQuery object

Throws:

BaseException - When the query could not be configured.

getData

HardwareData 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

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()

Description copied from interface: Annotatable

Get all parents objects which are annotatable and the logged in user has read permission to. If the item doesn't have any annotatable parents, it may return null or an empty set. The method should only return the immediate parent(s), not parents to parents, etc. As of BASE 3.1 this method may also return child items if the child item is a Subtypable item that has a subtype with the ItemSubtype.getPushAnnotations() flag set.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

Always null

Since:

3.3

getItemSubtype

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 if:

• a DerivedBioAssay is linked to this hardware
• an ArrayBatch is linked to this hardware
• a BioMaterialEvent is linked to this hardware
• a PlateEvent is linked to this hardware

Overrides:

isUsed in class BasicItem

Returns:

TRUE if this hardware is used.

Throws:

BaseException - if there is any error.

See Also:

• BasicItem.getUsingItems()

getUsingItems

public Set<ItemProxy> getUsingItems()

Get all:

• DerivedBioAssay:s with this hardware
• ArrayBatch:s with this hardware
• BioMaterial:s and PhysicalBioAssay:s with this hardware
• Plate:s with this hardware

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)

getVersionString

public String getVersionString()

Get the versionstring of this Hardware item.

Returns:

A string with the version of this item, or null if not known

setVersionString

public void setVersionString(String versionString)
                      throws StringTooLongException,
PermissionDeniedException

Set the versionstring for this Hardware item. The value must not be longer than the value specified by the MAX_VERSIONSTRING_LENGTH constant.

Parameters:

versionString - The new version for this item, or null if not known

Throws:

StringTooLongException - If versionString is longer then MAX_VERSIONSTRING_LENGTH

PermissionDeniedException - If the logged in user don't have write permission on this item