net.sf.basedb.core
Class ProtocolType

java.lang.Object
  net.sf.basedb.core.BasicItem<ProtocolTypeData>
      net.sf.basedb.core.ProtocolType

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Registered, Removable, SystemItem

public class ProtocolType
extends BasicItem<ProtocolTypeData>
implements Nameable, Removable, SystemItem, Registered

This class is used to represent the type of the Protocol items in BASE.

Version:

2.0

Author:

enell

See Also:

Protocol

Field Summary

static String	EXTRACTION The ID for the extraction protocol type, for example a protocol used when creating an Extract from a Sample.
static String	FEATURE_EXTRACTION The ID for the feature extraction protocol type, for example a protocol used for analysing one or more images to create a raw data file.
static String	HYBRIDIZATION The ID for the hybridization protocol type, for example a protocol used when creating a Hybridization from a set of LabeledExtract:s.
static String	LABELING The ID for the labeling protocol type, for example a protocol used when creating a LabeledExtract from an Extract.
static String	POOLING The ID for the pooling protocol type, for example a protocol used when creating a biomaterial item (Sample, Extract or LabeledExtract) from a set of other biomaterial items.
static String	PRINTING The ID for the printing protocol type, for example a protocol used when printing a batch of array slides using a print robot.
static String	SAMPLING The ID for the sampling protocol type, for example a protocol used when creating a Sample from a BioSource.
static String	SCANNING The ID for the scanning protocol type, for example a protocol used for scanning the microarray slide after an experiment.
static 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

Fields inherited from interface net.sf.basedb.core.SystemItem

MAX_SYSTEM_ID_LENGTH

Constructor Summary

ProtocolType(ProtocolTypeData data)
Creates a new protocoltype item.

Method Summary

static ProtocolType	getById(DbControl dc, int id) Get a ProtocolType object when you know the ID.
String	getDescription() Get the description for the item.
Date	getEntryDate() Get the date that the item was registered in the database.
String	getName() Get the name of the item.
static ProtocolType	getNew(DbControl dc) Create a new FileType item.
ItemQuery<Protocol>	getProtocols() Get a query that returns all protocols of this type
static ItemQuery<ProtocolType>	getQuery() Get a query configured to retrieve protocol types.
String	getSystemId() Get the system id for the item.
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get all: Protocol:s of this type PlateEventType:s using this protocol type
(package private) void	initPermissions(int granted, int denied) If this is a system protocol type, delete and create permissions are revoked.
boolean	isRemoved() Check if the removed flag is set for this item.
boolean	isSystemItem() Check if the item is a system item or not.
boolean	isUsed() Check if: A Protocol of this type exists A PlateEventType is linked to this protocol type
Protocol	newProtocol() Create a new Protocol item of this type.
void	setDescription(String description) Set the description for the item.
void	setName(String name) Set the name of the item.
void	setRemoved(boolean removed) Set the removed flag for this item.

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

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onBeforeCommit, onRollback, setDbControl, setProjectDefaults, 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.PROTOCOLTYPE, getType()

SAMPLING

public static final String SAMPLING

The ID for the sampling protocol type, for example a protocol used when creating a Sample from a BioSource.

See Also:

Constant Field Values

EXTRACTION

public static final String EXTRACTION

The ID for the extraction protocol type, for example a protocol used when creating an Extract from a Sample.

See Also:

Constant Field Values

LABELING

public static final String LABELING

The ID for the labeling protocol type, for example a protocol used when creating a LabeledExtract from an Extract.

See Also:

Constant Field Values

POOLING

public static final String POOLING

The ID for the pooling protocol type, for example a protocol used when creating a biomaterial item (Sample, Extract or LabeledExtract) from a set of other biomaterial items.

See Also:

Constant Field Values

HYBRIDIZATION

public static final String HYBRIDIZATION

The ID for the hybridization protocol type, for example a protocol used when creating a Hybridization from a set of LabeledExtract:s.

See Also:

Constant Field Values

PRINTING

public static final String PRINTING

The ID for the printing protocol type, for example a protocol used when printing a batch of array slides using a print robot.

See Also:

Constant Field Values

SCANNING

public static final String SCANNING

The ID for the scanning protocol type, for example a protocol used for scanning the microarray slide after an experiment.

See Also:

Constant Field Values

FEATURE_EXTRACTION

public static final String FEATURE_EXTRACTION

The ID for the feature extraction protocol type, for example a protocol used for analysing one or more images to create a raw data file.

See Also:

Constant Field Values

Constructor Detail

ProtocolType

ProtocolType(ProtocolTypeData data)

Creates a new protocoltype item.

Parameters:

data - The data

Method Detail

getNew

public static ProtocolType getNew(DbControl dc)
                           throws BaseException

Create a new FileType item.

Parameters:

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

Returns:

The new FileType item

Throws:

BaseException - If there is an error

getById

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

Get a ProtocolType object 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 ProtocolType 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 items

BaseException - If there is an error

getQuery

public static ItemQuery<ProtocolType> getQuery()

Get a query configured to retrieve protocol types.

Returns:

An ItemQuery object

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

getName

public String getName()

Description copied from interface: Nameable

Get the name of the item.

Specified by:

getName in interface Nameable

Returns:

A String with the name of the item

setName

public void setName(String name)
             throws PermissionDeniedException,
                    InvalidDataException

Description copied from interface: Nameable

Set the name of the item. The name cannot be null and mustn't be longer than the value specified by the Nameable.MAX_NAME_LENGTH constant.

Specified by:

setName in interface Nameable

Parameters:

name - The new name for the item

Throws:

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

InvalidDataException - If the name is null or longer than specified by the Nameable.MAX_NAME_LENGTH constant

getDescription

public String getDescription()

Description copied from interface: Nameable

Get the description for the item.

Specified by:

getDescription in interface Nameable

Returns:

A String with a description of the item

setDescription

public void setDescription(String description)
                    throws PermissionDeniedException,
                           InvalidDataException

Description copied from interface: Nameable

Set the description for the item. The description can be null but mustn't be longer than the value specified by the Nameable.MAX_DESCRIPTION_LENGTH constant.

Specified by:

setDescription in interface Nameable

Parameters:

description - The new description for the item

Throws:

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

InvalidDataException - If the description longer than specified by the Nameable.MAX_DESCRIPTION_LENGTH constant

isRemoved

public boolean isRemoved()

Description copied from interface: Removable

Check if the removed flag is set for this item.

Specified by:

isRemoved in interface Removable

Returns:

TRUE if the item is flagged as removed, FALSE otherwise

setRemoved

public void setRemoved(boolean removed)
                throws PermissionDeniedException

Description copied from interface: Removable

Set the removed flag for this item.

Specified by:

setRemoved in interface Removable

Parameters:

removed - TRUE if the item should be flagged as removed, FALSE otherwise

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.DELETE permission for setting the flag to TRUE or Permission.WRITE permission for setting the flag to FALSE

getSystemId

public String getSystemId()

Description copied from interface: SystemItem

Get the system id for the item.

Specified by:

getSystemId in interface SystemItem

Returns:

The id of the item or null if it is not a system item

isSystemItem

public boolean isSystemItem()

Description copied from interface: SystemItem

Check if the item is a system item or not. A system item have a non-null value for the system id.

Specified by:

isSystemItem in interface SystemItem

Returns:

TRUE if this item is a system item, FALSE otherwise

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

isUsed

public boolean isUsed()
               throws BaseException

Check if:

• A Protocol of this type exists
• A PlateEventType is linked to this protocol type

Overrides:

isUsed in class BasicItem<ProtocolTypeData>

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:

• Protocol:s of this type
• PlateEventType:s using this protocol type

  Overrides:

  getUsingItems in class BasicItem<ProtocolTypeData>

  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)

initPermissions

void initPermissions(int granted,
                     int denied)
               throws BaseException

If this is a system protocol type, delete and create permissions are revoked.

Overrides:

initPermissions in class BasicItem<ProtocolTypeData>

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

newProtocol

public Protocol newProtocol()
                     throws PermissionDeniedException,
                            BaseException

Create a new Protocol item of this type.

Returns:

The new Protocol object

Throws:

PermissionDeniedException - This exception is thrown if the logged in user doesn't have Permission.USE permission for this protocol type

BaseException - This exception is thrown if there is another error

getProtocols

public ItemQuery<Protocol> getProtocols()

Get a query that returns all protocols of this type

Returns:

An ItemQuery object