net.sf.basedb.core
Class Protocol

java.lang.Object
  net.sf.basedb.core.BasicItem<D>
      net.sf.basedb.core.OwnedItem<D>
          net.sf.basedb.core.SharedItem<D>
              net.sf.basedb.core.CommonItem<D>
                  net.sf.basedb.core.AnnotatedItem<ProtocolData>
                      net.sf.basedb.core.Protocol

All Implemented Interfaces:

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

public class Protocol
extends AnnotatedItem<ProtocolData>
implements FileAttachable, Registered

This class is used to represent individual protocol items and information about them.

Version:

2.0

Author:

enell

Field Summary

static int	MAX_EXTERNAL_ID_LENGTH The maximum length of the external id that can be stored in the database.
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

Constructor Summary

Protocol(ProtocolData data)
Creates a new protocol item.

Method Summary

void	addParameter(AnnotationType annotationType) Add an annotation type as a parameter to this protocol.
Set<Annotatable>	getAnnotatableParents() Get all parents objects which are annotatable and the logged in user has read permission to.
static Protocol	getById(DbControl dc, int id) Get a Protocol item when you know the ID.
Date	getEntryDate() Get the date that the item was registered in the database.
String	getExternalId() Get the external id of the protocol.
File	getFile() Get the file that is attached to the item.
static Protocol	getNew(DbControl dc, ProtocolType protocolType) Create a new Protocol item.
ItemQuery<AnnotationType>	getParameters() Get a query that returns all annotation types used as parameters for this protocol.
ProtocolType	getProtocolType() Get the associated ProtocolType item.
static ItemQuery<Protocol>	getQuery() Get a query configured to retrieve protocols.
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get all: a BioMaterial:s and Hybridization:s using this protocol a Plate:s using this protocol an ArrayBatch:s using this protocol a Scan:s using this protocol a RawBioAssay:s using this protocol
boolean	isParameter(Annotation annotation) Check if the annotation is parameter to this protocol.
boolean	isParameter(AnnotationType annotationType) Check if the annotation type is a parameter to this protocol.
boolean	isUsed() Check if this protocol is used by: a BioMaterialEvent a PlateEvent an ArrayBatch a Scan a RawBioAssay
void	removeParameter(AnnotationType annotationType) Remove an annotation type from the parameters for this protocol.
void	setExternalId(String externalId) Set the external id of the protocol.
void	setFile(File file) Attach a file to the item.
void	setProtocolType(ProtocolType protocolType) Set the protocol type of this Protocol item.

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

getAnnotationSet, getProtocol, isAnnotated, removeAnnotations, toTransferable

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

getDescription, getName, isRemoved, setDescription, setName, setRemoved, toTransferable

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

getItemKey, getProjectKey, initPermissions, isShared, onBeforeCommit, setItemKey, setProjectKey, toTransferable

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

getOwner, isOwner, setOwner, takeOwnership, toTransferable

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, 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

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

getOwner, isOwner, setOwner, takeOwnership

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.PROTOCOL, getType()

MAX_EXTERNAL_ID_LENGTH

public static final int MAX_EXTERNAL_ID_LENGTH

The maximum length of the external id that can be stored in the database.

Since:

2.15

See Also:

setExternalId(String), Constant Field Values

Constructor Detail

Protocol

Protocol(ProtocolData data)

Creates a new protocol item.

Parameters:

data - the data

Method Detail

getNew

public static Protocol getNew(DbControl dc,
                              ProtocolType protocolType)
                       throws BaseException

Create a new Protocol item.

Parameters:

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

protocolType - The type of the protocol

Returns:

The new Protocol item

Throws:

BaseException - If there is an error

getById

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

Get a Protocol 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 Protocol item

Throws:

ItemNotFoundException - This exception is thrown if an item with the specified ID is not found

PermissionDeniedException - This exception is thrown if the logged in user doesn't have READ permission to the item

BaseException - This exception is thrown if there is another error

getQuery

public static ItemQuery<Protocol> getQuery()

Get a query configured to retrieve protocols.

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

getFile

public File getFile()
             throws PermissionDeniedException,
                    BaseException

Description copied from interface: FileAttachable

Get the file that is attached to the item.

Specified by:

getFile in interface FileAttachable

Returns:

A File item, or null if no file is attached

Throws:

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

BaseException - If there is another error

setFile

public void setFile(File file)
             throws PermissionDeniedException

Description copied from interface: FileAttachable

Attach a file to the item.

Specified by:

setFile in interface FileAttachable

Parameters:

file - The file to attach to the item

Throws:

PermissionDeniedException - If the logged in user doesn't have use permission for the file or write permission for the 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

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.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

Always null

Since:

2.12

isUsed

public boolean isUsed()
               throws BaseException

Check if this protocol is used by:

• a BioMaterialEvent
• a PlateEvent
• an ArrayBatch
• a Scan
• a RawBioAssay

Overrides:

isUsed in class BasicItem<ProtocolData>

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:

• a BioMaterial:s and Hybridization:s using this protocol
• a Plate:s using this protocol
• an ArrayBatch:s using this protocol
• a Scan:s using this protocol
• a RawBioAssay:s using this protocol

  Overrides:

  getUsingItems in class BasicItem<ProtocolData>

  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)

getProtocolType

public ProtocolType getProtocolType()
                             throws PermissionDeniedException,
                                    BaseException

Get the associated ProtocolType item. All Protocol items must have a type.

Returns:

The ProtocolType item

Throws:

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

BaseException - If there is any error

setProtocolType

public void setProtocolType(ProtocolType protocolType)
                     throws PermissionDeniedException,
                            InvalidUseOfNullException

Set the protocol type of this Protocol item. This parameter mustn't be null.

Parameters:

protocolType - The new ProtocolType

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.WRITE permission to this protocol or Permission.USE permission for the protocol type

InvalidUseOfNullException - If protocoltype is null

getExternalId

public String getExternalId()

Get the external id of the protocol. This value can be used to link with information in external databases. It is not used by the BASE core and it doesn't have to be unique.

Returns:

The external id for the protocol

Since:

2.15

setExternalId

public void setExternalId(String externalId)
                   throws PermissionDeniedException,
                          InvalidDataException

Set the external id of the protocol. The value may be null but must not be longer than the value specified by the MAX_EXTERNAL_ID_LENGTH constant.

Parameters:

externalId - The new value for the external id

Throws:

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

InvalidDataException - If the string is too long

Since:

2.15

addParameter

public void addParameter(AnnotationType annotationType)
                  throws PermissionDeniedException,
                         InvalidDataException

Add an annotation type as a parameter to this protocol.

Parameters:

annotationType - The annotation type to add to this protocol

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.WRITE permission for the protocol and Permission.USE for the annotation type

InvalidDataException - If the annotationType is null, or the AnnotationType.isProtocolParameter() doesn't return true

Since:

2.2

removeParameter

public void removeParameter(AnnotationType annotationType)
                     throws PermissionDeniedException,
                            InvalidDataException

Remove an annotation type from the parameters for this protocol.

Parameters:

annotationType - The annotation type to remove from this protocol

Throws:

PermissionDeniedException - If the logged in user doesn't have Permission.WRITE permission for the protocol

InvalidDataException - If the annotationType is null

Since:

2.2

isParameter

public boolean isParameter(AnnotationType annotationType)

Check if the annotation type is a parameter to this protocol.

Parameters:

annotationType - The annotation type to check, null always return false

Returns:

TRUE if the annotation type is a parameter, FALSE otherwise

Since:

2.2

See Also:

AnnotationType.isProtocolParameter(Protocol)

isParameter

public boolean isParameter(Annotation annotation)

Check if the annotation is parameter to this protocol. This method is equivalent to isParameter(AnnotationType) but is not affected by possible permission problems with the annotation type.

Parameters:

annotation - The annotation to check, null always return false

Returns:

TRUE if the annotation is a parameter, FALSE otherwise

Since:

2.10

getParameters

public ItemQuery<AnnotationType> getParameters()

Get a query that returns all annotation types used as parameters for this protocol.

Returns:

An ItemQuery object

Since:

2.2