Package net.sf.basedb.core

Class Protocol

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.Protocol

All Implemented Interfaces:

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

public class Protocol
extends AnnotatedItem
implements FileAttachable, Registered, Subtypable

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

Version:

2.0

Author:

enell

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ALIGNMENT	The ID for the alignment protocol type, for example a protocol used when creating a DerivedBioAssay representing data that has been aligned against a reference genome.
static final String	CLUSTER_GENERATION	The ID for the cluster generation (in a flow cell) protocol type, for example a protocol used when creating a PhysicalBioAssay.
static final String	EXTRACTION	The ID for the extraction protocol type, for example a protocol used when creating an Extract from a Sample.
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.
static final String	HYBRIDIZATION	The ID for the hybridization protocol type, for example a protocol used when creating a PhysicalBioAssay from a set of (labeled) Extract:s.
static final String	LABELING	The ID for the labeling protocol type, for example a protocol used when creating a labeled extract from an Extract.
static final String	LIBRARY_PREPARATION	The ID for the library preparation protocol type, for example a protocol used when creating a library extract from an Extract.
static final int	MAX_EXTERNAL_ID_LENGTH	The maximum length of the external id that can be stored in the database.
static final String	POOLING	The ID for the pooling protocol type, for example a protocol used when creating a biomaterial item (Sample or Extract) from a set of other biomaterial items.
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.
static final String	SAMPLING	The ID for the sampling protocol type, for example a protocol used when creating a Sample from a BioSource.
static final String	SCANNING	The ID for the scanning protocol type, for example a protocol used for scanning the microarray slide after an experiment.
static final String	SEQUENCING	The ID for the sequencing protocol type, for example a protocol used when creating a DerivedBioAssay from a PhysicalBioAssay
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
Protocol(ProtocolData data)	Creates a new protocol item.

Method Summary

Modifier and Type	Method	Description
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.
(package private) ProtocolData	getData()	Get the BasicData object that holds all data for this item.
static String	getDefaultSystemId(Item itemType)	Get the system id for the protocol 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.
String	getExternalId()	Get the external id of the protocol.
File	getFile()	Get the file that is attached to the item.
ItemSubtype	getItemSubtype()	Get the subtype of the item.
static Protocol	getNew(DbControl dc)	Create a new Protocol item.
ItemQuery<AnnotationType>	getParameters()	Get a query that returns all annotation types used as parameters for this protocol.
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 PhysicalBioAssay:s using this protocol a Plate:s using this protocol an ArrayBatch:s using this protocol a DerivedBioAssay: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 DerivedBioAssay a RawBioAssay
void	removeParameter(AnnotationType annotationType)	Remove an annotation type from the parameters for this protocol.
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setExternalId(String externalId)	Set the external id of the protocol.
void	setFile(File file)	Attach a file to the item.
void	setItemSubtype(ItemSubtype subtype)	Set the subtype on the 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.PROTOCOL
• 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.

Since:

3.0

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.

Since:

3.0

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 labeled extract from an Extract.

Since:

3.0

See Also:

• Constant Field Values

LIBRARY_PREPARATION

public static final String LIBRARY_PREPARATION

The ID for the library preparation protocol type, for example a protocol used when creating a library extract from an Extract.

Since:

3.0

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 or Extract) from a set of other biomaterial items.

Since:

3.0

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 PhysicalBioAssay from a set of (labeled) Extract:s.

Since:

3.0

See Also:

• Constant Field Values

CLUSTER_GENERATION

public static final String CLUSTER_GENERATION

The ID for the cluster generation (in a flow cell) protocol type, for example a protocol used when creating a PhysicalBioAssay.

Since:

3.0

See Also:

• Constant Field Values

SEQUENCING

public static final String SEQUENCING

The ID for the sequencing protocol type, for example a protocol used when creating a DerivedBioAssay from a PhysicalBioAssay

Since:

3.0

See Also:

• Constant Field Values

ALIGNMENT

public static final String ALIGNMENT

The ID for the alignment protocol type, for example a protocol used when creating a DerivedBioAssay representing data that has been aligned against a reference genome.

Since:

3.0

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.

Since:

3.0

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.

Since:

3.0

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.

Since:

3.0

See Also:

• Constant Field Values

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 Details

Protocol

Protocol(ProtocolData data)

Creates a new protocol item.

Parameters:

data - the data

Method Details

getDefaultSystemId

public static String getDefaultSystemId(Item itemType)

Get the system id for the protocol 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 protocol.

Parameters:

itemType - The item type

Returns:

The system id of the default protocol or null

Since:

3.0

getNew

public static Protocol getNew(DbControl dc)
                       throws BaseException

Create a new Protocol item.

Parameters:

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

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

getData

ProtocolData 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

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

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:

2.12

getItemSubtype

@SubtypableRelatedItems(FILE)
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 this protocol is used by:

• a BioMaterialEvent
• a PlateEvent
• an ArrayBatch
• a DerivedBioAssay
• a RawBioAssay

Overrides:

isUsed in class BasicItem

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 PhysicalBioAssay:s using this protocol
• a Plate:s using this protocol
• an ArrayBatch:s using this protocol
• a DerivedBioAssay:s using this protocol
• a RawBioAssay:s using this protocol

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)

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