Package net.sf.basedb.core

Class Platform

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.Platform

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Removable

public class Platform
extends BasicItem
implements Nameable, Removable

This class is used to represent an experimental platform in BASE. An experimental platform is used to define the types of files that are used as data files. For example, the AFFYMETRIX platform defines CDF and CEL files.

A platform may have variants. A PlatformVariant has independent settings but may inherit file types from the main platform.

Some platforms are file-only platforms, and has data that can't be imported into the database, for example the Affymetrix platform. Platforms that are not file-only can also import data into the database. Such platforms may be locked to a single RawDataType or they may be GENERIC.

Version:

2.5

Author:

Nicklas

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	AFFYMETRIX	The external id for the Affymetrix platform.
static final String	GENERIC	The external id for the Generic platform.
static final int	MAX_EXTERNAL_ID_LENGTH	The maximum length of the external ID that can be stored in the database.
static final String	SEQUENCING	The external id for the generic Sequencing platform.
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
Platform(PlatformData data)	Creates a new filetype item from the given data.

Method Summary

Modifier and Type	Method	Description
static Platform	getByExternalId(DbControl dc, String externalId)	Get a Platform item when you know the external ID.
static Platform	getById(DbControl dc, int id)	Get a Platform object when you know the ID.
(package private) PlatformData	getData()	Get the BasicData object that holds all data for this item.
String	getDescription()	Get the description for the item.
String	getExternalId()	Get the external id for the platform.
PlatformFileType	getFileType(DataFileType type, PlatformVariant variant, boolean create)	Get information about a file type that has been registered with this platform/variant.
ItemQuery<PlatformFileType>	getFileTypes(PlatformVariant variant, boolean restrict)	Get the file types registered with this platform.
String	getName()	Get the name of the item.
static Platform	getNew(DbControl dc, String externalId, int channels)	Create a new file-only platform.
static Platform	getNew(DbControl dc, String externalId, RawDataType rawDataType)	Create a new platform which may optionally import data into the database.
static ItemQuery<Platform>	getQuery()	Get a query configured to retrieve Platform items.
RawDataType	getRawDataType()	Get the raw data type this platform is locked to.
User	getRemovedBy()	Get the user that flagged this item for removal.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: ArrayDesign:s and RawBioAssay:s using this platform
ItemQuery<PlatformVariant>	getVariants()	Get a query that returns variants of this platform.
protected void	initPermissions(int granted, int denied)	Deny deletion of the GENERIC and Affymetrix platform.
boolean	isFileOnly()	Check if the platform is a file-only platform or if it allows data to be imported into the database.
boolean	isRemoved()	Check if the removed flag is set for this item.
boolean	isUsed()	Check if: any raw bioassays or array design are using this platform
PlatformVariant	newVariant(String systemId)	Create a new PlatformVariant of this platform.
(package private) void	onAfterCommit(Transactional.Action action)	Register file-only platforms as raw data type after insert and unregister after delete.
void	removeFileType(DataFileType type, PlatformVariant variant)	Remove a file type from this platform/variant.
private void	setChannels(int channels)	Set the number of channels for a file-only platform.
void	setDescription(String description)	Set the description for the item.
private void	setExternalId(String externalId)
void	setName(String name)	Set the name of the item.
private void	setRawDataType(RawDataType rawDataType)	Set the raw data type.
void	setRemoved(boolean removed)	Set the removed flag for this item.

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, onAfterInsert, onBeforeCommit, 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

Field Details

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

• Item.PLATFORM
• getType()

GENERIC

public static final String GENERIC

The external id for the Generic platform. It allows importing raw data into the database for all raw data type.

See Also:

• getByExternalId(DbControl, String)
• Constant Field Values

AFFYMETRIX

public static final String AFFYMETRIX

The external id for the Affymetrix platform. It is a file-only platform.

See Also:

• getByExternalId(DbControl, String)
• Constant Field Values

SEQUENCING

public static final String SEQUENCING

The external id for the generic Sequencing platform. We don't defined any specific details at this level, but use variants for this.

Since:

3.0

See Also:

• PlatformVariant.SEQUENCING_EXPRESSION
• 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.

See Also:

• setExternalId(String)
• Constant Field Values

Constructor Details

Platform

Platform(PlatformData data)

Creates a new filetype item from the given data.

Parameters:

data - the data.

Method Details

getNew

public static Platform getNew(DbControl dc,
 String externalId,
 int channels)

Create a new file-only platform. Data for this platform can't be imported to the database.

Parameters:

dc - The DbControl to use for database access

externalId - The external ID of the platform, must be unique for all platforms

channels - Number of channels in this platform

Returns:

The new platform object

getNew

public static Platform getNew(DbControl dc,
 String externalId,
 RawDataType rawDataType)

Create a new platform which may optionally import data into the database.

Parameters:

dc - The DbControl to use for database access

externalId - The external ID of the platform, must be unique for all platforms

rawDataType - A specific raw data type this platform will be locked to or null if it is not locked to any specific raw data type

Returns:

The new platform object

getById

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

Get a Platform 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 Platform 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 another error

getByExternalId

public static Platform getByExternalId(DbControl dc,
 String externalId)
                                throws ItemNotFoundException,
PermissionDeniedException,
BaseException

Get a Platform item when you know the external ID.

Parameters:

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

externalId - The external ID of the item to load

Returns:

The Platform item.

Throws:

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

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

BaseException - If there is another error

getQuery

public static ItemQuery<Platform> getQuery()
                                    throws BaseException

Get a query configured to retrieve Platform items.

Returns:

An ItemQuery object

Throws:

BaseException - If the query could not be created.

getData

PlatformData getData()

Description copied from class: BasicItem

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

Specified by:

getData in class BasicItem

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

getRemovedBy

public User getRemovedBy()
                  throws PermissionDeniedException,
ItemNotFoundException

Description copied from interface: Removable

Get the user that flagged this item for removal.

Specified by:

getRemovedBy in interface Removable

Returns:

A User object, or null if this item has not been flagged

Throws:

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

ItemNotFoundException - If the user that removed this item can't be found

isUsed

public boolean isUsed()
               throws BaseException

Check if:

• any raw bioassays or array design are using this platform

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:

• ArrayDesign:s and RawBioAssay:s using this platform

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)

initPermissions

protected void initPermissions(int granted,
 int denied)

Deny deletion of the GENERIC and Affymetrix platform. The GENERIC platform is required by the system and the AFFYMETRIX platform is required for backwards compatibility reasons.

Overrides:

initPermissions in class BasicItem

Parameters:

granted - Permissions that have been granted by the subclass

denied - Permissions that have been denied by the subclass

onAfterCommit

void onAfterCommit(Transactional.Action action)

Register file-only platforms as raw data type after insert and unregister after delete.

Overrides:

onAfterCommit in class BasicItem

Since:

2.16.2

See Also:

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

getExternalId

public String getExternalId()

Get the external id for the platform.

setExternalId

private void setExternalId(String externalId)
                    throws PermissionDeniedException,
InvalidDataException,
BaseException

Throws:

PermissionDeniedException

InvalidDataException

BaseException

setChannels

private void setChannels(int channels)

Set the number of channels for a file-only platform.

setRawDataType

private void setRawDataType(RawDataType rawDataType)

Set the raw data type. The raw data type must allow data to be imported into the database.

Parameters:

rawDataType - The raw data type, null is allowed

isFileOnly

public boolean isFileOnly()

Check if the platform is a file-only platform or if it allows data to be imported into the database.

Returns:

TRUE if only file data is allowed, FALSE if import to database is allowed

getRawDataType

public RawDataType getRawDataType()

Get the raw data type this platform is locked to. File-only platforms are always locked to a raw data type. Platforms that support import of data to the database may or may not be locked. Note! If the variant is a file-only variant that hasn't been committed to the database a new instance of RawDataType is returned for each call to this method.

Returns:

The raw data type or null if the platform isn't locked

getVariants

public ItemQuery<PlatformVariant> getVariants()

Get a query that returns variants of this platform.

Returns:

An ItemQuery object

newVariant

public PlatformVariant newVariant(String systemId)

Create a new PlatformVariant of this platform.

Parameters:

systemId - The systemId of the new variant (must be unique)

Returns:

The new PlatformVariant object

See Also:

• PlatformVariant.getNew(DbControl, Platform, String)

getFileTypes

public ItemQuery<PlatformFileType> getFileTypes(PlatformVariant variant,
 boolean restrict)

Get the file types registered with this platform.

See Also:

• PlatformFileType.getQuery(Platform, PlatformVariant, boolean)

removeFileType

public void removeFileType(DataFileType type,
 PlatformVariant variant)

Remove a file type from this platform/variant. If the file type isn't registered this method does nothing. If a variant is given the file type is only removed from that variant. If no variant is given the file type is only removed from the platform, not from other variants that have registered with the file type.

Parameters:

type - The file type to remove

variant - An optional variant

Throws:

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

InvalidUseOfNullException - If type is null

getFileType

public PlatformFileType getFileType(DataFileType type,
 PlatformVariant variant,
 boolean create)

Get information about a file type that has been registered with this platform/variant.

Parameters:

type - The file type to get information for

variant - An optional variant

create - If TRUE, the file type will be added to the platform if it doesn't already exists

Returns:

Null if the file type isn't registered with the platform/variant (and create is false) or a PlatformFileType object

Since:

3.0