Package net.sf.basedb.core

Class PlatformVariant

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.BasicChildItem

net.sf.basedb.core.PlatformVariant

All Implemented Interfaces:

AccessControlled, Identifiable, Nameable, Removable

public class PlatformVariant
extends BasicChildItem
implements Nameable, Removable

Represents variants of a Platform.

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 int	MAX_EXTERNAL_ID_LENGTH	The maximum length of the external ID that can be stored in the database.
private static final QueryRuntimeFilter	RUNTIME_FILTER	This filter will only return items if the logged in user has generic read permission to platforms.
static final String	SEQUENCING_EXPRESSION	The external id for the expression-like sequencing data.
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
PlatformVariant(PlatformVariantData data)	Creates a new filetype item from the given data.

Method Summary

Modifier and Type	Method	Description
static PlatformVariant	getByExternalId(DbControl dc, String externalId)	Get a PlatformVariant item when you know the external ID.
static PlatformVariant	getById(DbControl dc, int id)	Get a PlatformVariant object when you know the ID.
(package private) PlatformVariantData	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 variant.
ItemQuery<PlatformFileType>	getFileTypes(boolean restrict)	Get a query returning file types registered with this platform variant.
String	getName()	Get the name of the item.
static PlatformVariant	getNew(DbControl dc, Platform platform, String externalId)	Create a new variant of a platform.
static PlatformVariant	getNew(DbControl dc, Platform platform, String externalId, int channels)	Create a new file-only variant of a platform.
static PlatformVariant	getNew(DbControl dc, Platform platform, String externalId, RawDataType rawDataType)	Create a new platform variant which may optionally import data into the database.
(package private) Item	getParentType()	Get the type of item that is the parent of this item.
Platform	getPlatform()	Get that platform this is a variant of.
static ItemQuery<PlatformVariant>	getQuery()	Get a query configured to retrieve PlatformVariant items.
RawDataType	getRawDataType()	Get the raw data type this platform variant 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 variant
boolean	isFileOnly()	Check if the platform variant is a file-only variant 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 variant
(package private) void	onAfterCommit(Transactional.Action action)	Register file-only platforms as raw data type after insert and unregister after delete.
private void	setChannels(int channels)	Set the number of channels for a file-only platform variant.
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	setPlatform(Platform platform)
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.BasicChildItem

getPermissionForWriteDeleteAndCreate, getPluginPermissions, initPermissions

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

addAnnotatableParents, addUsingItems, addUsingItems, breakCircularReferences, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, 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

SEQUENCING_EXPRESSION

public static final String SEQUENCING_EXPRESSION

The external id for the expression-like sequencing data.

Since:

3.0

See Also:

• Constant Field Values

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

• Item.PLATFORM
• getType()

RUNTIME_FILTER

private static final QueryRuntimeFilter RUNTIME_FILTER

This filter will only return items if the logged in user has generic read permission to platforms.

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

PlatformVariant

PlatformVariant(PlatformVariantData data)

Creates a new filetype item from the given data.

Parameters:

data - the data.

Method Details

getNew

public static PlatformVariant getNew(DbControl dc,
 Platform platform,
 String externalId)

Create a new variant of a platform. If the platform is a file-only platform the new variant will also be a file-only variant.

Parameters:

dc - The DbControl to use for database access

platform - The platform to create a variant for

externalId - The external ID of the variant, it must be unique for all variants

Returns:

The new PlatformVariant item

getNew

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

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

Parameters:

dc - The DbControl to use for database access

platform - The platform to create a variant for

externalId - The external ID of the variant, it must be unique for all variants

channels - Number of channels in this variant

Returns:

The new variant object

getNew

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

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

Parameters:

dc - The DbControl to use for database access

platform - The platform to create a variant for

externalId - The external ID of the platform variant, must be unique for all variants (including those for other 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 PlatformVariant getById(DbControl dc,
 int id)
                               throws ItemNotFoundException,
PermissionDeniedException,
BaseException

Get a PlatformVariant 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 PlatformVariant 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 PlatformVariant getByExternalId(DbControl dc,
 String externalId)
                                       throws ItemNotFoundException,
PermissionDeniedException,
BaseException

Get a PlatformVariant 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 PlatformVariant 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<PlatformVariant> getQuery()
                                           throws BaseException

Get a query configured to retrieve PlatformVariant items.

Returns:

An ItemQuery object

Throws:

BaseException - If the query could not be created.

getData

PlatformVariantData 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 variant

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 variant

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)

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

getParentType

Item getParentType()

Description copied from class: BasicChildItem

Get the type of item that is the parent of this item.

Specified by:

getParentType in class BasicChildItem

Returns:

The item type of the parent item

getPlatform

public Platform getPlatform()

Get that platform this is a variant of.

Returns:

A Platform item

Throws:

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

setPlatform

private void setPlatform(Platform platform)

getExternalId

public String getExternalId()

Get the external id for the platform variant.

setExternalId

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

Throws:

PermissionDeniedException

InvalidDataException

BaseException

isFileOnly

public boolean isFileOnly()

Check if the platform variant is a file-only variant 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

setChannels

private void setChannels(int channels)

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

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

getRawDataType

public RawDataType getRawDataType()

Get the raw data type this platform variant is locked to. File-only variants are always locked to a raw data type. Variants 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

getFileTypes

public ItemQuery<PlatformFileType> getFileTypes(boolean restrict)

Get a query returning file types registered with this platform variant.

Parameters:

restrict - If TRUE the query will only return file types that has been directly registered with this variant, if FALSE the query will also return file types that have been registered with the platform

See Also:

• PlatformFileType.getQuery(Platform, PlatformVariant, boolean)