Package net.sf.basedb.core

Class DataFileType

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.DataFileType

All Implemented Interfaces:

AccessControlled, Controlled, Identifiable, Nameable, Removable, Validatable

public class DataFileType
extends BasicItem
implements Nameable, Removable, Validatable

This class is used to represent types of files that are used to hold data instead of importing the data into into the database.

Version:

2.5

Author:

Nicklas

Last modified

$Date: 2019-02-26 11:10:15 +0100 (tis, 26 feb. 2019) $

Field Summary

Fields

Modifier and Type	Field	Description
static final String	AFFYMETRIX_CDF	The external ID for the file type representing Affymetrix CDF files.
static final String	AFFYMETRIX_CEL	The external ID for the file type representing Affymetrix CEL files.
static final String	BAM	The external ID for the file type representing a BAM (Binary Sequence Alignment/Map) file.
static final String	BASEFILE_MATRIX	The external ID for the file type representing a matrix BASEFile.
static final String	BASEFILE_SERIAL	The external ID for the file type representing a serial BASEFile.
static final String	BFS_METADATA	The external ID for the file type representing a BFS metadata file.
static final String	FPKM_TRACKING	The external ID for the file type representing a FPKM tracking file.
static final String	GENERIC_EXTRAVALUE_DATA	The external ID for the file type representing generic analysed extra value data.
static final String	GENERIC_PRINT_MAP	The external ID for the file type representing a generic print map (array design layout) of any type.
static final String	GENERIC_RAW_DATA	The external ID for the file type representing a generic raw data file of any type.
static final String	GENERIC_REPORTER_MAP	The external ID for the file type representing a generic reporter map (array design layout) of any type.
static final String	GENERIC_SPOT_DATA	The external ID for the file type representing generic analysed spot data.
static final int	MAX_EXTENSION_LENGTH	The maximum length of the file extension that can be stored in the database.
static final int	MAX_EXTERNAL_ID_LENGTH	The maximum length of the external ID that can be stored in the database.
static final String	MEV_TDMS	The external ID for the file type representing a MeV TDMS (Tab-Delimited Multiple Sample) file.
static final String	MICROARRAY_IMAGE	The external ID for the file type representing scanned microarray image.
static final String	REF_SEQ_GTF	The external ID for the file type representing a GTF reference file that define the features on an array design that we are interested in.
static final String	SAM	The external ID for the file type representing a SAM (Sequence Alignment/Map) file.
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
DataFileType(DataFileTypeData data)	Creates a new filetype item from the given data.

Method Summary

Modifier and Type	Method	Description
static DataFileType	getByExternalId(DbControl dc, String externalId)	Get a DataFileType item when you know the external ID.
static DataFileType	getById(DbControl dc, int id)	Get a DataFileType object when you know the ID.
(package private) DataFileTypeData	getData()	Get the BasicData object that holds all data for this item.
String	getDescription()	Get the description for the item.
String	getExtension()	Get the common file extension for data files of this type.
String	getExternalId()	Get the external id for the data file type.
ItemSubtype	getGenericType()	Get the generic file type for this data file type.
ItemQuery<ItemSubtype>	getItemSubtypes()	Get a query returning the item subtypes that files of this type can be used on.
Item	getItemType()	Get the type of item files of this type can be used on.
String	getName()	Get the name of the item.
static DataFileType	getNew(DbControl dc, String externalId, Item itemType)	Create a new data file type.
ItemQuery<PlatformFileType>	getPlatforms()	Get a query that returns all platforms/variants that are using this file type.
static ItemQuery<DataFileType>	getQuery()	Get a query configured to retrieve DataFileType items.
static ItemQuery<DataFileType>	getQuery(FileStoreEnabled item)	Get a query configured to retrieve DataFileType:s that can be used on a given item.
static ItemQuery<DataFileType>	getQuery(Platform platform, PlatformVariant variant, Item itemType, ItemSubtype genericType)	Get a query to retrieve DataFileType:s that can be used on specific platform/variant for a given item and/or generic file type.
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: FileSetMember:s using this file type Platform:s using this file type ItemSubtype:s using this file type
boolean	hasActiveValidator(DbControl dc)	Check if there is at least one extension that claims to support validation of files of this type.
boolean	isRemoved()	Check if the removed flag is set for this item.
boolean	isUsed()	Check if: A file has been tagged with this type in a file set A platform is using this file type
void	setDescription(String description)	Set the description for the item.
void	setExtension(String extension)	Set the most common gile extension for data file of this type.
private void	setExternalId(String externalId)
void	setGenericType(ItemSubtype genericType)	Set the generic file type of this item.
private void	setItemType(Item itemType)
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

addAnnotatableParents, addUsingItems, addUsingItems, breakCircularReferences, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, initPermissions, isDetached, isInDatabase, onAfterCommit, 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.DATAFILETYPE
• getType()

AFFYMETRIX_CDF

public static final String AFFYMETRIX_CDF

The external ID for the file type representing Affymetrix CDF files.

See Also:

• Constant Field Values

AFFYMETRIX_CEL

public static final String AFFYMETRIX_CEL

The external ID for the file type representing Affymetrix CEL files.

See Also:

• Constant Field Values

GENERIC_RAW_DATA

public static final String GENERIC_RAW_DATA

The external ID for the file type representing a generic raw data file of any type.

See Also:

• Constant Field Values

GENERIC_REPORTER_MAP

public static final String GENERIC_REPORTER_MAP

The external ID for the file type representing a generic reporter map (array design layout) of any type.

See Also:

• Constant Field Values

GENERIC_PRINT_MAP

public static final String GENERIC_PRINT_MAP

The external ID for the file type representing a generic print map (array design layout) of any type.

See Also:

• Constant Field Values

GENERIC_SPOT_DATA

public static final String GENERIC_SPOT_DATA

The external ID for the file type representing generic analysed spot data.

Since:

2.8

See Also:

• Constant Field Values

GENERIC_EXTRAVALUE_DATA

public static final String GENERIC_EXTRAVALUE_DATA

The external ID for the file type representing generic analysed extra value data.

Since:

2.8

See Also:

• Constant Field Values

BASEFILE_SERIAL

public static final String BASEFILE_SERIAL

The external ID for the file type representing a serial BASEFile.

Since:

2.11

See Also:

• Constant Field Values

BASEFILE_MATRIX

public static final String BASEFILE_MATRIX

The external ID for the file type representing a matrix BASEFile.

Since:

2.11

See Also:

• Constant Field Values

BFS_METADATA

public static final String BFS_METADATA

The external ID for the file type representing a BFS metadata file. The metadata file may reference additional files.

Since:

2.15

See Also:

• Constant Field Values

MEV_TDMS

public static final String MEV_TDMS

The external ID for the file type representing a MeV TDMS (Tab-Delimited Multiple Sample) file.

Since:

2.11

See Also:

• Constant Field Values

SAM

public static final String SAM

The external ID for the file type representing a SAM (Sequence Alignment/Map) file.

Since:

3.0

See Also:

• Constant Field Values

BAM

public static final String BAM

The external ID for the file type representing a BAM (Binary Sequence Alignment/Map) file.

Since:

3.0

See Also:

• Constant Field Values

MICROARRAY_IMAGE

public static final String MICROARRAY_IMAGE

The external ID for the file type representing scanned microarray image.

Since:

3.0

See Also:

• Constant Field Values

REF_SEQ_GTF

public static final String REF_SEQ_GTF

The external ID for the file type representing a GTF reference file that define the features on an array design that we are interested in.

Since:

3.0

See Also:

• Constant Field Values

FPKM_TRACKING

public static final String FPKM_TRACKING

The external ID for the file type representing a FPKM tracking file. http://cufflinks.cbcb.umd.edu/manual.html#tracking_format

Since:

3.0

See Also:

• Constant Field Values

MAX_EXTENSION_LENGTH

public static final int MAX_EXTENSION_LENGTH

The maximum length of the file extension that can be stored in the database.

See Also:

• setExtension(String)
• 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

DataFileType

DataFileType(DataFileTypeData data)

Creates a new filetype item from the given data.

Parameters:

data - the data.

Method Details

getNew

public static DataFileType getNew(DbControl dc,
 String externalId,
 Item itemType)

Create a new data file type.

Parameters:

dc - The DbControl to use for database access

externalId - The external ID of the new type, must be unique for all file types

itemType - The type of item that files of this type can be attached to. The item must implement the FileStoreEnabled interface

Returns:

The new file set member type object

getById

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

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

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

Get a query configured to retrieve DataFileType items.

Returns:

An ItemQuery object

Throws:

BaseException - If getting the query fails.

getQuery

public static ItemQuery<DataFileType> getQuery(FileStoreEnabled item)

Get a query configured to retrieve DataFileType:s that can be used on a given item. This method will check the FileStoreEnabled.getPlatform() and FileStoreEnabled.getVariant() values and restrict the query to only return items that can be used for that platform. If the item isn't attached to any platform or variant all data file types for the Identifiable.getType() are returned.

Parameters:

item - The item to get data file types for, or null to return all data file types

Returns:

An ItemQuery object

getQuery

public static ItemQuery<DataFileType> getQuery(Platform platform,
 PlatformVariant variant,
 Item itemType,
 ItemSubtype genericType)

Get a query to retrieve DataFileType:s that can be used on specific platform/variant for a given item and/or generic file type. All parameters are optional. If all are null the result is the same as getQuery().

Parameters:

platform - The platform, or null to not restrict by platform (unless a variant is given)

variant - The platform variant, or null to not restrict by variant

itemType - The type of item it should be possible to attach file to, or null to not restrict by item

genericType - The generic file type, or null to not restrict by file type

Returns:

A query returning data file types matching the specified restrictions

Since:

2.9

getData

DataFileTypeData 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:

• A file has been tagged with this type in a file set
• A platform is using this file type

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:

• FileSetMember:s using this file type
• Platform:s using this file type
• ItemSubtype:s using this file type

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)

getExternalId

public String getExternalId()

Get the external id for the data file type.

setExternalId

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

Throws:

PermissionDeniedException

InvalidDataException

BaseException

getGenericType

public ItemSubtype getGenericType()

Get the generic file type for this data file type.

Returns:

A file subtype item

Since:

3.0

setGenericType

public void setGenericType(ItemSubtype genericType)

Set the generic file type of this item. Null is not allowed.

Parameters:

genericType - The generic file type

Throws:

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

Since:

3.0

getExtension

public String getExtension()

Get the common file extension for data files of this type.

Returns:

A string or null if there is no common file extension

setExtension

public void setExtension(String extension)

Set the most common gile extension for data file of this type.

Parameters:

extension - The extension or null

Throws:

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

StringTooLongException - If the string is longer that MAX_EXTENSION_LENGTH.

setItemType

private void setItemType(Item itemType)

getItemType

public Item getItemType()

Get the type of item files of this type can be used on. The item should implement the FileStoreEnabled interface.

Returns:

An Item object

getItemSubtypes

public ItemQuery<ItemSubtype> getItemSubtypes()

Get a query returning the item subtypes that files of this type can be used on. The query should only be used if the main item type getItemType() is a Subtypable item.

Returns:

A query

Since:

3.0

hasActiveValidator

public boolean hasActiveValidator(DbControl dc)

Check if there is at least one extension that claims to support validation of files of this type. The extensions are not actually invoked, only prepared.

Since:

3.0

getPlatforms

public ItemQuery<PlatformFileType> getPlatforms()

Get a query that returns all platforms/variants that are using this file type.

Returns:

A query object