net.sf.basedb.core
Class Software

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<SoftwareData>
                  net.sf.basedb.core.Software

All Implemented Interfaces:

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

public class Software
extends CommonItem<SoftwareData>
implements Registered, Subtypable

This class is used to represent individual software items and information about them. In the current version of BASE the only type of software we keep information about is feature extraction software.

Version:

2.0

Author:

enell

Last modified

$Date: 2011-08-04 12:58:23 +0200 (Thu, 04 Aug 2011) $

Field Summary

static String	ALIGNMENT The id for the SoftwareType item representing software used for aligning sequenced data against a known reference database.
static String	FEATURE_EXTRACTION The id for the SoftwareType item representing the softwaretype "feature extraction software".
static int	MAX_VERSIONSTRING_LENGTH The maximum length of the version variable that can be stored in the database.
private 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

Software(SoftwareData data)
Creates a new software item.

Method Summary

static Software	getById(DbControl dc, int id) Get a Software item when you know the ID.
static String	getDefaultSystemId(Item itemType) Get the system id for the software 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.
ItemSubtype	getItemSubtype() Get the subtype of the item.
static Software	getNew(DbControl dc) Create a new Software item.
static ItemQuery<Software>	getQuery() Get a query configured to retrieve software.
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get all: RawBioAssay:s created with this software DerivedBioAssay: created with this software
String	getVersionString() Get the versionstring of this Software item.
boolean	isUsed() Check if: a RawBioAssay was created with this software a DerivedBioassay was created with this software
void	setItemSubtype(ItemSubtype subtype) Set the subtype on the item.
void	setVersionString(String versionString) Set the versionstring for this Software item.

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

private static final Item TYPE

The type of item represented by this class.

See Also:

Item.SOFTWARE, getType()

Last modified

$Date: 2011-08-04 12:58:23 +0200 (Thu, 04 Aug 2011) $

FEATURE_EXTRACTION

public static final String FEATURE_EXTRACTION

The id for the SoftwareType item representing the softwaretype "feature extraction software".

Since:

3.0

See Also:

Constant Field Values

ALIGNMENT

public static final String ALIGNMENT

The id for the SoftwareType item representing software used for aligning sequenced data against a known reference database.

Since:

3.0

See Also:

Constant Field Values

MAX_VERSIONSTRING_LENGTH

public static final int MAX_VERSIONSTRING_LENGTH

The maximum length of the version variable that can be stored in the database. Check the length against this value before calling the setVersionString(String) method to avoid exceptions.

See Also:

Constant Field Values

Constructor Detail

Software

Software(SoftwareData data)

Creates a new software item.

Parameters:

data - the data

Method Detail

getDefaultSystemId

public static String getDefaultSystemId(Item itemType)

Get the system id for the software 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 software.

Parameters:

itemType - The item type

Returns:

The system id of the default software type or null

Since:

3.0

getNew

public static Software getNew(DbControl dc)
                       throws BaseException

Create a new Software item.

Parameters:

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

Returns:

The new Software item

Throws:

BaseException - This exception is thrown if there is another error

getById

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

Get a Software 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 Software 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 item

BaseException - If there is another error

getQuery

public static ItemQuery<Software> getQuery()
                                    throws BaseException

Get a query configured to retrieve software.

Returns:

An ItemQuery object

Throws:

BaseException - If getting the query fails.

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

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

getItemSubtype

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:

• a RawBioAssay was created with this software
• a DerivedBioassay was created with this software

Overrides:

isUsed in class BasicItem<SoftwareData>

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:

• RawBioAssay:s created with this software
• DerivedBioAssay: created with this software

  Overrides:

  getUsingItems in class BasicItem<SoftwareData>

  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)

getVersionString

public String getVersionString()

Get the versionstring of this Software item.

Returns:

A string with the version of this item, or null if not known

setVersionString

public void setVersionString(String versionString)
                      throws StringTooLongException,
                             PermissionDeniedException

Set the versionstring for this Software item. The value must not be longer than the value specified by the MAX_VERSIONSTRING_LENGTH constant.

Parameters:

versionString - The new version for this item, or null if not known

Throws:

StringTooLongException - If the version is longer then MAX_VERSIONSTRING_LENGTH

PermissionDeniedException - If the logged in user don't have write permission on this item