net.sf.basedb.core
Class BioSource

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<D>
                  net.sf.basedb.core.AnnotatedItem<D>
                      net.sf.basedb.core.BioMaterial<BioSourceData>
                          net.sf.basedb.core.BioSource

All Implemented Interfaces:

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

public class BioSource
extends BioMaterial<BioSourceData>
implements Registered

This class represent biosource items. A biosource has information about the source of material used in an experiment, such as a cell line or patient. A biosource can be used to create Sample:s.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2010-06-08 12:43:14 +0200 (Tue, 08 Jun 2010) $

Field Summary

static Item

TYPE The type of item represented by this class.

Fields inherited from class net.sf.basedb.core.BioMaterial

MAX_EXTERNAL_ID_LENGTH

Fields inherited from interface net.sf.basedb.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

BioSource(BioSourceData bioSourceData)

Method Summary

long	countChildren(boolean pooled) Count the number of child samples.
long	countSamples() Counts all samples that have been created from this biosource.
Set<Annotatable>	getAnnotatableParents() Always null.
static BioSource	getById(DbControl dc, int id) Get an BioSource item when you know the id.
Date	getEntryDate() Get the date that the item was registered in the database.
static BioSource	getNew(DbControl dc) Create a new BioSource item.
static ItemQuery<BioSource>	getQuery() Get a query that returns biosource items.
ItemQuery<Sample>	getSamples() Get a query that returns all samples created from this biosource.
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get all: Sample:s created from this biosource
boolean	isUsed() Check that: no Sample has been created from this biosource
Sample	newSample() Create a new Sample from this biosource.

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

getExternalId, onBeforeCommit, setExternalId

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

getAnnotationSet, getProtocol, isAnnotated, removeAnnotations, toTransferable

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, 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

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.BIOSOURCE, getType()

Constructor Detail

BioSource

BioSource(BioSourceData bioSourceData)

Method Detail

getNew

public static BioSource getNew(DbControl dc)
                        throws BaseException

Create a new BioSource item.

Parameters:

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

Returns:

The new BioSource item

Throws:

BaseException - If there is an error

getById

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

Get an BioSource 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 BioSource item

Throws:

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

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

BaseException - If there is another error

getQuery

public static ItemQuery<BioSource> getQuery()

Get a query that returns biosource items.

Returns:

An ItemQuery object.

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

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Always null.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

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

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• no Sample has been created from this biosource

Overrides:

isUsed in class BasicItem<BioSourceData>

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:

• Sample:s created from this biosource

  Overrides:

  getUsingItems in class BasicItem<BioSourceData>

  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)

newSample

public Sample newSample()
                 throws PermissionDeniedException,
                        BaseException

Create a new Sample from this biosource.

Returns:

The new Sample item

Throws:

PermissionDeniedException - If the logged in user doesn't have use permission for this biosource

BaseException - If there is another error

getSamples

public ItemQuery<Sample> getSamples()

Get a query that returns all samples created from this biosource.

Returns:

An ItemQuery object

countSamples

public long countSamples()
                  throws BaseException

Counts all samples that have been created from this biosource. The count includes samples that the logged in user doesn't have access to.

Returns:

The number of samples

Throws:

BaseException - If counting the samples fails.

countChildren

public long countChildren(boolean pooled)

Count the number of child samples. Since biosources can't be pooled this method always return 0 if pooled=TRUE

Specified by:

countChildren in class BioMaterial<BioSourceData>

Parameters:

pooled - If TRUE, the count is for biomaterials of the same type, if FALSE the count is for biomaterials of the child type

Since:

2.16