net.sf.basedb.core
Class Sample

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<D>
                          net.sf.basedb.core.MeasuredBioMaterial<SampleData>
                              net.sf.basedb.core.Sample

All Implemented Interfaces:

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

public class Sample
extends MeasuredBioMaterial<SampleData>

This class is used to represent sample items. A sample is the actual sample taken from a BioSource. A sample can also be created by combining other samples into a new sample. A process is known as pooling. It is also possible to create standalone samples, with no reference to a biosource or to other samples.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2010-12-02 14:35:04 +0100 (Thu, 02 Dec 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

Sample(SampleData sampleData)

Method Summary

long	countChildren(boolean pooled) Count the number of child samples or extracts.
long	countExtracts() Counts all extracts that have been created from this sample.
long	countSamples() Counts all samples that have been created from this sample.
Set<Annotatable>	getAnnotatableParents() Get the biosource or pooled samples.
BioSource	getBioSource() Get the BioSource that is the parent of this sample.
static Sample	getById(DbControl dc, int id) Get an Sample item when you know the id.
ItemQuery<Sample>	getChildSamples() Creates a query that returns all child (pooled) samples that has this sample as one of it's sources.
ItemQuery<Extract>	getExtracts() Get a query that returns all extracts created from this sample.
static Sample	getNew(DbControl dc) Create a new Sample item.
static Sample	getNew(DbControl dc, BioPlateEventParticipant master) Create a new Sample item as part of a master bioplate event.
static ItemQuery<Sample>	getQuery() Get a query that returns samples.
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get all: Extract:s created from this sample Pooled samples
boolean	isUsed() Check that: no Extract:s has been created from this item no Sample:s has been created from this item
Extract	newExtract(Float usedQuantity) Create a new Extract from this sample.
Extract	newExtract(Float usedQuantity, BioPlateEventParticipant master) Create a new Extract from this sample as part of a master bioplate event.
void	setBioSource(BioSource bioSource) Set the BioSource item that is the parent of this sample.

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

getBioWell, getCreationEvent, getEntryDate, getEvents, getOriginalQuantity, getPoolingEvents, getProtocol, getRemainingQuantity, isInWell, isLockedInWell, isPooled, newEvent, newEvent, onBeforeCommit, setBioPlateEventParticipant, setBioWell, setOriginalQuantity, setPooled, updateRemainingQuantity

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

getExternalId, setExternalId

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

getAnnotationSet, 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.SAMPLE, getType()

Constructor Detail

Sample

Sample(SampleData sampleData)

Method Detail

getNew

public static Sample getNew(DbControl dc)
                     throws BaseException

Create a new Sample item.

Parameters:

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

Returns:

The new Sample item

Throws:

BaseException - If there is an error

getNew

public static Sample getNew(DbControl dc,
                            BioPlateEventParticipant master)
                     throws BaseException

Create a new Sample item as part of a master bioplate event.

Parameters:

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

master - The master bioplate event participant or null

Returns:

The new Sample item

Throws:

BaseException - If there is an error

Since:

2.17

getById

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

Get an Sample 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 Sample 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<Sample> getQuery()

Get a query that returns samples.

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.

Returns:

A value indicating the type of item

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the biosource or pooled samples.

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

isUsed

public boolean isUsed()
               throws BaseException

Check that:

• no Extract:s has been created from this item
• no Sample:s has been created from this item

Overrides:

isUsed in class MeasuredBioMaterial<SampleData>

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:

• Extract:s created from this sample
• Pooled samples

  Overrides:

  getUsingItems in class MeasuredBioMaterial<SampleData>

  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)

getBioSource

public BioSource getBioSource()
                       throws PermissionDeniedException,
                              BaseException

Get the BioSource that is the parent of this sample.

Returns:

A BioSource object or null if this is a pooled or standalone sample

Throws:

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

BaseException - If there is another error

setBioSource

public void setBioSource(BioSource bioSource)
                  throws PermissionDeniedException,
                         InvalidDataException

Set the BioSource item that is the parent of this sample.

Parameters:

bioSource - The parent BioSource item

Throws:

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

InvalidDataException - If this is a pooled sample

BaseException - If there is another error

newExtract

public Extract newExtract(Float usedQuantity)
                   throws PermissionDeniedException,
                          BaseException

Create a new Extract from this sample.

Parameters:

usedQuantity - The quantity used from this sample or null if not known

Returns:

The new Extract item

Throws:

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

BaseException - If there is another error

newExtract

public Extract newExtract(Float usedQuantity,
                          BioPlateEventParticipant master)
                   throws PermissionDeniedException,
                          BaseException

Create a new Extract from this sample as part of a master bioplate event.

Parameters:

usedQuantity - The quantity used from this sample or null if not known

master - The master bioplate event participant or null

Returns:

The new Extract item

Throws:

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

BaseException - If there is another error

Since:

2.17

getExtracts

public ItemQuery<Extract> getExtracts()
                               throws BaseException

Get a query that returns all extracts created from this sample.

Returns:

An ItemQuery object

Throws:

BaseException - If the query couldn't be created.

getChildSamples

public ItemQuery<Sample> getChildSamples()

Creates a query that returns all child (pooled) samples that has this sample as one of it's sources.

Returns:

A query

Since:

2.10

countExtracts

public long countExtracts()
                   throws BaseException

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

Returns:

The number of extracts

Throws:

BaseException - If there is some kind of error.

countSamples

public long countSamples()
                  throws BaseException

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

Returns:

The number of samples

Throws:

BaseException - If there is some kind of error.

Since:

2.16

countChildren

public long countChildren(boolean pooled)

Count the number of child samples or extracts.

Specified by:

countChildren in class BioMaterial<SampleData>

Parameters:

pooled - TRUE = count child samples, FALSE = count child extracts

Since:

2.16