net.sf.basedb.core
Class BioMaterial<D extends BioMaterialData>

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>

All Implemented Interfaces:

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

Direct Known Subclasses:

BioSource, MeasuredBioMaterial

public abstract class BioMaterial<D extends BioMaterialData>
extends AnnotatedItem<D>
implements Subtypable

This is the base class for for the three types of biomaterials: BioSource, Sample and Extract.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2012-02-23 15:45:07 +0100 (Thu, 23 Feb 2012) $

Field Summary

static int

MAX_EXTERNAL_ID_LENGTH The maximum length of the external id that can be stored in the database.

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

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

BioMaterial(D bioMaterialData)

Method Summary

abstract long	countChildren(boolean pooled) Count the number of already existing children to this biomaterial.
Set<Annotatable>	getAnnotatableParents() Get all child biomaterial items with a subtype that has the ItemSubtype.getPushAnnotations() flag set.
static BioMaterial	getById(DbControl dc, int id) Get a biomaterial item when you know the id.
SpecialQuery<BioMaterialEventSource>	getChildCreationEvents() Get a query returning all events where this biomaterial has been used as a source item.
String	getExternalId() Get the external id of the biomaterial.
ItemSubtype	getItemSubtype() Get the subtype of the item.
(package private) void	onBeforeCommit(Transactional.Action action) On delete action: issue an update to decrease the size of all BioMaterialList:s this is a member of.
void	setExternalId(String externalId) Set the external id of the biomaterial.
void	setItemSubtype(ItemSubtype subtype) Set the subtype on the item.

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, getUsingItems, getVersion, hashCode, hasPermission, isDetached, isInDatabase, isUsed, 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, getType, 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

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 Detail

BioMaterial

BioMaterial(D bioMaterialData)

Method Detail

getById

public static BioMaterial getById(DbControl dc,
                                  int id)

Get a biomaterial item when you know the id. This method can return any of the subclasses of BioMaterial. Eg. BioSource, Sample or Extract.

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

Since:

2.17

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)

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get all child biomaterial items with a subtype that has the ItemSubtype.getPushAnnotations() flag set.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

Since:

3.1

onBeforeCommit

void onBeforeCommit(Transactional.Action action)
              throws NotLoggedInException,
                     BaseException

On delete action: issue an update to decrease the size of all BioMaterialList:s this is a member of.

Overrides:

onBeforeCommit in class SharedItem<D extends BioMaterialData>

Throws:

NotLoggedInException - If no user is logged in

BaseException - If there is another error

See Also:

Transactional, Developer documentation: Transactions, Developer documentation: Coding rules and guidelines for item classes

getExternalId

public String getExternalId()

Get the external id of the biomaterial. This value can be used to link with information in external databases. It is not used by the BASE core and it doesn't have to be unique.

Returns:

The external id for the biomaterial

setExternalId

public void setExternalId(String externalId)
                   throws PermissionDeniedException,
                          InvalidDataException

Set the external id of the biomaterial. The value may be null but must not be longer than the value specified by the MAX_EXTERNAL_ID_LENGTH constant.

Parameters:

externalId - The new value for the external id

Throws:

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

InvalidDataException - If the string is too long

countChildren

public abstract long countChildren(boolean pooled)

Count the number of already existing children to this biomaterial. The count includes items that the logged in user doesn't have access to.

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

getChildCreationEvents

public SpecialQuery<BioMaterialEventSource> getChildCreationEvents()

Get a query returning all events where this biomaterial has been used as a source item.

Returns:

A special query

Since:

3.0