Package net.sf.basedb.core
Class BioSource
- All Implemented Interfaces:
AccessControlled
,Annotatable
,Identifiable
,Listable
,Nameable
,Ownable
,Registered
,Removable
,Shareable
,Subtypable
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: 2017-05-22 14:35:27 +0200 (må, 22 maj 2017) $
-
Field Summary
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
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionlong
countChildren
(boolean pooled) Count the number of child samples.long
Counts all samples that have been created from this biosource.static BioSource
Get anBioSource
item when you know the id.(package private) BioSourceData
getData()
Get theBasicData
object that holds all data for this item.Get the date that the item was registered in the database.static BioSource
Create a newBioSource
item.getQuery()
Get a query that returns biosource items.Get a query that returns all samples created from this biosource.getType()
Get the type of item represented by the object.Get all:Sample
:s created from this biosourceboolean
isUsed()
Check that: noSample
has been created from this biosourceCreate a newSample
from this biosource.void
setEntryDate
(Date entryDate) Set the date the entry was registered in the database.Methods inherited from class net.sf.basedb.core.BioMaterial
getAnnotatableParents, getChildCreationEvents, getExternalId, getItemSubtype, setExternalId, setItemSubtype
Methods inherited from class net.sf.basedb.core.AnnotatedItem
getAnnotationSet, getProtocol, isAnnotated, removeAnnotations
Methods inherited from class net.sf.basedb.core.CommonItem
getDescription, getName, getRemovedBy, isRemoved, setDescription, setName, setRemoved
Methods inherited from class net.sf.basedb.core.SharedItem
getItemKey, getProjectKey, initPermissions, isShared, onBeforeCommit, setItemKey, setProjectKey
Methods inherited from class net.sf.basedb.core.OwnedItem
getOwner, isOwner, setOwner, takeOwnership
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, isDetached, isInDatabase, onAfterCommit, onAfterInsert, 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
Methods inherited from interface net.sf.basedb.core.Nameable
getDescription, getName, setDescription, setName
Methods inherited from interface net.sf.basedb.core.Ownable
getOwner, isOwner, setOwner, takeOwnership
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Field Details
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TYPE
The type of item represented by this class.- See Also:
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Constructor Details
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BioSource
BioSource(BioSourceData bioSourceData)
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Method Details
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getNew
Create a newBioSource
item.- Parameters:
dc
- TheDbControl
which will be used for permission checking and database access- Returns:
- The new
BioSource
item - Throws:
BaseException
- If there is an error
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getById
public static BioSource getById(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException Get anBioSource
item when you know the id.- Parameters:
dc
- TheDbControl
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 foundPermissionDeniedException
- If the logged in user doesn't have read permission to the itemBaseException
- If there is another error
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getQuery
Get a query that returns biosource items.- Returns:
- An
ItemQuery
object.
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getData
BioSourceData getData()Description copied from class:BasicItem
Get theBasicData
object that holds all data for this item.- Overrides:
getData
in classBioMaterial
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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 theItem
enumeration.- Specified by:
getType
in interfaceIdentifiable
- Returns:
- A value indicating the type of item
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getEntryDate
Description copied from interface:Registered
Get the date that the item was registered in the database.- Specified by:
getEntryDate
in interfaceRegistered
- Returns:
- A date or null if this is not known
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setEntryDate
Description copied from interface:Registered
Set the date the entry was registered in the database. Implementations should only allow this property to be set before the item is first stored in the database. The intention of this method is to facilitate export/import of data between server.- Specified by:
setEntryDate
in interfaceRegistered
- Parameters:
entryDate
- A date or null to use today's date
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isUsed
Check that:- no
Sample
has been created from this biosource
- Overrides:
isUsed
in classBasicItem
- Returns:
- TRUE if this item is used, FALSE otherwise
- Throws:
BaseException
- If not able to tell if item is used or not.- See Also:
- no
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getUsingItems
Get all:Sample
:s created from this biosource
- Overrides:
getUsingItems
in classBasicItem
- Returns:
- A set containing proxies for the items, or an empty set if no items are using this item
- Since:
- 2.2
- See Also:
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newSample
Create a newSample
from this biosource.- Returns:
- The new
Sample
item - Throws:
PermissionDeniedException
- If the logged in user doesn't have use permission for this biosourceBaseException
- If there is another error
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getSamples
Get a query that returns all samples created from this biosource.- Returns:
- An
ItemQuery
object
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countSamples
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.
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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 classBioMaterial
- 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
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