Package net.sf.basedb.core

Class DerivedBioAssay

java.lang.Object

net.sf.basedb.core.BasicItem

net.sf.basedb.core.OwnedItem

net.sf.basedb.core.SharedItem

net.sf.basedb.core.CommonItem

net.sf.basedb.core.AnnotatedItem

net.sf.basedb.core.DerivedBioAssay

All Implemented Interfaces:

AccessControlled, Annotatable, FileStoreEnabled, Identifiable, Listable, Nameable, Ownable, Registered, Removable, Shareable, Subtypable

public class DerivedBioAssay
extends AnnotatedItem
implements Registered, FileStoreEnabled, Subtypable, Listable

Since:

3.0

Author:

Nicklas

Last modified

$Date: 2021-03-26 08:26:24 +0100 (Fri, 26 Mar 2021) $

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) static class	DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction	Whenever we modify the parent items to a derived bioassay, we must make sure that the physical bioassays for all child items are synchronized with the same changes.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ARRANGEMENT	The id for the DerivedBioAssayType item representing sequenced data that has been aligned to a reference database.
private boolean	extractHasBeenSet
private boolean	hardwareHasBeenSet
private boolean	protocolHasBeenSet
static final String	SCAN	The id for the DerivedBioAssayType item representing a scanned hybridization.
static final String	SEQUENCES	The id for the DerivedBioAssayType item representing original sequenced data.
private boolean	softwareHasBeenSet
static final 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

Constructors

Constructor	Description
DerivedBioAssay(DerivedBioAssayData data)

Method Summary

Modifier and Type	Method	Description
void	addParent(DerivedBioAssay bioAssay)	Add a derived bioassay as a parent to this derived bioassay.
void	addPhysicalBioAssay(PhysicalBioAssay bioAssay)	Add a physical bioassay as a parent to this derived bioassay.
(package private) int	breakCircularReferences(Set<ItemProxy> items)	Any parent bioassays found among the given items are removed from this item.
long	countRawBioAssays()	Counts all raw bioassays that have been created from this bioassay.
Set<Annotatable>	getAnnotatableParents()	Get the extract and parent bioassays or physical bioassays.
ArrayDesign	getArrayDesign()	Get the array design connected to this derived bioassay by following the path from the physical bioassay to the array slide to the array batch to the array design.
static DerivedBioAssay	getById(DbControl dc, int id)	Get a DerivedBioAssay item when you know the id.
ItemQuery<DerivedBioAssay>	getChildren()	Get all child derived bioassays.
(package private) DerivedBioAssayData	getData()	Get the BasicData object that holds all data for this item.
Date	getEntryDate()	Get the date that the item was registered in the database.
Extract	getExtract()	Get the extract that is the parent of the data in this derived bioassay.
FileSet	getFileSet()	Get the file set that collects all files that holds data for this item.
Hardware	getHardware()	Get the Hardware that was used when creating this bioassay set.
ItemSubtype	getItemSubtype()	Get the subtype of the item.
Job	getJob()	Get the job that created this bioassay.
Kit	getKit()	Get the Kit that was used when creating this bioassay.
static DerivedBioAssay	getNew(DbControl dc, boolean isRoot, Job job)	Create a new parent-less derived bioassay.
static DerivedBioAssay	getNew(DbControl dc, DerivedBioAssay parent, Job job)	Create a new child derived bioassay from a parent derived bioassay.
static DerivedBioAssay	getNew(DbControl dc, PhysicalBioAssay bioAssay, Job job)	Create a new (root) derived bioassay from a physical bioassay.
Collection<FileSet>	getParentFileSets()	Get the file sets of parent item(s) that are related to the current item.
ItemQuery<DerivedBioAssay>	getParents()	Get all parent derived bioassays.
ItemQuery<PhysicalBioAssay>	getPhysicalBioAssays()	Get a query that returns the physical bioassays used to create this derived bioassay.
Platform	getPlatform()	Get the platform the item is related to.
Protocol	getProtocol()	Default implementation returns null.
static ItemQuery<DerivedBioAssay>	getQuery()	Get a query that returns derived bioassay.
ItemQuery<RawBioAssay>	getRawBioAssays()
Software	getSoftware()	Get the Software that was used when creating this bioassay set.
Item	getType()	Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems()	Get all: Child derived bioassays Child raw bioassays
PlatformVariant	getVariant()	Get the platform variant the item is related to.
boolean	hasFileSet()	Check if this item has a file set.
boolean	isRoot()	Check if this bioassay set is derived from one or more physical bioassays or from derived bioassays.
boolean	isUsed()	Check if this item is used by some other item.
(package private) void	onBeforeCommit(Transactional.Action action)	Automatically try to assign an extract from parent items at creation time.
void	removeParent(DerivedBioAssay bioAssay)	Remove a derived bioassay as a parent item for this derived bioassay.
void	removePhysicalBioAssay(PhysicalBioAssay bioAssay)	Remove a physical bioassay as a parent item for this derived bioassay.
void	setEntryDate(Date entryDate)	Set the date the entry was registered in the database.
void	setExtract(Extract extract)	Set the extract that is the parent of data in this bioassay.
void	setHardware(Hardware hardware)	Set the Hardware that was used when creating this bioassay set.
void	setItemSubtype(ItemSubtype subtype)	Set the subtype on the item.
void	setJob(Job job)	Set the job on this derived bioassay that was used to create or import data for it.
void	setKit(Kit kit)	Set the Kit that was used when creating this bioassay.
(package private) void	setProjectDefaults(Project activeProject)	Set protocol, hardware and software from project default settings.
void	setProtocol(Protocol protocol)	Set the Protocol that describes the procedure used when creating this bioassay set.
void	setSoftware(Software software)	Set the Software that was used when creating this bioassay set.
void	testFixChildren()

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

getAnnotationSet, 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, 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, checkBatchAnnotatableUsage, checkPermission, equals, getBasicData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onRollback, setDbControl, 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

Field Details

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

• Item.DERIVEDBIOASSAY
• getType()

SCAN

public static final String SCAN

The id for the DerivedBioAssayType item representing a scanned hybridization.

See Also:

• Constant Field Values

SEQUENCES

public static final String SEQUENCES

The id for the DerivedBioAssayType item representing original sequenced data.

See Also:

• Constant Field Values

ARRANGEMENT

public static final String ARRANGEMENT

The id for the DerivedBioAssayType item representing sequenced data that has been aligned to a reference database.

See Also:

• Constant Field Values

extractHasBeenSet

private boolean extractHasBeenSet

protocolHasBeenSet

private boolean protocolHasBeenSet

hardwareHasBeenSet

private boolean hardwareHasBeenSet

softwareHasBeenSet

private boolean softwareHasBeenSet

Constructor Details

DerivedBioAssay

DerivedBioAssay(DerivedBioAssayData data)

Method Details

getById

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

Get a DerivedBioAssay 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 DerivedBioAssay 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

getNew

public static DerivedBioAssay getNew(DbControl dc,
 boolean isRoot,
 Job job)

Create a new parent-less derived bioassay. Parent items can be added by calling addPhysicalBioAssay(PhysicalBioAssay) or addParent(DerivedBioAssay).

Parameters:

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

isRoot - TRUE if the new item is a root derived bioassay (eg. it have physical bioassays as parent items)

job - The job that created the new bioassay

Returns:

A new DerivedBioAssay item

Since:

3.2

getNew

public static DerivedBioAssay getNew(DbControl dc,
 PhysicalBioAssay bioAssay,
 Job job)

Create a new (root) derived bioassay from a physical bioassay.

Parameters:

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

bioAssay - The parent physical bioassay

job - The job that created the new bioassay

Returns:

A new DerivedBioAssay item

getNew

public static DerivedBioAssay getNew(DbControl dc,
 DerivedBioAssay parent,
 Job job)

Create a new child derived bioassay from a parent derived bioassay.

Parameters:

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

parent - The parent bioassay

job - The job that created the new bioassay

Returns:

A new DerivedBioAssay item

getQuery

public static ItemQuery<DerivedBioAssay> getQuery()

Get a query that returns derived bioassay.

Returns:

An ItemQuery object

getData

DerivedBioAssayData getData()

Description copied from class: BasicItem

Get the BasicData object that holds all data for this item.

Overrides:

getData in class AnnotatedItem

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

getUsingItems

public Set<ItemProxy> getUsingItems()

Get all:

• Child derived bioassays
• Child raw bioassays

Overrides:

getUsingItems in class BasicItem

Returns:

A set containing proxies for the items, or an empty set if no items are using this item

See Also:

• BasicItem.addUsingItems(Set, Item, org.hibernate.query.Query)

isUsed

public boolean isUsed()
               throws BaseException

Description copied from class: BasicItem

Check if this item is used by some other item. With used we mean that another item is linking to this item in way that prevents this item from beeing deleted. Ie. if we tried to delete an item that is used, we would get a foreign key violation error from the database. If the subclass overrides this method it should propagate the call to the superclass, ie. super.isUsed(), unless it has decided that the item is used by some other means.

Overrides:

isUsed in class BasicItem

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()

breakCircularReferences

int breakCircularReferences(Set<ItemProxy> items)

Any parent bioassays found among the given items are removed from this item. NOTE! Due to DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction it should not be possible to create circular references between derived bioassays, but in case something changes in the future we have implemented this method anyway.

Overrides:

breakCircularReferences in class BasicItem

Since:

3.8

onBeforeCommit

void onBeforeCommit(Transactional.Action action)

Automatically try to assign an extract from parent items at creation time.

Overrides:

onBeforeCommit in class SharedItem

See Also:

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

setProjectDefaults

void setProjectDefaults(Project activeProject)
                 throws BaseException

Set protocol, hardware and software from project default settings.

Overrides:

setProjectDefaults in class BasicItem

Parameters:

activeProject - The currently active project

Throws:

BaseException

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the extract and parent bioassays or physical bioassays.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

getProtocol

public Protocol getProtocol()

Description copied from class: AnnotatedItem

Default implementation returns null. Should be overriden by subclasses that has protocols.

Specified by:

getProtocol in interface Annotatable

Overrides:

getProtocol in class AnnotatedItem

Returns:

Always null

getItemSubtype

@SubtypableRelatedItems({PHYSICALBIOASSAY,DERIVEDBIOASSAY,EXTRACT,SOFTWARE,HARDWARE,PROTOCOL,KIT})
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)

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

setEntryDate

public void setEntryDate(Date entryDate)

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 interface Registered

Parameters:

entryDate - A date or null to use today's date

getFileSet

public FileSet getFileSet()

Description copied from interface: FileStoreEnabled

Get the file set that collects all files that holds data for this item. If no file set exists a new one is created and automatically saved to the database when DbControl.commit() is called. To check if an item has files without creating a new file set use the FileStoreEnabled.hasFileSet() method.

Specified by:

getFileSet in interface FileStoreEnabled

Returns:

A file set

hasFileSet

public boolean hasFileSet()

Description copied from interface: FileStoreEnabled

Check if this item has a file set. Always call this method before FileStoreEnabled.getFileSet() to avoid creating a new file set when there is no need for it.

Specified by:

hasFileSet in interface FileStoreEnabled

Returns:

TRUE if a file set exists, FALSE if not

getPlatform

public Platform getPlatform()

Description copied from interface: FileStoreEnabled

Get the platform the item is related to. The platform is used to limit the DataFileType:s that can be added to the file set.

Specified by:

getPlatform in interface FileStoreEnabled

Returns:

A platform or null if the items is not related to any platform.

getVariant

public PlatformVariant getVariant()

Description copied from interface: FileStoreEnabled

Get the platform variant the item is related to. The platform is used to limit the DataFileType:s that can be added to the file set.

Specified by:

getVariant in interface FileStoreEnabled

Returns:

A platform or null if the items is not related to any variant.

getParentFileSets

public Collection<FileSet> getParentFileSets()

Description copied from interface: FileStoreEnabled

Get the file sets of parent item(s) that are related to the current item. If the item has no parent(s) or if the parent has no file set, null or an empty collection is returned.

Specified by:

getParentFileSets in interface FileStoreEnabled

Returns:

A collection of FileSet or null

testFixChildren

public void testFixChildren()

addPhysicalBioAssay

public void addPhysicalBioAssay(PhysicalBioAssay bioAssay)
                         throws PermissionDeniedException,
InvalidDataException

Add a physical bioassay as a parent to this derived bioassay. Note! Physical bioassays can only be added if this derived bioassay is a root bioassay. The physical bioassay for non-root derived bioassays are automatically assigned.

Parameters:

bioAssay - The parent bioassay to add

Throws:

PermissionDeniedException

InvalidDataException

Since:

3.2

removePhysicalBioAssay

public void removePhysicalBioAssay(PhysicalBioAssay bioAssay)
                            throws PermissionDeniedException,
InvalidDataException

Remove a physical bioassay as a parent item for this derived bioassay. Note! Physical bioassays can only be removed if this derived bioassay is a root bioassay. The physical bioassay for non-root derived bioassays are automatically assigned.

Parameters:

bioAssay - The parent bioassay to remove from this bioassay

Throws:

PermissionDeniedException

InvalidDataException

Since:

3.2

getPhysicalBioAssays

public ItemQuery<PhysicalBioAssay> getPhysicalBioAssays()

Get a query that returns the physical bioassays used to create this derived bioassay.

Returns:

An ItemQuery object

Since:

3.2

addParent

public void addParent(DerivedBioAssay bioAssay)
               throws PermissionDeniedException,
InvalidDataException

Add a derived bioassay as a parent to this derived bioassay. Note! Derived bioassays can only be added if this derived bioassay is not a root bioassay. The physical bioassays are automatically assigned.

Parameters:

bioAssay - The parent bioassay to add

Throws:

PermissionDeniedException

InvalidDataException

Since:

3.2

removeParent

public void removeParent(DerivedBioAssay bioAssay)
                  throws PermissionDeniedException,
InvalidDataException

Remove a derived bioassay as a parent item for this derived bioassay. Note! Derived bioassays can only be used as parents if this derived bioassay is not a root bioassay. The physical bioassays are automatically assigned.

Parameters:

bioAssay - The parent bioassay to remove from this bioassay

Throws:

PermissionDeniedException

InvalidDataException

Since:

3.2

getParents

public ItemQuery<DerivedBioAssay> getParents()

Get all parent derived bioassays.

Returns:

A query returning all parent bioassays

Since:

3.2

isRoot

public boolean isRoot()

Check if this bioassay set is derived from one or more physical bioassays or from derived bioassays. A root derived bioassay can only have physical bioassays as parent items. A non-root derived bioassay can only have other derived bioassays as parents, but the core keep automatically keep track of the physical bioassays.

Returns:

TRUE if this is a root bioassay set derived form a physical bioassay

getExtract

public Extract getExtract()

Get the extract that is the parent of the data in this derived bioassay. The extract should be an extract that is present on the physical bioassay that this bioassay is derived from. But this is not enforced by the core. If no extract is specified this bioassay applies to all extracts that are part of the physical bioassay.

Returns:

An extract or null

setExtract

public void setExtract(Extract extract)

Set the extract that is the parent of data in this bioassay. The extract should be an extract that is present on the physical bioassay that this bioassay is derived from. But this is not enforced by the core.

Parameters:

extract - The extract or null

getChildren

public ItemQuery<DerivedBioAssay> getChildren()

Get all child derived bioassays.

Returns:

A query returning all child bioassays

getJob

public Job getJob()

Get the job that created this bioassay.

Returns:

A job or null if not created by a job

setJob

public void setJob(Job job)
            throws PermissionDeniedException

Set the job on this derived bioassay that was used to create or import data for it.

Parameters:

job - The job or null to clear the existing job

Throws:

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

Since:

3.18.1

setProtocol

public void setProtocol(Protocol protocol)
                 throws PermissionDeniedException

Set the Protocol that describes the procedure used when creating this bioassay set.

Parameters:

protocol - A Protocol item, or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission on this event or use permission for the protocol

getKit

public Kit getKit()
           throws PermissionDeniedException,
BaseException

Get the Kit that was used when creating this bioassay.

Returns:

A Kit item, or null if not known

Throws:

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

BaseException - If there is another error

Since:

3.7

setKit

public void setKit(Kit kit)
            throws PermissionDeniedException

Set the Kit that was used when creating this bioassay.

Parameters:

kit - A Kit item, or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission on this event or use permission for the kit

Since:

3.7

getHardware

public Hardware getHardware()

Get the Hardware that was used when creating this bioassay set.

Returns:

A Hardware item, or null if not known

setHardware

public void setHardware(Hardware hardware)
                 throws PermissionDeniedException

Set the Hardware that was used when creating this bioassay set.

Parameters:

hardware - A Hardware item, or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission on this event or use permission for the hardware

getSoftware

public Software getSoftware()

Get the Software that was used when creating this bioassay set.

Returns:

A Software item, or null if not known

setSoftware

public void setSoftware(Software software)
                 throws PermissionDeniedException

Set the Software that was used when creating this bioassay set.

Parameters:

software - A Software item, or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission on this event or use permission for the software

getRawBioAssays

public ItemQuery<RawBioAssay> getRawBioAssays()

getArrayDesign

public ArrayDesign getArrayDesign()
                           throws PermissionDeniedException,
BaseException

Get the array design connected to this derived bioassay by following the path from the physical bioassay to the array slide to the array batch to the array design. If this derived bioasay has multiple parents that are linked to different array designs, null is returned.

Returns:

The array design, or null if no array design is connected

Throws:

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

BaseException - If there is another error.

countRawBioAssays

public long countRawBioAssays()
                       throws BaseException

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

Returns:

The number of raw bioassays

Throws:

BaseException - If the raw bioassays couldn't be counted.