Package net.sf.basedb.core
Class RawBioAssay
- All Implemented Interfaces:
AccessControlled
,Annotatable
,Controlled
,DiskConsumable
,FileStoreEnabled
,Identifiable
,Listable
,Nameable
,Ownable
,Registered
,Removable
,Shareable
public class RawBioAssay
extends AnnotatedItem
implements DiskConsumable, FileStoreEnabled, Registered, Listable
A rawbioassay represents the raw data generated from a single
DerivedBioAssay
. A raw bioassay must have a RawDataType
which specifies the data columns generated by the Software
.
Raw data is added by a RawDataBatcher
object. You can get a
batcher for this raw bioassay by calling the getRawDataBatcher(FeatureIdentificationMethod, Job)
method.
- Version:
- 2.0
- Author:
- Nicklas
- Last modified
- $Date: 2019-03-11 12:51:33 +0100 (mån, 11 mars 2019) $
-
Field Summary
Modifier and TypeFieldDescriptionprivate boolean
static final int
The maximum length of the name of a header that can be stored in the database.static final int
The maximum length of the value of a header that can be stored in the database.private boolean
private RawDataBatcher
private boolean
static final Item
The type of item represented by this class.Fields inherited from interface net.sf.basedb.core.Nameable
MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH
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Constructor Summary
-
Method Summary
Modifier and TypeMethodDescriptionvoid
Delete the raw data that has been added to the database for this raw bioassay.Get the parent derived bioassay and extract, if any.Get theArrayDesign
this raw data uses.static RawBioAssay
Get aRawBioAssay
object when you know the id.long
getBytes()
Get the absolute number of bytes this item uses.(package private) RawBioAssayData
getData()
Get theBasicData
object that holds all data for this item.long
Always 0.Get a dynamic query that returns the raw data of this raw bioassay.Get the date that the item was registered in the database.Get a query that returns all experiments where this raw bioassay is used.Get the file set that collects all files that holds data for this item.Get the value for the raw data header with the specified name.Get the names of all raw data headers.getJob()
Get the job that created or imported data to this raw bioassay.AlwaysLocation.PRIMARY
.static RawBioAssay
getNew
(DbControl dc, Platform platform, RawDataType rawDataType) Create a new raw bioassay for a specific platform and/or raw data type.static RawBioAssay
getNew
(DbControl dc, PlatformVariant variant, RawDataType rawDataType) Create a new raw bioassay for a specific platform variant.int
Get the number of spots on this raw bioassay that are stored in the database.int
Get the number of spots on this raw bioassay that are stored inside files.Get theDerivedBioAssay
this raw bioassay is created from.Get theExtract
this raw bioassay is created from.Get the file set from the array design, if it exists.Get the platform the item is related to.Get theProtocol
used while analysing the scanned images.static ItemQuery<RawBioAssay>
getQuery()
Get a query configured to retrieve raw bioassays.AlwaysQuotaType.RAW_DATA
.Get a query that returns the raw data of this raw bioassay.getRawDataBatcher
(FeatureIdentificationMethod fiMethod, Job job) Get a raw data batcher object which can be used to add raw data to the raw bioassay.getRawDataById
(int id) Get a raw data spot when you know the id.getRawDataById
(int id, boolean forceInitialization) Get a raw data spot when you know the id.Get the raw data type this raw bioassay uses for the raw data.Get a query that returns the reporters on this raw bioassay.Get theSoftware
used while analysing the scanned images.int
getSpots()
Utility method that either returns the number of db spots or the number of file spots.getType()
Get the type of item represented by the object.Get all:Experiment
:s using this raw bioassayTransformation
:s using this raw bioassayGet the platform variant the item is related to.boolean
Check if this raw bioassay is connected to an array design or not.boolean
hasData()
If raw data has been added to this raw bioassay or not.boolean
Check if this item has a file set.boolean
Check if this raw bioassay uses a file-only platform or variant.boolean
isPlatform
(String externalId) Check if the platform/variant of this raw bioassay has the given external ID.boolean
isSameArrayDesign
(ArrayDesign design) Checks if the given array design is the same as already set on this raw bioassay.boolean
isUsed()
Check if: AnExperiment
is using this raw bioassay ATransformation
is using this raw bio raw data type will also be updated.(package private) void
onBeforeCommit
(Transactional.Action action) Delete raw data if it exists.void
removeHeader
(String name) Remove a specific header from the raw bioassay.void
Remove all headers from the raw bioassay.void
setArrayDesign
(ArrayDesign arrayDesign) Set theArrayDesign
this raw data uses.void
setEntryDate
(Date entryDate) Set the date the entry was registered in the database.void
Set the value for a raw data header.void
Set the job on this raw bioassay that was used to create or import data for it.void
setNumFileSpots
(int numSpots) Set the number of spots that are stored in files.void
setParentBioAssay
(DerivedBioAssay parent) Set theDerivedBioAssay
this raw bioassay is created from.void
setParentExtract
(Extract extract) Set theExtract
this raw bioassay is created from.void
setPlatform
(Platform platform, RawDataType rawDataType) Set the platform and raw data type of the raw bioassay.(package private) void
setProjectDefaults
(Project activeProject) Set software, protocol and array design from project default settings.void
setProtocol
(Protocol protocol) Set theProtocol
used while analysing the scanned images.void
setSoftware
(Software software) Set theSoftware
used while analysing the scanned images.void
setVariant
(PlatformVariant variant, RawDataType rawDataType) Set the platform and variant of the raw bioassay.void
updateArrayDesign
(ArrayDesign arrayDesign, FeatureIdentificationMethod fiMethod, ProgressReporter progress) Set theArrayDesign
this raw data uses.boolean
Always FALSE.private void
validateFeatures
(DbControl dc, ArrayDesign design, FeatureIdentificationMethod fiMethod, boolean update, ProgressReporter progress) Validate that the features/reporters of the raw data matches the features/reporter on the array design.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, breakCircularReferences, 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
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Field Details
-
TYPE
The type of item represented by this class.- See Also:
-
MAX_HEADER_NAME_LENGTH
public static final int MAX_HEADER_NAME_LENGTHThe maximum length of the name of a header that can be stored in the database. Check the name length against this value before callingsetHeader(String, String)
to avoid exceptions.- See Also:
-
MAX_HEADER_VALUE_LENGTH
public static final int MAX_HEADER_VALUE_LENGTHThe maximum length of the value of a header that can be stored in the database. Check the value length against this value before callingsetHeader(String, String)
to avoid exceptions.- See Also:
-
rawDataBatcher
-
softwareHasBeenSet
private boolean softwareHasBeenSet -
protocolHasBeenSet
private boolean protocolHasBeenSet -
arrayDesignHasBeenSet
private boolean arrayDesignHasBeenSet
-
-
Constructor Details
-
RawBioAssay
RawBioAssay(RawBioAssayData data)
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-
Method Details
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getNew
Create a new raw bioassay for a specific platform and/or raw data type. If the platform is locked to a specific raw data type, therawDataType
parameter is ignored. If the platform isn't locked the raw data type is required and must be a database-based raw data type. Ie.RawDataType.isStoredInDb()
must return true.- Parameters:
dc
- TheDbControl
which will be used for permission checking and database accessplatform
- The platform of the new raw bioassay, null is not allowedrawDataType
- The raw data type of the raw bioassay (required if the platform isn't locked to a specific raw data type)- Returns:
- The new
RawBioAssay
item - Since:
- 2.5
-
getNew
Create a new raw bioassay for a specific platform variant. If the variant is locked to a specific raw data type, therawDataType
parameter is ignored. If the variant isn't locked the raw data type is required and must be a database-based raw data type. Ie.RawDataType.isStoredInDb()
must return true.- Parameters:
dc
- TheDbControl
which will be used for permission checking and database accessvariant
- The platform variant of the new raw bioassay, null is not allowedrawDataType
- The raw data type of the raw bioassay (required if the platform isn't locked to a specific raw data type)- Returns:
- The new
RawBioAssay
item - Since:
- 2.5
-
getById
public static RawBioAssay getById(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException Get aRawBioAssay
object 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
RawBioAssay
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 configured to retrieve raw bioassays.- Returns:
- An
ItemQuery
object
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getData
RawBioAssayData getData()Description copied from class:BasicItem
Get theBasicData
object that holds all data for this item.- Overrides:
getData
in classAnnotatedItem
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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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useDifference
public boolean useDifference()Always FALSE.- Specified by:
useDifference
in interfaceDiskConsumable
- Returns:
- TRUE if the item reports the difference, FALSE if it reports the absolute
- See Also:
-
getBytes
public long getBytes()Description copied from interface:DiskConsumable
Get the absolute number of bytes this item uses. All items must report this number.- Specified by:
getBytes
in interfaceDiskConsumable
- Returns:
- The absolute number of bytes the item uses
- See Also:
-
getDifference
public long getDifference()Always 0.- Specified by:
getDifference
in interfaceDiskConsumable
- Returns:
- The difference in bytes between now and when the item was loaded, or 0 if this item doesn't report differences
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getQuotaTypeSystemId
AlwaysQuotaType.RAW_DATA
.- Specified by:
getQuotaTypeSystemId
in interfaceDiskConsumable
- Returns:
- The systemid of the QuotaType
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getLocation
AlwaysLocation.PRIMARY
.- Specified by:
getLocation
in interfaceDiskConsumable
- Returns:
- The location
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getAnnotatableParents
Get the parent derived bioassay and extract, if any.- Specified by:
getAnnotatableParents
in interfaceAnnotatable
- Returns:
- A set containing annotatable items, or null
- Throws:
BaseException
- If there is an error
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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 whenDbControl.commit()
is called. To check if an item has files without creating a new file set use theFileStoreEnabled.hasFileSet()
method.- Specified by:
getFileSet
in interfaceFileStoreEnabled
- Returns:
- A file set
- Since:
- 2.5
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hasFileSet
public boolean hasFileSet()Description copied from interface:FileStoreEnabled
Check if this item has a file set. Always call this method beforeFileStoreEnabled.getFileSet()
to avoid creating a new file set when there is no need for it.- Specified by:
hasFileSet
in interfaceFileStoreEnabled
- Returns:
- TRUE if a file set exists, FALSE if not
- Since:
- 2.5
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getPlatform
Description copied from interface:FileStoreEnabled
Get the platform the item is related to. The platform is used to limit theDataFileType
:s that can be added to the file set.- Specified by:
getPlatform
in interfaceFileStoreEnabled
- Returns:
- A platform or null if the items is not related to any platform.
- Since:
- 2.5
-
getVariant
Description copied from interface:FileStoreEnabled
Get the platform variant the item is related to. The platform is used to limit theDataFileType
:s that can be added to the file set.- Specified by:
getVariant
in interfaceFileStoreEnabled
- Returns:
- A platform or null if the items is not related to any variant.
- Since:
- 2.5
-
getParentFileSets
Get the file set from the array design, if it exists.- Specified by:
getParentFileSets
in interfaceFileStoreEnabled
- Returns:
- A collection of
FileSet
or null - Since:
- 2.5
-
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 if:- An
Experiment
is using this raw bioassay - A
Transformation
is using this raw bio raw data type will also be updated. The platform can't be changed if raw data has been imported to the database.assay
- 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:
- An
-
getUsingItems
Get all:Experiment
:s using this raw bioassayTransformation
:s using this raw bioassay
- 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:
-
onBeforeCommit
Delete raw data if it exists.- Overrides:
onBeforeCommit
in classSharedItem
- Throws:
BaseException
- If there is another error- See Also:
-
setProjectDefaults
Set software, protocol and array design from project default settings.- Overrides:
setProjectDefaults
in classBasicItem
- Parameters:
activeProject
- The currently active project- Throws:
BaseException
- Since:
- 2.9
-
setPlatform
Set the platform and raw data type of the raw bioassay. This method will set the variant to null. UsesetVariant(PlatformVariant, RawDataType)
if you want to set a specific variant. If the platform is locked to a raw data type, therawDataType
parameter is ignored. If the platform isn't locked the raw data type must be a database-based raw data type. Ie.RawDataType.isStoredInDb()
must return true.- Parameters:
platform
- The new platform, null is not allowesrawDataType
- The raw data type, required if the platform doesn't specify a raw data type- Throws:
PermissionDeniedException
- If the logged in user doesn't have write permissionInvalidDataException
- If platform is null or if the raw data type is not properly specified- Since:
- 2.5
-
setVariant
Set the platform and variant of the raw bioassay. This method will automatically set the platform toPlatformVariant.getPlatform()
. If the platform variant is locked to a raw data type, the raw data type is also updated. The platform variant can't be changed if raw data has been imported to the database.- Parameters:
variant
- The new platform variantrawDataType
- The rawdata type for this platform variant. Null is allowed if rawDataType already has been set.- Throws:
PermissionDeniedException
- If the logged in user doesn't have write permissionInvalidDataException
- If variant is null- Since:
- 2.5
-
isPlatform
Check if the platform/variant of this raw bioassay has the given external ID.- Parameters:
externalId
- The external ID to match- Returns:
- TRUE if either the variant of platform matches the external ID
- Since:
- 2.5
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isFileOnlyPlatform
public boolean isFileOnlyPlatform()Check if this raw bioassay uses a file-only platform or variant. If the raw bioassay has a platform variant, the setting from the variant is returned, otherwise the setting from the platform.- Returns:
- TRUE if this raw bioassay use a file-only variant / platform
- Since:
- 2.5
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getRawDataType
Get the raw data type this raw bioassay uses for the raw data. The raw data type cannot be changed once the raw bioassay has been created.- Returns:
- A
RawDataType
object
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setJob
Set the job on this raw 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:
- 3.11.3
-
getJob
Get the job that created or imported data to this raw bioassay.- Returns:
- A
Job
object, ot null if this information is not available - Throws:
PermissionDeniedException
- If the logged in user doesn't have read permission to the jobBaseException
- If there is another error- Since:
- 2.7
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getParentBioAssay
Get theDerivedBioAssay
this raw bioassay is created from.- Returns:
- The
DerivedBioAssay
item or null if not known - Throws:
PermissionDeniedException
- If the logged in user doesn't have read permission for the scannerBaseException
- If there is another error.- Since:
- 3.0
-
setParentBioAssay
Set theDerivedBioAssay
this raw bioassay is created from.- Parameters:
parent
- The parent bioassay or null if not known- Throws:
PermissionDeniedException
- If the logged in user doesn't have write permission for the raw bioassay use permission for the scanBaseException
- If there is another error- Since:
- 3.0
-
getParentExtract
Get theExtract
this raw bioassay is created from.- Returns:
- The
Extract
item or null if not known - Throws:
PermissionDeniedException
- If the logged in user doesn't have read permission for the extractBaseException
- If there is another error.- Since:
- 3.0
-
setParentExtract
Set theExtract
this raw bioassay is created from.- Parameters:
extract
- The parent extract or null if not known- Throws:
PermissionDeniedException
- If the logged in user doesn't have write permission for the raw bioassay use permission for the scanBaseException
- If there is another error- Since:
- 3.0
-
getSoftware
Get theSoftware
used while analysing the scanned images.- Returns:
- The
Software
item or null if not known - Throws:
PermissionDeniedException
- If the logged in user doesn't have read permission for the softwareBaseException
- If there is another error.
-
setSoftware
Set theSoftware
used while analysing the scanned images.- Parameters:
software
- The software or null if not known- Throws:
PermissionDeniedException
- If the logged in user doesn't have write permission for the raw bioassay use permission for the scannerBaseException
- If there is another error
-
getProtocol
Get theProtocol
used while analysing the scanned images.- Specified by:
getProtocol
in interfaceAnnotatable
- Overrides:
getProtocol
in classAnnotatedItem
- Returns:
- The
Protocol
item or null if not known - Throws:
PermissionDeniedException
- If the logged in user doesn't have read permission for the protocolBaseException
- If there is another error.
-
setProtocol
Set theProtocol
used while analysing the scanned images.- Parameters:
protocol
- The protocol or null if not known- Throws:
PermissionDeniedException
- If the logged in user doesn't have write permission for the raw bioassay use permission for the protocolBaseException
- If there is another error
-
getArrayDesign
Get theArrayDesign
this raw data uses. This should normally be the same as the array design reached via the hybridization, but doesn't have to be.- Returns:
- The
ArrayDesign
item or null if not known - Throws:
PermissionDeniedException
- If the logged in user doesn't have read permission for the array designBaseException
- If there is another error.
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setArrayDesign
Set theArrayDesign
this raw data uses. The array design can't be changed with this method once raw data spots has been added. Use theupdateArrayDesign(ArrayDesign, FeatureIdentificationMethod, ProgressReporter)
to do that.- Parameters:
arrayDesign
- TheArrayDesign
item or null if not known- Throws:
PermissionDeniedException
- If the logged in user doesn't have write permission for the raw bioassay use permission for the array design or spots has already been addedBaseException
- If there is another error
-
isSameArrayDesign
Checks if the given array design is the same as already set on this raw bioassay.- Since:
- 3.0
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updateArrayDesign
public void updateArrayDesign(ArrayDesign arrayDesign, FeatureIdentificationMethod fiMethod, ProgressReporter progress) throws PermissionDeniedException, InvalidDataException Set theArrayDesign
this raw data uses. If data has already been imported to the raw bioassay, the reporters for each position on the new array design must match the positions of reporters already present in the raw bioassay.- Parameters:
arrayDesign
- TheArrayDesign
item or null if not knownfiMethod
- The method to use for identifying features on the new array design. Use null to use the method choosen by the new array design. TheFeatureIdentificationMethod.FEATURE_ID
will not work unless the raw bioassay is already connected to an array design which has features with external ID:sprogress
- An optional progress reporter- Throws:
PermissionDeniedException
- If the logged in user doesn't have write permission for the raw bioassay use permission for the array designInvalidDataException
- If the features of the new array design doesn't match the raw dataBaseException
- If there is another error- Since:
- 2.6
-
hasArrayDesign
public boolean hasArrayDesign()Check if this raw bioassay is connected to an array design or not.- Returns:
- TRUE if it has an array design, FALSE otherwise
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getSpots
public int getSpots()Utility method that either returns the number of db spots or the number of file spots. If there is spot data in the database, this number is returned, otherwise the number of file spots is returned.- Returns:
- The number of spots
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getNumDbSpots
public int getNumDbSpots()Get the number of spots on this raw bioassay that are stored in the database.- Returns:
- The number of spots in the database
- Since:
- 2.5
-
getNumFileSpots
public int getNumFileSpots()Get the number of spots on this raw bioassay that are stored inside files.- Returns:
- The number of spots in files
- Since:
- 2.5
-
setNumFileSpots
public void setNumFileSpots(int numSpots) Set the number of spots that are stored in files.- Parameters:
numSpots
- The number of spots- Since:
- 2.5
-
hasData
public boolean hasData()If raw data has been added to this raw bioassay or not. Note that this method checks both data in the database and data in the form of files. -
getHeader
Get the value for the raw data header with the specified name.- Parameters:
name
- The name of the header- Returns:
- The value of the header or null if no header with that name exists
-
setHeader
public void setHeader(String name, String value) throws PermissionDeniedException, InvalidDataException Set the value for a raw data header.- Parameters:
name
- The name of the headervalue
- The value of the header- Throws:
PermissionDeniedException
- If the logged in user doesn't have write permission or if spots already has been added to the raw bioassayInvalidDataException
- If the name or value is null or too long
-
removeHeaders
public void removeHeaders()Remove all headers from the raw bioassay.- Since:
- 2.5
-
removeHeader
Remove a specific header from the raw bioassay.- Parameters:
name
- The name of the header- Since:
- 2.5
-
getHeaderNames
Get the names of all raw data headers. The set is sorted by name.- Returns:
- A set containing the header names or an empty set if no headers have been defined
-
getExperiments
Get a query that returns all experiments where this raw bioassay is used.- Returns:
- An
ItemQuery
object
-
getRawDataBatcher
public RawDataBatcher getRawDataBatcher(FeatureIdentificationMethod fiMethod, Job job) throws PermissionDeniedException, BaseException Get a raw data batcher object which can be used to add raw data to the raw bioassay.- Parameters:
fiMethod
- The method to use for identifying features, or null to use the method choosen by the array design. This parameter has no meaning if the raw bioassay is not connected to an array design or if the array design has no features.job
- The job that is currently running, or null if the raw data import is not running as a job- Returns:
- A
RawDataBatcher
object. If this method is called multiple times thefiMethod
andjob
parameter is ignored and the same batcher as before is returned - Throws:
PermissionDeniedException
- If raw data has already been added or the logged in user doesn't have write permissionBaseException
- If there is another error- Since:
- 2.7
-
deleteRawData
Delete the raw data that has been added to the database for this raw bioassay. You should not call this method in the same transaction as adding raw data with the batcher fromgetRawDataBatcher(FeatureIdentificationMethod, Job)
.- Throws:
PermissionDeniedException
- If the logged in user doesn't have write permission or aRawDataBatcher
has been fetched using thegetRawDataBatcher(FeatureIdentificationMethod, Job)
method or the raw bioassay is used by some experimentBaseException
- If there is another error
-
getRawDataById
Get a raw data spot when you know the id. NOTE! This method may return an uninitialized proxy. If an initialized object is required usegetRawDataById(int, boolean)
instead.- Parameters:
id
- The id of the spot- Returns:
- An
RawData
object - Throws:
ItemNotFoundException
- If no raw data item was found for the given id.BaseException
- If there some other error.
-
getRawDataById
public RawData getRawDataById(int id, boolean forceInitialization) throws ItemNotFoundException, BaseException Get a raw data spot when you know the id.- Parameters:
id
- The id of the spotforceInitialization
- If TRUE the raw data and associated feature and reporter are sure to be initialized- Returns:
- An
RawData
object - Throws:
ItemNotFoundException
- If no raw data item was found for the given id.BaseException
- If there some other error.- Since:
- 2.15
-
getRawData
Get a query that returns the raw data of this raw bioassay.- Returns:
- A
DataQuery
object
-
getReporters
Get a query that returns the reporters on this raw bioassay. The query is rooted at the raw data, which means that:- All filters, sorting, etc. that works for
getRawData()
can be used without modifications on this query. - The same reporter may be returned multiple times if it is present on multiple spots.
- 'Null' values may be returned if there are spots without a reporter
- Returns:
- A
DataQuery
object - Since:
- 2.8
- All filters, sorting, etc. that works for
-
getDynamicRawData
Get a dynamic query that returns the raw data of this raw bioassay.- Returns:
- A
DynamicRawDataQuery
object
-
validateFeatures
private void validateFeatures(DbControl dc, ArrayDesign design, FeatureIdentificationMethod fiMethod, boolean update, ProgressReporter progress) Validate that the features/reporters of the raw data matches the features/reporter on the array design.- Parameters:
dc
- The DbControl to use for database accessdesign
- The array design to validate againstfiMethod
- The method to use for identifying features, or null to use the method choosen by the array designupdate
- If the raw data should be linked to the new feature or notprogress
- An optional progress reporter- Since:
- 2.6
-