net.sf.basedb.core
Class RawDataBatcher

java.lang.Object
  net.sf.basedb.core.AbstractBatcher
      net.sf.basedb.core.BasicBatcher<RawData>
          net.sf.basedb.core.RawDataBatcher

All Implemented Interfaces:

AccessControlled, Batcher

public class RawDataBatcher
extends BasicBatcher<RawData>

Batcher class for raw data. A single instance can be used for raw data belonging to a single RawBioAssay. If the raw bioassay is connected to an array design with features the raw data is verified against the features before it is inserted as follows:

• Find the feature located at the same coordinates as given by the row, column and block or row, column, metaGridX and metaGridY. A block number of zero signals that meta coordinates should be used. All other values use block coordinates.
• If a feature isn't found, an ItemNotFoundException is thrown
• If you have specified to verify the external reporter id by using the insert(RawData, String) method the external reporter id of the feature is checked against the supplied reporter id. If they don't match an InvalidDataException is thrown.
• Finally, the position and reporter is copied from the feature to the raw data. Note that any reporter you have set on the raw data yourself is overwritten and never used.

Note that if the raw bioassay isn't connected to an array design no checks are made and none of the above apply. The major difference is that you must alsways set a reporter youself in this case. We recommend that you use the insert(RawData) method if no array design is connected, and the insert(RawData, String) method otherwise.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2009-04-06 14:52:39 +0200 (Mon, 06 Apr 2009) $

Field Summary

private boolean	acceptInsertIfNullReporterOnFeature If we should always accept inserts when the feature has a NULL reporter.
private ArrayDesignData	arrayDesign The array design the raw bioassay is connected to, if any.
private long	bytes The number of bytes the spot data is occupying on disk.
private boolean	caseInsensitive If case should be ignored when comparing strings (external ID)
private int	currentPosition Keeps track of the position number unless the raw bioassay is connected to an array design with features.
private static boolean	debugSqlEnabled So we don't always have to call logSql.debug()
private FeatureIdentificationMethod	fiMethod The method to use for identifying features.
private org.hibernate.Query	findReporter A query to find reporters by the external id.
private static Logger	logSql Log all SQL statements.
private int	numAcceptedWithNullReporterOnFeature The number of accepted inserts were the feature had a NULL reporter
private int	numReportersNotFound The number of reporters that was not found.
private int	numSkippedMissingFeature The number of skipped inserts due to missing feature
private Map<Object,FeatureData>	preloaded Holds info about the features of an array design.
private RawBioAssay	rawBioAssay The raw bioassay this batcher adds raw data to.
private RawBioAssayData	rawBioAssayData Just a copy of the data object for the raw bioassay.
private RawDataType	rawDataType The type of raw data to batch.
private boolean	skipInsertIfMissingFeature If inserts that can't find a matching feature should be skipped or generate an error.
private Set<Object>	usedFeatures Keep track of the used features to make sure that no more than raw data spot references the same feature.
private boolean	useNullIfReporterNotFound If we should use the null reporter if a reporter isn't found.

Fields inherited from class net.sf.basedb.core.BasicBatcher

debugEnabled, logParam

Constructor Summary

RawDataBatcher(DbControl dc, RawBioAssay rawBioAssay, FeatureIdentificationMethod fim)

Method Summary

void	acceptInsertIfNullReporterOnFeature(boolean accept) Specify if inserts always should be accepted if there is a matching feature that has a NULL reporter.
void	delete(int id) Always throws a PermissionDeniedException, since raw data cannot be modifed once it has been created, except if all spots are deleted at the same time.
(package private) void	deleteAll() Delete all raw data.
private void	doInsert(RawData data, String externalReporterId, String externalFeatureId, boolean validateReporterId) Do the actual insert.
(package private) static RawDataBatcher	getNew(DbControl dc, RawBioAssay rawBioAssay, FeatureIdentificationMethod fiMethod) Create a new batcher for raw data.
int	getNumAcceptedWithNullReporterOnFeature() Get the number of accepted inserts because of features with a NULL reporter.
int	getNumReportersNotFound() Get the number of reporters that was not found.
int	getNumSkippedMissingFeature() Get the number of skipped inserts because of a missing feature.
(package private) PluginPermission	getPluginPermissions()
RawBioAssay	getRawBioAssay() Get the raw bioassay this batcher is used for.
Item	getType() Get the type of item supported by the batcher.
(package private) void	initPermissions(int granted, int denied) Grant read permission if the logged in user has read permission to the raw bioassay.
void	insert(RawData data) Insert a data object.
void	insert(RawData data, String externalReporterId) Deprecated. Use insert(RawData, String, String) instead
void	insert(RawData data, String externalReporterId, String externalFeatureId) Insert a raw data spot and verify the external id of the reporter.
RawData	newRawData() Create a new raw data object.
(package private) void	onBeforeClose() Update the spot count and disk usage on the raw bioassay.
void	skipInsertIfMissingFeature(boolean skip) Specify if the insert method should skip the insert if a feature for the spot can't be found.
void	update(RawData data) Always throws a PermissionDeniedException, since raw data cannot be modifed once it has been created.
void	useNullIfReporterNotFound(boolean useNull) Specify if the insert method should use a null reporter if a reporter with the given external ID isn't found.
void	validate(RawData data) Validate all properties for the raw data object: The data object is not null The data object belongs to the correct raw bioassay The position value is > 0 All of the extra properties using the ExtendedProperty.validateValue(Object) method

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

checkPermission, delete, flush, flushDelete, flushInsert, flushUpdate, getPermissions, getPropertyValue, getTotalInsertCount, hasPermission, onBeforeCommit, setPropertyValue

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

analyzeTable, close, getBatchSize, getDbControl, getSessionControl, isClosed, setBatchSize, setDbControl, updateLastAccess

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

logSql

private static final Logger logSql

Log all SQL statements.

debugSqlEnabled

private static final boolean debugSqlEnabled

So we don't always have to call logSql.debug()

rawBioAssay

private final RawBioAssay rawBioAssay

The raw bioassay this batcher adds raw data to.

rawBioAssayData

private final RawBioAssayData rawBioAssayData

Just a copy of the data object for the raw bioassay.

rawDataType

private final RawDataType rawDataType

The type of raw data to batch.

arrayDesign

private final ArrayDesignData arrayDesign

The array design the raw bioassay is connected to, if any.

caseInsensitive

private final boolean caseInsensitive

If case should be ignored when comparing strings (external ID)

currentPosition

private int currentPosition

Keeps track of the position number unless the raw bioassay is connected to an array design with features.

bytes

private long bytes

The number of bytes the spot data is occupying on disk. This value is calculated by the validate method for each spot and added to the raw bioassay by the close method.

findReporter

private org.hibernate.Query findReporter

A query to find reporters by the external id.

fiMethod

private FeatureIdentificationMethod fiMethod

The method to use for identifying features.

preloaded

private final Map<Object,FeatureData> preloaded

Holds info about the features of an array design. Using the feature identifier we can look up position number and reporter on each location and verify this against the raw data.

See Also:

FeatureIdentificationMethod

usedFeatures

private Set<Object> usedFeatures

Keep track of the used features to make sure that no more than raw data spot references the same feature.

useNullIfReporterNotFound

private boolean useNullIfReporterNotFound

If we should use the null reporter if a reporter isn't found.

numReportersNotFound

private int numReportersNotFound

The number of reporters that was not found.

skipInsertIfMissingFeature

private boolean skipInsertIfMissingFeature

If inserts that can't find a matching feature should be skipped or generate an error.

numSkippedMissingFeature

private int numSkippedMissingFeature

The number of skipped inserts due to missing feature

acceptInsertIfNullReporterOnFeature

private boolean acceptInsertIfNullReporterOnFeature

If we should always accept inserts when the feature has a NULL reporter.

numAcceptedWithNullReporterOnFeature

private int numAcceptedWithNullReporterOnFeature

The number of accepted inserts were the feature had a NULL reporter

Constructor Detail

RawDataBatcher

RawDataBatcher(DbControl dc,
               RawBioAssay rawBioAssay,
               FeatureIdentificationMethod fim)
         throws BaseException

Throws:

BaseException

Method Detail

getNew

static RawDataBatcher getNew(DbControl dc,
                             RawBioAssay rawBioAssay,
                             FeatureIdentificationMethod fiMethod)
                      throws BaseException

Create a new batcher for raw data.

Parameters:

dc - The DbControl to use for database access and permission checking

rawBioAssay - The raw bioassay this batcher should add raw data to

fiMethod - The method to use for identifying features, use null to use the method specified by the array design

Throws:

BaseException - If there is an error

See Also:

RawBioAssay.getRawDataBatcher(FeatureIdentificationMethod, Job)

getType

public Item getType()

Description copied from class: BasicBatcher

Get the type of item supported by the batcher. The returned value is one of the values defined in the Item enumeration.

Specified by:

getType in class BasicBatcher<RawData>

Returns:

A value indicating the type of item

See Also:

Item

validate

public void validate(RawData data)
              throws InvalidDataException

Validate all properties for the raw data object:

• The data object is not null
• The data object belongs to the correct raw bioassay
• The position value is > 0
• All of the extra properties using the ExtendedProperty.validateValue(Object) method

Specified by:

validate in class BasicBatcher<RawData>

Parameters:

data - Data object to validate

Throws:

InvalidDataException - If the data object is invalid

insert

public void insert(RawData data)
            throws BaseException

Description copied from class: BasicBatcher

Insert a data object. The data object will not be synchronized with the database. The object values may be modified.

Overrides:

insert in class BasicBatcher<RawData>

Parameters:

data - Data object to be inserted

Throws:

InvalidDataException - If the data is null or it doesn't validate against the BasicBatcher.validate(BatchableData) method

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

BaseException - If there is another error

update

public void update(RawData data)
            throws BaseException

Always throws a PermissionDeniedException, since raw data cannot be modifed once it has been created.

Overrides:

update in class BasicBatcher<RawData>

Parameters:

data - Data object to be updated

Throws:

InvalidDataException - If the data is null or it doesn't validate against the BasicBatcher.validate(BatchableData) method

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

BaseException - If there is another error

delete

public void delete(int id)
            throws BaseException

Always throws a PermissionDeniedException, since raw data cannot be modifed once it has been created, except if all spots are deleted at the same time.

Overrides:

delete in class BasicBatcher<RawData>

Parameters:

id - Id of the object to be deleted

Throws:

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

BaseException - If there is another error

See Also:

deleteAll()

initPermissions

void initPermissions(int granted,
                     int denied)
               throws BaseException

Grant read permission if the logged in user has read permission to the raw bioassay. Grant write, delete and create permission if the logged in user has write permission to the raw bioassay.

Overrides:

initPermissions in class BasicBatcher<RawData>

Parameters:

granted - Permissions that have been granted by the subclass

denied - Permissions that have been denied by the subclass

Throws:

BaseException - If the permissions couldn't be initialised

getPluginPermissions

PluginPermission getPluginPermissions()

Overrides:

getPluginPermissions in class BasicBatcher<RawData>

onBeforeClose

void onBeforeClose()
             throws BaseException

Update the spot count and disk usage on the raw bioassay.

Overrides:

onBeforeClose in class BasicBatcher<RawData>

Throws:

BaseException

useNullIfReporterNotFound

public void useNullIfReporterNotFound(boolean useNull)

Specify if the insert method should use a null reporter if a reporter with the given external ID isn't found. This setting only affects raw bioassays that are not connected to an array design.

Parameters:

useNull - TRUE if the insert should use a null reporter (default), FALSE otherwise

See Also:

skipInsertIfMissingFeature(boolean)

getNumReportersNotFound

public int getNumReportersNotFound()

Get the number of reporters that was not found.

Since:

2.7

See Also:

useNullIfReporterNotFound(boolean)

skipInsertIfMissingFeature

public void skipInsertIfMissingFeature(boolean skip)

Specify if the insert method should skip the insert if a feature for the spot can't be found. This setting only affects raw bioassays that are connected to an array design.

Parameters:

skip - TRUE if the insert should be skipped, FALSE to throw an ItemNotFoundException (default)

Since:

2.7

See Also:

useNullIfReporterNotFound(boolean)

getNumSkippedMissingFeature

public int getNumSkippedMissingFeature()

Get the number of skipped inserts because of a missing feature.

Since:

2.7

See Also:

skipInsertIfMissingFeature(boolean)

acceptInsertIfNullReporterOnFeature

public void acceptInsertIfNullReporterOnFeature(boolean accept)

Specify if inserts always should be accepted if there is a matching feature that has a NULL reporter. This settings only affects raw bioassays that are connected to an array design.

NOTE! The inserted data will also reference the NULL reporter.

Parameters:

accept - TRUE to always accept the insert, FALSE to throw an ItemNotFoundException if the insert doesn't specify a NULL reporter (default)

Since:

2.7

getNumAcceptedWithNullReporterOnFeature

public int getNumAcceptedWithNullReporterOnFeature()

Get the number of accepted inserts because of features with a NULL reporter.

Since:

2.7

See Also:

acceptInsertIfNullReporterOnFeature(boolean)

getRawBioAssay

public RawBioAssay getRawBioAssay()

Get the raw bioassay this batcher is used for.

insert

public void insert(RawData data,
                   String externalReporterId)
            throws BaseException

Deprecated. Use insert(RawData, String, String) instead

Throws:

BaseException

insert

public void insert(RawData data,
                   String externalReporterId,
                   String externalFeatureId)

Insert a raw data spot and verify the external id of the reporter. The external id is only verified if it is not null and the raw bioassay is connected to an array design with features. The external id is verified to match the external id of the reporter attached to feature of the spot's position. If the raw bioassay isn't connected to an array design, the batcher will automatically try to load the reporter with the given external ID. If you use this method you don't have the set the reporter with the RawData.setReporter(ReporterData) method.

The externalFeatureId is only needed if the FeatureIdentificationMethod.FEATURE_ID identification method is used. The other methods will use properties on the RawData object (postion or the coordinates) to find the feature. Feature identification is of course needed when the raw bioassay is connected to an array design but is also used when there is no array design to validate that duplicate spots are not inserted.

Parameters:

data - The raw data to insert

externalReporterId - The external id of the reporter expected to be found at the feature of this spot, or null to use the reporter attached to the feature

externalFeatureId - The feature ID of the feature if the FeatureIdentificationMethod.FEATURE_ID identification method is used

Throws:

BaseException - If the insertion failed

Since:

2.6

doInsert

private void doInsert(RawData data,
                      String externalReporterId,
                      String externalFeatureId,
                      boolean validateReporterId)
               throws BaseException

Do the actual insert.

Throws:

BaseException

newRawData

public RawData newRawData()
                   throws BaseException

Create a new raw data object. After you have set all properties, use one of the insert(RawData) or insert(RawData, String) methods to insert the raw data. You do not have to set the reporter if the raw bioassay is connected to an array design.

Returns:

A raw data object

Throws:

BaseException - If there is an error

deleteAll

void deleteAll()
         throws BaseException

Delete all raw data.

Throws:

BaseException

See Also:

RawBioAssay.deleteRawData()