gov.nih.nci.caarray.services.bioassaydata
Class IlluminaDbDataHanderDataSource

java.lang.Object
  extended by gov.nih.nci.caarray.services.bioassaydata.IlluminaDbDataHanderDataSource

public class IlluminaDbDataHanderDataSource
extends java.lang.Object


Constructor Summary
IlluminaDbDataHanderDataSource()
           
 
Method Summary
 void close(java.sql.Connection connection)
          Closes a JDBC connection.
 void close(java.sql.Statement statement)
          Closes a JDBC statement.
protected  gov.nih.nci.caarray.services.bioassaydata.DataHandlerDataSourceManagerDB createDataHandlerDataSourceManagerDB()
           
 CompositeSequenceDimension getCompositeSequenceDimension(ArrayDesign arrayDesign)
          Looks up an existing CompositeSequenceDimension for this array design.
 java.util.List<CompositeSequence> getCompositeSequences(CompositeGroup compositeGroup)
          Retrieve partial attributes of Feature only (id & identifier fields)
 java.util.List<CompositeSequence> getCompositeSequences(CompositeSequenceDimension dimension)
          Retrieve partial attributes of CompositeSequence only (id & identifier fields)
 java.sql.Connection getConnection()
          Returns a JDBC database connection to use to store raw data.
 java.util.List<Feature> getContainedFeatures(FeatureDimension dimension)
          Retrieve partial attributes of Feature only (id)
 FeatureDimension getFeatureDimension(ArrayDesign arrayDesign)
          Looks up an existing FeatureDimension for this array design.
 java.util.List<Feature> getFeatures(FeatureGroup featureGroup)
          Retrieve partial attributes of Feature only (id & identifier fields)
 java.util.List<Feature> getFeaturesWithLoacationAndZone(FeatureGroup featureGroup)
           
 QuantitationType getQuantitationType(QuantitationTypeDescriptor descriptor)
          Returns the quantitation type corresponding to the identifier provided.
 ReporterDimension getReporterDimension(ArrayDesign arrayDesign)
          Looks up an existing ReporterDimension for this array design.
 java.util.List<Reporter> getReporters(ReporterDimension dimension)
          Retrieve partial attributes of Reporter only (id )
 QuantitationType instantiate(QuantitationTypeDescriptor descriptor)
           
 void linkToExperiment(BioAssayData bioAssayData, Experiment experiment)
           
 void linkToExperiment(BioAssay bioAssay, Experiment experiment)
          Associates a BioAssay to an Experiment
 QuantitationType lookupQuantitationType(QuantitationTypeDescriptor descriptor)
           
 void save(BioAssay bioAssay)
          Saves the given BioAssay and its related elements.
 void save(DesignElement designElement)
          Saves the given DesignElement and its related elements.
 void setNewDesignElementDimensionOnCreateManagerDBForNextCreateOnly(boolean newDesignElementDimensionOnCreateManagerDBForNextCreateOnly)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

IlluminaDbDataHanderDataSource

public IlluminaDbDataHanderDataSource()
Method Detail

createDataHandlerDataSourceManagerDB

protected gov.nih.nci.caarray.services.bioassaydata.DataHandlerDataSourceManagerDB createDataHandlerDataSourceManagerDB()

setNewDesignElementDimensionOnCreateManagerDBForNextCreateOnly

public void setNewDesignElementDimensionOnCreateManagerDBForNextCreateOnly(boolean newDesignElementDimensionOnCreateManagerDBForNextCreateOnly)

getQuantitationType

public QuantitationType getQuantitationType(QuantitationTypeDescriptor descriptor)
                                     throws DataHandlerDataSourceException
Returns the quantitation type corresponding to the identifier provided.

Parameters:
descriptor - the quantitation type identifier.
Returns:
the matching QuantitationType.
Throws:
DataHandlerDataSourceException

instantiate

public QuantitationType instantiate(QuantitationTypeDescriptor descriptor)

lookupQuantitationType

public QuantitationType lookupQuantitationType(QuantitationTypeDescriptor descriptor)
                                        throws DataHandlerDataSourceException
Throws:
DataHandlerDataSourceException

getConnection

public java.sql.Connection getConnection()
                                  throws DataHandlerDataSourceException
Returns a JDBC database connection to use to store raw data.

Returns:
the database connection.
Throws:
DataHandlerDataSourceException

save

public void save(BioAssay bioAssay)
          throws DataHandlerDataSourceException
Saves the given BioAssay and its related elements.

Parameters:
bioAssay - the BioAssay to save.
Throws:
DataHandlerDataSourceException

close

public void close(java.sql.Connection connection)
Closes a JDBC connection.

Parameters:
connection - the connection to close.

close

public void close(java.sql.Statement statement)
Closes a JDBC statement.

Parameters:
statement - the statement to close.

save

public void save(DesignElement designElement)
          throws DataHandlerDataSourceException
Saves the given DesignElement and its related elements.

Throws:
DataHandlerDataSourceException

getFeatureDimension

public FeatureDimension getFeatureDimension(ArrayDesign arrayDesign)
                                     throws DataHandlerDataSourceException
Looks up an existing FeatureDimension for this array design.

Throws:
DataHandlerDataSourceException

getReporterDimension

public ReporterDimension getReporterDimension(ArrayDesign arrayDesign)
                                       throws DataHandlerDataSourceException
Looks up an existing ReporterDimension for this array design.

Throws:
DataHandlerDataSourceException

getCompositeSequenceDimension

public CompositeSequenceDimension getCompositeSequenceDimension(ArrayDesign arrayDesign)
                                                         throws DataHandlerDataSourceException
Looks up an existing CompositeSequenceDimension for this array design.

Throws:
DataHandlerDataSourceException

linkToExperiment

public void linkToExperiment(BioAssay bioAssay,
                             Experiment experiment)
                      throws DataHandlerDataSourceException
Associates a BioAssay to an Experiment

Throws:
DataHandlerDataSourceException

linkToExperiment

public void linkToExperiment(BioAssayData bioAssayData,
                             Experiment experiment)
                      throws DataHandlerDataSourceException
Throws:
DataHandlerDataSourceException

getFeatures

public java.util.List<Feature> getFeatures(FeatureGroup featureGroup)
                                    throws DataHandlerDataSourceException
Retrieve partial attributes of Feature only (id & identifier fields)

Returns:
Throws:
DataHandlerDataSourceException

getCompositeSequences

public java.util.List<CompositeSequence> getCompositeSequences(CompositeGroup compositeGroup)
                                                        throws DataHandlerDataSourceException
Retrieve partial attributes of Feature only (id & identifier fields)

Returns:
Throws:
DataHandlerDataSourceException

getContainedFeatures

public java.util.List<Feature> getContainedFeatures(FeatureDimension dimension)
                                             throws DataHandlerDataSourceException
Retrieve partial attributes of Feature only (id)

Returns:
Throws:
DataHandlerDataSourceException

getReporters

public java.util.List<Reporter> getReporters(ReporterDimension dimension)
                                      throws DataHandlerDataSourceException
Retrieve partial attributes of Reporter only (id )

Returns:
Throws:
DataHandlerDataSourceException

getCompositeSequences

public java.util.List<CompositeSequence> getCompositeSequences(CompositeSequenceDimension dimension)
                                                        throws DataHandlerDataSourceException
Retrieve partial attributes of CompositeSequence only (id & identifier fields)

Returns:
Throws:
DataHandlerDataSourceException

getFeaturesWithLoacationAndZone

public java.util.List<Feature> getFeaturesWithLoacationAndZone(FeatureGroup featureGroup)
                                                        throws DataHandlerDataSourceException
Returns:
Throws:
DataHandlerDataSourceException