adams.flow.transformer
Class RTransformer

java.lang.Object
  adams.core.ConsoleObject
      adams.core.option.AbstractOptionHandler
          adams.flow.core.AbstractActor
              adams.flow.transformer.AbstractTransformer
                  adams.flow.transformer.RTransformer

All Implemented Interfaces:

AdditionalInformationHandler, CleanUpHandler, Debuggable, DebugOutputHandler, Destroyable, OptionHandler, QuickInfoSupporter, ShallowCopySupporter<AbstractActor>, SizeOfHandler, Stoppable, VariableChangeListener, Actor, ErrorHandler, InputConsumer, OutputProducer, Serializable, Comparable

public class RTransformer
extends AbstractTransformer

Carries out an r command on the token passed in. The input can be accessed via 'X'.
Variables are supported as well, e.g. pow(X,@{exp}) with '@{exp}' being a variable available at execution time.
Returns a result from R.

Input/output:
- accepts:
java.lang.Integer
java.lang.String
java.lang.Double
java.lang.Double[]
java.lang.Double[][]
adams.data.spreadsheet.SpreadSheet
- generates:
java.lang.Integer

Valid options are:

-D <int> (property: debugLevel)
    The greater the number the more additional info the scheme may output to 
    the console (0 = off).
    default: 0
    minimum: 0
 

-name <java.lang.String> (property: name)
    The name of the actor.
    default: RTransformer
 

-annotation <adams.core.base.BaseText> (property: annotations)
    The annotations to attach to this actor.
    default: 
 

-skip (property: skip)
    If set to true, transformation is skipped and the input token is just forwarded 
    as it is.
 

-stop-flow-on-error (property: stopFlowOnError)
    If set to true, the flow gets stopped in case this actor encounters an error;
     useful for critical actors.
 

-script <adams.core.scripting.RScript> (property: script)
    Script to pass into r. The input value can be accessed via 'X'.
    default: 
 

-return-type <Integer|Double|DoubleArray|DoubleMatrix|String|DataFrame> (property: returnType)
    Data type of returned object
    default: Integer
 

-data-frame-columns <java.lang.String> (property: dataFrameColumns)
    The comma-separated list of dataframe column names to return only (if return 
    type is DataFrame)
    default: 
 

Version:

$Revision: 6830 $

Author:

rsmith

See Also:

Serialized Form

Field Summary

static String	INPUT the placeholder for the input value.
protected String	m_DataFrameColumns the comma-separated list of dataframe column names in case of .
protected org.rosuda.REngine.Rserve.RConnection	m_RConn Connection to Rserve
protected Object	m_returnedObject Object returned from r
protected RDataType	m_returnType Data type of object returned from r script
protected Rserve	m_Rserve the Rserve actor.
protected RScript	m_Script Script to pass to r

Fields inherited from class adams.flow.transformer.AbstractTransformer

BACKUP_INPUT, BACKUP_OUTPUT, m_InputToken, m_OutputToken

Fields inherited from class adams.flow.core.AbstractActor

m_Annotations, m_BackupState, m_DetectedObjectVariables, m_DetectedVariables, m_ErrorHandler, m_Executed, m_Executing, m_ExecutionListeningSupporter, m_FullName, m_Headless, m_Name, m_Parent, m_Root, m_ScopeHandler, m_Self, m_Skip, m_StopFlowOnError, m_StopMessage, m_Stopped, m_StorageHandler, m_VariablesUpdated

Fields inherited from class adams.core.option.AbstractOptionHandler

m_DebugLevel, m_OptionManager

Fields inherited from interface adams.flow.core.Actor

FILE_EXTENSION, FILE_EXTENSION_GZ

Constructor Summary

RTransformer()

Method Summary

Class[]	accepts() List of classes that can be used as input.
String	dataFrameColumnsTipText() A description of the return type.
void	defineOptions() Adds to the internal list of options.
protected String	doExecute() Executes the flow, including reading the input and returning R's output.
Class[]	generates() List of classes this flow can return.
String	getDataFrameColumns() Returns the comma-separated list of dataframe column names to retrieve only.
String	getQuickInfo() Returns a quick info about the actor, which will be displayed in the GUI.
RDataType	getReturnType() Gets the type of object this flow returns.
RScript	getScript() Gets the script.
String	globalInfo() Info about this flow.
boolean	hasPendingOutput() Returns true if the is pending output.
Token	output() Turns the returned object into a token to be passed through the system.
protected void	reset() Ressets the members.
String	returnTypeTipText() Tool tip about the return type.
String	scriptTipText() Tool tip about the script.
void	setDataFrameColumns(String value) Sets the comma-separated list of dataframe column names to retrieve only.
void	setReturnType(RDataType val) Sets the type of object this flow returns.
void	setScript(RScript val) Sets the script.
String	setUp() Sets up the connection to Rserve.
void	wrapUp() Closes the Rserve connection as the flow finishes.

Methods inherited from class adams.flow.transformer.AbstractTransformer

backupState, execute, input, postExecute, restoreState

Methods inherited from class adams.flow.core.AbstractActor

annotationsTipText, canInspectOptions, canPerformSetUpCheck, cleanUp, compareTo, debug, destroy, equals, findVariables, findVariables, findVariables, forceVariables, forCommandLine, forName, getAdditionalInformation, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowActors, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, handleException, hasErrorHandler, hasStopMessage, index, initialize, isBackedUp, isExecuted, isExecuting, isFinished, isHeadless, isStopped, nameTipText, performSetUpChecks, preExecute, pruneBackup, pruneBackup, setAnnotations, setErrorHandler, setHeadless, setName, setParent, setSkip, setStopFlowOnError, setVariables, shallowCopy, shallowCopy, sizeOf, skipTipText, stopExecution, stopExecution, stopFlowOnErrorTipText, updateDetectedVariables, updatePrefix, updateVariables, variableChanged

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, debug, debugLevelTipText, finishInit, getDebugLevel, getOptionManager, isDebugOn, newOptionManager, setDebugLevel, toCommandLine, toString

Methods inherited from class adams.core.ConsoleObject

getDebugging, getSystemErr, getSystemOut

Methods inherited from class java.lang.Object

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

Methods inherited from interface adams.flow.core.Actor

cleanUp, compareTo, debug, destroy, equals, findVariables, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, hasErrorHandler, hasStopMessage, index, isExecuted, isFinished, isHeadless, isStopped, setAnnotations, setErrorHandler, setHeadless, setName, setParent, setSkip, setStopFlowOnError, setVariables, sizeOf, stopExecution, stopExecution, variableChanged

Methods inherited from interface adams.core.AdditionalInformationHandler

getAdditionalInformation

Methods inherited from interface adams.core.option.OptionHandler

cleanUpOptions, getOptionManager

Field Detail

m_Script

protected RScript m_Script

Script to pass to r

INPUT

public static final String INPUT

the placeholder for the input value.

See Also:

Constant Field Values

m_returnType

protected RDataType m_returnType

Data type of object returned from r script

m_DataFrameColumns

protected String m_DataFrameColumns

the comma-separated list of dataframe column names in case of .

m_returnedObject

protected Object m_returnedObject

Object returned from r

m_RConn

protected org.rosuda.REngine.Rserve.RConnection m_RConn

Connection to Rserve

m_Rserve

protected Rserve m_Rserve

the Rserve actor.

Constructor Detail

RTransformer

public RTransformer()

Method Detail

globalInfo

public String globalInfo()

Info about this flow.

Specified by:

globalInfo in class AbstractOptionHandler

defineOptions

public void defineOptions()

Adds to the internal list of options.

Specified by:

defineOptions in interface OptionHandler

Overrides:

defineOptions in class AbstractActor

reset

protected void reset()

Ressets the members.

Overrides:

reset in class AbstractTransformer

setScript

public void setScript(RScript val)

Sets the script.

Parameters:

val - the script

getScript

public RScript getScript()

Gets the script.

Returns:

the script

scriptTipText

public String scriptTipText()

Tool tip about the script.

Returns:

tool tip message

setReturnType

public void setReturnType(RDataType val)

Sets the type of object this flow returns.

Parameters:

val - the type of object

getReturnType

public RDataType getReturnType()

Gets the type of object this flow returns.

Returns:

the type of object

returnTypeTipText

public String returnTypeTipText()

Tool tip about the return type.

Returns:

the tip

setDataFrameColumns

public void setDataFrameColumns(String value)

Sets the comma-separated list of dataframe column names to retrieve only.

Parameters:

value - the comma-separated list

getDataFrameColumns

public String getDataFrameColumns()

Returns the comma-separated list of dataframe column names to retrieve only.

Returns:

the comma-separated list

dataFrameColumnsTipText

public String dataFrameColumnsTipText()

A description of the return type.

Returns:

string description

getQuickInfo

public String getQuickInfo()

Returns a quick info about the actor, which will be displayed in the GUI.

Specified by:

getQuickInfo in interface QuickInfoSupporter

Specified by:

getQuickInfo in interface Actor

Overrides:

getQuickInfo in class AbstractActor

Returns:

null if no info available, otherwise short string

accepts

public Class[] accepts()

List of classes that can be used as input.

generates

public Class[] generates()

List of classes this flow can return.

output

public Token output()

Turns the returned object into a token to be passed through the system.

Specified by:

output in interface OutputProducer

Overrides:

output in class AbstractTransformer

hasPendingOutput

public boolean hasPendingOutput()

Returns true if the is pending output.

Specified by:

hasPendingOutput in interface OutputProducer

Overrides:

hasPendingOutput in class AbstractTransformer

setUp

public String setUp()

Sets up the connection to Rserve.

Specified by:

setUp in interface Actor

Overrides:

setUp in class AbstractActor

doExecute

protected String doExecute()

Executes the flow, including reading the input and returning R's output.

Specified by:

doExecute in class AbstractActor

wrapUp

public void wrapUp()

Closes the Rserve connection as the flow finishes.

Specified by:

wrapUp in interface Actor

Overrides:

wrapUp in class AbstractTransformer