org.gcube.dataanalysis.executor.rscripts.generic

Class GenericRScript

java.lang.Object

org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm

org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm

org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript

All Implemented Interfaces:

org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent, org.gcube.dataanalysis.ecoengine.interfaces.Transducerer

Direct Known Subclasses:

KnitrCompiler, TemplateRScripts

public abstract class GenericRScript
extends StandardLocalInfraAlgorithm

Field Summary

Fields

Modifier and Type	Field and Description
protected List<String>	environmentalvariables
protected List<String>	inputvariables
protected String	mainScriptName
protected LinkedHashMap<String,org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType>	output
protected HashMap<String,String>	outputValues
protected List<String>	outputvariables
protected String	packageURL

Fields inherited from class org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm

config, inputs, outputParameters, resourceManager, status

Constructor Summary

Constructors

Constructor and Description
GenericRScript()

Method Summary

Methods

Modifier and Type	Method and Description
protected String	analyseContent(String filecontent, String scriptfolder)
protected String	generateRemoteLogFile(String Rlog)
org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType	getOutput()
void	init()
protected void	initVariables()
protected void	process()
protected File	saveLogFile(String Rlog)
protected void	setInputParameters()
void	shutdown()

Methods inherited from class org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalInfraAlgorithm

sendNotification

Methods inherited from class org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm

addBooleanInput, addDoubleInput, addEnumerateInput, addFileInput, addIntegerInput, addOutputString, addRemoteDatabaseInput, addStringInput, compute, getDescription, getInfrastructure, getInputParameter, getInputParameters, getResourceLoad, getResources, getStatus, log, setConfiguration

Methods inherited from class java.lang.Object

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

Field Detail

outputValues

protected HashMap<String,String> outputValues

output

protected LinkedHashMap<String,org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType> output

mainScriptName

protected String mainScriptName

packageURL

protected String packageURL

environmentalvariables

protected List<String> environmentalvariables

inputvariables

protected List<String> inputvariables

outputvariables

protected List<String> outputvariables

Constructor Detail

GenericRScript

public GenericRScript()

Method Detail

shutdown

public void shutdown()

Specified by:

shutdown in interface org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent

Specified by:

shutdown in class org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm

init

public void init()
          throws Exception

Specified by:

init in interface org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent

Specified by:

init in class org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm

Throws:

Exception

process

protected void process()
                throws Exception

Specified by:

process in class org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm

Throws:

Exception

saveLogFile

protected File saveLogFile(String Rlog)
                    throws Exception

Throws:

Exception

generateRemoteLogFile

protected String generateRemoteLogFile(String Rlog)
                                throws Exception

Throws:

Exception

analyseContent

protected String analyseContent(String filecontent,
                    String scriptfolder)
                         throws Exception

Throws:

Exception

initVariables

protected void initVariables()

setInputParameters

protected void setInputParameters()

Specified by:

setInputParameters in class org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm

getOutput

public org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType getOutput()

Specified by:

getOutput in interface org.gcube.dataanalysis.ecoengine.interfaces.ComputationalAgent

Overrides:

getOutput in class org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm