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ecological-engine-smart-executor
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineSmartExecutor@122176 82a268e6-3cf1-43bd-a215-b396298e98cf

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Gianpaolo Coro 2016-01-10 18:51:15 +00:00
parent da5ee5cbb2
commit 627ce098b3
1 changed files with 42 additions and 0 deletions
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src/main/java/org/gcube/dataanalysis/executor/rscripts/KnitrCompiler.java Normal file
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package org.gcube.dataanalysis.executor.rscripts;
import java.io.File;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript;
public class KnitrCompiler extends GenericRScript {
@Override
public String getDescription() {
return "An algorithm to compile Knitr documents. Developed by IRD (reference Julien Bard, julien.barde@ird.fr)";
}
protected void initVariables(){
mainScriptName="IRDTunaAtlas-master/report/knitr/compileKnitR_CNR.R";
packageURL="http://goo.gl/T7V8LV";
environmentalvariables = new ArrayList<String>();
inputvariables.add("zipfile");
inputvariables.add("file.inout");
outputvariables.add("pdfresult");
}
@Override
protected void setInputParameters() {
inputs.add(new PrimitiveType(File.class.getName(), null, PrimitiveTypes.FILE, "zipfile", "The file containing R and the markdown (Rnw) files to compile","knitr_wfs.zip"));
inputs.add(new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "file.inout", "The name of the R file in the zip package", "main.r"));
}
@Override
public StatisticalType getOutput() {
output.put("pdfresult",new PrimitiveType(File.class.getName(), new File(outputValues.get("pdfresult")), PrimitiveTypes.FILE, "pdfresult", "The compiled PDF file"));
PrimitiveType o = new PrimitiveType(LinkedHashMap.class.getName(), output, PrimitiveTypes.MAP, "Output", "");
return o;
}
}