50 lines
1.9 KiB
Java
50 lines
1.9 KiB
Java
package org.gcube.dataanalysis.executor.rscripts;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.LinkedHashMap;
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import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
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import org.gcube.dataanalysis.executor.rscripts.generic.GenericRScript;
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public class KnitrCompiler extends GenericRScript {
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public static enum operators {
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EQUAL, NOT_EQUAL, CONTAINS, BEGINS_WITH, ENDS_WITH
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};
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@Override
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public String getDescription() {
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return "An algorithm to compile Knitr documents. Developed by IRD (reference Julien Bard, julien.barde@ird.fr)";
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}
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protected void initVariables(){
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mainScriptName="IRDTunaAtlas-master/report/knitr/compileKnitR_CNR.R";
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packageURL="http://goo.gl/T7V8LV";
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environmentalvariables = new ArrayList<String>();
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inputvariables.add("zipfile");
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inputvariables.add("file.inout");
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outputvariables.add("pdfresult");
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}
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@Override
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protected void setInputParameters() {
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inputs.add(new PrimitiveType(Enum.class.getName(), operators.values(), PrimitiveTypes.ENUMERATED, name, description, defaultvalue));
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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"));
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inputs.add(new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "file.inout", "The name of the R file in the zip package", "main.r"));
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}
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@Override
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public StatisticalType getOutput() {
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output.put("pdfresult",new PrimitiveType(File.class.getName(), new File(outputValues.get("pdfresult")), PrimitiveTypes.FILE, "pdfresult", "The compiled PDF file"));
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PrimitiveType o = new PrimitiveType(LinkedHashMap.class.getName(), output, PrimitiveTypes.MAP, "Output", "");
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return o;
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}
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}
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