49 lines
2.1 KiB
Java
Executable File
49 lines
2.1 KiB
Java
Executable File
package org.gcube.dataanalysis.executor.nodes.transducers.bionym.implementations.parsers;
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import java.io.File;
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import java.util.HashMap;
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import java.util.List;
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import org.gcube.dataanalysis.executor.nodes.transducers.bionym.abstracts.MatcherInput;
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import org.gcube.dataanalysis.executor.nodes.transducers.bionym.interfaces.Parser;
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import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenFileTools;
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import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters;
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public class YasmeenParser implements Parser{
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public static String parserLib = "YASMEEN-parser-1.2.0.jar";
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protected String sandboxFolder = "./";
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public HashMap<String, String> parameters;
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@Override
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public void init(String sandboxfolder, HashMap<String, String> parameters) {
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this.sandboxFolder = sandboxfolder;
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this.parameters = parameters;
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}
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@Override
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public MatcherInput parse (List<String> rawnames) throws Exception{
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String parserName = parameters.get(YasmeenGlobalParameters.parserNameParam);
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String inputFileName = parameters.get(YasmeenGlobalParameters.parserInputFileParam);
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String outputFileName = parameters.get(YasmeenGlobalParameters.parserOutputFileParam);
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Boolean preparsing = Boolean.valueOf(parameters.get(YasmeenGlobalParameters.activatePreParsingProcessing));
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YasmeenFileTools.writeYasmeenParserInput(sandboxFolder, inputFileName, rawnames);
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if (parserName==null || parserName.equalsIgnoreCase(YasmeenGlobalParameters.BuiltinParsers.NONE.name()) )
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parserName = "IDENTITY";
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String execution = "java -Xmx512m -Xmx1024m -jar "+new File(sandboxFolder,parserLib)+" -inFile "+new File(sandboxFolder,inputFileName).getAbsolutePath()+" -outFile "+new File(sandboxFolder,outputFileName).getAbsolutePath()+" -parser "+parserName;
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if (preparsing)
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execution+= " -preParsingRuleset commonPreparsingRules -preParsingRuleset bionymPreparsingRules -postParsingRuleset bionymPostparsingRules";
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YasmeenFileTools.callYasmeen(execution);
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MatcherInput input = YasmeenFileTools.getYasmeenParserOutput(sandboxFolder, outputFileName);
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return input;
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}
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}
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