[UIMA-3357] CONTAINS fails when running script as AE in a pipeline with a new CAS

• Type: Bug
• Status: Closed
• Priority: Minor
• Resolution: Fixed
• Affects Version/s: 2.0.1ruta, 2.1.0ruta
• Fix Version/s: 2.2.0ruta
• Component/s: Ruta, uimaFIT
• Assignee: Peter Klügl
• Reporter: Daniel Maeurer
• Created: 21/Oct/13 10:18
• Updated: 09/Dec/13 10:25
• Resolved: 09/Dec/13 10:25

Description

When running my Ruta script as an analysis engine in a pipeline, it does not work correctly when creating a new CAS and processing the pipeline a second time with the new CAS.
While reusing the old cas with "cas.reset()" is working, creating a new CAS results in failing rules including "CONTAINS" in the ruta script.

The ruta script used in the example:

mystic.ruta

PACKAGE de.tudarmstadt.algo.vpino.ruta;
DECLARE test;
Document{CONTAINS(CW)->MARK(test)};

The following Java class can reproduce the error. It creates four xmi files. The last xmi file is missing the annotations created with rules including "CONTAINS".

MysticPipe.java

package org.uimafit.pipeline;

import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.List;

import org.apache.uima.UIMAFramework;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.impl.XmiCasSerializer;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.fit.pipeline.SimplePipeline;
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.resource.metadata.ResourceMetaData;
import org.apache.uima.util.CasCreationUtils;
import org.apache.uima.util.InvalidXMLException;
import org.apache.uima.util.XMLInputSource;
import org.apache.uima.util.XMLSerializer;
import org.xml.sax.SAXException;

public class MysticPipe {

	public static void main(String[] args) throws Exception {
		working("This is a test.", initPipeline());
		failing("This is a test.", initPipeline());
	}

	private static AnalysisEngine initPipeline() throws ResourceInitializationException, IOException, InvalidXMLException {
		File specFile = new File("./descriptor/de/tudarmstadt/algo/vpino/ruta/mysticEngine.xml");
		XMLInputSource in = new XMLInputSource(specFile);
		AnalysisEngineDescription ruta = (AnalysisEngineDescription) UIMAFramework.getXMLParser().parseResourceSpecifier(in);
		return AnalysisEngineFactory.createEngine(ruta);
	}

	private static void working(String input, AnalysisEngine theEngine) throws ResourceInitializationException, AnalysisEngineProcessException, IOException,
	        SAXException {
		final List<ResourceMetaData> metaData = new ArrayList<ResourceMetaData>();
		metaData.add(theEngine.getMetaData());
		final CAS cas = CasCreationUtils.createCas(metaData);
		System.out.println("create a new cas...");
		cas.setDocumentLanguage("de");
		cas.setDocumentText(input);
		SimplePipeline.runPipeline(cas, theEngine);
		writeXmiFile(cas, "works_test1");//CHECK
		//THE DIFFERENCE
		cas.reset();
		//END DIFFERENCE
		System.out.println("create a new cas...");
		cas.setDocumentLanguage("de");
		cas.setDocumentText(input);
		SimplePipeline.runPipeline(cas, theEngine);
		writeXmiFile(cas, "works_test2");//CHECK
	}

	private static void failing(String input, AnalysisEngine theEngine) throws ResourceInitializationException, AnalysisEngineProcessException, IOException,
	        SAXException {
		final List<ResourceMetaData> metaData = new ArrayList<ResourceMetaData>();
		metaData.add(theEngine.getMetaData());
		final CAS cas = CasCreationUtils.createCas(metaData);
		System.out.println("create a new cas...");
		cas.setDocumentLanguage("de");
		cas.setDocumentText(input);
		SimplePipeline.runPipeline(cas, theEngine);
		writeXmiFile(cas, "works_test3"); // CHECK
		//THE DIFFERENCE
		final CAS cas2 = CasCreationUtils.createCas(metaData);
		//END DIFFERENCE
		System.out.println("create a new cas...");
		cas2.setDocumentLanguage("de");
		cas2.setDocumentText(input);
		SimplePipeline.runPipeline(cas2, theEngine);
		writeXmiFile(cas2, "fail_test4"); //FAIL
		return;
	}
	
	public static void writeXmiFile(CAS aCas, String Fname) throws IOException, SAXException {
		File outFile = new File("output", Fname + ".xmi");
		OutputStream out = null;

		try {
			// out = new StringOutputStream();
			out = new FileOutputStream(outFile);
			XmiCasSerializer ser = new XmiCasSerializer(aCas.getTypeSystem());
			XMLSerializer xmlSer = new XMLSerializer(out, false);
			ser.serialize(aCas, xmlSer.getContentHandler());
		} finally {
			if (out != null) {
				out.close();
			}
		}
	}
}