001/** 
002 * Copyright (c) 2007-2008, Regents of the University of Colorado 
003 * All rights reserved.
004 * 
005 * Redistribution and use in source and binary forms, with or without
006 * modification, are permitted provided that the following conditions are met:
007 * 
008 * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 
009 * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 
010 * Neither the name of the University of Colorado at Boulder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 
011 * 
012 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
013 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
014 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
015 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
016 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
017 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
018 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
019 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
020 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
021 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
022 * POSSIBILITY OF SUCH DAMAGE. 
023 */
024package org.cleartk.corpus.ace2005;
025
026import java.io.File;
027import java.io.FileOutputStream;
028import java.io.IOException;
029
030import org.apache.uima.UimaContext;
031import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
032import org.apache.uima.cas.FSIterator;
033import org.apache.uima.cas.FeatureStructure;
034import org.apache.uima.jcas.JCas;
035import org.apache.uima.jcas.cas.FSArray;
036import org.apache.uima.jcas.tcas.Annotation;
037import org.apache.uima.resource.ResourceInitializationException;
038import org.cleartk.ne.type.Ace2005Document;
039import org.cleartk.ne.type.NamedEntity;
040import org.cleartk.ne.type.NamedEntityMention;
041import org.cleartk.util.ViewUriUtil;
042import org.jdom2.Document;
043import org.jdom2.Element;
044import org.jdom2.output.Format;
045import org.jdom2.output.XMLOutputter;
046import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
047import org.apache.uima.fit.descriptor.ConfigurationParameter;
048import org.apache.uima.fit.util.JCasUtil;
049
050/**
051 * <br>
052 * Copyright (c) 2007-2008, Regents of the University of Colorado <br>
053 * All rights reserved.
054 * 
055 * 
056 * @author Philip Ogren
057 * 
058 */
059
060public class Ace2005Writer extends JCasAnnotator_ImplBase {
061
062  public static final String PARAM_OUTPUT_DIRECTORY_NAME = "outputDirectoryName";
063
064  @ConfigurationParameter(
065      name = PARAM_OUTPUT_DIRECTORY_NAME,
066      mandatory = true,
067      description = "provides the path of the directory where the XML files should be written.")
068  private String outputDirectoryName;
069
070  private File outputDirectory;
071
072  private int idIndex = 0;
073
074  @Override
075  public void initialize(UimaContext context) throws ResourceInitializationException {
076    super.initialize(context);
077
078    outputDirectory = new File(outputDirectoryName);
079    if (!outputDirectory.exists()) {
080      outputDirectory.mkdirs();
081    }
082  }
083
084  private Element createExtentElement(String elementName, Annotation annotation) {
085    Element extent = new Element(elementName);
086    Element charseq = new Element("charseq");
087    charseq.setAttribute("START", "" + annotation.getBegin());
088    charseq.setAttribute("END", "" + (annotation.getEnd() - 1));
089    charseq.setText(annotation.getCoveredText());
090    extent.addContent(charseq);
091    return extent;
092  }
093
094  @Override
095  public void process(JCas jCas) throws AnalysisEngineProcessException {
096    String uri = new File(ViewUriUtil.getURI(jCas)).getName();
097    String docId = uri.substring(0, uri.indexOf(".sgm"));
098    Ace2005Document document;
099    document = JCasUtil.select(jCas, Ace2005Document.class).iterator().next();
100
101    Document xml = new Document();
102
103    Element sourceFileElement = new Element("source_file");
104    sourceFileElement.setAttribute("URI", uri);
105    sourceFileElement.setAttribute("SOURCE", document.getAceSource());
106    sourceFileElement.setAttribute("TYPE", document.getAceType());
107    xml.addContent(sourceFileElement);
108
109    Element documentElement = new Element("document");
110    documentElement.setAttribute("DOCID", docId);
111    sourceFileElement.addContent(documentElement);
112
113    FSIterator<FeatureStructure> namedEntities = jCas.getFSIndexRepository().getAllIndexedFS(
114        jCas.getCasType(NamedEntity.type));
115    while (namedEntities.hasNext()) {
116      NamedEntity namedEntity = (NamedEntity) namedEntities.next();
117      Element namedEntityElement = new Element("entity");
118      namedEntityElement.setAttribute("ID", "" + idIndex++);
119      namedEntityElement.setAttribute("TYPE", namedEntity.getEntityType());
120      String entitySubtype = namedEntity.getEntitySubtype();
121      if (entitySubtype != null)
122        namedEntityElement.setAttribute("SUBTYPE", entitySubtype);
123      String entityClass = namedEntity.getEntityClass();
124      if (entityClass != null)
125        namedEntityElement.setAttribute("CLASS", entityClass);
126
127      FSArray namedEntityMentions = namedEntity.getMentions();
128      for (int i = 0; i < namedEntityMentions.size(); i++) {
129        NamedEntityMention namedEntityMention = (NamedEntityMention) namedEntityMentions.get(i);
130        Element namedEntityMentionElement = new Element("entity_mention");
131        namedEntityMentionElement.setAttribute("ID", "" + idIndex++);
132        namedEntityMentionElement.setAttribute("TYPE", namedEntityMention.getMentionType());
133
134        namedEntityMentionElement.addContent(createExtentElement(
135            "extent",
136            namedEntityMention.getAnnotation()));
137        namedEntityMentionElement.addContent(createExtentElement(
138            "head",
139            namedEntityMention.getHead()));
140        namedEntityElement.addContent(namedEntityMentionElement);
141      }
142      documentElement.addContent(namedEntityElement);
143    }
144
145    XMLOutputter xmlOut = new XMLOutputter(Format.getPrettyFormat());
146    try {
147      FileOutputStream stream = new FileOutputStream(new File(outputDirectory, docId
148          + ".cleartk.xml"));
149      xmlOut.output(xml, stream);
150      stream.close();
151    } catch (IOException e) {
152      throw new AnalysisEngineProcessException(e);
153    }
154
155  }
156
157  public void setOutputDirectoryName(String outputDirectoryName) {
158    this.outputDirectoryName = outputDirectoryName;
159  }
160
161}