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1 package de.mpiwg.anteater.species.common.impl;
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2
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3 import java.io.InputStream;
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4 import java.util.HashMap;
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5 import java.util.List;
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6 import java.util.Map;
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7
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3
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8 import org.apache.commons.lang3.StringEscapeUtils;
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9
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2
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10 import uk.ac.man.documentparser.dataholders.Document;
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11 import uk.ac.man.entitytagger.Mention;
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12 import uk.ac.man.entitytagger.doc.TaggedDocument;
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13 import uk.ac.man.entitytagger.matching.MatchOperations;
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14 import uk.ac.man.entitytagger.matching.Matcher;
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15 import uk.ac.man.entitytagger.matching.Matcher.Disambiguation;
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16 import uk.ac.man.entitytagger.matching.Postprocessor;
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17 import uk.ac.man.entitytagger.matching.matchers.MatchPostProcessor;
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18 import uk.ac.man.entitytagger.matching.matchers.VariantDictionaryMatcher;
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19 import de.mpiwg.anteater.logging.IAnteaterLogger;
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20 import de.mpiwg.anteater.species.common.ICommonNameFinder;
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21
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22 public class LinnaeusNameFinder implements ICommonNameFinder {
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23
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24 public final static String COMPONENT_NAME = LinnaeusNameFinder.class
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25 .getSimpleName();
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26
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27 private IAnteaterLogger logger;
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28
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29 public LinnaeusNameFinder(IAnteaterLogger logger) {
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30 this.logger = logger;
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31 }
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32
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33 @Override
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34 public String findCommonNames(String text) {
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35 Matcher matcher = VariantDictionaryMatcher.load(getClass()
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36 .getResourceAsStream("resources-linnaeus/species-light.tsv"),
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37 true);
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38
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39 Disambiguation disambiguation = Disambiguation.ON_WHOLE;
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40
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41 matcher = new MatchPostProcessor(matcher, disambiguation, true, null,
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42 getPostprocessor(new HashMap<String, String>(), ""));
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43
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44 matcher.match("test", new Document("none", null, null, null, null,
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45 null, null, null, null, null, null, null, null, null, null));
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46
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47 Document doc = new Document("id", "title", "", text, text, Document.Text_raw_type.TEXT, "", null, Document.Type.OTHER, null, "", "", "", "", null);
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48 TaggedDocument tagged = MatchOperations.matchDocument(matcher, doc);
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49 List<Mention> species = tagged.getAllMatches();
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3
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50 StringBuffer sb = new StringBuffer();
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51 sb.append("<linnaeus>");
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52
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53 for (Mention s : species) {
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54 sb.append("<species id=\"" + StringEscapeUtils.escapeXml(s.getMostProbableID()) + "\" ");
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55 sb.append("start=\"" + s.getStart() + "\" ");
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56 sb.append("end=\"" + s.getEnd() + "\" ");
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57 sb.append("text=\"" + StringEscapeUtils.escapeXml(s.getText()) + "\" ");
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58 sb.append("/>");
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59 }
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60
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61 sb.append("</linnaeus>");
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62 System.out.println(sb.toString());
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63 return sb.toString();
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2
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64 }
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65
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66 public Postprocessor getPostprocessor(Map<String, String> comments,
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67 String tag) {
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68 InputStream stop = getClass().getResourceAsStream(
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69 "resources-linnaeus/stoplist.tsv");
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70 InputStream acr = getClass().getResourceAsStream(
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71 "resources-linnaeus/synonyms-acronyms.tsv");
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72 InputStream spf = getClass().getResourceAsStream(
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73 "resources-linnaeus/species-frequency.tsv");
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74
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75 Postprocessor res = new Postprocessor(new InputStream[] { stop },
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76 new InputStream[] { acr }, new InputStream[] { spf }, comments,
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77 null);
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78
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79 try {
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80 if (stop != null)
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81 stop.close();
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82 if (acr != null)
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83 acr.close();
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84 if (spf != null)
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85 spf.close();
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86 } catch (Exception e) {
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87 System.err.println(e);
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88 e.printStackTrace();
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89 System.exit(0);
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90 }
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91 return res;
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92 }
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93 }
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