Package org.mitre.medfacts.i2b2.cli

Examples of org.mitre.medfacts.i2b2.cli.BatchRunner.execute()

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      b.processEnabledFeaturesFile(featuresFile);

      b.setRunConfiguration(currentRunConfiguration);

      b.execute();

      logger.info(String.format("====== END RUN # %d WITH %d FILES IN TRAINING SET =====", i, size));
      i++;
    }
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       File negationCueFile = new File(negationCueFileUri);
       System.out.format("negation cue list url: %s%n", negationCueFile);

       CueListScanner scanner = new CueListScanner(negationCueFile, CueWordType.NEGATION);
       scanner.setTextLookup(textLookup);
       scanner.execute();
       List<Annotation> annotationList = scanner.getAnnotationList();
       System.out.println("ANNOTATIONS:");
       if (annotationList == null)
       {
         System.out.println("no annotations returned.");
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       File negationCueFile = new File(negationCueFileUri);
       System.out.format("negation cue list url: %s%n", negationCueFile);

       CueListScanner scanner = new CueListScanner(negationCueFile, CueWordType.SPECULATION);
       scanner.setTextLookup(textLookup);
       scanner.execute();
       List<Annotation> annotationList = scanner.getAnnotationList();
       System.out.println("ANNOTATIONS:");
       if (annotationList == null)
       {
         System.out.println("no annotations returned.");
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      InputStreamReader inputStreamReader = new InputStreamReader(cueFileInputStream);
      BufferedReader bufferedReader = new BufferedReader(inputStreamReader);

      CueListScanner scanner = new CueListScanner(bufferedReader, cueWordType);
      scanner.setTextLookup(textLookup);
      scanner.execute();
      annotationList = scanner.getAnnotationList();

      bufferedReader.close();
      inputStreamReader.close();
      cueFileInputStream.close();
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