Initializing and using clinical pipleline from java

[Mansour Al Akeel]

I am using the following code to test initialization for the clinical
annotator from a junit test case:


    AnalysisEngineDescription description =
UmlsDictionaryLookupAnnotator.createAnnotatorDescription();

    AnalysisEngine ae = UIMAFramework.produceAnalysisEngine(description);

    URL testFile = this.getClass().getResource("/clinical-text-1.txt");

    byte[] encoded = Files.readAllBytes(Paths.get(testFile.toURI()));

    String encoding = "UTF-8";

    String textContent = new String(encoded, encoding);

    JCas jcas = ae.newJCas();

    jcas.setDocumentText(textContent);

    long start = System.currentTimeMillis();
    ae.process(jcas);
    long end = System.currentTimeMillis();

    System.out.println("processing done in : " + ((end - start) / 1000.0));

    XmlCasSerializer.serialize(jcas.getCas(), System.out);

    jcas.reset();


The output is produced, however, there's no annotations added, and no
error or exception is thrown.

Am I missing something here??

Thank you.