@Override
protected List<Keyterm> getKeyterms(String question) {
String document = question;
System.out.println("CHECK " + question);
// int indexSpace = documentLine.indexOf(' ');
// String docID = documentLine.substring(0, indexSpace);
// String document = documentLine.substring(indexSpace + 1);
Chunker extractor = null;
try {
extractor = (Chunker) AbstractExternalizable.readObject(modelFile);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (ClassNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
List<Keyterm> keyterms = new ArrayList<Keyterm>();
Chunking entities = extractor.chunk(document);
for (Chunk ne : entities.chunkSet()) {
// Annotations
String keyWord = question.substring(ne.start(), ne.end());
keyterms.add(new Keyterm(keyWord));
}
// store the keyterms from chunker here from annotator
return keyterms;
}
/**
* Initializes this resource
*
* @return Resource
* @throws ResourceInstantiationException
*/
@SuppressWarnings("rawtypes")
public Resource init() throws ResourceInstantiationException {
if (modelFileUrl == null) throw new ResourceInstantiationException("No model file provided!");
try {
modelFile = new File(modelFileUrl.toURI());
} catch (URISyntaxException e) {
throw new ResourceInstantiationException(e);
}
if (modelFile == null || !modelFile.exists()) {
throw new ResourceInstantiationException(
"modelFile:" + modelFileUrl.toString() + " does not exists");
}
try {
classifier = (LMClassifier) AbstractExternalizable.readObject(modelFile);
} catch (IOException e) {
throw new ResourceInstantiationException(e);
} catch (ClassNotFoundException e) {
throw new ResourceInstantiationException(e);
}
return this;
}
@Override
public void initialize(UimaContext c) throws ResourceInitializationException {
super.initialize(c);
try {
nerModelFile =
new File(
new URI(
AustinMaKeytermExtractor.class
.getResource("/ne-en-bio-genetag.HmmChunker")
.toString()));
chunker = (Chunker) AbstractExternalizable.readObject(nerModelFile);
} catch (IOException e) {
System.err.println("IOException in creating chunker");
throw new ResourceInitializationException(
"Unable to load NER model file", "load_ner_model_error", new Object[] {nerModelFile}, e);
} catch (ClassNotFoundException e) {
System.err.println("ClassNotFoundException in creating chunker");
throw new ResourceInitializationException(
"Unable to load NER model file", "load_ner_model_error", new Object[] {nerModelFile}, e);
} catch (URISyntaxException e) {
e.printStackTrace();
throw new ResourceInitializationException(
"Unable to load NER model file", "load_ner_model_error", new Object[] {nerModelFile}, e);
}
// Read in the geneDictionary
geneDictionary = new HashSet<String>();
try {
File geneDictionaryFile =
new File(new URI(AustinMaKeytermExtractor.class.getResource("/ref.dic").toString()));
BufferedReader reader = new BufferedReader(new FileReader(geneDictionaryFile));
String line;
try {
while ((line = reader.readLine()) != null) geneDictionary.add(line);
} catch (IOException e) {
System.err.println("IOException in reading gene dictionary file");
throw new ResourceInitializationException(
"Unable to load gene dictionary file", "load_gene_dic_error", new Object[] {}, e);
}
} catch (FileNotFoundException e) {
System.err.println("FileNotFoundException in reading gene dictionary file");
throw new ResourceInitializationException(
"Unable to find gene dictionary file", "load_gene_dic_error", new Object[] {}, e);
} catch (URISyntaxException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
throw new ResourceInitializationException(
"Unable to find gene dictionary file", "load_gene_dic_error", new Object[] {}, e1);
}
}
public static void main(String[] args) {
String modelFile = "src/main/resources/models/ne-en-bio-genetag.HmmChunker";
String question =
"What is the role of PrnP in mad cow disease (bovine spongiform encephalitis, BSE)?";
try {
Chunker achunker = (Chunker) AbstractExternalizable.readObject(new File(modelFile));
Chunking chunking = achunker.chunk(question);
for (Chunk chunk : chunking.chunkSet()) {
System.out.println(question.substring(chunk.start(), chunk.end()));
}
} catch (Exception e) {
System.err.println("oops");
}
}
public ChunkerFeatureExtractor() throws ClassNotFoundException, IOException {
@SuppressWarnings("unchecked") // req for deserialize
CodeSource src = this.getClass().getProtectionDomain().getCodeSource();
String loc = src.getLocation().toString();
File hmmFile =
new File(
loc.substring(5, loc.length() - 10)
+ "/objects/pos-en-general-brown.HiddenMarkovModel");
// File hmmFile = new
// File("C:/Users/D059348/dev/HU/MaschinelleSprachverarbeitung/objects/pos-en-general-brown.HiddenMarkovModel");
HiddenMarkovModel posHmm = (HiddenMarkovModel) AbstractExternalizable.readObject(hmmFile);
FastCache<String, double[]> emissionCache = new FastCache<String, double[]>(100000);
mPosTagger = new HmmDecoder(posHmm, null, emissionCache);
}
@Override
public void initialize(UimaContext aContext) throws ResourceInitializationException {
super.initialize(aContext);
// initialization part from annotator
String model = (String) aContext.getConfigParameterValue("TrainedModel");
modelFile = new File(model);
try {
extractor = (Chunker) AbstractExternalizable.readObject(modelFile);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (ClassNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
/**
* @param fileName
* @return
* @throws IOException
* @throws ClassNotFoundException
*/
private LMClassifier<?, ?> deserialize(String fileName)
throws ClassNotFoundException, IOException {
return (LMClassifier<?, ?>)
AbstractExternalizable.readObject(new File(classLoader.getResource(fileName).getFile()));
}
