/**
* @param aContext
* @throws ResourceInitializationException
*/
@Override
public void initialize(UimaContext aContext) throws ResourceInitializationException {
debug("initialize ()");
super.initialize(aContext);
GenResourceLoader loader = new GenResourceLoader();
int i = 0;
String text = loader.getTextResource2(stopwordFile);
if (text == null) {
debug("Input error, unable to read stopword file: " + stopwordFile);
return;
}
stopList = new HashMap<String, Integer>();
String lines[] = text.split("\\n");
for (i = 0; i < lines.length; i++) {
String aWord = lines[i];
stopList.put(aWord.toLowerCase(), i);
}
debug("Loaded " + stopList.size() + " stopwords");
}
@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);
}
}
@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 aContext
* @throws ResourceInitializationException
*/
@Override
public void initialize(UimaContext aContext) throws ResourceInitializationException {
debug("initialize ()");
super.initialize(aContext);
}
