private boolean hasConceptTopic(SurfaceElement surf) {
Document doc = surf.getSentence().getDocument();
LinkedHashSet<SemanticItem> sems = surf.getSemantics();
if (sems == null) return false;
for (SemanticItem sem : sems) {
Ontology ont = sem.getOntology();
if (doc.getTopics() != null && doc.getTopics().contains(ont)) return true;
}
return false;
}
private boolean hasStringTopic(SurfaceElement surf) {
Document doc = surf.getSentence().getDocument();
LinkedHashSet<SemanticItem> sems = surf.getSemantics();
if (sems == null) return false;
for (SemanticItem sem : sems) {
if (sem instanceof Term == false) continue;
Term term = (Term) sem;
if (doc.getTopics() != null && doc.getTopics().contains(term.getText().toUpperCase()))
return true;
}
return false;
}
/**
* Adds term annotations to a document.
*
* @param doc the document to add annotations to
* @param annFilename the name of the file with annotations
* @return XML representation of the document after adding annotations.
*/
public static Element processSingleFile(Document doc, String annFilename) {
Map<String, List<String>> lines =
StandoffAnnotationReader.readAnnotationFiles(
Arrays.asList(annFilename), Constants.UMLS_SEMTYPES);
Map<Class, List<Annotation>> annotations =
StandoffAnnotationReader.parseAnnotations(doc.getId(), lines, null);
SemanticItemFactory sif = doc.getSemanticItemFactory();
Class[] processOrder = new Class[] {TermAnnotation.class, Reference.class};
for (int i = 0; i < processOrder.length; i++) {
Class c = processOrder[i];
List<Annotation> anns = annotations.get(c);
if (anns == null) continue;
for (Annotation ann : anns) {
if (ann instanceof TermAnnotation) {
Entity ent = sif.newEntity(doc, (TermAnnotation) ann);
int maxId = doc.getMaxId(Term.class);
ent.setId("T" + ++maxId);
}
}
}
return doc.toXml();
}