GateGazMed.java

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package com.uem.gsi.cleim.nlp;

import gate.Annotation;
import gate.Document;
import gate.Corpus;
import gate.CorpusController;
import gate.AnnotationSet;
import gate.FeatureMap;
import gate.Gate;
import gate.Factory;
import gate.util.*;
import gate.util.persistence.PersistenceManager;

import java.util.List;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.Vector;

import java.io.File;
import java.io.IOException;

public class GateGazMed {
  private String xmlGate="";
  private String sWebInf="";
        private List<String> annotTypesToWrite;
  private Vector<String> vAnnotListMinor;
  private Vector<List<String>> vAnnotList;
  private Vector<List<String>> vAnnotListLan; //Language
  private Vector<List<String>> vAnnotListSource; //(Major)
  private Vector<List<String>> vAnnotListGroup;
        private Vector<List<String>> vAnnotListFrom;
        private Vector<List<String>> vAnnotListTo;
        private Vector<List<String>> vAnnotListUrl;
  
  //private String encoding = null;
  
  public GateGazMed(String pWebInf){
        sWebInf=pWebInf;
        //List of anotations
                annotTypesToWrite = new ArrayList<String>(1);
                annotTypesToWrite.add("Medicine");
                //Init vectors
                vAnnotListMinor=new Vector<String>();
                //Freebase
                vAnnotListMinor.addElement("disease");
                vAnnotListMinor.addElement("symptom");
                vAnnotListMinor.addElement("treatment");
                //Medlineplus
                vAnnotListMinor.addElement("medlineplus");
                //Snomed ct
                vAnnotListMinor.addElement("snomed");
                //
                vAnnotList=new Vector<List<String>>(vAnnotListMinor.size());
                vAnnotListLan=new Vector<List<String>>(vAnnotListMinor.size());
                vAnnotListSource=new Vector<List<String>>(vAnnotListMinor.size());
                vAnnotListGroup=new Vector<List<String>>(vAnnotListMinor.size());
                vAnnotListFrom=new Vector<List<String>>(vAnnotListMinor.size());
                vAnnotListTo=new Vector<List<String>>(vAnnotListMinor.size());
                vAnnotListUrl=new Vector<List<String>>(vAnnotListMinor.size());
                for (int i=0;i<vAnnotListMinor.size();i++){
                        vAnnotList.insertElementAt(new ArrayList<String>(), i);
                        vAnnotListLan.insertElementAt(new ArrayList<String>(), i);
                        vAnnotListSource.insertElementAt(new ArrayList<String>(), i);
                        vAnnotListGroup.insertElementAt(new ArrayList<String>(), i);
                        vAnnotListFrom.insertElementAt(new ArrayList<String>(), i);
                        vAnnotListTo.insertElementAt(new ArrayList<String>(), i);
                        vAnnotListUrl.insertElementAt(new ArrayList<String>(), i);
                }
  }

  private void initGate(){
        try {
                  //System.out.println("gate.home: "+Gate.getGateHome());
                if (Gate.getGateHome()==null){
                                //Gate home, config -> webapp/WEB-INF/gate.xml, plugins -> webapp/WEB-INF/plugins
                        File gateHome = new File(sWebInf);
                                Gate.setGateHome(gateHome); 
                                // user config -> webapp/WEB-INF/user-gate.xml 
                                Gate.setUserConfigFile(new File(gateHome, "user-gate.xml"));
                }
                //System.out.println("Is Gate initialized? "+Gate.isInitialised());
                        if (!Gate.isInitialised())
                                Gate.init(); 

        } catch (Exception e) {
                        e.printStackTrace();
                }
  }

  public void runGazetteer(String sDocText,String sGapp){
        try {
        initGate(); 
                  // load the gapp application
            CorpusController application =
              //(CorpusController)PersistenceManager.loadObjectFromFile(new File(sWebInf+"/CLEiM.gapp"));
                (CorpusController)PersistenceManager.loadObjectFromFile(new File(sWebInf+"/"+sGapp));
            // Create a temporally Corpus, process and clear
            Corpus corpus = Factory.newCorpus("Medicine Corpus");
            application.setCorpus(corpus);
            Document doc = Factory.newDocument(sDocText);
            corpus.add(doc);
            application.execute();
            // remove the document from the corpus again
            corpus.clear();
            
            // Extract annotations
            Iterator<String> annotTypesIt = annotTypesToWrite.iterator();
            while(annotTypesIt.hasNext()) {
              String annotSelected=annotTypesIt.next();
                AnnotationSet annotsOfThisType = doc.getAnnotations(annotSelected);
                if(annotsOfThisType != null) {
                for (int i=0; i<annotsOfThisType.size();i++){
                        Annotation annot=annotsOfThisType.get(i);
                        if (annot!=null){
                                FeatureMap features=annot.getFeatures();
                                //String anotName=(String)features.get("name");
                                String anotLan=(String)features.get("language");
                                String minorType=(String)features.get("minorType");
                                String majorType=(String)features.get("majorType");
                                String groups=(String)features.get("groups");
                                String url=(String)features.get("url");
                                String from=annot.getStartNode().getOffset().toString();
                                String to=annot.getEndNode().getOffset().toString();
                                String anotName=sDocText.substring(new Integer(from), new Integer(to));
                                int j=vAnnotListMinor.indexOf(minorType);
                                if (j>-1){
                                        vAnnotList.get(j).add(anotName.toUpperCase());
                                        vAnnotListLan.get(j).add(anotLan);
                                        vAnnotListSource.get(j).add(majorType);
                                        vAnnotListGroup.get(j).add(groups);
                                        vAnnotListFrom.get(j).add(from);
                                        vAnnotListTo.get(j).add(to);
                                        vAnnotListUrl.get(j).add(url);
                        }
                        }
                }
                }
            }
            Factory.deleteResource(doc);
            Factory.deleteResource(application); 
    } catch (GateException e) {
                        e.printStackTrace();
    } catch (IOException e) {
                        e.printStackTrace();
                }
  }
  public Vector<String> getMinor(){
        return this.vAnnotListMinor;
  }
  public Vector<List<String>> getAnnot(){
        return this.vAnnotList;
  }
  public Vector<List<String>> getAnnotLan(){
        return this.vAnnotListLan;
  }
  public Vector<List<String>> getAnnotSource(){
        return this.vAnnotListSource;
  }
  public Vector<List<String>> getAnnotGroup(){
        return this.vAnnotListGroup;
  }
  public Vector<List<String>> getAnnotFrom(){
        return this.vAnnotListFrom;
  }
  public Vector<List<String>> getAnnotTo(){
        return this.vAnnotListTo;
  }
  public Vector<List<String>> getAnnotUrl(){
        return this.vAnnotListUrl;
  }
  public String getXmlGate(){
        return this.xmlGate;
  }
  public static void main(String args[]) {
        String path="WebContent/WEB-INF";
        String sGapp="CLEiM.gapp";
                String text= "UNDERLYING MEDICAL CONDITION: "+
    " 56 year old man with history of colon and testicular cancer, pons glioma now"+  
    " with significant hilar lymphadeonpathry, pulmonary pathology on CXR."+
    " REASON FOR THIS EXAMINATION: extracto de genciana colirio/gotas óticas"+
    " vagina no hiperestésica  56 year old man with history of colon and testicular cancer, pons glioma now"+  
    " Salmonella Irumu SIDA con visión deficiente with significant hilar lymphadeonpathry, pulmonary pathology on CXR."+
    " Suture of wound of forelimb Lumbar chemical sympathectomy"+
    " vía fístula mucosa No contraindications for IV contrast  pain back pain aspirin cáncer de próstata";
                GateGazMed gateMed=new GateGazMed(path);
                gateMed.runGazetteer(text,sGapp);
                Vector<String> vMinor=gateMed.getMinor();
                Vector<List<String>> vAnnot=gateMed.getAnnot();
                Vector<List<String>> vAnnotSource=gateMed.getAnnotSource();
                Vector<List<String>> vAnnotGroup=gateMed.getAnnotGroup();
                Vector<List<String>> vAnnotFrom=gateMed.getAnnotFrom();
                Vector<List<String>> vAnnotTo=gateMed.getAnnotTo();
                Vector<List<String>> vAnnotUrl=gateMed.getAnnotUrl();
                for (int i=0;i<vMinor.size();i++){
                        System.out.println("Minor: "+vMinor.get(i));
                        for (int j=0;j<vAnnot.get(i).size();j++){
                                System.out.println("->Annot: "+vAnnot.get(i).get(j));
                                System.out.println("->AnnotSource: "+vAnnotSource.get(i).get(j));
                                System.out.println("->AnnotGroup: "+vAnnotGroup.get(i).get(j));
                                System.out.println("->AnnotFrom: "+vAnnotFrom.get(i).get(j));
                                System.out.println("->AnnotTo: "+vAnnotTo.get(i).get(j));
                                System.out.println("->AnnotUrl: "+vAnnotUrl.get(i).get(j));
                        }
                }
        }
}