SNOMEDToFile.java

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package com.uem.gsi.cleim.rpd;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.io.Writer;
import java.util.ArrayList;
import java.util.List;

import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;

import com.uem.gsi.cleim.util.Constants;

import java.util.regex.*;
public class SNOMEDToFile {
        /*private String sWebInf="";
        private int count=0;
  private int countSpanish=0;
  private int countEnglish=0;
  private List<String> lTopicLang;
  private List<String> lID;
        private List<String> lTopicName;
        private List<String> lUrl;
  private List<String> lFullSummary;
  private List<String> lGroupNames;
  private List<ArrayList<String>> lSynonyms;
  private ArrayList<String> lSynonym;
        
  public SNOMEDToFile(String pWebInf){
        sWebInf=pWebInf;
                lTopicLang = new ArrayList<String>();
                lID = new ArrayList<String>();
                lTopicName = new ArrayList<String>();
                lUrl = new ArrayList<String>();
                lFullSummary = new ArrayList<String>();
                lGroupNames = new ArrayList<String>();
                lSynonyms = new ArrayList<ArrayList<String>>();
        }
        
  public void textToList(){
                try {
                        Document doc;
                        //Local
                        if (sWebInf!="")
                                doc = MyDOMParser.getDocument(sWebInf+Constants.MLP_XML_VOCAB, 1);
                        //Remote
                        else
                                doc = MyDOMParser.getDocument(Constants.MLP_XML_VOCAB, 0);
                        this.count=new Integer(doc.getElementsByTagName("MedicalTopics").item(0).getAttributes().getNamedItem("total").getNodeValue());
                        this.countEnglish=new Integer(doc.getElementsByTagName("MedicalTopics").item(0).getAttributes().getNamedItem("totalEnglish").getNodeValue());
                        this.countSpanish=new Integer(doc.getElementsByTagName("MedicalTopics").item(0).getAttributes().getNamedItem("totalSpanish").getNodeValue());
                        
                        NodeList listRes=doc.getElementsByTagName("MedicalTopic");
                        String id="",name="",url="",fullsum="",groups="";
                        for (int j=0;j<listRes.getLength();j++){
                                lSynonym = new ArrayList<String>();
                    Node annotNode=listRes.item(j);
                                //English or spanish
                                lTopicLang.add(annotNode.getAttributes().getNamedItem("langcode").getNodeValue());
                                NodeList listChildAnnot=annotNode.getChildNodes();
                                for (int i=0;i<listChildAnnot.getLength();i++){
                                        Node nodeContent=listChildAnnot.item(i);
                            if (nodeContent.getNodeName().equals("ID"))
                                id=nodeContent.getTextContent();
                            if (nodeContent.getNodeName().equals("MedicalTopicName"))
                                name=nodeContent.getTextContent();
                            if (nodeContent.getNodeName().equals("URL"))
                                url=nodeContent.getTextContent();
                            if (nodeContent.getNodeName().equals("FullSummary"))
                                fullsum=nodeContent.getTextContent();
                            //Groups names
                            if (nodeContent.getNodeName().equals("Groups")){
                                NodeList listGroups=nodeContent.getChildNodes();
                                groups="";
                                for (int k=0;k<listGroups.getLength();k++){
                                        if (listGroups.item(k).getNodeType()==1)
                                                groups+=(groups.equals(""))?
                                                        listGroups.item(k).getChildNodes().item(3).getTextContent():
                                                        " | "+listGroups.item(k).getChildNodes().item(3).getTextContent();
                                }
                            }
                            //Synonyms
                            if (nodeContent.getNodeName().equals("Synonyms")){
                                NodeList listSynonyms=nodeContent.getChildNodes();
                                for (int k=0;k<listSynonyms.getLength();k++){
                                        if (listSynonyms.item(k).getNodeType()==1)
                                                lSynonym.add(listSynonyms.item(k).getTextContent());
                                }
                            }
                                }
                                lID.add(id);
                                lTopicName.add(name);
                                lUrl.add(url);
                                lFullSummary.add(fullsum);
                                lGroupNames.add(groups);
                                lSynonyms.add(lSynonym);
                        }
                } catch (Exception e) {
                        System.out.println("Exception reading medlineplus xml: "+e.toString());
                }
        }

  private void loadListFileLan(String filePath,String lan){
                try {
                        Writer out = new BufferedWriter(new OutputStreamWriter(
                new FileOutputStream(filePath), "UTF8"));
                        //      Write english data
                        for (int i=0;i<lID.size();i++){
                                if (lTopicLang.get(i).equals(lan)){
                                        //out.write(lTopicName.get(i)+"&name="+lTopicName.get(i)+"&url="+lUrl.get(i)+"&groups="+lGroupNames.get(i)+"\n");
                                        out.write(lTopicName.get(i)+"&url="+lUrl.get(i)+"&groups="+lGroupNames.get(i)+"\n");
                                        for (int j=0;j<lSynonyms.get(i).size();j++){
                                                //out.write(lSynonyms.get(i).get(j)+"&name="+lSynonyms.get(i).get(j)+"&url="+lUrl.get(i)+"&groups="+lGroupNames.get(i)+"\n");
                                                out.write(lSynonyms.get(i).get(j)+"&url="+lUrl.get(i)+"&groups="+lGroupNames.get(i)+"\n");
                                                
                                        }
                                }
                        }
            out.close();
                } catch (IOException e) {
                        e.printStackTrace();
                }
        }

        public static void main(String[] args) {
                try{
                        // PUT HERE YOUR ABSOLUTE PATH IF YOU WANT LOCAL PROCESS, KEEP EMPTY IF NOT
                        String xmlpath="";
                        // PUT HERE YOUR LOCAL WEB-INF PATH TO AUTOMATICALLY UPDATE GATE FILES
                        String webinf="WebContent/WEB-INF";
                        SNOMEDToFile mlp=new SNOMEDToFile(xmlpath);
                        System.out.println("READING XML FILES...");
                        mlp.xmlToList();
                        System.out.println("Topics number: "+mlp.count+
                                        " In English: "+mlp.countEnglish+". In Spanish: "+mlp.countSpanish);
                        for(int i=0; i<mlp.lID.size();i++){
                                System.out.println("lang: "+mlp.lTopicLang.get(i));
                                System.out.println("ID: "+mlp.lID.get(i));
                                System.out.println("Name: "+mlp.lTopicName.get(i));
                                System.out.println("Url: "+mlp.lUrl.get(i));
                                System.out.println("FullSummary: "+mlp.lFullSummary.get(i));
                                System.out.println("Groups: "+mlp.lGroupNames.get(i));
                                for (int j=0;j<mlp.lSynonyms.get(i).size();j++)
                                        System.out.println("Synonyms: "+mlp.lSynonyms.get(i).get(j));
                        }
                        System.out.println("LOADING GATE LIST FILE...");
                        //TO LOAD DISJOINTED LANGUAGE FILES TO THE TERMS
                        mlp.loadListFileLan(webinf+Constants.PATH_MLP_LST_EN, "English");
                        mlp.loadListFileLan(webinf+Constants.PATH_MLP_LST_SP, "Spanish");
                        //USE THIS TO LOAD ENGLISH AND SPANISH TERMS IN THE SAME LIST
                        //mlp.loadListFile(Constants.PATH_MLP_LST);
                        System.out.println("DONE");
                        
                }catch(Exception e){
                        System.out.println("Error: "+e.toString());
                }
        }
*/
        public void replacePattern(String filePathInput, String filePathOutput, 
                        String sPattern, String sReplacement){  
    try {  
        FileReader fr = new FileReader(filePathInput);  
        BufferedReader br = new BufferedReader(fr);  
        FileWriter fw = new FileWriter(filePathOutput);  
        PrintWriter pw = new PrintWriter(fw);   
        String line = null;  
  
        while((line=br.readLine()) != null) {  
                line=line.replaceAll(sPattern, sReplacement);    
                pw.write(line);  
        }  
    }catch(Exception e){
        System.out.println("Exception: "+e.toString());
    }  
        }
        public static void main(String[] args) {
                
        }
}