CallPMSoap.java

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package com.uem.gsi.cleim.scl;
import java.rmi.RemoteException;
import java.util.ArrayList;
import java.util.List;

import org.apache.axis2.AxisFault;
import org.apache.commons.httpclient.util.URIUtil;

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

import gov.nih.nlm.ncbi.www.soap.eutils.*;

public class CallPMSoap {
        private String term;
        private String lan="";
        private String logic="+";
  private int limit=20;
        private int pmPage=0;
        private int count=0;
        private int totalpages=0;
        private String idList="";
        private List<String> lIDList;
        private List<String> lTitle;
        private List<String> lPubDate;
        private List<String> lAuthors;
  private List<String> lAbstractUrl;
  
        public CallPMSoap() {
                lIDList = new ArrayList<String>();
                lTitle = new ArrayList<String>();
        lPubDate = new ArrayList<String>();
        lAuthors = new ArrayList<String>();
        lAbstractUrl = new ArrayList<String>();
  }
        
        private void queryPMID(){
                try {
                        EUtilsServiceStub stub = new EUtilsServiceStub();
                        EUtilsServiceStub.ESearchRequest eSearchRequest=new EUtilsServiceStub.ESearchRequest();
                        eSearchRequest.setTool(Constants.ENTREZ_TOOL);
                        eSearchRequest.setEmail(Constants.ENTREZ_EMAIL);
                        eSearchRequest.setDb("pubmed");
                        String termUrlenc=URIUtil.encodeQuery(this.term).replaceAll("%20", this.logic);
                        eSearchRequest.setTerm(termUrlenc+this.lan);
                        eSearchRequest.setSort("PublicationDate");
                        eSearchRequest.setDatetype("edat");
                        eSearchRequest.setUsehistory("y");
                        eSearchRequest.setRetMax(""+this.limit);
                        eSearchRequest.setRetStart(""+this.pmPage*this.limit);
                        EUtilsServiceStub.ESearchResult res = stub.run_eSearch(eSearchRequest);
                        this.count=new Integer(res.getCount());
                        totalpages=new Integer(count/limit);
                        if (res.getIdList().getId()!=null){
                                int i = 0;
                                int resLength=res.getIdList().getId().length;
                                for (i = 0; i < resLength-1; i++){
                                        String id=res.getIdList().getId()[i];
                                        lIDList.add(id);
                                        idList+=id+",";
                                }
                                String id=res.getIdList().getId()[resLength-1];
                                lIDList.add(id);
                                idList+=id;
                        }
                } catch (AxisFault e) {
                        e.printStackTrace();
                } catch (RemoteException e) {
                        e.printStackTrace();
                } catch (Exception e){
                        e.printStackTrace();
                }
        }
        
        public void queryPMInit(){
                queryPMID();
                if (!idList.equals("")){
                        try {
                                EUtilsServiceStub stub = new EUtilsServiceStub();
                                EUtilsServiceStub.ESummaryRequest eSummaryRequest = new  EUtilsServiceStub.ESummaryRequest();
                                eSummaryRequest.setTool(Constants.ENTREZ_TOOL);
                                eSummaryRequest.setEmail(Constants.ENTREZ_EMAIL);
                                eSummaryRequest.setDb("pubmed");
                                eSummaryRequest.setId(this.idList);
                                //eSummaryRequest.setRetmax("10");
                                //eSummaryRequest.setRetstart(0);
                                EUtilsServiceStub.ESummaryResult res = stub.run_eSummary(eSummaryRequest);
                                int resLength=res.getDocSum().length;
                                for (int i = 0; i < resLength; i++){
                                        String title="",pubdate="",abstracturl="",authors="";
                                        for (int k = 0; k < res.getDocSum()[i].getItem().length; k++){
                                                if (res.getDocSum()[i].getItem()[k].getItem()==null){
                                                        String name=res.getDocSum()[i].getItem()[k].getName();
                                                        String value=res.getDocSum()[i].getItem()[k].getItemContent();
                                                        if (name.equals("Title")) title=value;
                                                        else if (name.equals("PubDate")) pubdate=value;
                                                        else if (name.equals("HasAbstract") && value.equals("1")) 
                                                                abstracturl=Constants.ENTREZ_BASE+"efetch.fcgi?db=pubmed&id="+
                                                       this.lIDList.get(i)+"&rettype=abstract&retmode=text";
                                                }else{
                                                        if (res.getDocSum()[i].getItem()[k].getName().equals("AuthorList")){
                                                                int subLength=res.getDocSum()[i].getItem()[k].getItem().length;
                                                                for (int w = 0; w < subLength; w++){
                                                                        String value=res.getDocSum()[i].getItem()[k].getItem()[w].getItemContent();
                                                                        authors+=value+". ";
                                                                }
                                                        }
                                                }
                                                
                                        }
                                        lTitle.add(title);
                                        lPubDate.add(pubdate);
                                        lAbstractUrl.add(abstracturl);
                                        lAuthors.add(authors);
                                }
                        } catch (AxisFault e) {
                                e.printStackTrace();
                        } catch (RemoteException e) {
                                e.printStackTrace();
                        }
                }
        }
        public void setTerm(String pterm){
                this.term=pterm;
        }
        public void setLanSpa(){
                this.lan="+(spa[LANG])";
        }
        public void setLan(String pLan){
                this.lan=pLan;
        }
        public void setLogic(String plogic){
                this.logic=plogic;
        }
        public void setLimit(int plimit){
                this.limit=plimit;
        }
        public void setPage(int pPage){
                this.pmPage=pPage;
        }
        public int getCount(){
        return this.count;
  }
        public int getTotalPages(){
        return this.totalpages;
  }
        public List<String> getTitles(){
        return this.lTitle;
  }
  public List<String> getPubDates(){
        return this.lPubDate;
  }
  public List<String> getAuthors(){
        return this.lAuthors;
  }
  public List<String> getAbstractUrl(){
        return this.lAbstractUrl;
  }
  
        public static void main (String[] args){
                CallPMSoap oPM=new CallPMSoap();
                oPM.setTerm("Cáncer de próstata");
                try {
                oPM.setPage(0);
                //oPM.setLanSpa();
                oPM.queryPMInit();
            List<String> l0=oPM.getTitles();
            List<String> l1=oPM.getPubDates();
            List<String> l2=oPM.getAuthors();
            List<String> l3=oPM.getAbstractUrl();
            System.out.println("Resultados: "+oPM.getCount());
            for (int i=0;i<l1.size();i++){
                System.out.println("<tr>");
                System.out.println("<td>"+l0.get(i)+"<br><a href='"+l3.get(i)+
                                "' target=_blank>Go to Abstract</a></td>"+
                                "<td>"+l1.get(i)+"</td>"+
                                "<td>"+l2.get(i)+"</td>");
                System.out.println("</tr>");
            }
          } catch (Exception e) {
                System.out.println(e.toString());
          }
     
        }
        
}