CallNCBO.java

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package com.uem.gsi.cleim.nlp;

import java.io.File;

import org.apache.commons.httpclient.HttpClient;
import org.apache.commons.httpclient.methods.PostMethod;
import org.apache.commons.io.FileUtils;

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

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

public class CallNCBO {
  
        //HTTP REST Web service parameter defaults
  private String text = "";
  //ICD10(44103),Medlineplus(40397),MeSH(42142),Human disease(44172)
  private String ontologiesToKeepInResult="40397";
  private String levelMax="0";
  private String longestOnly="false";
  private String wholeWordOnly="true";
  private String filterNumber="false";
  private String stopWords="null";
  private String withDefaultStopWords="true";
  private String withSynonyms="true";
  private String scored="true";
  private String ontologiesToExpand="";
  private String semanticTypes="";
  private String mappingTypes="all";
  private String format="xml"; //"text","tabDelimited"
  
        public CallNCBO(){
        }
        public String doRESTQuery() throws Exception{
                String sSource="";
                //try {
          HttpClient client = new HttpClient();
      PostMethod method = new PostMethod(Constants.NCBO_BASE+Constants.NCBO_ANNOT);

      // Configure the form parameters
      method.addParameter("apikey", Constants.NCBO_APIKEY);
      method.addParameter("email", Constants.NCBO_EMAIL);
      method.addParameter("longestOnly", longestOnly);
      method.addParameter("wholeWordOnly", wholeWordOnly);
      method.addParameter("filterNumber", filterNumber);
      method.addParameter("stopWords", stopWords);
      method.addParameter("withDefaultStopWords", withDefaultStopWords);
      method.addParameter("withSynonyms", withSynonyms);
      method.addParameter("scored", scored);
      method.addParameter("ontologiesToExpand", ontologiesToExpand);
      method.addParameter("ontologiesToKeepInResult", ontologiesToKeepInResult);
      method.addParameter("semanticTypes", semanticTypes);
      method.addParameter("levelMax", levelMax);
      method.addParameter("mappingTypes", mappingTypes);
      method.addParameter("textToAnnotate", text);
      //method.addParameter("format", "asText");
      //method.addParameter("format", "tabDelimited");
      method.addParameter("format", format);
      
      // Execute the POST method
       int statusCode = client.executeMethod(method);
        if( statusCode != -1 ) {
          sSource = method.getResponseBodyAsString();
          method.releaseConnection();
          //System.out.println(contents);
        }else{
                sSource="<statusCode>"+statusCode+"</statusCode>";
                //System.out.println("status: "+statusCode);
        }
    //} catch( Exception e ) {
    //  e.printStackTrace();
    //}
                return sSource;
        }
        public void setText(String ptext){
                this.text=ptext;
        }
        public void setOntInRes(String pontologiesToKeepInResult){
                this.ontologiesToKeepInResult=pontologiesToKeepInResult;
        }
        public void setLevelMax(String plevelMax){
                this.levelMax=plevelMax;
        }
        public void setLongestOnly(String plongestOnly){
                this.longestOnly=plongestOnly;
        }
        public void setWholeWordOnly(String pwholeWordOnly){
                this.wholeWordOnly=pwholeWordOnly;
        }
        public void setFilterNumber(String pfilterNumber){
                this.filterNumber=pfilterNumber;
        }
        public void setStopWords(String pstopWords){
                this.stopWords=pstopWords;
        }
        public void setWithDefaultStopWords(String pwithDefaultStopWords){
                this.withDefaultStopWords=pwithDefaultStopWords;
        }
        public void setWithSynonyms(String pwithSynonyms){
                this.withSynonyms=pwithSynonyms;
        }
        public void setScored(String pscored){
                this.scored=pscored;
        }
        public void setOntologiesToExpand(String pontologiesToExpand){
                this.ontologiesToExpand=pontologiesToExpand;
        }
        public void setSemanticTypes(String psemanticTypes){
                this.semanticTypes=psemanticTypes;
        }
        public void setMappingTypes(String pmappingTypes){
                this.mappingTypes=pmappingTypes;
        }
        public void setFormat(String pformat){
                this.format=pformat;
        }
        
  public static void main( String[] args ) {
         //System.out.println("********************* NCBO ANNOTATOR CLIENT TEST ************************* \n");
         try {
                 CallNCBO oNCBO=new CallNCBO();
                 File fClinicalCase=new File("D:/UEM/MedicalMiner/ClinicalCases/CasoClinicoNCBO.txt");
                 //File fClinicalCase=new File("D:/UEM/MedicalMiner/ClinicalCases/CasoClinico20.txt");
                 // Read the entire contents of sample.txt
                 String text=FileUtils.readFileToString(fClinicalCase);
                 oNCBO.setText("diabetes");
                 //System.out.print(oNCBO.doRESTQuery());
                 //System.exit(0);
                 Document doc = MyDOMParser.getDocument(oNCBO.doRESTQuery());
                 //String elementName = doc.getNodeName();
                 //String textInXml=doc.getElementsByTagName("textToAnnotate").item(0).getFirstChild().getNodeValue();
                 NodeList listAnnot=doc.getElementsByTagName("annotationBean");
                 
                 for (int i=0;i<listAnnot.getLength();i++){
                         //Initialize data to show
                         String localOntologyId="",fullId="",preferredName="";
                         String contextName="",isDirect="",from="",to="",nameInText="";
                         Node annotNode=listAnnot.item(i);
                         //System.out.println(listAnnot.item(i).getNodeName());
                         NodeList listChildAnnot=annotNode.getChildNodes();
                         for (int j=0;j<listChildAnnot.getLength();j++){
                                 Node nodeTemp1=listChildAnnot.item(j);
                                 //System.out.println(nodeTemp1.getNodeName());
                                 //Concept
                         if (nodeTemp1.getNodeName().equals("concept")){
                                 //System.out.println(nodeTemp1.getNodeName());
                                 NodeList listChildRes=nodeTemp1.getChildNodes();
                                 for (int k=0;k<listChildRes.getLength();k++){
                                         Node node1=listChildRes.item(k);
                                         String node1name=node1.getNodeName();
                                         //Elements selection
                                         if (node1name.equals("localOntologyId"))
                                                 localOntologyId=node1.getFirstChild().getNodeValue().trim();
                                         else if (node1name.equals("fullId"))
                                                 fullId=node1.getFirstChild().getNodeValue().trim();
                                         else if (node1name.equals("preferredName"))
                                                 preferredName=node1.getFirstChild().getNodeValue().trim();
                 }
                                        
                         }//Context
                         else if (nodeTemp1.getNodeName().equals("context")){
                                 //System.out.println(nodeTemp1.getNodeName());
                                 NodeList listChildRes=nodeTemp1.getChildNodes();
                                 for (int k=0;k<listChildRes.getLength();k++){
                                         Node node1=listChildRes.item(k);
                                         String node1name=node1.getNodeName();
                                         //System.out.println(node1.getNodeName()+"="+node1.getNodeValue());
                                         //Seleccionar elementos
                                         if (node1name.equals("contextName"))
                                                 contextName=node1.getFirstChild().getNodeValue().trim();
                                         else if (node1name.equals("isDirect"))
                                                 isDirect=node1.getFirstChild().getNodeValue().trim();
                                         else if (node1name.equals("from"))
                                                 from=node1.getFirstChild().getNodeValue().trim();
                                         else if (node1name.equals("to"))
                                                 to=node1.getFirstChild().getNodeValue().trim();
                                                 
                                                 }/*else if (node1name.equals("term")){
                                                         if (node1.getFirstChild()!=null && node1.getFirstChild().getFirstChild()!=null)
                                                                 System.out.println("***"+node1.getFirstChild().getNodeName()+"="+node1.getFirstChild().getFirstChild().getNodeValue().trim());
                                 }else if (node1name.equals("concept")){
                                                         
                                                 }*/
                                 }
                         }
                                 nameInText=text.substring(new Integer(from)-1,new Integer(to));
                                 //nameInText=textInXml.substring(new Integer(from)-1,new Integer(to));
                         
                                 System.out.println(localOntologyId+","+fullId+","+preferredName+","+
                                                 contextName+","+isDirect+","+from+","+to+","+nameInText);
                         }
         }
         catch( Exception e ) {
           e.printStackTrace();
         }
  }

}