TestAnnotations.java

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package com.uem.gsi.cleim.test;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.UnsupportedEncodingException;
import java.io.Writer;

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

import com.uem.gsi.cleim.nlp.GateGazMed;
import com.uem.gsi.cleim.nlp.IntegrateAnnot;
import com.uem.gsi.cleim.nlp.NCBOAnnot;
import com.uem.gsi.cleim.util.Constants;

public class TestAnnotations {
        private String path="WebContent/WEB-INF";
        private String text="";
        private String onts="";
        private String lev="0";
        private String[] localSrc=new String[]{"","",""};
        private String[] localLan=new String[]{"",""};
        private IntegrateAnnot ia;
        //private GateGazMed gateAnnot;
        //private NCBOAnnot ncboAnnot;
        public TestAnnotations() {
                
                //gateAnnot=new GateGazMed(path);
                //ncboAnnot=new NCBOAnnot();
        }
        public void setText(String ptext){
                text=ptext;
        }
        public void setOnts(String ponts){
                onts=ponts;
        }
        public void setLev(String plev){
                lev=plev;
        }
        public void setLocalSrc(String[] plocalSrc){
                localSrc=plocalSrc;
        }
        public void setLocalLan(String[] plocalLan){
                localLan=plocalLan;
        }
        public void initIntegrateAnnot(){
                ia=new IntegrateAnnot(text,path,onts,lev,localSrc,localLan);
        }
        private long takeTime(){
                //return System.nanoTime();
                return System.currentTimeMillis();
        }
        private void avoidInitialization(){
                try {
                        ia.gateWithoutFormat();
                        ia.ncboWithoutFormat();
                } catch (Exception e) {
                        System.out.println(e.toString());
                }
        }
        public long testGate(String formatType){
                String output="";
                long res=0;
                try{
                        if (formatType.equals("")){
                                long start = takeTime();
                                ia.gateWithoutFormat();
                                long end = takeTime();
                                res=end-start;
                        }else if (formatType.equals("html")){
                                long start = takeTime();
                                output=ia.htmlGateTree();
                                long end = takeTime();
                                res=end-start;
                        }else if(formatType.equals("xml")){
                                long start = takeTime();
                                ia.initXmlDocument();
                                ia.xmlGateTree();
                                output=ia.getNormalizedXml();
                                long end = takeTime();
                                res=end-start;
                        }
                }catch(Exception e){
                        System.out.println("Exception: "+e.toString());
                }
                System.out.println("GATE Time (format="+formatType+"): "+res);
                //System.out.println(output);
                return res;
        }
        public long testOba(String formatType){
                String output="";
                long res=0;
                try{
                        if (formatType.equals("")){
                                long start = takeTime();
                                ia.ncboWithoutFormat();
                                long end = takeTime();
                                res=end-start;
                        }else if (formatType.equals("html")){
                                long start = takeTime();
                          output=ia.htmlNCBOTree();
                                long end = takeTime();
                                res=end-start;
                        }else if(formatType.equals("xml")){
                                long start = takeTime();
                                ia.initXmlDocument();
                                ia.xmlNCBOTree();
                                output=ia.getNormalizedXml();
                                long end = takeTime();
                                res=end-start;
                        }
                }catch(Exception e){
                        System.out.println("Exception: "+e.toString());
                }
                System.out.println("NCBO Time (format="+formatType+"): "+res);
                //System.out.println(output);
                return res;
        }
        public void testHTTPGATE(String src){
                String sSource="";
                HttpClient client = new HttpClient();
    PostMethod method = new PostMethod("http://orion.esp.uem.es:8080/CLEiM/NLPServ");
    // Configure the form parameters
    method.addParameter("text", text);
    method.addParameter("src", src);
    try{
        long start = takeTime();
            int statusCode = client.executeMethod(method);
            sSource = method.getResponseBodyAsString();
            long end = takeTime();
                        System.out.println("GATE HTTP Time (src="+src+"): "+ (end-start));
            if( statusCode != -1 ) {
              //sSource = method.getResponseBodyAsString();
              method.releaseConnection();
              //System.out.println(contents);
            }else{
                System.out.println("ERROR, statusCode = "+statusCode);
            }
    }catch(Exception e){
        System.out.println("Exception: "+e.toString());
    }
        }
        public static void main(String[] args) {
                String text="";
                int testNumber=3;
                int longTestNumber=10;
                int caseNumber=6;
                int longCaseNumber=3;
                String testCase="";
                String[] sResults;
                TestAnnotations ta=new TestAnnotations();
                ta.setLev("0");
                                
                //Test UPMC cases
                sResults=new String[testNumber+1];
                for (int i=0;i<sResults.length;i++)
                        sResults[i]="";
                
                for (int k=0;k<caseNumber;k++){
                        //Text and ontologies
                        switch (k) {
                        case 0:
                                ta.setOnts("40397"); //P1,P2,P3
                                ta.setLocalSrc(new String[]{"","MedlinePlus",""}); //P4,P5,P6 
                                ta.setLocalLan(new String []{"en",""});
                                testCase="P1;P2;P3;P4;P5;P6";
                                break;
                        case 1:
                                ta.setOnts("46116"); //P7,P8,P9
                                ta.setLocalSrc(new String[]{"","","Snomed"}); //P10,P11,P12
                                ta.setLocalLan(new String []{"en",""});
                                testCase="P7;P8;P9;P10;P11;P12";
                                break;
                        case 2:
                                ta.setOnts("40397,46116"); //P13,P14,P15
                                ta.setLocalSrc(new String[]{"","MedlinePlus","Snomed"}); //P16,P17,P18
                                ta.setLocalLan(new String []{"en",""});
                                testCase="P13;P14;P15;P16;P17;P18";
                                break;
                        case 3:
                                ta.setLocalSrc(new String[]{"","MedlinePlus",""}); //P19,P20,P21
                                ta.setLocalLan(new String []{"en","sp"});
                                testCase="P19;P20;P21";
                                break;
                        case 4:
                                ta.setLocalSrc(new String[]{"","","Snomed"}); //P22,P23,P24
                                ta.setLocalLan(new String []{"en","sp"});
                                testCase="P22;P23;P24";
                                break;
                        case 5:
                                ta.setLocalSrc(new String[]{"","MedlinePlus","Snomed"}); //P25,P26,P27
                                ta.setLocalLan(new String []{"en","sp"});
                                testCase="P25;P26;P27";
                                break;
                        }
                        
                        System.out.println("********************************");
                        System.out.println("TEST CASE: "+testCase);
                        System.out.println("********************************");
                        
                        for (int i=715;i<727;i++){
                                //Text from file
                                try {
                                        File fClinicalCase=new File("D:/UEM/MedicalMiner/ClinicalCases/upmc_2012/"+i);
                                        text=FileUtils.readFileToString(fClinicalCase);
                                } catch (IOException e1) {
                                        System.out.println("Exception: "+e1.toString());
                                }
                                //Text
                                ta.setText(text);
                                ta.initIntegrateAnnot();
                                //Avoid initialization times
                                ta.avoidInitialization();
                                
                                System.out.println(" -> CLINICAL CASE "+i);
                                System.out.println("----------------------");
                                sResults[0]+=(sResults[0].equals(""))?testCase:";"+testCase;
                                //Repeat Test testNumber times
                                for (int n=0;n<testNumber;n++){
                                        System.out.println("+++++++++++++++++++++");
                                        System.out.println("TEST NUMER: N="+n);
                                        System.out.println("+++++++++++++++++++++");
                                        //Test GATE
                                        System.gc();
                                        sResults[n+1]+=(sResults[n+1].equals(""))?ta.testGate(""):";"+ta.testGate("");
                                        System.gc();
                                        sResults[n+1]+=";"+ta.testGate("html");
                                        System.gc();
                                        sResults[n+1]+=";"+ta.testGate("xml");
                                        
                                        //Test OBA
                                        if (k<3) {
                                                System.gc();
                                                sResults[n+1]+=";"+ta.testOba("");
                                                System.gc();
                                                sResults[n+1]+=";"+ta.testOba("html");
                                                System.gc();
                                                sResults[n+1]+=";"+ta.testOba("xml");
                                        }
                                }
                        }
                        Writer out;
                        try {
                                out = new BufferedWriter(new OutputStreamWriter(
                                    new FileOutputStream("data/case"+k+".txt", false), "UTF8"));
                        
                                for (int y=0;y<sResults.length;y++){
                                        out.write(sResults[y]+"\n");
                                        sResults[y]="";
                                }
                                out.close();
                        } catch (Exception e) {
                                System.out.println("Exception: "+e.toString());
                        }
                        
                }
                /*
                //Test long texts
                sResults=new String[longTestNumber+1];
                for (int i=0;i<sResults.length;i++)
                        sResults[i]="";
                
                for (int k=0;k<longCaseNumber;k++){ 
                        //Text and ontologies
                        switch (k) {
                        case 0:
                                ta.setLocalSrc(new String[]{"Freebase","MedlinePlus",""}); //P28,P29,P30
                                ta.setLocalLan(new String []{"en","sp"});
                                ta.setOnts("40397"); //P31,P32,P33
                                testCase="P28;P29;P30;P31;P32;P33";
                                break;
                        case 1:
                                ta.setLocalSrc(new String[]{"","","Snomed"}); //P34,P35,P36
                                ta.setLocalLan(new String []{"en","sp"});
                                ta.setOnts("46116");  //P37,P38,P39
                                testCase="P34;P35;P36;P37;P38;P39";
                                break;
                        case 2:
                                ta.setLocalSrc(new String[]{"Freebase","MedlinePlus","Snomed"}); //P40,P41,P42 
                                ta.setLocalLan(new String []{"en","sp"});
                                ta.setOnts("40397,46116"); //P43,P44,P45
                                testCase="P40;P41;P42;P43;P44;P45";
                                break;
                        }
                        System.out.println("********************************");
                        System.out.println("TEST CASE: "+testCase);
                        System.out.println("********************************");
                        for (int i=0;i<3;i++){
                                //Text from file
                                try {
                                        File fClinicalCase=new File("D:/UEM/MedicalMiner/ClinicalCases/upmc_2012/long"+i);
                                        text=FileUtils.readFileToString(fClinicalCase);
                                } catch (IOException e1) {
                                        System.out.println("Exception: "+e1.toString());
                                }
                                //Text
                                ta.setText(text);
                                ta.initIntegrateAnnot();
                                //Avoid initialization times
                                ta.avoidInitialization();
                                
                                System.out.println(" -> CLINICAL CASE LONG "+i);
                                System.out.println("----------------------");
                                sResults[0]+=(sResults[0].equals(""))?testCase:";"+testCase;
                                for (int n=0;n<longTestNumber;n++){
                                        System.out.println("+++++++++++++++++++++");
                                        System.out.println("TEST NUMER: N="+n);
                                        System.out.println("+++++++++++++++++++++");
                                        
                                        //Test GATE
                                        System.gc();
                                        sResults[n+1]+=(sResults[n+1].equals(""))?ta.testGate(""):";"+ta.testGate("");
                                        System.gc();
                                        sResults[n+1]+=";"+ta.testGate("html");
                                        System.gc();
                                        sResults[n+1]+=";"+ta.testGate("xml");
                                        //ta.testHTTPGATE("-1");
                
                                        //Test OBA
                                        System.gc();
                                        sResults[n+1]+=";"+ta.testOba("");
                                        System.gc();
                                        sResults[n+1]+=";"+ta.testOba("html");
                                        System.gc();
                                        sResults[n+1]+=";"+ta.testOba("xml");
                                }
                        }
                        Writer out;
                        try {
                                out = new BufferedWriter(new OutputStreamWriter(
                                    new FileOutputStream("data/caseLong"+k+".txt", false), "UTF8"));
                        
                                for (int y=0;y<sResults.length;y++){
                                        out.write(sResults[y]+"\n");
                                        sResults[y]="";
                                }
                                out.close();
                        } catch (Exception e) {
                                System.out.println("Exception: "+e.toString());
                        }
                }*/
        }
}