edu.harvard.i2b2.util.I2b2UtilTest.java Source code

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Here is the source code for edu.harvard.i2b2.util.I2b2UtilTest.java

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/*
 * Copyright (c) 2006-2007 Massachusetts General Hospital 
 * All rights reserved. This program and the accompanying materials 
 * are made available under the terms of the i2b2 Software License v1.0 
 * which accompanies this distribution. 
 * 
 * Contributors:
 *       Kavishwar Wagholikar (kavi)
 *       July 4, 2015
 */

package edu.harvard.i2b2.util;

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

import javax.xml.bind.JAXBException;

import org.apache.commons.io.IOUtils;
import org.hl7.fhir.Bundle;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import edu.harvard.i2b2.fhir.AuthenticationFailure;
import edu.harvard.i2b2.fhir.I2b2Util;
import edu.harvard.i2b2.fhir.Utils;
import edu.harvard.i2b2.fhir.WebServiceCall;
import edu.harvard.i2b2.fhir.XQueryUtil;
import edu.harvard.i2b2.fhir.XQueryUtilException;
import edu.harvard.i2b2.fhir.core.FhirCoreException;
import edu.harvard.i2b2.fhir.core.Project;

public class I2b2UtilTest {
    Logger logger = LoggerFactory.getLogger(I2b2UtilTest.class);
    String i2b2User;
    String i2b2Password;
    String i2b2Url;
    String i2b2Domain;
    String projectId;
    String patientId;
    List<String> items;

    @Before
    public void init() {
        i2b2User = "demo";//pcori
        i2b2Password = "demouser";
        i2b2Url = "http://services.i2b2.org:9090/i2b2";
        i2b2Domain = "i2b2demo";
        projectId = "Demo";//"pcori";
        patientId = "1000000005";
        items = new ArrayList<String>();
        items.add("\\\\i2b2_LABS\\i2b2\\Labtests\\");
    }

    @Test
    public void getAllPatientMin()
            throws XQueryUtilException, IOException, JAXBException, AuthenticationFailure, FhirCoreException {
        String requestXml = IOUtils
                .toString(I2b2Util.class.getResourceAsStream("/i2b2query/getAllPatientsMin.xml"));

        requestXml = I2b2Util.insertI2b2ParametersInXml(requestXml, i2b2User, i2b2Password, i2b2Url, i2b2Domain);

        if (patientId != null)
            requestXml = requestXml.replaceAll("PATIENTID", patientId);

        String responseXml = WebServiceCall.run(i2b2Url + "/services/QueryToolService/pdorequest", requestXml);
        logger.trace("got response:" + responseXml);
        logger.trace("" + XQueryUtil.getStringSequence("//observation", responseXml).size());
    }

    @Test
    public void validateUser()
            throws XQueryUtilException, IOException, JAXBException, AuthenticationFailure, FhirCoreException {
        String pmResponse = I2b2Util.getPmResponseXml(i2b2User, i2b2Password, i2b2Url, i2b2Domain);
        String i2b2Token = I2b2Util.getToken(pmResponse);
        pmResponse = I2b2Util.getPmResponseXml(i2b2User, i2b2Token, i2b2Url, i2b2Domain);

        List<Project> projMap = I2b2Util.getUserProjectMap(pmResponse);

        Assert.assertEquals(projectId, projMap.get(0).getId());
        //Assert.assertEquals("i2b2 Demo",projMap.get(0).getName());
        //logger.info(pmResponse);
        //logger.info("i2b2Token:"+i2b2Token);
        I2b2Util.getAllPatients(i2b2User, i2b2Token, i2b2Url, i2b2Domain, projMap.get(0).getId());
        String pdoXml = I2b2Util.getAllDataPDO(i2b2User, i2b2Password, i2b2Url, i2b2Domain, projectId, patientId,
                items);
        Bundle b = I2b2Util.getAllDataForAPatientAsFhirBundle(pdoXml);
        logger.info("projMap:" + projMap.toString());
        //logger.info("pdoAllPtDataXml:"+pdoXml);
        logger.info("Patient Bundle size:" + b.getEntry().size());
    }

    @Test
    public void getPDO()
            throws XQueryUtilException, IOException, JAXBException, AuthenticationFailure, FhirCoreException {
        String pdoResponse = I2b2Util.getAllDataPDO(i2b2User, i2b2Password, i2b2Url, i2b2Domain, projectId,
                patientId, items);

        //logger.info("responseXml:"+pdoResponse);
    }

    @Test
    public void getPatientListForAProject()
            throws XQueryUtilException, IOException, JAXBException, AuthenticationFailure {
        String i2b2ResponseXml = I2b2Util.getAllPatients(i2b2User, i2b2Password, i2b2Url, i2b2Domain, projectId);

        logger.info("i2b2ResponseXm:" + i2b2ResponseXml);
        ArrayList<String> list = I2b2Util.getAllPatientsAsList(i2b2ResponseXml);

        logger.info("list:" + list.toString());
    }

    // @Test
    public void getProjectsTest() throws XQueryUtilException {
        String pmResponseXml = Utils.getFile("pmResponse.xml");
        I2b2Util.getUserProjectMap(pmResponseXml);
        // logger.info("::"+I2b2Util.getUserProjectMap(pmResponseXml));
    }

    @Test
    public void getDataForAPatient() throws IOException, XQueryUtilException {
        String requestXml = IOUtils
                .toString(I2b2Util.class.getResourceAsStream("/i2b2query/i2b2RequestNullForAPatient.xml"));

        requestXml = I2b2Util.insertI2b2ParametersInXml(requestXml, i2b2User, i2b2Password, i2b2Url, i2b2Domain);

        if (patientId != null)
            requestXml = requestXml.replaceAll("PATIENTID", patientId);

        String responseXml = WebServiceCall.run(i2b2Url + "/services/QueryToolService/pdorequest", requestXml);
        logger.trace("got response:" + responseXml);
        logger.trace("" + XQueryUtil.getStringSequence("//observation", responseXml).size());
    }

    @Test
    public void getMedsAndLabsForAPatient() throws IOException, XQueryUtilException {
        String requestXml = IOUtils
                .toString(I2b2Util.class.getResourceAsStream("/i2b2query/i2b2RequestMEdsAndLabsForAPatient.xml"));

        requestXml = I2b2Util.insertI2b2ParametersInXml(requestXml, i2b2User, i2b2Password, i2b2Url, i2b2Domain);

        if (patientId != null)
            requestXml = requestXml.replaceAll("PATIENTID", patientId);

        String responseXml = WebServiceCall.run(i2b2Url + "/services/QueryToolService/pdorequest", requestXml);
        logger.trace("got response:" + responseXml);
        logger.trace("" + XQueryUtil.getStringSequence("//observation", responseXml).size());
    }

    @Test
    public void getDocuments() throws IOException {
        /*   
           String path="\\\\i2b2_REP\\i2b2\\Reports\\";
           path="\\\\i2b2_MEDS\\i2b2\\Medications\\";
           List<String> pathList=new ArrayList<String>();
           pathList.add(path);
           I2b2Util.getAllDataForAPatient(Config.getOpenI2b2User(), Config.getOpenI2b2Password(), Config.getI2b2Url(), Config.getI2b2Domain(), Config.getOpenI2b2Project(), Config.getDemoPatientId(), pathList);
        */

        String requestXml = IOUtils
                .toString(I2b2UtilTest.class.getResourceAsStream("/i2b2RequestMedsForAPatient.xml"));
        //   I2b2Util.getI2b2Response(Config.getI2b2Url(), requestXml);

    }
}