edu.harvard.i2b2.FhirUtilTest.java Source code

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Here is the source code for edu.harvard.i2b2.FhirUtilTest.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;

import static org.junit.Assert.*;

import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
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.hl7.fhir.Medication;
import org.hl7.fhir.MedicationOrder;
import org.hl7.fhir.Patient;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import edu.harvard.i2b2.fhir.FhirUtil;
import edu.harvard.i2b2.fhir.JAXBUtil;
import edu.harvard.i2b2.fhir.MetaResourceDb;
import edu.harvard.i2b2.fhir.Utils;
import edu.harvard.i2b2.fhir.core.FhirCoreException;
import edu.harvard.i2b2.fhir.query.SearchParameterMap;

public class FhirUtilTest {

    static Logger logger = LoggerFactory.getLogger(FhirUtilTest.class);

    @Test
    public void contain() {
        try {
            // URL path=FhirUtil.class.getResource("validation.zip");
            // System.out.println(FhirUtil.isValid(Utils.getFile("example/fhir/singlePatient.xml")));
            String mpXml = IOUtils.toString(
                    FhirUtilTest.class.getResourceAsStream("/example/fhir/DSTU2/singleMedicationOrder.xml"));
            String mXml = IOUtils
                    .toString(FhirUtilTest.class.getResourceAsStream("/example/fhir/DSTU2/singleMedication.xml"));

            MedicationOrder mp = JAXBUtil.fromXml(mpXml, MedicationOrder.class);
            Medication m = JAXBUtil.fromXml(mXml, Medication.class);

            // logger.info("MP:"+JAXBUtil.toXml(mp));
            // logger.info("MP:"+JAXBUtil.toXml(m));

            logger.info("after containing:" + JAXBUtil.toXml(FhirUtil.containResource(mp, m, m.toString())));
        } catch (Exception e) {
            logger.error(e.getMessage(), e);
        }
    }

    @Test
    public void readMedicationOrder() {
        try {
            String mpXml = IOUtils
                    .toString(FhirUtilTest.class.getResourceAsStream("/example/fhir/DSTU2/MedicationOrder.xml"));

            MedicationOrder mp = JAXBUtil.fromXml(mpXml, MedicationOrder.class);
        } catch (Exception e) {
            logger.error(e.getMessage(), e);
        }
    }

    @Test
    public void extractPatientId() {

        String url = "?Patient=123";
        String id = FhirUtil.extractPatientId(url);
        logger.info("id:" + id);

        url = "?patient=1000000005&_include=medication";
        id = FhirUtil.extractPatientId(url);
        logger.info("id:" + id);

        url = "?_include=medication&patient=1000000005";
        id = FhirUtil.extractPatientId(url);
        logger.info("id:" + id);
    }

    @Test
    public void include() throws IOException, IllegalAccessException, IllegalArgumentException,
            InvocationTargetException, NoSuchMethodException, SecurityException, JAXBException, FhirCoreException {
        Bundle b1 = createMedicationOrderAndMedicationBundle();
        Bundle b2 = createMedicationOrderBundle();
        List<String> includeList = new ArrayList<String>();
        includeList.add("medication");
        MetaResourceDb md1 = new MetaResourceDb();
        md1.addBundle(b1);

        md1.getIncludedResources(MedicationOrder.class, FhirUtil.getResourceListFromBundle(b2), includeList);

    }

    private Bundle createMedicationOrderAndMedicationBundle() throws IOException, JAXBException {
        Bundle b = new Bundle();
        String mpXml = IOUtils
                .toString(FhirUtilTest.class.getResourceAsStream("/example/fhir/DSTU2/singleMedicationOrder.xml"));
        String mXml = IOUtils
                .toString(FhirUtilTest.class.getResourceAsStream("/example/fhir/DSTU2/singleMedication.xml"));

        MedicationOrder mp = JAXBUtil.fromXml(mpXml, MedicationOrder.class);
        Medication m = JAXBUtil.fromXml(mXml, Medication.class);
        MetaResourceDb db = new MetaResourceDb();
        db.addResource(m);
        db.addResource(mp);
        return FhirUtil.getResourceBundle(db.getAll(), "basePath", "url");
    }

    private Bundle createMedicationOrderBundle() throws IOException, JAXBException {
        Bundle b = new Bundle();
        String mpXml = IOUtils
                .toString(FhirUtilTest.class.getResourceAsStream("/example/fhir/DSTU2/singleMedicationOrder.xml"));

        MedicationOrder mp = JAXBUtil.fromXml(mpXml, MedicationOrder.class);
        MetaResourceDb db = new MetaResourceDb();
        db.addResource(mp);
        return FhirUtil.getResourceBundle(db.getAll(), "basePath", "url");
    }
}