edu.harvard.i2b2.fhirserver.ws.I2b2Helper.java Source code

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Here is the source code for edu.harvard.i2b2.fhirserver.ws.I2b2Helper.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.fhirserver.ws;

import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import javax.annotation.Resource;
import javax.ejb.EJB;
import javax.inject.Inject;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpSession;
import javax.ws.rs.core.Response;
import javax.xml.bind.JAXBException;
import javax.xml.parsers.ParserConfigurationException;

import org.apache.commons.io.IOUtils;
import org.hl7.fhir.Bundle;
import org.hl7.fhir.Patient;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;

import edu.harvard.i2b2.fhir.AuthenticationFailure;
import edu.harvard.i2b2.fhir.FhirEnrich;
import edu.harvard.i2b2.fhir.FhirUtil;
import edu.harvard.i2b2.fhir.I2b2Util;
import edu.harvard.i2b2.fhir.JAXBUtil;
import edu.harvard.i2b2.fhir.MetaResourceDb;
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.fhirserver.ejb.PatientBundleService;

public class I2b2Helper {

    static Logger logger = LoggerFactory.getLogger(I2b2Helper.class);

    static Bundle allPatients = null;

    static Bundle initAllPatients(HttpSession session)
            throws AuthenticationFailure, FhirServerException, XQueryUtilException, JAXBException, IOException {
        if (session == null) {
            return null;
        }
        if (allPatients == null) {// avoid redundant run
            // if (session.getAttribute("INIT_ALL_PATIENTS") != null)
            // return;

            // MetaResourceDb md = I2b2Helper.getMetaResourceDb(session, sbb);
            allPatients = I2b2Util.getAllPatientsAsFhirBundle(session);
            logger.info("Got ResourceSet of size::" + allPatients.getEntry().size());
            // md.addBundle(b);
            // I2b2Helper.saveMetaResourceDb(session, md, sbb);
        }
        return allPatients;
    }

    private static Bundle getPdo(HttpSession session, String patientId, PatientBundleService service)
            throws InterruptedException {
        return service.getPatientBundle(session, patientId);
    }

    static String processXquery(String query, String input) throws XQueryUtilException {
        logger.trace("will run query:" + query + "\n input" + input);
        return XQueryUtil.processXQuery(query, input);
    }

    static String removeSpace(String input) throws ParserConfigurationException, SAXException, IOException {
        // return Utils.getStringFromDocument(Utils.xmltoDOM(input.replaceAll(
        // "(?m)^[ \t]*\r?\n", "")));
        return input.replaceAll("(?m)^[ \t]*\r?\n", "");
        // return input;
    }

    static Bundle parsePatientIdToFetchPDO(HttpServletRequest request, HttpSession session, String resourceName,
            PatientBundleService service) throws XQueryUtilException, JAXBException, IOException,
            AuthenticationFailure, FhirServerException, InterruptedException {
        String patientId = I2b2Helper.extractPatientId(request.getQueryString());
        if (patientId == null)
            patientId = I2b2Helper.extractPatientId2(request.getRequestURL().toString(), resourceName);
        logger.info("PatientId:" + patientId);
        if (patientId != null) {
            // filter.put("Patient", "Patient/" + patientId);
            return I2b2Helper.getPdo(session, patientId, service);
        } else {
            if (resourceName.equals("Patient"))
                return I2b2Helper.initAllPatients(session);

        }
        return null;
    }

    static String extractPatientId(String input) {
        if (input == null)
            return null;
        String id = null;
        Pattern p = Pattern.compile("[Subject:subject|Patient|patient|_id]=([a-zA-Z0-9]+)");
        Matcher m = p.matcher(input);

        if (m.find()) {
            id = m.group(1);
            logger.trace(id);
        }
        return id;
    }

    static String extractPatientId2(String string, String resourceName) {
        logger.debug("requestUrl is:" + string);
        if (string == null)
            return null;
        String id = null;

        Pattern p = Pattern.compile(".*/([a-zA-Z0-9]+)[-]*.*$");
        Matcher m = p.matcher(string);

        if (m.find()) {
            id = m.group(1);
            logger.trace("id:" + id);
        }
        if (id.equals(resourceName))
            id = null;
        return id;
    }

}