edu.harvard.i2b2.fhir.server.ws.I2b2Helper.java Source code

Introduction

Here is the source code for edu.harvard.i2b2.fhir.server.ws.I2b2Helper.java

Source

/*
 * 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.fhir.server.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.oauth2.core.ejb.PatientBundleManager;
import edu.harvard.i2b2.oauth2.core.ejb.ProjectPatientMapManager;
import edu.harvard.i2b2.oauth2.core.entity.AccessToken;

public class I2b2Helper {

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

    static Bundle initAllPatients(AccessToken tok, ProjectPatientMapManager service) throws FhirServerException {
        logger.info("Got request:" + tok);
        Bundle allPatients = service.getProjectPatientBundle(tok);
        logger.info("Got ResourceSet of size::" + allPatients.getEntry().size());
        return allPatients;
    }

    private static Bundle getPdo(AccessToken accessTok, String patientId, PatientBundleManager pBundleMgr,
            ProjectPatientMapManager projPatMapMgr) throws FhirServerException {

        if (projPatMapMgr.hasAccessToPatient(accessTok, patientId)) {
            return pBundleMgr.getPatientBundle(accessTok, patientId);
        } else {
            throw new FhirServerException(
                    "the patientId is invalid for the given access Token: Either the patient Id is invalid or the accessToken is not credientialed to access the given patient");
        }
    }

    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(HttpSession session, String requestUri, String queryString,
            String resourceName, PatientBundleManager service, ProjectPatientMapManager ppmservice,
            String patientId) throws XQueryUtilException, JAXBException, IOException, AuthenticationFailure,
            FhirServerException, InterruptedException {
        AccessToken tok = (AccessToken) session.getAttribute("accessToken");

        //if not specified in call extract from Url
        if (patientId == null) {
            patientId = FhirUtil.extractPatientId(queryString);
        }

        logger.info("PatientId:" + patientId);
        //if also not found in url 
        if (patientId == null)
            patientId = FhirUtil.extractPatientIdFromRequestById(requestUri, resourceName);
        logger.info("PatientId:" + patientId);

        if (patientId != null) {
            // filter.put("Patient", "Patient/" + patientId);
            return I2b2Helper.getPdo(tok, patientId, service, ppmservice);
        } else {
            if (resourceName.equals("Patient")) {
                //throw new FhirServerException("Search on patients is not allowed. Patient id needs to be specified");
                return I2b2Helper.initAllPatients(tok, ppmservice);
            }
        }
        return null;
    }

}