edu.harvard.i2b2.PreProcessFhirSpec.java Source code

Introduction

Here is the source code for edu.harvard.i2b2.PreProcessFhirSpec.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
 */

/*
 * 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)
 */
package edu.harvard.i2b2;

import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;

import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import edu.harvard.i2b2.fhir.Utils;
import edu.harvard.i2b2.fhir.XQueryUtil;
import edu.harvard.i2b2.fhir.XQueryUtilException;

public class PreProcessFhirSpec {
    static Logger logger = LoggerFactory.getLogger(PreProcessFhirSpec.class);

    public PreProcessFhirSpec() throws IOException, XQueryUtilException {
        logger.trace("hi");
        ArrayList<String> resourceList = new ArrayList<String>();
        resourceList.add("Patient".toLowerCase());
        resourceList.add("Medication".toLowerCase());
        resourceList.add("MedicationStatement".toLowerCase());
        resourceList.add("Observation".toLowerCase());
        ZipFile zipFile = new ZipFile(Utils.getFilePath("fhir-spec.zip"));// fhir-all-xsd.zip
        logger.trace("" + zipFile.getName());

        Enumeration<? extends ZipEntry> entries = zipFile.entries();

        for (String rName : resourceList) {
            String fName = "site/" + rName + ".profile.xml";
            logger.trace("" + zipFile.getEntry(fName));
            String fContent = IOUtils.toString(zipFile.getInputStream(zipFile.getEntry(fName)));
            logger.trace("" + XQueryUtil.processXQuery(
                    "declare default element namespace \"http://hl7.org/fhir\";//searchParam", fContent));

        }

        /*while (entries.hasMoreElements()) {
           ZipEntry entry = entries.nextElement();
           if(!entry.getName().matches(".*\\.html$")) continue;
           Pattern p = Pattern.compile("^site/([^\\.\\\\]*)\\..*$");
           Matcher m = p.matcher(entry.getName());
           String rname="";
           if (m.matches()) {
        //logger.trace("" + entry.getName() + "->" + m.group(1));
        rname=m.group(1).toLowerCase();
           }
               
           if (resourceList.contains(rname))
        logger.trace(entry.getName()+"->" + rname);
           // InputStream stream = zipFile.getInputStream(entry);
               
        }*/

    }

    public static void main(String[] args) throws IOException, XQueryUtilException {
        new PreProcessFhirSpec();

    }

}