org.LexGrid.LexBIG.admin.LoadMrMap.java Source code

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Here is the source code for org.LexGrid.LexBIG.admin.LoadMrMap.java

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/*
 * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and 
 * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
 * triple-shield Mayo logo are trademarks and service marks of MFMER.
 *
 * Except as contained in the copyright notice above, or as used to identify 
 * MFMER as the author of this software, the trade names, trademarks, service
 * marks, or product names of the copyright holder shall not be used in
 * advertising, promotion or otherwise in connection with this software without
 * prior written authorization of the copyright holder.
 * 
 * Licensed under the Eclipse Public License, Version 1.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at 
 * 
 *       http://www.eclipse.org/legal/epl-v10.html
 * 
 */
package org.LexGrid.LexBIG.admin;

import java.net.URI;
import java.util.HashMap;
import java.util.Map;

import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException;
import org.LexGrid.LexBIG.Extensions.Load.MrMap_Loader;
import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl;
import org.LexGrid.LexBIG.LexBIGService.LexBIGService;
import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager;
import org.LexGrid.relations.Relations;
import org.apache.commons.cli.BasicParser;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.lexevs.system.ResourceManager;

import edu.mayo.informatics.lexgrid.convert.directConversions.mrmap.MappingRelationsUtil;

public class LoadMrMap {

    public static void main(String[] args) {
        try {
            new LoadMrMap().run(args);
        } catch (LBResourceUnavailableException e) {
            Util.displayTaggedMessage(e.getMessage());
        } catch (Exception e) {
            Util.displayAndLogError("REQUEST FAILED !!!", e);
        }
    }

    public LoadMrMap() {
        super();
    }

    /**
         * Primary entry point for the program.
         * 
         * @throws Exception
         */
    public void run(String[] args) throws Exception {
        synchronized (ResourceManager.instance()) {

            // Parse the command line ...
            CommandLine cl = null;
            Options options = getCommandOptions();
            try {
                cl = new BasicParser().parse(options, args);

            } catch (Exception e) {
                Util.displayCommandOptions("LoadMrMapp", options,
                        "\n LoadMrMapp -inMap \"file:///path/to/MRMAP.RRF \" -inSat \"file:///path/to/MRSAT.RRF\" "
                                + Util.getURIHelp(),
                        e);
                return;
            }

            // Interpret provided values ...
            URI source = Util.string2FileURI(cl.getOptionValue("inMap"));
            URI sourceSat = Util.string2FileURI(cl.getOptionValue("inSat"));

            Util.displayTaggedMessage("LOADING FROM URI FOR MRMAP: " + source.toString());
            Util.displayTaggedMessage("LOADING FROM URI FOR MRSAT: " + sourceSat.toString());
            Util.displayTaggedMessage("POST LOAD AND ACTIVATION AVAILABLE ONLY ON MRMAP LOADS");

            // Find the registered extension handling this type of load ...
            LexBIGService lbs = LexBIGServiceImpl.defaultInstance();
            LexBIGServiceManager lbsm = lbs.getServiceManager(null);
            MappingRelationsUtil mapUtil = new MappingRelationsUtil();
            HashMap<String, Relations> relations = mapUtil.processMrSatBean(sourceSat.getPath(), source.getPath());

            for (Map.Entry<String, Relations> rel : relations.entrySet()) {
                Relations relation = rel.getValue();
                System.out.println("relation : " + relation.getSourceCodingScheme());
                MrMap_Loader loader = (MrMap_Loader) lbsm
                        .getLoader(org.LexGrid.LexBIG.Extensions.Load.MrMap_Loader.name);

                loader.load(source, sourceSat, null, null, null, null, null, null, null, null, null, rel, false,
                        true);
                Util.displayLoaderStatus(loader);
            }

        }
    }

    /**
     * Return supported command options.
     * 
     * @return org.apache.commons.cli.Options
     */
    private Options getCommandOptions() {
        Options options = new Options();
        Option o;

        o = new Option("inMap", "input", true, "URI or path specifying location of the source file.");
        o.setArgName("uri");
        o.setRequired(true);
        options.addOption(o);

        o = new Option("inSat", "input", true, "URI or path specifying location of the source file.");
        o.setArgName("uri");
        o.setRequired(true);
        options.addOption(o);

        return options;
    }

}