public class testkinetikit {
    private SPDBManager dbm;
    private EntityManager em;
    private static Logger log=Logger.getLogger(testkinetikit.class);

    public testkinetikit() {
        try {
            dbm = new SPDBManager();
            em = dbm.getEntityManager();
        } catch (SigPathDatabaseException e) {
            e.printStackTrace();
        }
    }

    private static void initConsoleLogging() {
        String slash = File.separator;
        String loggingConfigFileName = new String ("config" + slash + "logging_console_file.cfg");
        PropertyConfigurator.configure (loggingConfigFileName);
    }

    public static void main(String[] args) {


        testkinetikit tester = new testkinetikit();
        Category root = Category.getRoot();
        //root.setPriority(Priority.INFO);

        initConsoleLogging();
        String model_spid = CLI.getOption(args, "-spid", null);
        String filename=CLI.getOption(args,"-o", model_spid + "-export");

        if (model_spid == null) {
            System.err.println("usage: testkinetikit -spid <model-spid> -o <output filename>");
            System.exit(1);
        }
        try {
            tester.export(model_spid, filename);
        } catch (SigPathDatabaseException e) {
            e.printStackTrace();

        }
        System.out.println("done.");

    }

    /**
     * Export a model in SBML format. Just print the model on stdout.
     */
    public void export(String model_spid, String filename) throws SigPathDatabaseException {

        FileOutputStream out;
        PrintStream p;
        String outTxt;

        TExportModel texport = new TExportModelKK(model_spid);
        texport.setHideDate(true);
        XDebug xdebug = new XDebug();
        xdebug.startTimer();
        texport.execute(xdebug);
        outTxt = ((TExportModel) texport).getOutFile();
        try {
             out = new FileOutputStream(filename);
             out.write(outTxt.getBytes());
             out.flush();
             out.close();

        } catch (Exception e) {
            System.err.println("Error writing to file");
            e.printStackTrace();
            System.exit(10);
        }

    }

}