edu.utah.bmi.ibiomes.cli.CLIUtils.java Source code

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Here is the source code for edu.utah.bmi.ibiomes.cli.CLIUtils.java

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/*
 * iBIOMES - Integrated Biomolecular Simulations
 * Copyright (C) 2014  Julien Thibault, University of Utah
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package edu.utah.bmi.ibiomes.cli;

import java.io.BufferedReader;
import java.io.Console;
import java.io.IOException;
import java.io.InputStreamReader;

import org.apache.commons.compress.compressors.CompressorException;
import org.irods.jargon.core.exception.AuthenticationException;
import org.irods.jargon.core.exception.JargonException;
import org.irods.jargon.core.pub.IRODSAccessObjectFactory;

import edu.utah.bmi.ibiomes.security.IRODSConnector;
import edu.utah.bmi.ibiomes.security.IRODSEnvironmentFile;

/**
 * Utility functions for iBIOMES command-line interface
 * @author Julien Thibault
 *
 */
public class CLIUtils {

    /**
     * Connect to iBIOMES
     * @return Connection
     * @throws IOException
     * @throws CompressorException 
     */
    public static IRODSConnector getConnection() throws IOException, JargonException, CompressorException {
        return getConnection(null);
    }

    /**
     * Connect to iBIOMES
     * @param password Password
     * @return Connection
     * @throws IOException
     * @throws CompressorException 
     */
    public static IRODSConnector getConnection(String password)
            throws IOException, JargonException, CompressorException {
        return getConnection(null, password, null);
    }

    /**
     * Connect to iBIOMES
     * @param password Password
     * @return Connection
     * @throws IOException
     * @throws CompressorException 
     */
    public static IRODSConnector getConnection(String password, String server)
            throws IOException, JargonException, CompressorException {
        return getConnection(null, password, server);
    }

    /**
     * Connect to iBIOMES
     * @param password Password
     * @return Connection
     * @throws IOException
     * @throws CompressorException 
     */

    public static IRODSConnector getConnection(String username, String password, String server)
            throws IOException, JargonException, CompressorException {
        IRODSEnvironmentFile envFile = null;
        IRODSConnector cnx = null;

        Console objConsole = System.console();
        if (objConsole == null) {
            System.err.println("Console Object is not available.");
            System.exit(1);
        }

        System.out.println("Authentication... ");
        try {
            envFile = IRODSEnvironmentFile.instance();
        } catch (IOException e) {
            System.out.println("IRODS user info file not found!");
            System.out.println("Make sure your .irodsEnv file exists in $HOME/.irods or $IBIOMES_HOME");
            System.exit(1);
        }

        //while login fails
        while (cnx == null) {
            //retrieve iRODS password
            if (password == null) {
                if (username == null)
                    username = envFile.getIrodsUserName();
                System.out.println("iBIOMES password for " + username + ":");
                char[] pwdArray = objConsole.readPassword();
                password = String.copyValueOf(pwdArray);
            }

            //try to connect to iRODS system using default settings
            try {
                cnx = new IRODSConnector(username, password, server);
                try {
                    //try to login
                    IRODSAccessObjectFactory aoFactory = cnx.getFileSystem().getIRODSAccessObjectFactory();
                    aoFactory.getUserAO(cnx.getAccount());
                } catch (JargonException exc) {
                    System.out.println("\nLogin failed. Try again.");
                    cnx = null;
                }
            } catch (IOException ioe) {
                System.out.println("\nCould not find login info...");
                cnx = null;
            } catch (AuthenticationException ae) {
                System.out.println("\nLogin failed. Try again.");
                cnx = null;
            }
            password = null;
        }
        System.out.println("Authentication successful!");
        return cnx;
    }

    /**
     * Connect to iRODS using parameters given in command-line interface.
     * @return Connection object
     * @throws IOException
     * @throws JargonException
     */
    public static IRODSConnector getConnectionFromCLI() throws IOException, JargonException {
        Console objConsole = System.console();
        if (objConsole == null) {
            System.err.println("Console Object is not available.");
            System.exit(1);
        }

        BufferedReader in = new BufferedReader(new InputStreamReader(System.in, "UTF-8"));

        System.out.println("Host:");
        String host = in.readLine();

        System.out.println("Port [1247]:");
        String iPort = in.readLine();

        int port = 1247;
        if (iPort != null && iPort.length() > 0)
            port = Integer.parseInt(iPort);

        System.out.println("Zone:");
        String zone = in.readLine();

        System.out.println("Default resource:");
        String server = in.readLine();

        System.out.println("Username:");
        String userName = in.readLine();

        //retrieve iRODS password
        System.out.println("Password:");
        char[] pwdArray = objConsole.readPassword();
        String password = String.copyValueOf(pwdArray);

        IRODSConnector cnx = new IRODSConnector(host, port, userName, password, "", zone, server);
        try {
            //try to login
            IRODSAccessObjectFactory aoFactory = cnx.getFileSystem().getIRODSAccessObjectFactory();
            aoFactory.getUserAO(cnx.getAccount());
            System.out.println("\nConnected! (" + cnx.getAccount().toURI(false) + ")");
        } catch (JargonException exc) {
            System.out.println("Login info: " + cnx.getAccount().getUserName() + "@" + cnx.getAccount().getHost()
                    + ":" + cnx.getAccount().getPort() + ").");
            System.out.println("Login failed. Try again.");
            cnx = null;
        }
        return cnx;
    }
}