/**
 * \file    validateSBML.java
 * \brief   Validates an SBML document using the SBML.org Online Validator
 * \author  Ben Bornstein <sbml-team@caltech.edu>
 * \author  Akiya Jouraku <sbml-team@caltech.edu>
 *
 * $Id$
 * $Source$
 *
 * Copyright (C) 2009-2011 jointly by the following organizations: 
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
 *  
 * Copyright (C) 2006-2008 by the California Institute of Technology,
 *     Pasadena, CA, USA 
 *  
 * Copyright (C) 2002-2005 jointly by the following organizations: 
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. Japan Science and Technology Agency, Japan
 * 
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published
 * by the Free Software Foundation; either version 2.1 of the License, or
 * any later version.
 * 
 * This software 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.  The software and
 * documentation provided hereunder is on an "as is" basis, and the
 * copyright holders have no obligations to provide maintenance, support,
 * updates, enhancements or modifications.  In no event shall the copyright
 * holders be liable to any party for direct, indirect, special, incidental
 * or consequential damages, including lost profits, arising out of the use
 * of this software and its documentation, even if the copyright holders
 * have been advised of the possibility of such damage.  See the GNU Lesser
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; if not, write to the Free Software Foundation,
 * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
 */


import java.net.URL;
import java.net.URLConnection;

import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.IOException;

import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Random;
import java.util.regex.Pattern;
import java.util.regex.Matcher;


/**
 * Performs a Multipart HTTP post to the given URL.  A post operation
 * is started with the creation of a MultipartPost object.  Post
 * parameters are sent with writeParameter() and may be eithier
 * strings or the contents of an XML file.  A post is finished by
 * calling done() which returns an InputStream for reading the servers
 * response.
 *
 * NOTE: This class is meant to communicate with the SBML.org online
 * validator.  As such, it assumes uploaded files are XML and always
 * sends a Content-Type: text/xml.
 */
class MultipartPost
{
  public MultipartPost (String url) throws IOException
  {
    Random random = new Random();

    connection  = ( new URL(url) ).openConnection();
    boundary    = "<<" + Long.toString(random.nextLong(), 30);
    String type = "multipart/form-data; boundary=" + boundary;

    connection.setDoOutput(true);
    connection.setRequestProperty("Content-Type", type);

    stream = connection.getOutputStream();
  }

  public InputStream done () throws IOException
  {
    writeln("--" + boundary + "--");
    writeln();

    stream.close();

    return connection.getInputStream();
  }

  public void writeParameter (String name, String value) throws IOException
  {
    writeln("--" + boundary);
    writeln("Content-Disposition: form-data; name=\"" + name + "\"");
    writeln();
    writeln(value);
  }

  public void writeParameter (String name, File file) throws IOException
  {
    String prefix = "Content-Disposition: form-data; name=\"file\"; filename=";

    writeln("--" + boundary);
    writeln(prefix + '"' + file.getName() + '"');
    writeln("Content-Type: text/xml");
    writeln();

    InputStream source = new FileInputStream(file);
    copy(source, stream);

    writeln()
    stream.flush();
    source.close();
  }

  void copy (InputStream source, OutputStream destination) throws IOException
  {
    byte[] buffer = new byte[8192];
    int    nbytes = 0;

    while ((nbytes = source.read(buffer, 0, buffer.length)) >= 0)
    {
      destination.write(buffer, 0, nbytes);
    }
  }

  void writeln (String s) throws IOException
  {
    write(s);
    writeln();
  }

  void writeln () throws IOException
  {
    write('\r');
    write('\n');
  }

  void write (char c) throws IOException
  {
    stream.write(c);
  }

  void write (String s) throws IOException
  {
    stream.write(s.getBytes());
  }


  URLConnection connection;
  OutputStream  stream;
  String        boundary;
}


/**
 * SBMLValidator is simply a container for the static method
 * validateSBML(filename, parameters).
 */
class SBMLValidator
{
  public static String validatorURL = "http://sbml.org/validator/";

  /**
   * Validates the given SBML filename (or http:// URL) by calling the
   * SBML.org online validator. The results are returned as an
   * InputStream whose format may be controlled by setting
   * parameters.put("output", ...) to one of: "xml", "xhtml", "json",
   * "text" (default: xml).
   *
   * @return an InputStream containing the validation results.
   */
  public static InputStream validateSBML (String filename, Map parameters)
    throws IOException
  {
    if (parameters.get("output") == null)
    {
      parameters.put("output", "xml");
    }

    MultipartPost post   = new MultipartPost(validatorURL);
    InputStream   result = null;

    if (filename.startsWith("http://"))
    {
      post.writeParameter("url", filename);
    }
    else
    {
      post.writeParameter("file", new File(filename));
    }

    try
    {
      Iterator iter = parameters.keySet().iterator();

      while ( iter.hasNext() )
      {
        String name  = (String) iter.next();
        String value = (String) parameters.get(name);

        post.writeParameter(name, value);
      }
    }
    catch (NoSuchElementException e)
    {
      e.printStackTrace();
    }

    return post.done();
  }
}


/**
 * usage: java validateSBML [-h] [-o output-format] [-d opt1[,opt2,...]] filename.xml  
 * usage: java validateSBML [-h] [-o output-format] [-d opt1[,opt2,...]] http://... 
 *
 * Validates the SBML document given by filename.xml or located at
 * the http:// URL.  Output-format is optional and may be one of:
 * xml, xhtml, json, text (default: xml)
 */
public class validateSBML
{
  static void usage ()
  {
    String usage =
      "usage: java validateSBML [-h] [-o output-format] [-d opt1[,opt2,...]] filename.xml\n" + 
      "usage: java validateSBML [-h] [-o output-format] [-d opt1[,opt2,...]] http://..." + 
      "\n\n" +
      "  Validates the SBML document given by filename.xml or located at\n" +
      "  the http:// URL." + 
      "\n\n" + 
      "Options:\n\n" +
      "  -o output-format\n" +
      "    Specify an output format.\n\n" +
      "      xml   : XML (Default)\n" +
      "      xhtml : XHTML\n" +
      "      text  : plain text\n" +
      "      json  : JavaScript Object Notation\n\n" +
      "  -d opt1[,opt2,...]\n" +
      "    Disable the given consistency check options.\n" +
      "    The options are given as comma-separated characters.\n" +
      "    Each character is one of the followings:\n\n" +
      "      u : disable the units consistency check\n" +
      "      g : disable the overall SBML consistency check\n" +
      "      i : disable the identifier consistency check\n" +
      "      m : disable the MathML consistency check\n" +
      "      s : disable the SBO consistency check\n" +
      "      o : disable the overdetermined model check\n" +
      "      p : disable the modeling practice check\n\n" +
      "  -h  : Print this usage and exit.\n"; 

    System.out.println(usage);
    System.exit(1);
  }

  public static void main (String[] args)
  {
    String filename = null;
    String output   = "xml";
    String offcheck = null;

    /**
     *
     * Parse the command-line arguments.
     *
     */
    for (int i=0; i < args.length; i++)
    {
      if ( args[i].equals("-h") )
      {
        usage();
      }
      else if ( args[i].equals("-o") )
      {
        if ( (i+1) >= args.length ) 
        {
         usage();
        }

        Pattern p = Pattern.compile("(xml|xhtml|json|text)"); 
        Matcher m = p.matcher(args[i+1]);
        if ( ! m.matches() )
        {
          usage();
        }

        output = args[++i]; 
      }
      else if ( args[i].equals("-d") )
      {
        if ( (i+1) >= args.length ) 
        {
         usage();
        }
        Pattern p = Pattern.compile("[a-zA-Z](,[a-zA-Z])*"); 
        Matcher m = p.matcher(args[i+1]);
        if ( ! m.matches() )
        {
          usage();
        }

        offcheck = args[++i]; 
      }
      else if ( args[i].startsWith("-") )
      {
        // invalid option 
        usage();
      }
      else
      {
        // currently only one filename (url) can be given.
        if ( (i+1) < args.length )
        {
          usage();
        }
        filename = args[i];
      }
    }

    if ( filename == null)
    {
      usage();
    }

    try
    {
      HashMap       parameters = new HashMap();
      InputStream   result     = null;

      parameters.put("output", output);
      if ( offcheck != null )
      {
        parameters.put("offcheck", offcheck);
      }

      result = SBMLValidator.validateSBML(filename, parameters);

      print(result, System.out);
      result.close();
    }
    catch (IOException e)
    {
      e.printStackTrace();
    }
  }

  static void print (InputStream source, OutputStream destination)
    throws IOException
  {
    byte[] buffer = new byte[8192];
    int    nbytes = 0;

    while ((nbytes = source.read(buffer, 0, buffer.length)) >= 0)
    {
      destination.write(buffer, 0, nbytes);
    }

    destination.flush();
  }
}