jembossfileauthserver.java

emboss的linux版本的源代码

/****************************************************************
*  
*  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 2
*  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, write to the Free Software
*  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
*
*  @author: Copyright (C) Tim Carver
*
***************************************************************/

package org.emboss.jemboss.server;

import org.emboss.jemboss.JembossParams;
import org.emboss.jemboss.parser.Ajax;

import java.io.*;
import java.util.*;

/**
*
* File manager methods
*
*/
public class JembossFileAuthServer
{

  /** path separator */
  private String ps = new String(System.getProperty("path.separator"));

//get paths to EMBOSS
  /** jemboss properties */
  JembossParams jp = new JembossParams();
  /** emboss binary directory */
  String embossBin = jp.getEmbossBin();
  /** emboss path */
  String embossPath = jp.getEmbossPath();
  /** emboss run environment */
  private String environ = "PATH=" + embossBin + ps + embossPath;


  /**
  *
  * Retrieves the file manager roots on the server
  * @param userName	username
  * @param passwd	passwd
  * @return		file manager roots
  *
  */
  public Vector embreo_roots(String userName, byte[] passwd)
  {
    Ajax aj = new Ajax();
    Vector vans = new Vector();
    if(!verifyUser(aj,userName,passwd,vans))
      return vans;

    String userHomeDir = aj.home+"/";

    vans.add("status");
    vans.add("0");
    vans.add("msg");
    vans.add("");

    vans.add("default-root");
    vans.add("HOME");

    vans.add("HOME");
    vans.add(userHomeDir);

    vans.add("EMBOSS results");
    vans.add("/tmp/SOAP/emboss/"+userName);
 
//ADD IN OTHER USER ROOT DIRECTORIES HERE

//  System.out.println(userHomeDir);
//  vans.add("SCRATCH");
//  vans.add("/m3/users/tim/soap");
  
    return vans;
  }


  /**
  *
  * Given a file manager root alias e.g. "HOME" return
  * the directory this represents
  * @param s		root alias (e.g "HOME")
  * @param userName	username
  * @param passwd	passwd
  * @return 		directory path
  *
  */
  private String getRoot(String s, String userName, byte[] passwd)
  {
    String rt = null;
    Vector userRoots = embreo_roots(userName,passwd);
 
    for(int i=0; i<userRoots.size();i+=2)
    {
      String root = (String)userRoots.get(i);
      if(root.equalsIgnoreCase(s))
        return (String)userRoots.get(i+1);
    }

    return rt;
  }


  /**
  *
  * Get a directory listing
  * @param option	root alias
  * @param dirname	direcory name
  * @param userName     username
  * @param passwd       passwd
  * @return             directory listing
  *
  */
  public Vector directory_shortls(String options, String dirname,
                           String userName, byte[] passwd)
  {

    Vector vans = new Vector();
    Ajax aj = new Ajax();
    if(!verifyUser(aj,userName,passwd,vans))
      return vans;

    int split = options.indexOf("=")+1;

    aj.listFiles(userName,passwd,environ,
                 getRoot(options.substring(split),userName,passwd)
                 + "/" + dirname);
    String listAll = aj.getOutStd();

//  System.out.println("listAll "+listAll+" STDERR "+aj.getErrStd());
    aj.listDirs(userName,passwd,environ,
                 getRoot(options.substring(split),userName,passwd)
                 + "/" + dirname);
    String listDir = aj.getOutStd();

    listAll = listAll.concat("\n"+listDir); 

    vans.add("status");
    vans.add("0");
    vans.add("msg");
    vans.add("");
    vans.add("list");
    vans.add(listAll);
    vans.add("dirlist");
    vans.add(listDir);

    for(int i=0;i<passwd.length;i++)
      passwd[i] = '\0';

    return vans;
  }

  /**
  *
  * Get the contents of a file
  * @param option       root alias
  * @param dirname      file name
  * @param userName     username
  * @param passwd       passwd
  * @return             file contents
  *
  */
  public Vector get_file(String options, String filename,
                           String userName, byte[] passwd)
  {

    Vector vans = new Vector();
    Ajax aj = new Ajax();

    int split = options.indexOf("=")+1;    
    String fullFileName = getRoot(options.substring(split),userName,passwd)
                         + "/" + filename;

    byte fbuf[] =  aj.getFile(userName,passwd,environ,
                              fullFileName);
    
    if(aj.getFileok()==1)
    {
      vans.add("contents");
      if(aj.getPrnt() == 1)
        vans.add(new String(fbuf));
      else
        vans.add(fbuf);
    }
    else
      System.out.println("Cannot getFile "+fullFileName);

    vans.add("status");
    vans.add("0");
    vans.add("msg");
    vans.add("");

    for(int i=0;i<passwd.length;i++)
      passwd[i] = '\0';

    return vans;
  } 


  /**
  *
  * Make a directory
  * @param option 	root alias
  * @param dirname	name of new directory
  * @param userName     username
  * @param passwd       passwd
  * @return         	message
  *    
  */
  public Vector mkdir(String options, String dirname,
                      String userName, byte[] passwd)
  {
    Vector vans = new Vector();
    Ajax aj = new Ajax();

    int split = options.indexOf("=")+1;
    String fullDirname = getRoot(options.substring(split),userName,passwd)+
                           "/" + dirname;
    boolean ok=true;
    try
    {
      ok = aj.makeDir(userName,passwd,environ,fullDirname);
    }
    catch(Exception exp){}
    vans.add("msg");
    if(ok)
      vans.add("");
    else
      vans.add("NOT OK");

    for(int i=0;i<passwd.length;i++)
      passwd[i] = '\0';

    return vans;
  }

  /**
  *
  * Delete a file
  * @param option       root alias
  * @param filename	file name
  * @param userName     username
  * @param passwd       passwd
  * @return             message
  *
  */
  public Vector delFile(String options, String filename,
                        String userName, byte[] passwd)
  {
    Vector vans = new Vector();
    Ajax aj = new Ajax();
  
    int split = options.indexOf("=")+1;
    String fullname = getRoot(options.substring(split),userName,passwd)+
                             "/" + filename;
    boolean ok=true;
    try
    {
      ok = aj.delFile(userName,passwd,environ,fullname);
    }
    catch(Exception exp){}

    vans.add("msg");
    if(ok)
      vans.add("");
    else
      vans.add("NOT OK");

    for(int i=0;i<passwd.length;i++)
      passwd[i] = '\0';

    return vans;
  }

  /**
  *
  * Delete a directory
  * @param option       root alias
  * @param filename     directory name
  * @param userName     username
  * @param passwd       passwd
  * @return             message
  *
  */
  public Vector delDir(String options, String filename,
                       String userName, byte[] passwd)
  {
    Vector vans = new Vector();
    Ajax aj = new Ajax();

    int split = options.indexOf("=")+1;
    String fullname = getRoot(options.substring(split),userName,passwd)+
                             "/" + filename;
    boolean ok=true;
    try
    {
      ok = aj.delDir(userName,passwd,environ,fullname);
    }
    catch(Exception exp){}

    vans.add("msg");
    if(ok)
      vans.add("");
    else
      vans.add("NOT OK");

    for(int i=0;i<passwd.length;i++)
      passwd[i] = '\0';

    return vans;
  }


  /**
  *
  * Rename a file
  * @param option       root alias
  * @param oldfile	old file name
  * @param newfile	new file name
  * @param userName     username
  * @param passwd       passwd
  * @return             message
  *
  */
  public Vector rename(String options, String oldfile, String newfile,
                       String userName, byte[] passwd)
  {
    Vector vans = new Vector();
    Ajax aj = new Ajax();

    int split = options.indexOf("=")+1;
    String oldname = getRoot(options.substring(split),userName,passwd)+
                             "/" + oldfile;
    boolean ok=true;
    try
    {
      ok = aj.renameFile(userName,passwd,environ,oldname,newfile);
    }
    catch(Exception exp){}
    vans.add("msg");
    if(ok)
      vans.add("");
    else
      vans.add("NOT OK");

    for(int i=0;i<passwd.length;i++)
      passwd[i] = '\0';

    return vans;
  }


  /**
  *
  * Put a file on the server file system
  * @param option 	root alias
  * @param filename 	name of file to add
  * @param filedata 	file contents
  * @param userName     username
  * @param passwd       passwd
  * @return             message
  *
  */
  public Vector put_file(String options, String filename, byte[] filedata,
                           String userName, byte[] passwd)
  {
    Vector vans = new Vector();
    Ajax aj = new Ajax();

    int split = options.indexOf("=")+1;
    String fullFilename = getRoot(options.substring(split),userName,passwd)+
                            "/" + filename;
    aj.putFile(userName,passwd,environ,fullFilename,filedata);

    vans.add("msg");
    vans.add("");
 
    for(int i=0;i<passwd.length;i++)
      passwd[i] = '\0';

    return vans;
  }
 
  /**
  *
  * Verify the username/passwd
  * @param aj           ajax/jni
  * @param userName     username
  * @param passwd       password
  * @param res          results vector
  * @return             true if authenticated ok
  *
  */
  private boolean verifyUser(Ajax aj, String userName,
                             byte[] passwd, Vector res)
  {

    if(userName == null || passwd == null)
    {
//    System.out.println("Failed Authorisation "+userName);
      res.add("msg");
      res.add("Failed Authorisation ");
      res.add("status");
      res.add("1");
      return false;
    }

    boolean ok = false;

    try
    {
      ok = aj.userAuth(userName,passwd,environ);
    }
    catch(Exception exp) 
    {
      ok = false;
    }

    if(!ok)
    {
      System.out.println("Failed Authorisation "+userName);
      System.out.println("STDERR "+aj.getErrStd());
      res.add("msg");
      res.add("Failed Authorisation "+userName);
      res.add("status");
      res.add("1");
      return false;
    }

    return true;
  }

}