jembossauthserver.java

emboss的linux版本的源代码

  /**
  *
  * Returns the results for a saved project.
  * @param project 	project directory name
  * @param cl		unused if showing all results 
  *			otherwise this is the name of 
  *    			the file to display
  * @param userName	username
  * @param passwd	passwd
  * @return 		saved results files
  *
  */
  public Vector show_saved_results(String project, String cl,
                              String userName, byte[] passwd)
  {

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

    project = tmproot.concat(userName+fs+project);

    if(cl.equals(""))
    {
      File projectDir = new File(project);
      ssr = loadFilesContent(aj,userName,passwd,
                      projectDir,project,ssr,null);
    }
    else
    {
      byte fbuf[]=null;
      try
      {
        fbuf =  aj.getFile(userName,passwd,environ,
                                  project+fs+cl);
        ssr.add(cl);
        ssr.add(new String(fbuf));
      }
      catch(Exception exp){}
    }
 
    ssr.add("status");
    ssr.add("0");
    ssr.add("msg");
    ssr.add("OK");

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

    return ssr;
  }

  /**
  *  
  * Save a file to a project directory on the server.
  * @return 	message
  *
  */
  public Vector save_project_file(String project, String filename, 
                    String notes, String userName, byte[] passwd)
  {
    Ajax aj = new Ajax();
    Vector v = new Vector(4);
    if(!verifyUser(aj,userName,passwd,v))
    {
      v.trimToSize();
      return v;
    }

    final String fn = tmproot + fs + userName+ fs + 
                     project + fs + filename;
    boolean ok = aj.putFile(userName,passwd,environ,
                            fn,notes.getBytes());

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

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

    if(ok)
      v.add("OK"); 
    else
      return returnError(aj,"Failed to save file "+fn,userName);
        
    return v;
  }

  /**
  *  
  * Deletes a projects saved results.
  * @param project	project directory name
  * @param cl		unused
  * @param userName	username
  * @param passwd	passwd
  * @return message
  *
  */
  public Vector delete_saved_results(String project, String cl,
                                String userName, byte[] passwd)
  {
    Vector dsr = new Vector(4);
    Ajax aj = new Ajax();
    if(!verifyUser(aj,userName,passwd,dsr))
    {
      dsr.trimToSize();
      return dsr;
    }

    tmproot = tmproot.concat(userName+fs);

    StringTokenizer st = new StringTokenizer(project,"\n");
    while(st.hasMoreTokens()) 
    {
      String proj = tmproot.concat(st.nextToken());
      boolean ok = aj.delDir(userName,passwd,environ,proj);
      if(!ok || !aj.getErrStd().equals(""))
        return returnError(aj,"Failed deletion of directory "+proj,userName);
    }

    dsr.add("status");
    dsr.add("0");
    dsr.add("msg");
    dsr.add("Results deleted successfully.");

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

    return dsr;
  }


  /**
  *
  * List of the saved results on the server.
  * @param userName     username
  * @param passwd       passwd
  * @return 		list of the saved results.
  *
  */
  public Vector list_saved_results(String userName, byte[] passwd)
  {
    Ajax aj = new Ajax();
    Vector lsr = new Vector();
    if(!verifyUser(aj,userName,passwd,lsr))
      return lsr;

    tmproot = tmproot.concat(userName+fs);

    lsr.add("status");
    lsr.add("0");
    lsr.add("msg");
    lsr.add("OK");

    aj.setErrStd();
    boolean lsd = aj.listDirs(userName,passwd,environ,tmproot);
    
    String outStd = aj.getOutStd();

    int indStart = 0;
    int indEnd   = 0;
//  StringTokenizer stok = new StringTokenizer(outStd,"\n");
//  while(stok.hasMoreTokens())
    while((indEnd = outStd.indexOf("\n",indStart)) > -1) 
    {
//    String dirname = stok.nextToken();
      String dirname = outStd.substring(indStart,indEnd);
      indStart = indEnd+1;

      lsr.add(dirname);
      byte fbuf[] = aj.getFile(userName,passwd,environ,
                     tmproot + dirname + fs + ".desc");
      lsr.add(new String(fbuf));

      if(aj.getFileok()!=1)
      {
        String dat = new Date().toString();
        dat = dat.replace(':','_');

        appendToLogFile(userName+":: "+dat+" Calling getFile : "+tmproot +
                        dirname + fs + ".desc\n"+
                        "STDERR "+aj.getErrStd()+"\n"+
                        "STDOUT "+aj.getOutStd(),errorLog);
      }
    }
    
    lsr.add("list");
    lsr.add(outStd);

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

    return lsr;
  }


  /**
  *
  * Appends a log entry to the log file
  * @param logEntry	entry to add to log file
  * @param logFileName 	log file name
  *
  */ 
  private void appendToLogFile(String logEntry, String logFileName)
  {
    BufferedWriter bw = null;
    try 
    {
      bw = new BufferedWriter(new FileWriter(logFileName, true));
      bw.write(logEntry);
      bw.newLine();
      bw.flush();
    } 
    catch (Exception ioe) 
    {
      System.out.println("Error writing to log file "+logFile);
      ioe.printStackTrace();
    } 
    finally                     // always close the file
    {                       
      if(bw != null) 
      try
      {
        bw.close();
      } 
      catch (IOException ioe2) {}
    }

  }


  /**
  *
  * Reads in files from EMBOSS output
  * @param aj		ajax/jni
  * @param userName	username
  * @param passwd	passwd
  * @param projectDir	project directory
  * @param project     	project name
  * @param result	results
  * @param inFiles	input files
  * @return		result
  *
  */
  private Vector loadFilesContent(Ajax aj, String userName, 
            byte[] passwd, File projectDir, String project,
            Vector result, Vector inFiles)
  {

    boolean ls = false;

    try
    {
      ls = aj.listFiles(userName,passwd,environ,project);
    }
    catch(Exception exp){}

    if(!ls)
    {
      String dat = new Date().toString();
      dat = dat.replace(':','_');

      appendToLogFile(userName+":: "+dat+
                      " Failed loadFilesContent\n"+
                      "STDERR "+aj.getErrStd()+"\n"+
                      "STDOUT "+aj.getOutStd(),errorLog);
    }

    StringTokenizer stok = new StringTokenizer(aj.getOutStd(),"\n");
    String fn =  null;
    while(stok.hasMoreTokens()) 
    {
      fn = stok.nextToken();
      if(inFiles == null || !inFiles.contains(fn))
      {
        byte fbuf[]=null;
        try
        {
          fbuf =  aj.getFile(userName,passwd,environ,
                                    project+fs+fn);
        }
        catch(Exception exp){}
        if(aj.getFileok()==1)
        {
          result.add(fn);
          result.add(fbuf);
        }
        else
        {
          String dat = new Date().toString();
          dat = dat.replace(':','_');

          appendToLogFile(userName+":: "+dat+
                          " Cannot getFile "+project+fs+fn,errorLog);
        }
      }
    }

    return result;
  }


  /**
  *
  * Used to provide information on the batch/background
  * processes.
  * @param prog         program
  * @param opt          options
  * @param resToQuery   results to query
  * @param userName     username
  * @param passwd       passwd
  *
  */
  public Vector update_result_status(String prog, String opt,
                        Vector resToQuery,String userName,
                        byte[] passwd)
  {
    Ajax aj = new Ajax();
    Vector vans = new Vector();
    if(!verifyUser(aj,userName,passwd,vans))
      return vans;

    tmproot = tmproot.concat(userName+fs);

    for(Enumeration e = resToQuery.elements() ; e.hasMoreElements() ;)
    {
      String thiskey = (String)e.nextElement();
      e.nextElement();

      try
      {
        aj.getFile(userName,passwd,environ,
                 tmproot+thiskey+fs+".finished");
      }
      catch(Exception ex){}

      if((aj.getErrStd().indexOf("stat error") == -1) &&
         (aj.getFileok()==1))
      {
        vans.add(thiskey);
        vans.add("complete");
        
        byte fbuf[] = aj.getFile(userName,passwd,environ,
                tmproot + fs + thiskey+ fs + ".desc");

        if(aj.getFileok()==1)
        {
          vans.add(thiskey+"-description");
          vans.add(new String(fbuf));
        }
      }
      else
      {
        vans.add(thiskey);
        vans.add("pending");
      }
    }

    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)
    {
      String dat = new Date().toString();
      dat = dat.replace(':','_');

      appendToLogFile(userName+":: "+dat+
                      " Failed Authorisation "+userName+"\n"+
                      "STDERR "+aj.getErrStd(),errorLog);
      res.add("msg");
      res.add("Failed Authorisation "+userName);
      res.add("status");
      res.add("1");
      return false;
    }

    return true;
  }

  /**
  *
  * Report the stderr and stdout to error logs
  * @param aj	ajax/jni
  * @param msg 	message
  * @return	vector containing the message 
  *
  */
  private Vector returnError(Ajax aj, String msg, String userName)
  {
    String dat = new Date().toString();
    dat = dat.replace(':','_');

    appendToLogFile(userName+":: "+dat+
                    " STDERR "+aj.getErrStd()+"\n"+
                    "STDOUT "+aj.getOutStd()+"\n"+
                    "MSG    "+msg,errorLog);

    Vector vans = new Vector(4);
    vans.add("msg");
    vans.add(aj.getErrStd());

    vans.add("status");
    vans.add("1");
    return vans;
  }

  public final Object clone() throws java.lang.CloneNotSupportedException
  {
    throw new java.lang.CloneNotSupportedException();
  }

}