jembossauthserver.java

emboss的linux版本的源代码

      matrices.append(dataFile[i]+"\n");
    showdbOut.add("codons");
    showdbOut.add(matrices.toString());

    return showdbOut;
  }


  /**
  *
  * Run an emboss application
  * @param embossCommand        command line to run
  * @param options              options
  * @param inFiles              input files
  * @param userName             userName
  * @param passwd               passwd
  * @return 			output files from application run
  *
  */
  public synchronized Vector run_prog(String embossCommand, String options,
                            Vector inFiles, String userName, byte[] passwd)
  {
    tmproot = tmproot.concat(userName+fs);
    Ajax aj = new Ajax();
    Vector result = new Vector(6,1);

    if(!verifyUser(aj,userName,passwd,result))
      return result;

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

    //disallow multiple command constructions
    if(embossCommand.indexOf(";") > -1) 
    {
      String warn = new String(userName+":: "+dat+
                               " ERROR: Disallowed command syntax "+
                               embossCommand);
      appendToLogFile(warn,errorLog);
      result.add("msg");
      result.add(warn);
      result.add("status");
      result.add("1");
      result.trimToSize();
      return result;
    }

    //trap anything that is trying to write to stdout
    int stdIndex = embossCommand.indexOf(" stdout ");
    if(stdIndex > -1)
    {
      String startCmd = embossCommand.substring(0,stdIndex+7);
      String endCmd = embossCommand.substring(stdIndex+8);
      embossCommand = startCmd.concat("file ");
      embossCommand = embossCommand.concat(endCmd);
    }

    boolean ok = false; 
// listing of users root directory
    try
    { 
      aj.setErrStd();
      ok = aj.listDirs(userName,passwd,environ,tmproot);
    }
    catch(Exception exp){}


// create the results directory structure for this user if necessary
    if(!ok)
    {
      try
      {
        aj.setErrStd();
        ok = aj.makeDir(userName,passwd,environ,tmproot);
      }
      catch(Exception exp){}

//    if(ok && aj.getErrStd().equals(""))
//    Linux fix - ignore stderr here
      if(ok)
        appendToLogFile(userName+":: "+dat+" Created directory "+tmproot,errorLog);
      else
      {
        String warnmsg = new String(userName+":: "+dat+" Failed to create dir "+tmproot+
                                    "\nSTDERR :"+ aj.getErrStd());
        appendToLogFile(warnmsg,errorLog);
        result.add("msg");
        result.add(warnmsg);
        result.add("status");
        result.add("1");
        result.trimToSize();
        return result;
      }
    }

//get a unique project name
    String appl = embossCommand.substring(0,embossCommand.indexOf(" "));
    Random rnd = new Random();
    String project = new String(tmproot + appl + "_" +
         dat.replace(' ','_') + "_" + rnd.nextInt(99999));

    try
    {
      aj.setErrStd();
      ok = aj.makeDir(userName,passwd,environ,project);
    }
    catch(Exception exp){}

    if(!ok) 
      return returnError(aj,"run_prog failed to create dir "+
                          project,userName);

//create description file & input files
    StringBuffer descript = new StringBuffer();
    descript.append("EMBOSS run details for ");
    descript.append(appl);
    descript.append(ls);
    descript.append(ls);
    descript.append("Parameters Used: ");
    descript.append(embossCommand);
    descript.append(ls);
    descript.append("Started: ");
    descript.append(dat);
    descript.append(ls);
    descript.append(ls);
    descript.append("Input files:");
    descript.append(ls);

//write input files to project directory
    Vector inFileNames = new Vector();
    for(Enumeration e = inFiles.elements() ; e.hasMoreElements() ;)
    {
      String thiskey = (String)e.nextElement();  // file name
      inFileNames.add(thiskey);

      descript.append(project);
      descript.append(fs);
      descript.append(thiskey);
      descript.append(ls);

      ok = false;
      try
      {
        aj.setErrStd();
        ok = aj.putFile(userName,passwd,environ,
                 new String(project+fs+thiskey),
                 (byte[])e.nextElement());
      }
      catch(Exception exp){}

      if(!ok)
        return returnError(aj,"Failed to make file "+
                           project+fs+thiskey,userName);
    }

//write decription file to project directory
    ok = false;
    try
    {
      aj.setErrStd();
      ok = aj.putFile(userName,passwd,environ,
           new String(project + fs + ".desc"),
           descript.toString().getBytes());
    }
    catch(Exception exp){}

    if(!ok)
      return returnError(aj,"Failed to make file "+
                         project+fs+".desc",userName);

    new AppendToLogFileThread(userName+":: "+dat+" "+options+
                              " "+embossCommand,logFile,true).start();

    result.add("cmd");
    result.add(embossCommand);
    result.add("status");
    result.add("0");

    File projectDir = new File(project);
    if(options.toLowerCase().indexOf("interactive") > -1)
    {
      ok=true;
      try
      {
        aj.setErrStd();
        ok = aj.forkEmboss(userName,passwd,environ,
                             embossCommand,project);
      }
      catch(Exception exp){} 
 
//include any stderr from EMBOSS
      result.add("msg");
      result.add(aj.getErrStd());

//add a finished file
      try
      {
        aj.setErrStd();
        ok = aj.putFile(userName,passwd,environ,
             new String(project+fs+".finished"),
            (new Date()).toString().getBytes());
      }
      catch(Exception exp){}

      if(!ok)
        return returnError(aj,"putFile error in run_prog",userName);

//get the output files
      result = loadFilesContent(aj,userName,passwd,
                      projectDir,project,result,inFileNames);

      for(int i=0;i<passwd.length;i++)
        passwd[i] = '\0';
    }
    else      //batch or background
    {

// COMMENT THIS LINE TO USE QUEUEING SOFTWARE
      boolean lforkB = aj.forkBatch(userName,passwd,environ,
                                    embossCommand,project);

// UNCOMMENT ONE OF THESE LINE TO USE QUEUEING SOFTWARE
//    runAsBatch(aj,userName,passwd,project,quoteMe(embossCommand));
//    runAsGNQSBatch(aj,userName,passwd,project,quoteMe(embossCommand));
//    runAsPBSBatch(aj,userName,passwd,project,quoteMe(embossCommand));
      result.add("msg");
      result.add("");
      result.add("job_submitted");
      result.add("Job " + projectDir.getName() + "submitted.");
      result.add("jobid");
      result.add(projectDir.getName());
      result.add("description");
      result.add(descript+ls+"Application pending"+ls);
    }

    return result;
  }


  /**
  *
  * Quote all tokens ready for shell scripts
  * @param s	text to quote
  * @return	quoted text
  *
  */
  private String quoteMe(String s)
  {
    StringBuffer qs = new StringBuffer();
    StringTokenizer st = new StringTokenizer(s.trim()," ");
    String tok;
    while (st.hasMoreTokens())
    {
      tok = st.nextToken().trim();
      if(!tok.equals(" "))
      {
        qs.append("\"");
        qs.append(tok);
        qs.append("\" ");
      }
    }
    return qs.toString();
  }

  /**
  *
  * Submit to a OpenPBS batch queue. This method creates a script for
  * submission to a batch queueing system.
  * @param aj			ajax/jni
  * @param userName		username
  * @param passwd		passwd
  * @param project		project directory
  * @param embossCommand	emboss command
  *
  */
  private void runAsPBSBatch(Ajax aj, String userName, byte[] passwd,
                              String project, String embossCommand)
  {
    StringBuffer scriptIt = new StringBuffer();
    scriptIt.append("#PBS -j oe\n");
    scriptIt.append("#PBS -S /bin/sh\n");
    scriptIt.append(environ.replace(' ','\n'));
    scriptIt.append("\nexport PATH\n");
    scriptIt.append("export PLPLOT_LIB\n");
    scriptIt.append("export EMBOSS_DATA\n");
    scriptIt.append("cd "+project+"\n"+embossCommand+"\n");
    scriptIt.append("date > "+project+"/.finished\n");

    String scriptFile = new String(project+fs+".scriptfile");
    boolean ok = false;
    try
    {
      ok = aj.putFile(userName,passwd,environ,scriptFile,
                      scriptIt.toString().getBytes());
    }
    catch(Exception exp){}

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

      appendToLogFile(userName+":: "+dat+
                      " Failed to make file "+project+fs+".scriptfile\n"+
                      "STDERR "+aj.getErrStd()+"\n"+
                      "STDOUT "+aj.getOutStd(),errorLog);
    }

    boolean lfork=true;
    try
    {
      //EDIT batchCommand
      String batchCommand = "/hgmp/local/openpbs/bin/qsub "+scriptFile;
      lfork = aj.forkEmboss(userName,passwd,environ,
                            batchCommand,project);
    }
    catch(Exception exp){}

    if(!lfork || !aj.getErrStd().equals(""))
    {
      String dat = new Date().toString();
      dat = dat.replace(':','_');

      appendToLogFile(userName+":: "+dat+
                      " Fork batch process failed "+embossCommand,errorLog);
    }

    return;
  }

  /**
  *
  * Submit to a Generic NQS batch queue. This method creates a script for
  * submission to a batch queueing system.
  * @param aj                   ajax/jni
  * @param userName             username
  * @param passwd               passwd
  * @param project              project directory
  * @param embossCommand        emboss command
  *
  */
  private void runAsGNQSBatch(Ajax aj, String userName, byte[] passwd,
                              String project, String embossCommand)
  {
    String scriptIt = "#QSUB -q jemboss-queue\n";
    scriptIt = scriptIt.concat("#QSUB -s /bin/sh\n");
    scriptIt = scriptIt.concat("#QSUB -eo -o report.nqs\n");
    scriptIt = scriptIt.concat(environ.replace(' ','\n'));
    scriptIt = scriptIt.concat("\nexport PATH\n");
    scriptIt = scriptIt.concat("export PLPLOT_LIB\n");
    scriptIt = scriptIt.concat("export EMBOSS_DATA\n");
    scriptIt = scriptIt.concat("cd "+project+"\n"+embossCommand+"\n");
    scriptIt = scriptIt.concat("date > "+project+"/.finished\n");

    String scriptFile = new String(project+fs+".scriptfile");
    boolean ok = false;
    try
    {
      ok = aj.putFile(userName,passwd,environ,scriptFile,
                      scriptIt.getBytes());
    }
    catch(Exception exp){}

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

      appendToLogFile(userName+":: "+dat+" Failed to make file "+project+fs+".scriptfile",errorLog);
      appendToLogFile(userName+":: "+dat+" STDERR "+aj.getErrStd(),errorLog);
      appendToLogFile(userName+":: "+dat+" STDOUT "+aj.getOutStd(),errorLog);
    }

    boolean lfork=true;
    try
    {
      //EDIT batchCommand
      String batchCommand = "/hgmp/local/nqs/bin/qsub "+scriptFile;
      lfork = aj.forkEmboss(userName,passwd,environ,
                            batchCommand,project);
    }
    catch(Exception exp){}

    if(!lfork || !aj.getErrStd().equals(""))
    {
      String dat = new Date().toString();
      dat = dat.replace(':','_');

      appendToLogFile(userName+":: "+dat+
                      " Fork batch process failed "+embossCommand,errorLog);
    }
    
    return;
  }

  /**
  *
  * Submit to a batch queue
  * @param aj                   ajax/jni
  * @param userName             username
  * @param passwd               passwd
  * @param project              project directory
  * @param embossCommand        emboss command
  *
  */
  private void runAsBatch(Ajax aj, String userName, byte[] passwd,
                    String project, String embossCommand)
  {
    String scriptIt = "#!/bin/sh\n";
    scriptIt = scriptIt.concat(environ.replace(' ','\n'));
    scriptIt = scriptIt.concat("\nexport PATH\n");
    scriptIt = scriptIt.concat("export PLPLOT_LIB\n");
    scriptIt = scriptIt.concat("export EMBOSS_DATA\n");
    scriptIt = scriptIt.concat("cd "+project+"\n"+embossCommand+"\n");
    scriptIt = scriptIt.concat("date > "+project+"/.finished\n");
    
    boolean ok = false;
    try
    {
      ok = aj.putFile(userName,passwd,environ,
               new String(project+fs+".scriptfile"),
               scriptIt.getBytes());
    }
    catch(Exception exp){}

    if(!ok)
    {
      String dat = new Date().toString();
      dat = dat.replace(':','_');
    
      appendToLogFile(userName+":: "+dat+" Failed to make file "+project+fs+".scriptfile",errorLog);
      appendToLogFile(userName+":: "+dat+" STDERR "+aj.getErrStd(),errorLog);
      appendToLogFile(userName+":: "+dat+" STDOUT "+aj.getOutStd(),errorLog);
    }
  
    boolean lfork=true;
    try
    {
      //EDIT batchCommand 
      String batchCommand = "/bin/batchQueue.sh " + project +
                            "/.scriptfile ";
                         
      lfork = aj.forkEmboss(userName,passwd,environ,
                            batchCommand,project);
    }
    catch(Exception exp){}

    if(!lfork || !aj.getErrStd().equals(""))
    {
      String dat = new Date().toString();
      dat = dat.replace(':','_');

      appendToLogFile(userName+":: "+dat+
                      " Fork batch process failed "+embossCommand,errorLog);
    }
    return;
  }