jembossserver.java

emboss的linux版本的源代码

      }
      
      dout.close();
    }
    catch (IOException ioe) {} 

    RunEmbossApplication2 rea = new RunEmbossApplication2(embossCommand,
                                               envp,new File(project));
    
    result.add("cmd");
    result.add(appl + " " + rest);
    result.add("msg");
    result.add(msg);
    result.add("status");
    result.add("0");

    if(options.toLowerCase().indexOf("interactive") > -1)
    { 
      String stdout = "";
      try
      {
        rea.getProcess().waitFor();
        stdout = rea.getProcessStdout();
      }
      catch(InterruptedException iexp){}    
      if(!stdout.equals(""))
      {
        result.add("stdout");
        result.add(stdout);
      }
      createFinishedFile(project);
    }
    else      //batch or background
    {
      JembossThread jt = new JembossThread(rea,project);
      jt.start();

//    if(jt.isAlive())
//      System.out.println("THREAD IS ALIVE!");

      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);
    }

//get the output files
    result = loadFilesContent(projectDir,project,result,inFiles);
    result = loadPNGContent(projectDir,project,result);

    return result;
  }

  /**
  *
  * Creates a file named "finished" in the project directory,
  * that contains a time stamp.
  * @param project	project directory name
  *
  */ 
  private void createFinishedFile(String project)
  {
    File finished = new File(new String(project + fs + ".finished"));
    try
    {
      PrintWriter fout = new PrintWriter(new FileWriter(finished));
      fout.println((new Date()).toString());
      fout.close();
    }
    catch (IOException ioe) {}
  }


  /**
  *
  * 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
  * @return 		saved results files
  *
  */
  public Vector show_saved_results(String project, String cl,
                                   String userName)
  {
    Vector ssr = new Vector();
    tmproot = tmproot.concat(userName+fs); 
    ssr = show_saved_results(project,cl);
    return ssr;
  }

  /**
  *
  * 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
  * @return             saved results files
  *
  */
  public Vector show_saved_results(String project, String cl)
  {
    Vector ssr = new Vector();
   
    project = tmproot.concat(project);
    File projectDir = new File(project);

    if(cl.equals(""))
    {
      ssr = loadFilesContent(projectDir,project,ssr,null);
      ssr = loadPNGContent(projectDir,project,ssr);
    }
    else
    {
      try
      {
        String fc = "";
        String line;
        File fn = new File(project + fs + cl);

        if(fn.exists())
        {
          BufferedReader in = new BufferedReader(new FileReader(project +
                                                       fs + cl));
          while((line = in.readLine()) != null)
            fc = fc.concat(line + "\n");
        }
  
        ssr.add(cl);
        ssr.add(fc);
      }
      catch (IOException ioe){}
    }

    ssr.add("status");
    ssr.add("0");

    ssr.add("msg");
    ssr.add("OK");

    return ssr;
  }


  /**
  *
  * Save a file to a project directory on the server.
  * @param project      project directory to save file in
  * @param filename     filename
  * @param notes        text to write to file
  * @param userName     username
  * @return             message
  *
  */
  public Vector save_project_file(String project, String filename,
                                  String notes, String userName)
  {
    return save_project_file(userName+ fs +project, filename, notes);
  }


  /**
  *
  * Save a file to a project directory on the server.
  * @param project	project directory to save file in
  * @param filename	filename
  * @param notes	text to write to file
  * @param userName	username
  * @return 		message
  *
  */
  public Vector save_project_file(String project, String filename,
                                  String notes)
  {
    Vector v = new Vector();
    String msg = "OK";

    String fn = tmproot + fs + 
                     project + fs + filename;

    File f = new File(fn);
    try
    {
      if(!f.exists())
        f.createNewFile();
      FileOutputStream out = new FileOutputStream(f);
      out.write(notes.getBytes());
      out.close();
    }
    catch(IOException ioe)
    {
      msg = new String("Error making input file");
    }

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

    return v;
  }


  /**
  *  
  * Deletes a projects saved results.
  * @param project	project directory name
  * @param cl		unused
  * @param userName     username
  * @return 		message
  *
  */
  public Vector delete_saved_results(String project, String cl,
                                     String userName)
  {
    Vector dsr = new Vector();
    tmproot = tmproot.concat(userName+fs);
    dsr = delete_saved_results(project,cl);
    return dsr;
  }

  /**
  * 
  * Deletes a projects saved results.
  * @param project      project directory name
  * @param cl           unused
  * @return             message
  *
  */
  public Vector delete_saved_results(String project, String cl)
  {
    Vector dsr = new Vector();

    StringTokenizer st = new StringTokenizer(project,"\n");
    while(st.hasMoreTokens()) 
    {
      String proj = tmproot.concat(fs+st.nextToken());
    
      File projectDir = new File(proj);
      File resFiles[] = projectDir.listFiles();
      for(int i=0;i<resFiles.length;i++)
        resFiles[i].delete();
      
      projectDir.delete();
    }

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


  /**
  *
  * List of the saved results on the server.
  * @param userName	username
  * @return 		list of the saved results.
  *
  */
  public Vector list_saved_results(String userName)
  {
    Vector lsr = new Vector();
    tmproot = tmproot.concat(userName+fs);
    tmprootDir = new File(tmproot);
    lsr = list_saved_results();
    return lsr;
  }

  /**
  *
  * List of the saved results on the server.
  * @return             list of the saved results.
  *
  */
  public Vector list_saved_results()
  {
    Vector lsr = new Vector();
   
    lsr.add("status");
    lsr.add("0");
    lsr.add("msg");
    lsr.add("OK");


    String resFiles[] = tmprootDir.list(new FilenameFilter()
    {
      public boolean accept(File cwd, String name)
      {
        return !name.startsWith(".");
      };
    });
    
    String list = "";
    for(int i=0;i<resFiles.length;i++)
    {
      String line = new String("");
      String fc = new String("");
     
      try
      {
        BufferedReader in = new BufferedReader(new FileReader(tmproot + fs + 
                                               resFiles[i] + fs + ".desc"));
        while((line = in.readLine()) != null)
          fc = fc.concat(line + "\n");
        lsr.add(resFiles[i]);
        lsr.add(fc);
        list = list.concat(resFiles[i] + "\n");
      }
      catch (IOException ioe)
      {
        System.out.println("IOException in list_saved_results " +tmproot + fs +
                                               resFiles[i] + fs + ".desc");
      }
    }

    lsr.add("list");
    lsr.add(list);

    return lsr;
  
  }


  /**
  *
  * Reads in files from EMBOSS output
  * @param projectDir   project directory
  * @param project      project name
  * @param result       results
  * @param inFiles      input files
  * @return             result
  *
  */
  private Vector loadFilesContent(File projectDir, String project, 
                                  Vector result, Hashtable inFiles)
  {

    String outFiles[] = projectDir.list(new FilenameFilter()
    {
      public boolean accept(File cwd, String name)
      {
        return (!name.startsWith(".") && !name.endsWith(".png"));
      };
    });

    for(int i=0;i<outFiles.length;i++)
    {
      String line = new String("");
      String fc = new String("");
      String key = new String(outFiles[i]);


      if(inFiles != null)
      {
        if(!inFiles.containsKey(key))        // leave out input files
        {
          try
          {
            BufferedReader in = new BufferedReader(new FileReader(project + fs +
                                                                  outFiles[i]));
            while((line = in.readLine()) != null)
              fc = fc.concat(line + "\n");
          }
          catch (IOException ioe){}
        }
      }
      else
      {
        try
        {
          BufferedReader in = new BufferedReader(new FileReader(project + fs +
                                                                outFiles[i]));
          while((line = in.readLine()) != null)
            fc = fc.concat(line + "\n");
        }
        catch (IOException ioe){}
      }

      if(!fc.equals(""))
      {
        result.add(key);
        result.add(fc);
      }
    }
    return result;

  }

  /**
  *
  * Reads in png files from EMBOSS output
  * @param projectDir   project directory
  * @param project      project name
  * @param result       results
  * @return             result
  *
  */
  private Vector loadPNGContent(File projectDir, String project, Vector result)
  {

    String pngFiles[] = projectDir.list(new FilenameFilter()
    {
      public boolean accept(File cwd, String name)
      {
        if( name.endsWith(".png") ||
            name.endsWith(".dat") )
          return true;
        return false;
      };
    });

    for(int i=0;i<pngFiles.length;i++)
    {
      String key = new String(pngFiles[i]);
      DataInputStream dis = null;
      FileInputStream fis = null;
      int nby = 0;
      byte data[] = readByteFile(project + fs + pngFiles[i]);
      if(data != null)
      {
        result.add(key);
        result.add(data);
      }
    }
    return result;
  }

  /**
  *
  * Read a file into a byte array.
  * @param filename	file name
  * @return 		byte[] contents of file
  *
  */
  protected static byte[] readByteFile(String filename)
  {

    File fn = new File(filename);
    byte[] b = null;
    try
    {
      long s = fn.length();
      if(s == 0)
        return b;
      b = new byte[(int)s];
      FileInputStream fi = new FileInputStream(fn);
      fi.read(b);
      fi.close();
    }
    catch (IOException ioe)
    {
      System.out.println("Cannot read file: " + filename);
    }
    return b;

  }


  /**
  *
  * Used to provide information on the batch/background
  * processes.
  * @param prog         program
  * @param opt          options
  * @param resToQuery   results to query
  * @param userName     username
  *
  */
  public Vector update_result_status(String prog, String opt,
                        Vector resToQuery,String userName)
  {
    return update_result_status(prog,opt,getHashtable(resToQuery),
                                userName);
  }

  /**
  *
  * Used to provide information on the batch/background
  * processes.
  * @param prog         program
  * @param opt          options
  * @param resToQuery   results to query
  * @param userName     username
  *
  */
  public Vector update_result_status(String prog, String opt,
                        Hashtable resToQuery,String userName)
  {
    tmproot = tmproot.concat(userName+fs);
    return update_result_status(prog, opt, resToQuery);
  }

  /**
  *
  * Used to provide information on the batch/background
  * processes.
  * @param prog         program
  * @param opt          options
  * @param resToQuery   results to query
  *
  */
  public Vector update_result_status(String prog, String opt, 
                                     Hashtable resToQuery)
  {

    Vector vans = new Vector();
    Enumeration enumRes = resToQuery.keys();
    while (enumRes.hasMoreElements())
    {
      String thiskey = (String)enumRes.nextElement().toString();
      String thiselm = (String)resToQuery.get(thiskey);
//    System.out.println("KEY : "+thiskey+" ELEMENT: "+thiselm);
      File f = new File(tmproot+fs+thiskey+fs+".finished");
      if(f.exists())
      {
        vans.add(thiskey);
        vans.add("complete");
        String fc = "";
        try
        {
          String line;
          BufferedReader in = new BufferedReader(new FileReader(tmproot+
                                                fs+thiskey+fs+".desc"));
          while((line = in.readLine()) != null)
            fc = fc.concat(line + "\n");
        }
        catch (IOException ioe)
        {
          fc = "Error in reading information file";
        }
        vans.add(thiskey+"-description");
        vans.add(fc);
      }
      else
      {
        vans.add(thiskey);
        vans.add("pending");
      }
    }

    return vans;
  }

  /**
  *
  * Convert contents from a Vector to a Hashtable
  * @param v    Vector
  *
  */
  private Hashtable getHashtable(Vector v)
  {
    Hashtable h = new Hashtable();
    for(Enumeration e = v.elements() ; e.hasMoreElements() ;)
    {
      String s = (String)e.nextElement();
      h.put(s,e.nextElement());
    }
    return h;
  }


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

}