jembossserver.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.programs.RunEmbossApplication;
import org.emboss.jemboss.programs.RunEmbossApplication2;
import org.emboss.jemboss.parser.Ajax;

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

/**
*
* Jemboss Non-authenticated Server for Apache Axis (SOAP)
* web services
*
*/
public class JembossServer
{

  /** file separator */
  private String fs = System.getProperty("file.separator");

//get paths to EMBOSS
  /** jemboss properties */
  JembossParams jp = new JembossParams();
  /** plplot path */
  String plplot = jp.getPlplot();
  /** emboss data directory */
  String embossData = jp.getEmbossData();
  /** emboss binary directory */
  String embossBin = jp.getEmbossBin();
  /** emboss path */
  String embossPath = jp.getEmbossPath();
  /** acd directory */
  String acdDirToParse = jp.getAcdDirToParse();

  /** user home directory */
  private String homeDirectory = System.getProperty("user.home") + fs;
  /** user name */
  private String username = System.getProperty("user.name") + fs;
  /** results directory */
  private String tmproot  = "/tmp/SOAP/emboss/" + username;
  /** results directory */
  private File tmprootDir = new File(tmproot);

  /** emboss run environment */
  private String[] envp_emboss = 
  {
    "PATH=" + embossPath + System.getProperty("path.separator")
            + embossBin,
    "PLPLOT_LIB=" + plplot,
// cygwin: embossdata application does not like 
//         EMBOSS_DATA specified - it fails to 
//         fetch files
//  "EMBOSS_DATA=" + embossData,
    "HOME=" + homeDirectory,
    "EMBOSSCYGROOT=" + JembossParams.getCygwinRoot()
//  ,"LD_LIBRARY_PATH=/usr/local/lib"
// FIX FOR SOME SUNOS OR USE embossEnvironment

  };

  /** emboss run environment */
  private String[] envp = jp.getEmbossEnvironmentArray(envp_emboss);
 

  public JembossServer(){}

  public JembossServer(String tmproot)
  {
    this.tmproot = tmproot;
    tmprootDir = new File(tmproot);
  }

  public String name()
  {
    return "The EMBOSS Application Suite";
  }

  public String version()
  {
    String embossCommand = new String(embossBin + "embossversion");
    RunEmbossApplication2 rea = new RunEmbossApplication2(embossCommand,
                                                           envp,null);
    try
    {
      Process p = rea.getProcess();
      p.waitFor();
    }
    catch(InterruptedException iexp){}

    return rea.getProcessStdout();
  }


  public String appversion()
  {
    String embossCommand = new String(embossBin + "embossversion");
    RunEmbossApplication2 rea = new RunEmbossApplication2(embossCommand,
                                                           envp,null);
    try
    {
      Process p = rea.getProcess();
      p.waitFor();
    }
    catch(InterruptedException iexp){}

    return rea.getProcessStdout();
  }


  public String about()
  {
    return "Jemboss is an interface to the EMBOSS suite of programs.";
  }

  public String helpurl()
  {
    return "http://www.uk.embnet.org/Software/EMBOSS/";
  }

  public String abouturl()
  {
    return "http://www.uk.embnet.org/Software/EMBOSS/overview.html";
  }

  public String docurl()
  {
     return "http://www.uk.embnet.org/Software/EMBOSS/general.html";
  }

  public Hashtable servicedesc()
  {
     Hashtable desc = new Hashtable();
     desc.put("name",name());
     desc.put("version",version());
     desc.put("appversion",appversion());
     desc.put("about",about());
     desc.put("helpurl",helpurl());
     desc.put("abouturl",abouturl());
     desc.put("docurl",docurl());
     return desc;
  }


  /**
  *
  * Retrieves the ACD file of an application.
  * @param appName	application name
  * @return 		ACD string
  *
  */
  public Vector show_acd(String appName)
  {

    Vector acd = new Vector();
    String acdText = new String("");
    String line;
    String acdToParse = new String(acdDirToParse + appName + ".acd");

    try
    {
      BufferedReader in = new BufferedReader(new FileReader(acdToParse));
      while((line = in.readLine()) != null )
      {
        if(!line.startsWith("#") && !line.equals(""))
        { 
          line = line.trim();
          line = line.replace('}',')');
          acdText = acdText.concat(line + "\n");
        }
      }
    }
    catch (IOException e)
    {
      System.out.println("Cannot open EMBOSS acd file " + acdToParse);
    }

    acd.add("status");
    acd.add("0");
    acd.add("acd");
    acd.add(acdText);

    return acd;
  }

  /**
  *
  * Returns the output of the EMBOSS utility wossname
  * @return 	wossname output
  *
  */
  public Vector getWossname()
  {
    Vector wossOut = new Vector();
    String embossCommand = new String(embossBin + "wossname -colon -auto");
    RunEmbossApplication2 rea = new RunEmbossApplication2(embossCommand,
                                                           envp,null);
    wossOut.add("status");
    wossOut.add("0");
    try
    {
      Process p = rea.getProcess();
      p.waitFor();
    }
    catch(InterruptedException iexp){}

    wossOut.add("wossname");
    wossOut.add(rea.getProcessStdout());

    return wossOut;

  }


  /**
  *
  * Returns the help for an application as given by 'tfm'
  * @param applName	application name
  * @return 		help 
  *
  */
  public Vector show_help(String applName)
  {
    String command = embossBin.concat("tfm " + applName + 
                                       " -html -nomore");
    RunEmbossApplication2 rea = new RunEmbossApplication2(command,
                                                     envp,null);

    try
    {
      Process p = rea.getProcess();
      p.waitFor();
    }
    catch(InterruptedException iexp){}

    String helptext = rea.getProcessStdout();
    if(helptext.equals(""))
      helptext = "No help available for this application.";

    Vector vans = new Vector();
    vans.add("helptext");
    vans.add(helptext);

    return vans;
  }


  /**
  *
  * Uses JNI to calculate sequence attributes using EMBOSS library call.
  * @param fileContent  sequence filename or database entry
  * @param seqtype      sequence type (seqset/sequence)
  * @param userName     username
  * @return     	sequence length, weight & type (protein/nucleotide)
  *
  */
  public Vector call_ajax(String fileContent, String seqtype, String userName)
  {
    return call_ajax(fileContent,seqtype);
  }

  /**
  *
  * Uses JNI to calculate sequence attributes using EMBOSS library call.
  * @param fileContent  sequence filename or database entry
  * @param seqtype      sequence type (seqset/sequence)
  * @return     	sequence length, weight & type (protein/nucleotide)
  *
  */
  public Vector call_ajax(String fileContent, String seqtype)
  {
    boolean afile = false;
    String fn = null;
    File tf = null;

    Vector vans = new Vector();

    // create temporary file
    if( ((fileContent.indexOf(":") < 0) || 
         (fileContent.indexOf("\n") > 0) ) &&
       !((new File(fileContent)).exists()) ) 
    {
      afile = true;
      try
      {
        tf = File.createTempFile("tmp",".jembosstmp", tmprootDir);
        PrintWriter out = new PrintWriter(new FileWriter(tf));
        out.println(fileContent);
        out.close();
    
        fn = new String(tf.getCanonicalPath());
      }
      catch (IOException ioe) 
      {
        System.out.println("IOException : STATUS NOT OK");
        vans.add("status");
        vans.add("1");
        return vans;
      }
    }
    else
    {
      fn = fileContent;     //looks like db entry or local file name
    }

    boolean ok = false;
    Ajax aj = null;

    if( ((new File(fn)).exists()) ||    //call ajax if sequence file
         (fn.indexOf(":") > 0) )        //or db
    {
      try
      {
        aj = new Ajax();
        if(seqtype.startsWith("seqset"))
          ok = aj.seqsetType(fn);
        else
          ok = aj.seqType(fn);
      }
      catch (Exception e)
      {
        System.out.println("AjaxException : STATUS NOT OK");
        vans.add("status");
        vans.add("1");
        return vans;
      }
    }

    if(ok)
    {
      vans.add("length");
      vans.add(new Integer(aj.length));
      vans.add("protein");
      vans.add(new Boolean(aj.protein));
      vans.add("weight");
      vans.add(new Float(aj.weight));
      vans.add("status");
      vans.add("0");
    }
    else
    {
      vans.add("status");
      vans.add("1");
    }

    if(afile)
      tf.delete();

    return vans;
  }


  /**
  *
  * Returns the databases held on the server
  * @return 	output from 'showdb'
  *
  */
  public Vector show_db()
  {
    Vector showdbOut = new Vector();
    String embossCommand = new String(embossBin + "showdb -auto");
    RunEmbossApplication2 rea = new RunEmbossApplication2(embossCommand,
                                                          envp,null);
    showdbOut.add("status");
    showdbOut.add("0");

    try
    {
      Process p = rea.getProcess();
      p.waitFor();
    }
    catch(InterruptedException iexp){}

    showdbOut.add("showdb");
    showdbOut.add(rea.getProcessStdout());
     
    // find available matrices
    String dataFile[] = (new File(embossData)).list(new FilenameFilter()
    {
      public boolean accept(File dir, String name)
      {
        File fileName = new File(dir, name);
        return !fileName.isDirectory();
      };
    });
    String matrices ="";
    for(int i=0;i<dataFile.length;i++)
      matrices=matrices.concat(dataFile[i]+"\n");
    showdbOut.add("matrices");
    showdbOut.add(matrices);

    // find available codon usage tables
    
    dataFile = (new File(embossData+fs+"CODONS")).list(new FilenameFilter()
    {
      public boolean accept(File dir, String name)
      {
        File fileName = new File(dir, name);
        return !fileName.isDirectory();
      };
    });
    matrices ="";
    for(int i=0;i<dataFile.length;i++)
      matrices=matrices.concat(dataFile[i]+"\n");
    showdbOut.add("codons");
    showdbOut.add(matrices);

    return showdbOut;
  }


  /**
  *
  * Run an EMBOSS application
  * @param embossCommand	command line to run
  * @param options		unused
  * @param inFiles		input files and names
  * @return 			output files from application run
  *
  */
  public Vector run_prog(String embossCommand, String options, 
                                             String[] inFiles)
  {
    Vector result = new Vector();

    Hashtable inF = new Hashtable();
    for(int i=0; i<inFiles.length;i+=2)
      inF.put(inFiles[i],inFiles[i+1]);

    result = run_prog(embossCommand,options,inF);

    return result;
  }

  /**
  *
  * Run an EMBOSS application
  * @param embossCommand        command line to run
  * @param options              unused
  * @param inFiles              input files and names
  * @param userName		username
  * @return                     output files from application run
  *
  */
  public Vector run_prog(String embossCommand, String options,
                         Vector inFiles, String userName)
  {
    Hashtable hashInFiles = getHashtable(inFiles);
    tmproot = tmproot.concat(userName+fs);
    return run_prog(embossCommand,options,hashInFiles);
/*   return run_prog(embossCommand,options,hashInFiles,userName); */
  }

  /**
  *
  * Run an EMBOSS application
  * @param embossCommand	command line to run
  * @param options		unused 
  * @param inFiles		input files
  * @return 			output files from application run
  *
  */
  public Vector run_prog(String embossCommand, String options, 
                                            Hashtable inFiles)
  {

    Vector result = new Vector();

    //disallow multiple command constructions
    if(embossCommand.indexOf(";") > -1) 
    {
       result.add("msg");
       result.add("ERROR: Disallowed command syntax "+embossCommand);
       result.add("status");
       result.add("1");

       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);
    }

    Enumeration enumFiles = inFiles.keys();
    String appl   = embossCommand.substring(0,embossCommand.indexOf(" "));
    String rest   = embossCommand.substring(embossCommand.indexOf(" "));
    embossCommand = embossBin.concat(embossCommand);
    String msg = new String("");

    boolean ok;
    
    if(!tmprootDir.isDirectory())
    {
      ok = tmprootDir.mkdirs();
      if(ok)
        System.out.println("Created directory "+tmproot);
      else
        System.out.println("Failed to create directory "+tmproot);
    }

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

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

    File projectDir = new File(project);
    ok = projectDir.mkdirs();

//create description file
    File desc = new File(new String(project + fs + ".desc"));

    String ls = System.getProperty("line.separator");
    String descript = "";
    try
    {
      PrintWriter dout = new PrintWriter(new FileWriter(desc));

      descript = descript.concat("EMBOSS run details"+ls+ls+
                                 "Application: "+appl+ls+rest+
                                 "Started at "+dat+ls+ls+"Input files:");
      dout.println("EMBOSS run details" + ls + ls);
      dout.println("Application: " + appl + ls + rest);
      dout.println("Started at " + dat + ls + ls + "Input files:");
  
      while (enumFiles.hasMoreElements())
      {
        String thiskey = (String)enumFiles.nextElement().toString();
        File f = new File(project + fs + thiskey);
        descript = descript.concat(project+fs+thiskey);
        dout.println(project + fs + thiskey);

        try
        {
          f.createNewFile();
          FileOutputStream out = new FileOutputStream(f);
          out.write((byte []) inFiles.get(thiskey));
          out.close();
        }
        catch(IOException ioe)
        {
          msg = new String("Error making input file");
        }