jembossauthserver.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.RunEmbossApplication2;
import org.emboss.jemboss.parser.Ajax;

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

/**
*
* Jemboss Authenticated Server for Apache Axis (SOAP)
* web services
*
*/
public class JembossAuthServer
{

  /** SOAP results directory */
  private String tmproot = new String("/tmp/SOAP/emboss/");
  /** Jemboss log file       */
  private final String logFile = new String(tmproot+"/jemboss.log");
  /** Jemboss error log file */
  private final String errorLog = new String(tmproot+"/jemboss_error.log");
  /** file separator */
  private final String fs = new String(System.getProperty("file.separator"));
  /** path separator */
  private final String ps = new String(System.getProperty("path.separator"));
  /** line seperator */
  private final String ls = System.getProperty("line.separator");

//get paths to EMBOSS
  /** jemboss properties */
  final JembossParams jp  = new JembossParams();
  /** plplot path */
  final String plplot     = jp.getPlplot();
  /** emboss data path */
  final String embossData = jp.getEmbossData();
  /** emboss binary path */
  final String embossBin  = jp.getEmbossBin();
  /** path environment variable */
  final String embossPath = embossBin + ps + jp.getEmbossPath();

  /** emboss run environment */
  final private String[] env = 
  {
    "PATH=" + embossPath,
    "PLPLOT_LIB=" + plplot,
    "EMBOSS_DATA=" + embossData
//  ,"LD_LIBRARY_PATH=/usr/local/lib"
// FIX FOR SOME SUNOS
  };
 
  /** emboss run environment as a string */ 
  private final String environ = "PATH=" + embossPath+ " "+
                           "PLPLOT_LIB=" + plplot +" "+
                           "EMBOSS_DATA=" + embossData +" "+
                           jp.getEmbossEnvironment();
// "LD_LIBRARY_PATH=/usr/local/lib"+" ";
// FIX FOR SOME SUNOS


  /**
  *
  * Retrieves the ACD file of an application.
  * @param appName 	application name
  * @return 		Vector of containing the ACD string
  *
  */
  public Vector show_acd(String appName)
  {
    Vector acd = new Vector(4);
    StringBuffer acdText = new StringBuffer();
    final String acdToParse = new String(jp.getAcdDirToParse() + appName + ".acd");

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

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

    return acd;
  }


  /**
  *
  * Returns the output of the EMBOSS utility wossname
  * @return 	wossname output
  *
  */
  public Vector getWossname()
  {
    final String[] envp = jp.getEmbossEnvironmentArray(env);
    Vector wossOut = new Vector(4);
    final String embossCommand = new String(embossBin + 
                   "wossname -colon -gui -auto");
 
    RunEmbossApplication2 rea = new RunEmbossApplication2(embossCommand,
                                                           envp,null);
    rea.waitFor();
    wossOut.add("status");
    wossOut.add(rea.getStatus());
    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)
  {
    final String[] envp = jp.getEmbossEnvironmentArray(env);
    final String command = embossBin.concat("tfm " + applName + " -html -nomore");
    RunEmbossApplication2 rea = new RunEmbossApplication2(command,
                                                       envp,null);
    rea.waitFor();
    String helptext = rea.getProcessStdout();
 
    if(helptext.equals(""))
      helptext = "No help available for this application.";

    Vector vans = new Vector(2);
    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
  * @param passwd       passwd
  * @return 	sequence length, weight & type (protein/nucleotide)
  *
  */
  public Vector call_ajax(String fileContent, String seqtype,
                          String userName, byte[] passwd)
  {
    Vector vans = new Vector(8);
    Ajax aj = new Ajax();
    if(!verifyUser(aj,userName,passwd,vans))
    {
      vans.trimToSize();
      return vans;
    }

    boolean afile = false;
    boolean fexists = false;

    // local file exists?
    if(fileContent.startsWith(fs))
    {
      int ind = fileContent.lastIndexOf(fs);
      String fdir  = fileContent.substring(0,ind);
      String ffile = fileContent.substring(ind+1).trim(); 
      boolean ok = aj.listFiles(userName,passwd,environ,fdir);

      if(!ok)
        return returnError(aj,"listFiles error in call_ajax",userName);

      if(aj.getOutStd().indexOf(fs+ffile+"\n") > -1)
        fexists = true;
      else 
        return returnError(aj,"listFiles error in call_ajax",userName);
    }

    // create temporary file
    String fn = null;
    if( ((fileContent.indexOf(":") < 0) || 
         (fileContent.indexOf("\n") > 0) ) &&
         (!fexists) ) 
    {
      try
      {
        fn = tmproot+fs+userName+fs+".jembosstmp";
        boolean ok = aj.putFile(userName,passwd,environ,
                             fn,fileContent.getBytes());

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

        afile = true;
      }
      catch (Exception ioe) 
      {
        String dat = new Date().toString();
        dat = dat.replace(':','_');

        appendToLogFile(userName+":: "+dat+
                        " Exception: call_ajax creating "+fn,
                         errorLog);
        vans.add("status");
        vans.add("1");
        vans.trimToSize();
        return vans;
      }
    }
    else
    {
      fn = fileContent;     //looks like db entry or local file name
    }

    if( fexists  || afile ||    //call ajax if sequence file
        fn.indexOf(":") > 0 )   //or db
    {
      boolean ok = false;
      try
      {
        if(seqtype.startsWith("seqset"))
          ok = aj.seqsetAttrib(userName,passwd,environ,fn);
        else
          ok = aj.seqAttrib(userName,passwd,environ,fn);

        if(!ok)
          return returnError(aj,"seqAttrib or seqsetAttrib error",userName);

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

        appendToLogFile(userName+":: "+dat+
                        " Exception: call_ajax status not ok",
                         errorLog);
        vans.add("status");
        vans.add("1");
        vans.trimToSize();
        return vans;
      }
    }

    if(afile)
      aj.delFile(userName,passwd,environ,fn);

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

    vans.add("length");
    vans.add(new Integer(aj.length_soap));
    vans.add("protein");
    vans.add(new Boolean(aj.protein_soap));
    vans.add("weight");
    vans.add(new Float(aj.weight_soap));
    vans.add("status");
    vans.add("0");

    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)
  * @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(8);

    // create temporary file
    if( ((fileContent.indexOf(":") < 0) ||
         (fileContent.indexOf("\n") > 0) ) &&
       !((new File(fileContent)).exists()) )
    {
      afile = true;
      try
      {
        File tmprootDir = new File(tmproot);
        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)
      {
        appendToLogFile("IOException: call_ajax creating tmp.jembosstmp",
                         errorLog);
        vans.add("status");
        vans.add("1");
        vans.trimToSize();
        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)
      {
         appendToLogFile("Exception: call_ajax status not ok",
                         errorLog);
        vans.add("status");
        vans.add("1");
        vans.trimToSize();
        return vans;
      }
    }

    if(ok)
    {
//    System.out.println("STATUS 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
    {
      appendToLogFile("Error: call_ajax status not ok",
                         errorLog);
      vans.add("status");
      vans.add("1");
      vans.trimToSize();
    }

    if(afile)
      tf.delete();

    return vans;
  }


  /**
  *
  * Returns the databases held on the server
  * @return 	output from 'showdb'
  *
  */
  public Vector show_db()
  {
    final String[] envp = jp.getEmbossEnvironmentArray(env);
    Vector showdbOut = new Vector(8);
    final String embossCommand = new String(embossBin + "showdb -auto");

    RunEmbossApplication2 rea = new RunEmbossApplication2(embossCommand,
                                                          envp,null);
    rea.waitFor();

    showdbOut.add("status");
    showdbOut.add(rea.getStatus());
     
    if(!rea.getStatus().equals("0"))
    {
      showdbOut.trimToSize();
      return showdbOut;
    }
                        
    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();
      };
    });
    StringBuffer matrices = new StringBuffer();
    for(int i=0;i<dataFile.length;i++)
      matrices.append(dataFile[i]+"\n");
    showdbOut.add("matrices");
    showdbOut.add(matrices.toString());

    // 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 = new StringBuffer();
    for(int i=0;i<dataFile.length;i++)