Run galfit using a votable

Script

import java.io.BufferedInputStream;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import java.util.Vector;
import java.util.regex.Pattern;

import uk.ac.starlink.table.ColumnInfo;
import uk.ac.starlink.table.RowSequence;
import uk.ac.starlink.table.StarTable;
import uk.ac.starlink.table.StarTableFactory;

public StarTable loadVOTable( File file ) throws IOException {
    return new StarTableFactory().makeStarTable( file.toString(), "votable" );
}

void writeStringToAFile(String filepath, String content) throws IOException{
	BufferedWriter out = new BufferedWriter(new FileWriter(filepath));
	out.write(content);
	out.close();
}

	    String fileVotablePath = "";
	    File tmpfile = File.createTempFile("astro", null);
	    FileWriter writer = new FileWriter(tmpfile);
	    writer.write(votable);
	    writer.close();

	    fileVotablePath = tmpfile.getAbsolutePath();

	    script = "";
		Map mapping = new HashMap();
		Vector mappingPos = new Vector();
		//Map mappingIds = new HashMap();
		int nCol;
		try{
			
		   //open the table
		   File file = new File(fileVotablePath);
		   StarTable table = loadVOTable(file);
		   
		   //get the column info
		   nCol = table.getColumnCount();
		   for(int i =0; i< nCol; i++){
			   ColumnInfo colInfo = table.getColumnInfo(i);
			   mapping.put(colInfo.getName(), i);  //names to positions
			   mappingPos.add(colInfo.getName());  //positions to names
		   }
		   
		   if(mapping.get(columnNameWithConfigFile)==null)
			   throw new Exception(columnNameWithConfigFile+" is not a column on the votable");
		   if(mapping.get(columnNameWithNewConfigFile)==null)
			   throw new Exception(columnNameWithNewConfigFile+" is not a column on the votable");
		   
		   script="#!/bin/bash \n" +
				"cd " + experimentFolder + " \n" +
		   		"path=$(pwd) \n" +
		   		"file=\"/galfit.01\" \n" +
		   		"orig=$path$file \n";
		   
		   RowSequence rseq = table.getRowSequence();
	       while ( rseq.next() ) {
	        	String fileName = (String) rseq.getCell(  (int) mapping.get(columnNameWithConfigFile)  );
	        	String fileName2 = (String) rseq.getCell(  (int) mapping.get(columnNameWithNewConfigFile)  );
	        	script += "galfit " + fileName + "\n";
	        	script += "mv $orig "+ fileName2 + "\n";
	       }
	        rseq.close();
	        
		}catch (Exception ex){
		   script = "Exception during the process: \n"+ ex.getMessage();
		   throw new Exception(script);
		}