JSP Uploader on Linux Issue

Hi.
I have a JSP uploader. This works fine on Windows platforms. The linux version works well too, but only with text files. Any other file (.gpeg, .odt, .pdf etc) get corrupted in some way or another on uploading.
Kindly look at the code involved and help me out. Thanks.
<%@ page import="java.io.*, java.lang.*" %>
<%
out.println("Uploading your file. Please wait...");%><br><%
String operatingSystemVersion = String.valueOf(System.getProperty("os.name"));
FileOutputStream fileOut = null;
if(operatingSystemVersion.startsWith("Linux"))
     String contentType = request.getContentType();
     String file = null;
     String saveFile = "";
     if ((contentType != null) && (contentType.indexOf("multipart/form-data") >= 0))
          DataInputStream in = new DataInputStream(request.getInputStream());
          int formDataLength = request.getContentLength();
          byte dataBytes[] = new byte[formDataLength];
          int byteRead = 0;
          int totalBytesRead = 0;
          while (totalBytesRead < formDataLength)
               byteRead = in.read(dataBytes, totalBytesRead, formDataLength);
               totalBytesRead += byteRead;
          try
               file = new String(dataBytes);
               saveFile = file.substring(file.indexOf("filename=\"") + 10);
               saveFile = saveFile.substring(0, saveFile.indexOf("\n"));
               saveFile = saveFile.substring(saveFile.lastIndexOf("/") + 1,saveFile.indexOf("\""));
               int lastIndex = contentType.lastIndexOf("=");
               String boundary = contentType.substring(lastIndex + 1,contentType.length());
               int pos;
               pos = file.indexOf("filename=/" + 1);
               pos = file.indexOf("\n", pos) + 1;
               pos = file.indexOf("\n", pos) + 1;
               pos = file.indexOf("\n", pos) + 1;
               int boundaryLocation = file.indexOf(boundary, pos) - 4;
               out.print("Boundary: " + boundaryLocation + "   ");
               int startPos = ((file.substring(0, pos)).getBytes()).length;
               out.print("startPos: " + startPos + "   ");
               int endPos = ((file.substring(0, boundaryLocation)).getBytes()).length;
               out.print("endPos: " + endPos + "   ");
               //Specify the folder here that you want the file uploaded into
               // Note that you need read/write permissions to that folder
               String folder = "/home/arthur/uploads/";
               fileOut = new FileOutputStream(folder + saveFile);
               for(int i = 0; i < dataBytes.length; i++)
                    byte data = dataBytes;
                    fileOut.write(data);
               fileOut.write(dataBytes, startPos, (endPos - startPos));
//               out.print("Writing out OK");
               out.print("flushing...");
               fileOut.flush();
               //     here </TD>
               //     <meta HTTP-EQUIV="Refresh" content="5; URL=index.jsp">
               //     <br>
          catch(Exception e)
               out.print(e);
else
     String saveFile = "";
     String contentType = request.getContentType();
     if ((contentType != null) && (contentType.indexOf("multipart/form-data") >= 0))
          DataInputStream in = new DataInputStream(request.getInputStream());
          int formDataLength = request.getContentLength();
          byte dataBytes[] = new byte[formDataLength];
          int byteRead = 0;
          int totalBytesRead = 0;
          while (totalBytesRead < formDataLength)
               byteRead = in.read(dataBytes, totalBytesRead, formDataLength);
               totalBytesRead += byteRead;
          try
               String file = new String(dataBytes);
               saveFile = file.substring(file.indexOf("filename=\"") + 10);
               saveFile = saveFile.substring(0, saveFile.indexOf("\n"));
               saveFile = saveFile.substring(saveFile.lastIndexOf("\\") + 1,saveFile.indexOf("\""));
               int lastIndex = contentType.lastIndexOf("=");
               String boundary = contentType.substring(lastIndex + 1,contentType.length());
               int pos;
               pos = file.indexOf("filename=\"");
               pos = file.indexOf("\n", pos) + 1;
               pos = file.indexOf("\n", pos) + 1;
               pos = file.indexOf("\n", pos) + 1;
               int boundaryLocation = file.indexOf(boundary, pos) - 4;
               int startPos = ((file.substring(0, pos)).getBytes()).length;
               int endPos = ((file.substring(0, boundaryLocation)).getBytes()).length;
               // Specify the folder here that you want the file uploaded into
               // Note that you need read/write permissions to that folder
               String folder = "C:/Program Files/Apache Software Foundation/Tomcat5.5/webapps/upload/images/";
               fileOut = new FileOutputStream(folder + saveFile);
               fileOut.write(dataBytes, startPos, (endPos - startPos));
               fileOut.flush();
               fileOut.close();
               %>
                    <meta HTTP-EQUIV="Refresh" content="5; URL=index.jsp">
               <%
          catch(Exception e)
               out.print(e);
          finally
               try{fileOut.close();}catch(Exception err){}
%>
{code}

I have acquired Apache file upload and modified upload.jsp and this is how it looks:
<%@ page import="java.io.*, java.lang.*, org.apache.commons.io.*, org.apache.commons.fileupload.*" %>
<%
          out.println("Uploading your file. Please wait...");%><br><%
          DiskFileItemFactory factory = new DiskFileItemFactory();
        // maximum size that will be stored in memory
        factory.setSizeThreshold(4096);
        // the location for saving data that is larger than getSizeThreshold()
        factory.setRepository(new File("C:/tmp"));
        ServletFileUpload upload = new ServletFileUpload(factory);
        // maximum size before a FileUploadException will be thrown
        upload.setSizeMax(1000000);
        List fileItems = upload.parseRequest(req);
        // assume we know there are two files. The first file is a small
        // text file, the second is unknown and is written to a file on
        // the server
        Iterator i = fileItems.iterator();
        String comment = ((FileItem)i.next()).getString();
        FileItem fi = (FileItem)i.next();
        // filename on the client
        String fileName = fi.getName();
        // save comment and filename to database
        // write the file
        fi.write(new File("C:/", fileName));
%>However, Tomcat complains that
HTTP Status 500 -
type Exception report
message
description The server encountered an internal error () that prevented it from fulfilling this request.
exception
org.apache.jasper.JasperException: Unable to compile class for JSP:
An error occurred at line: 4 in the jsp file: /upload.jsp
DiskFileItemFactory cannot be resolved to a type
1: <%@ page import="java.io.*, java.lang.*, org.apache.commons.io.*, org.apache.commons.fileupload.*" %>
2: <%
3: out.println("Uploading your file. Please wait...");%><br><%
4: DiskFileItemFactory factory = new DiskFileItemFactory();
5:
6: // Set factory constraints
7: factory.setSizeThreshold(yourMaxMemorySize);
An error occurred at line: 4 in the jsp file: /upload.jsp
DiskFileItemFactory cannot be resolved to a type
1: <%@ page import="java.io.*, java.lang.*, org.apache.commons.io.*, org.apache.commons.fileupload.*" %>
2: <%
3: out.println("Uploading your file. Please wait...");%><br><%
4: DiskFileItemFactory factory = new DiskFileItemFactory();
5:
6: // Set factory constraints
7: factory.setSizeThreshold(yourMaxMemorySize);
An error occurred at line: 7 in the jsp file: /upload.jsp
yourMaxMemorySize cannot be resolved
4: DiskFileItemFactory factory = new DiskFileItemFactory();
5:
6: // Set factory constraints
7: factory.setSizeThreshold(yourMaxMemorySize);
8: factory.setRepository(new File("C:/Documents and Settings/Arthur/Desktop/"));
9:
10: // Create a new file upload handler
An error occurred at line: 11 in the jsp file: /upload.jsp
ServletFileUpload cannot be resolved to a type
8: factory.setRepository(new File("C:/Documents and Settings/Arthur/Desktop/"));
9:
10: // Create a new file upload handler
11: ServletFileUpload upload = new ServletFileUpload(factory);
12:
13: // Set overall request size constraint
14: upload.setSizeMax(yourMaxRequestSize);
An error occurred at line: 11 in the jsp file: /upload.jsp
ServletFileUpload cannot be resolved to a type
8: factory.setRepository(new File("C:/Documents and Settings/Arthur/Desktop/"));
9:
10: // Create a new file upload handler
11: ServletFileUpload upload = new ServletFileUpload(factory);
12:
13: // Set overall request size constraint
14: upload.setSizeMax(yourMaxRequestSize);
An error occurred at line: 14 in the jsp file: /upload.jsp
yourMaxRequestSize cannot be resolved
11: ServletFileUpload upload = new ServletFileUpload(factory);
12:
13: // Set overall request size constraint
14: upload.setSizeMax(yourMaxRequestSize);
15:
16: // Parse the request
17: List /* FileItem */ items = upload.parseRequest(request);
An error occurred at line: 17 in the jsp file: /upload.jsp
List cannot be resolved to a type
14: upload.setSizeMax(yourMaxRequestSize);
15:
16: // Parse the request
17: List /* FileItem */ items = upload.parseRequest(request);
18: %>
Stacktrace:
     org.apache.jasper.compiler.DefaultErrorHandler.javacError(DefaultErrorHandler.java:85)
     org.apache.jasper.compiler.ErrorDispatcher.javacError(ErrorDispatcher.java:330)
     org.apache.jasper.compiler.JDTCompiler.generateClass(JDTCompiler.java:435)
     org.apache.jasper.compiler.Compiler.compile(Compiler.java:298)
     org.apache.jasper.compiler.Compiler.compile(Compiler.java:277)
     org.apache.jasper.compiler.Compiler.compile(Compiler.java:265)
     org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:564)
     org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:299)
     org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315)
     org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
     javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
note The full stack trace of the root cause is available in the Apache Tomcat/5.5.23 logs.
Apache Tomcat/5.5.23Any help?

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    The after paramform does some major data manipulations, writing to temporary tables (on commit preserve rows), that are used in queries from the reports.
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    [2007/10/8 11:40:40:536] Error 50103 (rwfdt:rwfdtfl_FreeDistList): running
    [2007/10/8 11:40:40:536] Error 50103 (rwfdt:rwfdtfl_FreeDistList): quit
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    at com.sun.corba.se.internal.corba.ServerDelegate.dispatch(ServerDelegate.java:353)
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    Message was edited by:
    user599601

    I have a rather frustrating problem on our production servers...
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    The after paramform does some major data manipulations, writing to temporary tables (on commit preserve rows), that are used in queries from the reports.
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    Message was edited by:
    user599601

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    Thanks.

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    This is what changes the tools release, sometimes people just run this one update to gain quick and dirty access to a different version.
    I pulled this download and ran through it myself without incident doing all the steps you say, adding in 4-3-2 which you seemed to have skipped.  I built a system database.
    My hcengs.log shows
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    Creating Table  PSSTATUS
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    Building required indexes for PSSTATUS
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    After import, PSSTATUS is
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