Yurong Chen

Hello, I met two problems in my project:
1. I wrote the following application. It can be complied. However, when I run it, i get the error message:
java.lang.ClassNotFoundException: org.gjt.mm.mysql.Driver at java.net.URLClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClassInternal(Unknown Source) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Unknown Source) at Application.run(Application.java:55) at java.lang.Thread.run(Unknown Source)
My Application.java is as followed:
import java.io.*; import java.util.*; import java.sql.*; import java.util.Properties; import javax.mail.*; import javax.mail.internet.*; class Application extends Thread { boolean isOkay = true; public static void main(String args[]) { new Thread(new Application()).start(); } public void run() { while(isOkay) { try { sleep(120000); System.out.println("Sleep Finished!"); } catch (InterruptedException e) { isOkay = false; } // main application of connect to database here String fileName = ""; String email =""; String firstName=""; String applied ="no"; Connection con = null; //set relevant variables about JMatLink JMatLink engine = new JMatLink(); String command ="perceptron " + fileName; String directory="cd C://Tomcat4//webapps//project//matlab"; int EpI; //set relevant variable about sending email Send resultEmail = new Send(); String fromName="Chen Yurong"; String fromAddress ="lip01yc@shef.ac.uk"; String resultFile="C://Tomcat4//webapps//project//matlab//results.mat"; String smtpHost = "broadstone.sheffield.ac.uk"; String subject1="Successful Result!"; String subject2="Failed Result!"; String body = "Welcome to Bioinformatics webserver!We are sorry that the request you submitted cannot get a satisfied result now " ; resultEmail.setFromName(fromName); resultEmail.setSmtpHost(smtpHost); resultEmail.setFromAddress(fromAddress); resultEmail.setToAddress(email); resultEmail.setToName(firstName); // Load the Database Driver and catch the Exception try { Class.forName("org.gjt.mm.mysql.Driver").newInstance(); }catch (Exception e) { e.printStackTrace(); // Sending failed information to client by email resultEmail.setBody(body); resultEmail.setSubject(subject2); resultEmail.send(); System.out.println("failed!"); System.exit(1); } System.out.println("Load database!"); // Declare the Query Elements Statement stmt = null; ResultSet result = null; ResultSet result2 = null; // Make the connection with the database and report any errors try{ con=DriverManager.getConnection("jdbc:mysql://localhost/project?user=m1yc3&password=124124"); stmt=con.createStatement(); result= stmt.executeQuery("SELECT name, email, status FROM File WHERE status = \""+applied+"\" LIMIT 1 "); System.out.println("choose out!"); fileName = result.getString(1); email = result.getString(2); applied="yes"; stmt.executeUpdate("UPDATE File SET status =\"" + applied + "\" WHERE name =\"" + fileName + "\""); System.out.println("updated succesfully!"); result2 = stmt.executeQuery("SELECT f_name FROM Client WHERE email = \""+email+"\""); firstName = result2.getString(1); System.out.println("First name out!"); //Empty the Query statements if (result!=null) result.close(); if (result2!=null) result2.close(); if (stmt != null) stmt.close(); } catch (SQLException e) {} catch (Exception e) { e.printStackTrace(); } // Using JMatLink to open Matlab envirnment to process request and send result try { EpI= engine.engOpen(); engine.engEvalString(directory); engine.engEvalString(command); System.out.println("succesfully!"); engine.engClose(); //Sending Result to client by email resultEmail.setSubject(subject1); resultEmail.attachfile(resultFile); resultEmail.sendFile(); System.out.println("send Email!"); }catch (Exception e) { // Sending failed information to client by email resultEmail.setBody(body); resultEmail.setSubject(subject2); resultEmail.send(); System.out.println("failed!"); } } } }
2. I want to count rows when I select something from tables. I use the following jsp programming. However, I cannot get the variable "count"'s value after I execute the SQL. The SQL is stmt.executeQuery("SELECT COUNT(*) FROM File WHERE status = \""+applied+"\" GROUP BY status"); The method I want to get the value of "Count" is count = resultOfSort.getInt(1);
My whole program is as followed:
<jsp:useBean id="currentDate" class = "project.NewDate" scope="request"> </jsp:useBean> <%@ page import= "java.sql.*" %> <% String fileSize = request.getParameter("fileSize").trim(); String fileName = (String)session.getAttribute("fileName"); String email = (String)session.getAttribute("email"); String filePathName = request.getParameter("filePathName").trim(); String queue = (String)session.getAttribute("queue"); String directory = "C://Tomcat4//webapps//project//matlab//"; String applied="no"; int count=0; Connection con = null; // Load the Database Driver and catch the Exception try { Class.forName("org.gjt.mm.mysql.Driver").newInstance(); }catch (Exception e) { e.printStackTrace(); } boolean duplicateError = false; int times =0; response.setContentType("text/html"); // Set the content type response.setHeader("Expires","Mon, 01 Jan 1990 00:00:00 GMT"); // Force the browser to reload each time. // Declare the Query Elements Statement stmt = null; ResultSet result = null; //ResultSet resultOfSort = null; // Make the connection with the database and report any errors try{ con=DriverManager.getConnection("jdbc:mysql://localhost/project?user=m1yc3&password=124124"); stmt=con.createStatement(); //stmt2=con.createStatement(); resultOfSort = stmt.executeQuery("SELECT COUNT(*) FROM File WHERE status = \""+applied+"\" GROUP BY status"); //result= stmt.executeQuery("SELECT * FROM File WHERE status = \""+applied+"\""); count = resultOfSort.getInt(1); if (count >=10) { %> <jsp:forward page="bioinformatics.jsp"> <jsp :-P aram name="fail" value="1" /> </jsp:forward> <% } else { result = stmt.executeQuery("SELECT name,size,ID, email FROM File ORDER BY ID "); while(result.next()) { times = result.getInt(3); if((fileName.equals(result.getString(1)))&&(email.equals(result.getString(4)))&&(fileSize.equals(result.getString(2)))) duplicateError = true; } // Update the database; if(duplicateError){ session.invalidate(); %> <jsp:forward page="sequenceTry.jsp"> <jsp :-P aram name="fail" value="2" /> </jsp:forward> <% } else{ stmt.executeUpdate("INSERT INTO File VALUES(\""+(times+1)+"\",\""+fileName+"\",\""+fileSize+"\",\""+directory+"\",\""+email+"\",\""+applied+"\")"); stmt.executeUpdate("INSERT INTO Statistics VALUES(\""+(times+1)+"\",\""+fileName+"\",\""+currentDate.getYear()+"\",\""+currentDate.getMonth()+"\",\""+currentDate.getDay()+"\",\""+currentDate.getDayOfMonth()+"\",\""+currentDate.getZoneOffset()+"\")"); // session.setAttribute("queue",count); %> <jsp:forward page="successfulRequest.jsp"> <jsp :-P aram name="fileSize" value="<%=fileSize%>"/> <jsp :-P aram name="filePathName" value="<%=filePathName%>"/> <jsp :-P aram name="queue" value="<%=count%>"/> </jsp:forward> <% } } //Empty the Query statements if (result!=null) result.close(); if (stmt != null) stmt.close(); } catch (SQLException e) {} catch (Exception e) { e.printStackTrace(); } %>
Can anybody help me ?? Thank you in advance!
Yurong

Hello,
I met a problem in sending email. I want to send a email with both body content and attachment content. I try the following code:
public boolean sendFile(){ try { InternetAddress from = new InternetAddress(getFromAddress(), getFromName()); InternetAddress to = new InternetAddress(getToAddress(), getToName()); Properties props = new Properties(); props.put("mail.smtp.host", fieldSmtpHost); // Create a mail session Session session = Session.getDefaultInstance(props, null); session.setDebug(true); mail = new MimeMessage(session); mail.setFrom(from); mail.addRecipient(Message.RecipientType.TO, to); mail.setSubject(getSubject()); //mail.setContent(getBody(), "text/plain"); int n=1; Multipart mp = new MimeMultipart(); MimeBodyPart mbp1= new MimeBodyPart(); mbp1.setContent(getBody(), "text/plain"); mp.addBodyPart(mbp1,n); Enumeration efile=fileVector.elements(); while(efile.hasMoreElements()){ MimeBodyPart mbp=new MimeBodyPart(); fileName=efile .nextElement().toString(); FileDataSource fds=new FileDataSource(fileName); mbp.setDataHandler(new DataHandler(fds)); mbp.setFileName(fds.getName()); mp.addBodyPart(mbp,++n); } fileVector.removeAllElements(); //new try mail.setContent(mp); mail.setSentDate(new Date()); Transport.send(mail); } catch (MessagingException mex) { mex.printStackTrace(); Exception ex = null; if ((ex=mex.getNextException())!=null){ ex.printStackTrace(); } return false; } catch (Exception exc) { } return true; } }
However, I received the email only with the attachment. I cannot find any body content in my email. Could anybody help me? Thank you in advance!
Yurong

Hello,
I am a new beginner here. I am doing a small project about web server design. I meet a problem now.
In one step of my project, after the client submitting request, the server should do two things: one is send the main page back to the client, the other is invoking a algorithm to process the request and send the result to client by email. Is it a multiple threads problem? Should I use java servlet to solve the problem? I only use JSP in my project. Can I use JSP to solve the problem? If Java servlet is the only choice, could you give me some advice to do? I really don't know how to begin?? Thank you in advance!
Yurong Chen

I have solved the above problem. I didn't put the javabean in one specific package and put it inside the classes folder directly. Now I put the javabean in one specific package. It works well.
Yurong

Hello,
I have installed Tomcat4.0 in my Windows2000. I can run the examples provided by Tomcat4.0 successfully. However, when I run my own jsp program, the Tomcat gives me error message as followed:
An error occurred at line: 2 in the jsp file: /FinishRegistration.jsp Generated servlet error: C:\Tomcat4\work\Standalone\localhost\project\FinishRegistration$jsp.java:60: Class org.apache.jsp.Email not found. Email email = null; ^ An error occurred at line: 2 in the jsp file: /FinishRegistration.jsp Generated servlet error: C:\Tomcat4\work\Standalone\localhost\project\FinishRegistration$jsp.java:63: Class org.apache.jsp.Email not found. email= (Email) ^ An error occurred at line: 2 in the jsp file: /FinishRegistration.jsp Generated servlet error: C:\Tomcat4\work\Standalone\localhost\project\FinishRegistration$jsp.java:68: Class org.apache.jsp.Email not found. email = (Email) java.beans.Beans.instantiate(this.getClass().getClassLoader(), "Email"); ^ 3 errors, 1 warning
I don't know why this happens. I have runned the same program on the Host Tomcat of our department. It works well. I think the problem should be the classpath. How to set the right classpath??
Thank you in advance!
Yurong

Dear Frank and Michael,
Thank you for your kind help!
I have tried to make a "shell script" as followed:
#!/sbin/sh LD_LIBRARY_PATH=/usr/local/matlab/extern/lib/sol2:'pwd':$LD_LIBRARY_PATH export LD_LIBRARY_PATH java Test
At the same time, I wrote a java program to run this "shell script". The source code is followed:
import java.io.*; public class TestRun{ public static void main(String[] args) { String s = null; //Get the Runtime object try { Runtime r = Runtime.getRuntime ( ) ; // Execute the Unix command Process p1 = r.exec ( "cd /home/m1yc3/try/" ) ; System.out.println("Unix!"); Process p = r.exec("testrun"); InputStream in = p.getInputStream ( ) ; BufferedReader stdInput = new BufferedReader(new InputStreamRead er(in)); while ((s = stdInput.readLine()) != null ) { System.out.println(s); } stdInput.close(); } catch (IOException e){ System.out.println(e); System.exit(1); } } }
This program can run sccessfully with the output " Succesfully" which is from the Test.java file.
import java.io.*; public class Test{ public static void main(String[] args) { JMatLink engine = new JMatLink(); String fileName ="perceptron"; String directory="cd /home/m1yc3/try"; int EpI; EpI= engine.engOpen(); engine.engEvalString(directory); engine.engEvalString(fileName); System.out.println("succesfully!"); engine.engClose(); } }
However, when I put this code in my JSP and run it, it always give me the error page and make the Tomcat cannot be located any more. I have tried this for several days and failed again and again. Could you help me to solve the problem? The source code of my jsp is as followed:
<%@ page import= "java.io.*" %> <% out.println("Unix!"); String s = null; //Get the Runtime object try { Runtime r = Runtime.getRuntime ( ) ; // Execute the Unix command Process p1 = r.exec ( "cd /home/m1yc3/try/" ) ; Process p = r.exec("testrun"); InputStream in = p.getInputStream ( ) ; BufferedReader stdInput = new BufferedReader(new InputStreamReader(in)); while ((s = stdInput.readLine()) != null ) { System.out.println(s); } stdInput.close(); } catch (IOException e){ System.out.println(e); System.exit(1); } %>
Thank you in advance!
Yurong

Dear Frank,
In this project, I should design a web server which can allow the users to make use some algorithms.
1. The algorithms are written in Matlab.
2. The users submit the Excel files which contains the input data of the algorithms.
3. I should use Java to finish the project.
4. I have used the jspSmartUpload Package to upload the excel files from the client side.
5. I have used the JMatLink package to call Matlab in java.
6. I should pass the different file which is uploaded from client side to my algorithms which is written in Matlab.
However, my problem is how to pass the different file names to the "shell script" file ( You taught me yesterday) in JSP and execute the "shell script" file in JSP.

Thank you very much!
Yurong

Dear Frank ,
Thank you very much! I have tried the way you said and it works successfully.
However, I still have one more problem. I should call the JMatLink package in my JSP in tomcat. Everytime I should pass different parameters (different file names) to call my JMatLink package. How can I do that? Should I ask this question in JSP forum?
Thank you very much!
Yurong

Hello, I met a problem when I try to set the UNIX environment variable in my java program for calling matlab. I used a package named JMatLink for calling matlab in java. However, before I starting the following environment variable must be set:
setenv LD_LIBRARY_PATH /usr/local/matlab/extern/lib/sol2:'pwd'
I have used the followng sorce code to try that:
import java.io.*; public class Test{ public static void main(String[] args) { String s = null; //Get the Runtime object try { Runtime r = Runtime.getRuntime ( ) ; // Execute the Unix command Process p1 = r.exec ( "setenv LD_LIBRARY_PATH /usr/local/matlab/extern/lib/sol2:'pwd'" ) ; System.out.println("Unix!"); Process p = r.exec("host $LD_LIBRARY_PATH"); InputStream in = p.getInputStream ( ) ; BufferedReader stdInput = new BufferedReader(new InputStreamReader(in)); while ((s = stdInput.readLine()) != null ) { System.out.println(s); } stdInput.close(); } catch (IOException e){ System.out.println(e); System.exit(1); } JMatLink engine = new JMatLink(); String fileName ="perceptron"; String directory="cd /home/m1yc3/try"; int EpI; EpI= engine.engOpen(); engine.engEvalString(directory); engine.engEvalString(fileName); System.out.println("succesfully!"); engine.engClose(); } }
However, when I compiled the program, it gave me error message about "cannot find the setenv command".
Could somebody tell me how to set the environment variable in java program?? Thank you in advance!
Yurong

Dear All,
Thank you very much! I have solved the problem in Windows. However, I am still trying to set the right path in my web server.
Yurong

Dear Andres,
I want to try the JSTL to send email after my program running. It should be brilliant. I need time to learn that.
Yurong

Dear Andres and Ankur,

I think my problem is on setting the environment variables. However, I have set the package into my classpath. It still gave me the error message when I compiled the program:
javax.activation.UnsupportedDataTypeException: no object DCH for MIME type text/plain at javax.activation.ObjectDataContentHandler.writeTo(DataHandler.java:841) at javax.activation.DataHandler.writeTo(DataHandler.java:295) at javax.mail.internet.MimeBodyPart.writeTo(MimeBodyPart.java:1147) at javax.mail.internet.MimeMessage.writeTo(MimeMessage.java:1600) at com.sun.mail.smtp.SMTPTransport.sendMessage(SMTPTransport.java:324) at javax.mail.Transport.send0(Transport.java:163) at javax.mail.Transport.send(Transport.java:80) at SendEmail.main(SendEmail.java:43) javax.mail.SendFailedException: Sending failed; nested exception is: class javax.mail.MessagingException: IOException while sending message; nested exception is: javax.activation.UnsupportedDataTypeException: no object DCH for MIME type text/plain at javax.mail.Transport.send0(Transport.java:218) at javax.mail.Transport.send(Transport.java:80) at SendEmail.main(SendEmail.java:43)
Should I put the source code of my program here? It is a little long.
import java.util.Properties; import javax.mail.*; import javax.mail.internet.*; public class SendEmail{ public static void main (String args[]) throws Exception { String password = "124124"; String challengeQuestion = "How are you?"; String answer = "I am fine"; String toAddr = "cyrcr@yahoo.com.cn"; String toName = "Chen Yurong"; String body = "Welcome to Bioinformatics webserver!Thank you for registering with our bioinformatics webserver." + "This automated reply is for your reference only. User Name: " + toName+" Email: "+toAddr + "Password: "+password+"Challenge Words: "+challengeQuestion+" , the answer is " + answer; String fromAddr = "lip01yc@sheffield.ac.uk"; String fromName = "Yurong Chen"; String subject= "Registration on the bioinformatics web server"; //Specify the SMTP Host Properties props = new Properties(); props.put("mail.smtp.host", "broadstone.sheffield.ac.uk"); //Create a mail session, turn on the debug flag Session ssn = Session.getDefaultInstance(props,null); ssn.setDebug(true); try{ //set the from information InternetAddress from = new InternetAddress(fromAddr, fromName); //set the to information InternetAddress toUser = new InternetAddress(toAddr, toName); //Create the message Message msg = new MimeMessage(ssn); msg.setFrom(from); msg.addRecipient(Message.RecipientType.TO, toUser); msg.setSubject(subject); msg.setContent(body, "text/plain"); //Send the message across Transport.send(msg); System.out.println("send successful!"); } catch (MessagingException mex) { mex.printStackTrace(); } } }

Thank you for your kind help!

Yurong
[ June 22, 2006: Message edited by: Ulf Dittmer ]

It is the problem! Thank you ! I ignored that package when I imported the javax.*.
However, I met a new problem now. I sent out the message without any error now. But I didn't receive the email in the destination email address. I wrote a test program for that and got the following message:
javax.mail.SendFailedException: Sending failed; nested exception is: class javax.mail.MessagingException: IOException while sending message; nested exception is: javax.activation.UnsupportedDataTypeException: no object DCH for MIME type text/plain at javax.mail.Transport.send0(Transport.java:218) at javax.mail.Transport.send(Transport.java:80) at SendEmail.main(SendEmail.java:43)
Could you help me to explain that?
Thanks in advance!
Yurong

Hello, I use javaMail for my javabean to send email in my web server. However I got the following error message when I compile it.:
java.lang.NoClassDefFoundError: com/sun/mail/util/BEncoderStream at javax.mail.internet.InternetAddress.setPersonal(InternetAddress.java:168) at javax.mail.internet.InternetAddress.(InternetAddress.java:119) at javax.mail.internet.InternetAddress.(InternetAddress.java:105) at Email.send(Email.java:78)
my javabean Email.java has the source code as followed:
public void send() { validate(); if (!errors.isEmpty()) return; try { InternetAddress from = new InternetAddress(getFromAddress(), getFromName()); InternetAddress to = new InternetAddress(getToAddress(), getToName()); Properties props = new Properties(); props.put("mail.smtp.host", fieldSmtpHost); // Create a mail session Session session = Session.getDefaultInstance(props, null); session.setDebug(true); mail = new MimeMessage(session); mail.setFrom(from); mail.addRecipient(Message.RecipientType.TO, to); mail.setSubject(getSubject()); mail.setContent(getBody(), "text/plain"); } catch (Exception exc) { } (new Thread(this)).start(); return; }

My application FinishRegister.jsp have the followed source code:
<% java.lang.String userName = (String)session.getAttribute("forename")+(String)session.getAttribute("lastname"); java.lang.String userEmail = (String)session.getAttribute("email"); java.lang.String password = (String)session.getAttribute("password"); java.lang.String challengeQuestion = (String)session.getAttribute("question"); java.lang.String answer = (String)session.getAttribute("answer"); java.lang.String body = "Welcome to Bioinformatics webserver!Thank you for registering with our bioinformatics webserver." + " This automated reply is for your reference only. User Name: " + userName+" Email: "+userEmail + "Password: "+password+"Challenge Words: "+challengeQuestion+" , the answer is " + answer; java.lang.String fromName = "Yurong Chen"; java.lang.String smtpHost = "mailhost.dcs.shef.ac.uk"; java.lang.String fromAddress = "sheng@dcs.shef.ac.uk"; java.lang.String subject = "Registration";%> <% email.setFromName(fromName); email.setSmtpHost(smtpHost); email.setFromAddress(fromAddress); email.setBody(body); email.setSubject(subject); email.setToAddress(userEmail); email.setToName(userName); email.send(); %>

Thank you in advanced!
Yurong Chen
[ June 22, 2006: Message edited by: Ulf Dittmer ]

Hello, I use javamail to create a javebean for send email from the webserver. However, when I run the program, I get the following error message:
java.lang.NoClassDefFoundError: com/sun/mail/util/BEncoderStream
I don't know why it gives me such error message. When I compile my javabean, it works well and no error message.
Any help will be appreciated !