database connection - Tomcat6 can't connect to MySql (The driver has not received any packets from the server)

Question

i'm running an Apache Tomcat 6.0.20 / MySQL 5.1.37-lubuntu / sun-java6-jdk /sun-java6-jre / sun-java6-bin on my local machine using Ubuntu 9.10 as OS. I'm trying to get a simple DB-query example running for 2 days now, but i still get this Exception:

org.apache.jasper.JasperException: javax.servlet.ServletException: javax.servlet.jsp.JspException: Unable to get connection, DataSource invalid: "org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.)"
 org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServletWrapper.java:522)
 org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:398)
 org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
 org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
 javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

root cause

javax.servlet.ServletException: javax.servlet.jsp.JspException: Unable to get connection, DataSource invalid: "org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.)"
 org.apache.jasper.runtime.PageContextImpl.doHandlePageException(PageContextImpl.java:862)
 org.apache.jasper.runtime.PageContextImpl.handlePageException(PageContextImpl.java:791)
 org.apache.jsp.index_jsp._jspService(index_jsp.java:104)
 org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
 javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
 org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374)
 org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
 org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
 javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

root cause

javax.servlet.jsp.JspException: Unable to get connection, DataSource invalid: "org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (Communications link failure

The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.)"
 org.apache.taglibs.standard.tag.common.sql.QueryTagSupport.getConnection(QueryTagSupport.java:285)
 org.apache.taglibs.standard.tag.common.sql.QueryTagSupport.doStartTag(QueryTagSupport.java:168)
 org.apache.jsp.index_jsp._jspx_meth_sql_005fquery_005f0(index_jsp.java:274)
 org.apache.jsp.index_jsp._jspx_meth_c_005fotherwise_005f0(index_jsp.java:216)
 org.apache.jsp.index_jsp._jspx_meth_c_005fchoose_005f0(index_jsp.java:130)
 org.apache.jsp.index_jsp._jspService(index_jsp.java:93)
 org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
 javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
 org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374)
 org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
 org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
 javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

my web.xml looks like this :

<?xml version="1.0" encoding="utf-8"?>
<web-app xmlns="http://java.sun.com/xml/ns/javaee"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"
    version="2.5">
  <resource-ref>
      <description>DB Connection</description>
      <res-ref-name>jdbc/testDB</res-ref-name>
      <res-type>javax.sql.DataSource</res-type>
      <res-auth>Container</res-auth>
  </resource-ref>
</web-app>

the context.xml looks like this :

<?xml version="1.0" encoding="UTF-8"?>
<Context path="/my1stApp" docBase="/var/www/jsp/my1stApp" debug="5" reloadable="true" crossContext="true">
    <Resource name="jdbc/testDB" auth="Container" type="javax.sql.DataSource"
    maxActive="5" maxIdle="5" maxWait="10000"
    username="user" password="password" driverClassName="com.mysql.jdbc.Driver"
    url="jdbc:mysql://localhost:3306/some"/>
</Context>

and the jsp file looks like this:

<%@ page contentType="text/html" %>

<%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>

<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions" %>

<%@ taglib prefix="fmt" uri="http://java.sun.com/jsp/jstl/fmt" %>
<%@ taglib prefix="sql" uri="http://java.sun.com/jsp/jstl/sql" %>


<html>

  <head>

    <title>DroneLootTool</title>

  </head>

  <body bgcolor="white">



 <sql:query var="res" dataSource="jdbc/testDB">
  select name, othername 
  from mytable
 </sql:query>

  <h2>Results</h2>

<c:forEach var="row" items="${res.rows}">
    Name ${row.name}<br/>
    MoreName ${row.othername}<br/><br/>
</c:forEach>


  </body>

</html>

• read lots of forum entries / tried lots of different settings (always changed back to original settings when it didnt' work)
• set TOMCAT6_SECURITY=no in /etc/default/tomcat6 because TOMCAT6_SECURITY=yes was causing trouble too
• the skip-networking flag is not set for the DB (BIND 127.0.0.1 is set)
• firewall is swiched off (sudo ufw disable)
• MySQL works (tested several times with user used in this skript)

• telnet localhost 3306 says

  Trying ::1... Trying 127.0.0.1... Connected to localhost. Escape character is '^]'. Connection closed by foreign host.

---

The TestConnection.java produced the following output:

me@my-laptop:~/Desktop$ java -classpath '/usr/share/java/mysql.jar:./' TestConnection com.mysql.jdbc.Driver jdbc:mysql://localhost:3306/testDB myuser mypassword

com.mysql.jdbc.CommunicationsException: Communications link failure
    Last packet sent to the server was 0 ms ago.
        at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1070)
        at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2103)
        at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:718)
        at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:298)
        at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
        at java.sql.DriverManager.getConnection(DriverManager.java:582)
        at java.sql.DriverManager.getConnection(DriverManager.java:185)
        at TestConnection.checkConnection(TestConnection.java:40)
        at TestConnection.main(TestConnection.java:21)
    Caused by: com.mysql.jdbc.CommunicationsException: Communications link failure

    Last packet sent to the server was 0 ms ago.
        at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1070)
        at com.mysql.jdbc.MysqlIO.readPacket(MysqlIO.java:666)
        at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1069)
        at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2031)
        ... 7 more
    Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost.
        at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:2431)
        at com.mysql.jdbc.MysqlIO.readPacket(MysqlIO.java:590)
        ... 9 more
    Connection failed.

---

i don't know if there is a difference between the way the java driver connects to the DB and the Perl DBI module does, but this PERL skript works

#!/usr/bin/perl -w 

use CGI;
use DBI;
use strict;

print CGI::header();

my $dbh = DBI->connect("dbi:mysql:some:localhost", "user", "password");

my $sSql = "SELECT * from mytable";

my $ppl = $dbh->selectall_arrayref( $sSql );

foreach my $pl (@$ppl)
{
  my @array = @$pl;
  print @array;
}

$dbh->disconnect;

---

enabled --log-warnings on the mysql, but i didn't get any new warnings. When i was searching the logs for warnings i found this messages when i restart the tomcat, don't know if it helps to find the problem :

Feb  2 19:50:37 tobias-laptop jsvc.exec[3129]: 02.02.2010 19:50:37 org.apache.catalina.startup.HostConfig checkResources#012INFO: Undeploying context [/myapp]
Feb  2 19:50:37 tobias-laptop jsvc.exec[3129]: 02.02.2010 19:50:37 org.apache.catalina.loader.WebappClassLoader clearReferencesThreads#012SCHWERWIEGEND: A web application appears to have started a thread named [MySQL Statement Cancellation Timer] but has failed to stop it. This is very likely to create a memory leak.
Feb  2 19:50:37 tobias-laptop jsvc.exec[3129]: 02.02.2010 19:50:37 org.apache.catalina.startup.HostConfig deployDescriptor#012INFO: Deploying configuration descriptor myapp.xml

Answer 1

I solved this problem. The reason why this error occurs is tomcat security restrictions.

You have to add following line to your $TOMCAT-CONFIG/policy.d/04webapps.policy

permission java.net.SocketPermission "127.0.0.1:3306", "connect";

Works for me, hope it will work for you too :)