Jchem connection problem

Hi,





I am using the jchem.jar for registration and search in substructes. (www.chemicainventory.org). I am setting up the system on a debian server using jdk1.5.0_08 and jchem.jar (version JCHEM_VERSION = 3.1.6).





The application is runnig fine, and I can search and register text based info, but when trying to register structure data the error beneath is shown, and as it appears, the connection handler cannot connect to the mysql database... (jdbc version : mysql-connector-java-3.1.12-bin.jar):





Error start: *************************************************





** BEGIN NESTED EXCEPTION **





java.net.SocketException


MESSAGE: java.net.ConnectException: Connection refused





STACKTRACE:





java.net.SocketException: java.net.ConnectException: Connection refused


at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:156)


at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:284)


at com.mysql.jdbc.Connection.createNewIO(Connection.java:2555)


at com.mysql.jdbc.Connection.<init>(Connection.java:1485)


at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:266)


at java.sql.DriverManager.getConnection(DriverManager.java:525)


at java.sql.DriverManager.getConnection(DriverManager.java:171)


at chemaxon.util.ConnectionHandler.setConnected(ConnectionHandler.java:206)


at chemaxon.util.ConnectionHandler.connect(ConnectionHandler.java:246)


at chemicalinventory.beans.ChemicalRegBean.checkChemicalRegistration(ChemicalRegBean.java:261)


at chemicalinventory.beans.ChemicalRegBean.regOK(ChemicalRegBean.java:228)


at org.apache.jsp.administration.compound.chemical_005fadministration_005fnew_jsp._jspService(chemic


al_005fadministration_005fnew_jsp.java:180)


at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)


at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332)


at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)


at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)


at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)


at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)


at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)


at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463)


at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398)


at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)


at org.apache.jsp.administration.adminController_jsp._jspService(adminController_jsp.java:191)


at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)


at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332)


at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)


at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)


at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)


at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)


at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)


at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)


at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:524)


at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)


at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)


at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)


at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)


at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)


at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseP


rotocol.java:664)


at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)


at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)


at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)


at java.lang.Thread.run(Thread.java:595)








** END NESTED EXCEPTION **











Last packet sent to the server was 13 ms ago.


at com.mysql.jdbc.Connection.createNewIO(Connection.java:2621)


at com.mysql.jdbc.Connection.<init>(Connection.java:1485)


at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:266)


at java.sql.DriverManager.getConnection(DriverManager.java:525)


at java.sql.DriverManager.getConnection(DriverManager.java:171)


at chemaxon.util.ConnectionHandler.setConnected(ConnectionHandler.java:206)


at chemaxon.util.ConnectionHandler.connect(ConnectionHandler.java:246)


at chemicalinventory.beans.ChemicalRegBean.checkChemicalRegistration(ChemicalRegBean.java:261)


at chemicalinventory.beans.ChemicalRegBean.regOK(ChemicalRegBean.java:228)


at org.apache.jsp.administration.compound.chemical_005fadministration_005fnew_jsp._jspService(chemic


al_005fadministration_005fnew_jsp.java:180)


at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)


at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332)


at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)


at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)


at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)


at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)


at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672)


at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463)


at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398)


at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)


at org.apache.jsp.administration.adminController_jsp._jspService(adminController_jsp.java:191)


at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)


at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332)


at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)


at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)


at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)


at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)


at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)


at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)


at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)


at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:524)


at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)


at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)


at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)


at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)


at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)


at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseP


rotocol.java:664)


at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)


at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)


at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)


at java.lang.Thread.run(Thread.java:595)





Error end:****************************************************








Hope that you can give some feed back on this issue...!





Dann

Hi,





It seems that the JDBC connection cannot be established.





Please check if the URL you pass on to our API (ConnectionHandler) is correct.








Best regards,





Szilard

For obtaining connecting I am usign your connection handler:





ConnectionHandler ch = new ConnectionHandler();


ch.setDriver(Attributes.DB_DRIVER);


ch.setUrl(Attributes.DB_NAME);


ch.setLoginName(Attributes.DB_USER);


ch.setPassword(Attributes.DB_PWD);


ch.setPropertyTable(Attributes.J_PROP_TABLE);





ch.connect();





this utilizes the following url: jdbc:mysql://130.225.252.212:3306/chemicals





which is the same as I use for my connection pooling, without problems...!!

Hi,





The ConnectionHandler class hasn't been changed for ages, and works fine for all of our users.





You say you can connect fine with the same URL.


In this case:





- Are there any new connections created, or you are just using the old ones ?


- Is your code running on the same machine ?


(please note that in MySQL a user can have different rights if connecting from localhost)


- Is there any kind of firewall that could interfere with the connection ?


- Is your code running in the same JVM ?


- Does your code use the same username and password ?


- How do you connect ?


This is the actual code how we create the connection:

Code:

Class.forName (driver).newInstance(); con = DriverManager.getConnection(url, loginName, password);

Best regards,





Szilard

Hi,





I will try to install different versions of jdk and propably also mysql...





I will get back with information about this solving the problem..





Dann

The problem was the mysql package distributed with the Debian system.





After installing mysql from www.mysql.com in 4.1.21, the application now works as intended..





Dann