Opened 17 years ago

Closed 17 years ago

Last modified 17 years ago

#362 closed defect (wontfix)

Stack trace is output to catalina.out when it shouldn't

Reported by: Jari Häkkinen Owned by: Johan Enell
Priority: trivial Milestone:
Component: web Version: trunk
Keywords: Cc:


The below exception is thrown when ones tries to run an analysis plugin on 1 channel data. Obviously there is no 1 channel analysis plugin available, and a pop-up windows is shown saying the same as the burp below. Shouldn't this exception be caught?

22:51:26,643 ERROR [jsp]:253 - Servlet.service() for servlet jsp threw exception net.sf.basedb.clients.web.WebException?: No plugins found:<br>No plugins can be used in this context, for the following reasons:<br><ul><li>Normalization: Lowess: Lowess normalization requires 2-channel data, not 1-channel.<li>Normalization: Median ratio: Normalization requires 2-channel data, not 1-channel.</ul>

at org.apache.jsp.common.plugin.index_jsp._jspService( 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 net.sf.basedb.clients.web.servlet.CharacterEncodingFilter?.doFilter(CharacterEncodingFilter?.java:71) at org.apache.catalina.core.ApplicationFilterChain?.internalDoFilter(ApplicationFilterChain?.java:202) 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.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( at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection( at at at org.apache.tomcat.util.threads.ThreadPool?$ControlRunnable?.run(ThreadPool?.java:684) at

Change History (4)

comment:1 Changed 17 years ago by Nicklas Nordborg

Priority: majortrivial
Summary: Exception thrown when trying to run analysis plugin on 1 channel dataStack trace is displayed instead of proper error message

This exception shouldn't be displayed as a stacktrace. There are two reasons that it is:

  1. The web.xml file is missing or doesn't contain information about exception handling. The web.xml file should be located in the <basedir>/www/WEB-INF directory and must contain the following tags:


<exception-type>java.lang.Throwable</exception-type> <location>/exception/exception.jsp</location>


  1. There is a bug in the exception.jsp page that prevents it from displaying a proper error message. In this case the catalina.out file should contain more information about the bug in the exception.jsp page. The catalina.out file is located in the <tomcat-dir>/logs directory.

comment:2 Changed 17 years ago by Jari Häkkinen

Sorry, I was not clear enogh in my first report. I have web.xml properly installed, and it is a copy of, also there is no information about exception.jsp in catalina.out. This is to be expected since the BASE gui is behaving properly, i.e., a pop-up appears with a deceant message.

What I was refering to was the message in catalina.out (which I submitted in the inital report). If the exception is caught and properly dealt with (printing a message to the user), should it report an exception stack trace in the log file? I mean, missing plugins in some contexts is not an error but to be expected. This should only generate an report to the user without any stack trace anywhere.

comment:3 Changed 17 years ago by Nicklas Nordborg

Resolution: wontfix
Status: newclosed

If you wish to do this you have to configure Tomcat differently. The logging into catalina.out and maybe other log files is not controlled by BASE. For more information see:

comment:4 Changed 17 years ago by Nicklas Nordborg

Summary: Stack trace is displayed instead of proper error messageStack trace is output to catalina.out when it shouldn't
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