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

[Jari Häkkinen]

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(index_jsp.java:224) 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(Http11Processor.java:869) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) at java.lang.Thread.run(Thread.java:613)

[Nicklas Nordborg]

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:

<error-page>

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

</error-page>

2. 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.

[Jari Häkkinen]

Sorry, I was not clear enogh in my first report. I have web.xml properly installed, and it is a copy of web.xml.in, 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.

[Nicklas Nordborg]

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: ​http://tomcat.apache.org/faq/logging.html