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Main page is blank

Paulo Nuin
Hi

We successfully built and deployed the webapp for an instance or WormMine. Outputs were fine, no errors or warnings displayed, some errors were found on Tomcat access, later corrected, but lately we experiencing an error on Tomcat were files required to the main page of the webapp are not found. Both errors (shown below) are on exceptions on the java.io.FileNotFoundException class on the /header?desktop=true of the web app.

Any help is appreciated. Don’t know if it is relevant, but most ports on our instance are closed, with the exception of 8080.

Thanks in advance

Paulo


Jun 25, 2015 2:29:08 AM org.apache.catalina.core.ApplicationDispatcher invoke
SEVERE: Servlet.service() for servlet jsp threw exception
java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
        at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
        at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
        at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
        at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
        at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
        at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
        at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
        at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
        at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
        at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
        at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
        at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
        at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
        at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
        at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
        at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
        at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
        at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
        at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
        at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
        at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Thread.java:745)

Jun 25, 2015 2:29:08 AM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [action] in context with path [/wormmine] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: Problem accessing the absolute URL "http://im-dev.wormbase.org:8080/header?desktop=true". java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true] with root cause
java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
        at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
        at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
        at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
        at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
        at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
        at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
        at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
        at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
        at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
        at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
        at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
        at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
        at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
        at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
        at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
        at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
        at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
        at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
        at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
        at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
        at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Thread.java:745)
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Re: Main page is blank

Julie Sullivan
Hi Paulo,

I've never seen that error before! "header?desktop=true" isn't a valid
path, it makes me think there is a merging issue maybe?

I can try to deploy your webapp and see what I find. Which is the one
you are using? Is this it:

        https://github.com/WormBase/intermine/tree/dev/wormmine

Also, I would be testing on tomcat 7, I haven't updated InterMine to use
tomcat 8 yet.

Julie

On 25/06/15 04:52, Paulo Nuin wrote:

> Hi
>
> We successfully built and deployed the webapp for an instance or WormMine. Outputs were fine, no errors or warnings displayed, some errors were found on Tomcat access, later corrected, but lately we experiencing an error on Tomcat were files required to the main page of the webapp are not found. Both errors (shown below) are on exceptions on the java.io.FileNotFoundException class on the /header?desktop=true of the web app.
>
> Any help is appreciated. Don’t know if it is relevant, but most ports on our instance are closed, with the exception of 8080.
>
> Thanks in advance
>
> Paulo
>
>
> Jun 25, 2015 2:29:08 AM org.apache.catalina.core.ApplicationDispatcher invoke
> SEVERE: Servlet.service() for servlet jsp threw exception
> java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
> at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
> at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
> at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
> at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
> at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
> at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
> at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
> at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
> at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
> at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
> at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
> at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
> at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
> at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
> at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
> at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
> at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
> at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
> at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
> at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
> at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
> at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
> at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
> at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
> at java.lang.Thread.run(Thread.java:745)
>
> Jun 25, 2015 2:29:08 AM org.apache.catalina.core.StandardWrapperValve invoke
> SEVERE: Servlet.service() for servlet [action] in context with path [/wormmine] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: Problem accessing the absolute URL "http://im-dev.wormbase.org:8080/header?desktop=true". java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true] with root cause
> java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
> at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
> at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
> at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
> at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
> at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
> at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
> at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
> at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
> at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
> at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
> at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
> at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
> at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
> at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
> at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
> at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
> at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
> at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
> at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
> at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
> at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
> at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
> at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
> at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
> at java.lang.Thread.run(Thread.java:745)
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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Re: Main page is blank

Paulo Nuin
Hi

That’s the one. And we are using Tomcat 7, not installed by the package manager.

Thanks a lot

Paulo


> On Jun 25, 2015, at 2:21 AM, Julie Sullivan <[hidden email]> wrote:
>
> Hi Paulo,
>
> I've never seen that error before! "header?desktop=true" isn't a valid path, it makes me think there is a merging issue maybe?
>
> I can try to deploy your webapp and see what I find. Which is the one you are using? Is this it:
>
> https://github.com/WormBase/intermine/tree/dev/wormmine
>
> Also, I would be testing on tomcat 7, I haven't updated InterMine to use tomcat 8 yet.
>
> Julie
>
> On 25/06/15 04:52, Paulo Nuin wrote:
>> Hi
>>
>> We successfully built and deployed the webapp for an instance or WormMine. Outputs were fine, no errors or warnings displayed, some errors were found on Tomcat access, later corrected, but lately we experiencing an error on Tomcat were files required to the main page of the webapp are not found. Both errors (shown below) are on exceptions on the java.io.FileNotFoundException class on the /header?desktop=true of the web app.
>>
>> Any help is appreciated. Don’t know if it is relevant, but most ports on our instance are closed, with the exception of 8080.
>>
>> Thanks in advance
>>
>> Paulo
>>
>>
>> Jun 25, 2015 2:29:08 AM org.apache.catalina.core.ApplicationDispatcher invoke
>> SEVERE: Servlet.service() for servlet jsp threw exception
>> java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
>> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
>> at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
>> at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
>> at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>> at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
>> at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
>> at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
>> at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
>> at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
>> at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
>> at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
>> at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
>> at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
>> at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
>> at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
>> at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
>> at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>> at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
>> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
>> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
>> at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>> at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
>> at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
>> at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
>> at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
>> at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>> at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>> at java.lang.Thread.run(Thread.java:745)
>>
>> Jun 25, 2015 2:29:08 AM org.apache.catalina.core.StandardWrapperValve invoke
>> SEVERE: Servlet.service() for servlet [action] in context with path [/wormmine] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: Problem accessing the absolute URL "http://im-dev.wormbase.org:8080/header?desktop=true". java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true] with root cause
>> java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
>> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
>> at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
>> at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
>> at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>> at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
>> at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
>> at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
>> at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
>> at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
>> at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
>> at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
>> at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
>> at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
>> at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
>> at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
>> at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
>> at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>> at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
>> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
>> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
>> at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>> at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
>> at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
>> at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
>> at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
>> at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>> at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>> at java.lang.Thread.run(Thread.java:745)
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>


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Re: Main page is blank

Julie Sullivan
Hi Paulo,

I just noticed this commit:

https://github.com/WormBase/intermine/commit/25fb13f133773e4e3164a51f2895be05724da7a8

"Layout.jsp -> use desktop version of site "

Do you know why that was added? Can you try to revert that change and
see if that helps?

But that seems like custom code so I am not sure if I am going to be of
much help to you.

Julie

On 25/06/15 14:47, Paulo Nuin wrote:

> Hi
>
> That’s the one. And we are using Tomcat 7, not installed by the package manager.
>
> Thanks a lot
>
> Paulo
>
>
>> On Jun 25, 2015, at 2:21 AM, Julie Sullivan <[hidden email]> wrote:
>>
>> Hi Paulo,
>>
>> I've never seen that error before! "header?desktop=true" isn't a valid path, it makes me think there is a merging issue maybe?
>>
>> I can try to deploy your webapp and see what I find. Which is the one you are using? Is this it:
>>
>> https://github.com/WormBase/intermine/tree/dev/wormmine
>>
>> Also, I would be testing on tomcat 7, I haven't updated InterMine to use tomcat 8 yet.
>>
>> Julie
>>
>> On 25/06/15 04:52, Paulo Nuin wrote:
>>> Hi
>>>
>>> We successfully built and deployed the webapp for an instance or WormMine. Outputs were fine, no errors or warnings displayed, some errors were found on Tomcat access, later corrected, but lately we experiencing an error on Tomcat were files required to the main page of the webapp are not found. Both errors (shown below) are on exceptions on the java.io.FileNotFoundException class on the /header?desktop=true of the web app.
>>>
>>> Any help is appreciated. Don’t know if it is relevant, but most ports on our instance are closed, with the exception of 8080.
>>>
>>> Thanks in advance
>>>
>>> Paulo
>>>
>>>
>>> Jun 25, 2015 2:29:08 AM org.apache.catalina.core.ApplicationDispatcher invoke
>>> SEVERE: Servlet.service() for servlet jsp threw exception
>>> java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
>>> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
>>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
>>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
>>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
>>> at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
>>> at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
>>> at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>> at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
>>> at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
>>> at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
>>> at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
>>> at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
>>> at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
>>> at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
>>> at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
>>> at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
>>> at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
>>> at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
>>> at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
>>> at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>>> at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
>>> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
>>> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
>>> at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>> at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
>>> at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
>>> at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
>>> at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
>>> at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
>>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>> at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>> at java.lang.Thread.run(Thread.java:745)
>>>
>>> Jun 25, 2015 2:29:08 AM org.apache.catalina.core.StandardWrapperValve invoke
>>> SEVERE: Servlet.service() for servlet [action] in context with path [/wormmine] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: Problem accessing the absolute URL "http://im-dev.wormbase.org:8080/header?desktop=true". java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true] with root cause
>>> java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
>>> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
>>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
>>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
>>> at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
>>> at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
>>> at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
>>> at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>> at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
>>> at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
>>> at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
>>> at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
>>> at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
>>> at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
>>> at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
>>> at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
>>> at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
>>> at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
>>> at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
>>> at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
>>> at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>>> at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
>>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
>>> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
>>> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
>>> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
>>> at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>> at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
>>> at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
>>> at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
>>> at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
>>> at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
>>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>> at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>> at java.lang.Thread.run(Thread.java:745)
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>
>

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Re: Main page is blank

Todd Harris-2
Possibly related to branding our intermine instance with our boilerplate? Looks like it is trying to force the desktop (not mobile) site.

Perhaps worth simply removing for testing?

Todd

Sent from my iPhone

> On Jun 25, 2015, at 6:52 AM, Julie Sullivan <[hidden email]> wrote:
>
> Hi Paulo,
>
> I just noticed this commit:
>
> https://github.com/WormBase/intermine/commit/25fb13f133773e4e3164a51f2895be05724da7a8
>
> "Layout.jsp -> use desktop version of site "
>
> Do you know why that was added? Can you try to revert that change and see if that helps?
>
> But that seems like custom code so I am not sure if I am going to be of much help to you.
>
> Julie
>
>> On 25/06/15 14:47, Paulo Nuin wrote:
>> Hi
>>
>> That’s the one. And we are using Tomcat 7, not installed by the package manager.
>>
>> Thanks a lot
>>
>> Paulo
>>
>>
>>> On Jun 25, 2015, at 2:21 AM, Julie Sullivan <[hidden email]> wrote:
>>>
>>> Hi Paulo,
>>>
>>> I've never seen that error before! "header?desktop=true" isn't a valid path, it makes me think there is a merging issue maybe?
>>>
>>> I can try to deploy your webapp and see what I find. Which is the one you are using? Is this it:
>>>
>>>    https://github.com/WormBase/intermine/tree/dev/wormmine
>>>
>>> Also, I would be testing on tomcat 7, I haven't updated InterMine to use tomcat 8 yet.
>>>
>>> Julie
>>>
>>>> On 25/06/15 04:52, Paulo Nuin wrote:
>>>> Hi
>>>>
>>>> We successfully built and deployed the webapp for an instance or WormMine. Outputs were fine, no errors or warnings displayed, some errors were found on Tomcat access, later corrected, but lately we experiencing an error on Tomcat were files required to the main page of the webapp are not found. Both errors (shown below) are on exceptions on the java.io.FileNotFoundException class on the /header?desktop=true of the web app.
>>>>
>>>> Any help is appreciated. Don’t know if it is relevant, but most ports on our instance are closed, with the exception of 8080.
>>>>
>>>> Thanks in advance
>>>>
>>>> Paulo
>>>>
>>>>
>>>> Jun 25, 2015 2:29:08 AM org.apache.catalina.core.ApplicationDispatcher invoke
>>>> SEVERE: Servlet.service() for servlet jsp threw exception
>>>> java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
>>>>    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
>>>>    at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
>>>>    at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
>>>>    at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
>>>>    at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
>>>>    at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
>>>>    at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>>>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>    at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
>>>>    at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
>>>>    at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
>>>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
>>>>    at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
>>>>    at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
>>>>    at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
>>>>    at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
>>>>    at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
>>>>    at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
>>>>    at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
>>>>    at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
>>>>    at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
>>>>    at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>>>>    at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
>>>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
>>>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
>>>>    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
>>>>    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
>>>>    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>>>    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
>>>>    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>>>    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
>>>>    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
>>>>    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
>>>>    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
>>>>    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>>>    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>>>    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>>>    at java.lang.Thread.run(Thread.java:745)
>>>>
>>>> Jun 25, 2015 2:29:08 AM org.apache.catalina.core.StandardWrapperValve invoke
>>>> SEVERE: Servlet.service() for servlet [action] in context with path [/wormmine] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: Problem accessing the absolute URL "http://im-dev.wormbase.org:8080/header?desktop=true". java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true] with root cause
>>>> java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
>>>>    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
>>>>    at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
>>>>    at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
>>>>    at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
>>>>    at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
>>>>    at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
>>>>    at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>>>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>    at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
>>>>    at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
>>>>    at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
>>>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
>>>>    at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
>>>>    at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
>>>>    at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
>>>>    at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
>>>>    at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
>>>>    at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
>>>>    at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
>>>>    at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
>>>>    at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
>>>>    at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>>>>    at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
>>>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
>>>>    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
>>>>    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
>>>>    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
>>>>    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>>>    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
>>>>    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>>>    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
>>>>    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
>>>>    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
>>>>    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
>>>>    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>>>    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>>>    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>>>    at java.lang.Thread.run(Thread.java:745)
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>
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Re: Main page is blank

Paulo Nuin
Hi

Indeed the error was on that line. Deploying the app without that line (and the footer, after another similar error) worked fine. The web app works and things look good.

Thanks a lot, Julie for the help. Again, learned a little bit more about Intermine.

Cheers
Paulo


> On Jun 25, 2015, at 2:05 PM, Todd Harris <[hidden email]> wrote:
>
> Possibly related to branding our intermine instance with our boilerplate? Looks like it is trying to force the desktop (not mobile) site.
>
> Perhaps worth simply removing for testing?
>
> Todd
>
> Sent from my iPhone
>
>> On Jun 25, 2015, at 6:52 AM, Julie Sullivan <[hidden email]> wrote:
>>
>> Hi Paulo,
>>
>> I just noticed this commit:
>>
>> https://github.com/WormBase/intermine/commit/25fb13f133773e4e3164a51f2895be05724da7a8
>>
>> "Layout.jsp -> use desktop version of site "
>>
>> Do you know why that was added? Can you try to revert that change and see if that helps?
>>
>> But that seems like custom code so I am not sure if I am going to be of much help to you.
>>
>> Julie
>>
>>> On 25/06/15 14:47, Paulo Nuin wrote:
>>> Hi
>>>
>>> That’s the one. And we are using Tomcat 7, not installed by the package manager.
>>>
>>> Thanks a lot
>>>
>>> Paulo
>>>
>>>
>>>> On Jun 25, 2015, at 2:21 AM, Julie Sullivan <[hidden email]> wrote:
>>>>
>>>> Hi Paulo,
>>>>
>>>> I've never seen that error before! "header?desktop=true" isn't a valid path, it makes me think there is a merging issue maybe?
>>>>
>>>> I can try to deploy your webapp and see what I find. Which is the one you are using? Is this it:
>>>>
>>>>   https://github.com/WormBase/intermine/tree/dev/wormmine
>>>>
>>>> Also, I would be testing on tomcat 7, I haven't updated InterMine to use tomcat 8 yet.
>>>>
>>>> Julie
>>>>
>>>>> On 25/06/15 04:52, Paulo Nuin wrote:
>>>>> Hi
>>>>>
>>>>> We successfully built and deployed the webapp for an instance or WormMine. Outputs were fine, no errors or warnings displayed, some errors were found on Tomcat access, later corrected, but lately we experiencing an error on Tomcat were files required to the main page of the webapp are not found. Both errors (shown below) are on exceptions on the java.io.FileNotFoundException class on the /header?desktop=true of the web app.
>>>>>
>>>>> Any help is appreciated. Don’t know if it is relevant, but most ports on our instance are closed, with the exception of 8080.
>>>>>
>>>>> Thanks in advance
>>>>>
>>>>> Paulo
>>>>>
>>>>>
>>>>> Jun 25, 2015 2:29:08 AM org.apache.catalina.core.ApplicationDispatcher invoke
>>>>> SEVERE: Servlet.service() for servlet jsp threw exception
>>>>> java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
>>>>>   at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
>>>>>   at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
>>>>>   at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
>>>>>   at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
>>>>>   at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
>>>>>   at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
>>>>>   at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>>>>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>>   at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
>>>>>   at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
>>>>>   at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
>>>>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
>>>>>   at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
>>>>>   at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
>>>>>   at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
>>>>>   at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
>>>>>   at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
>>>>>   at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
>>>>>   at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
>>>>>   at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
>>>>>   at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
>>>>>   at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>>>>>   at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
>>>>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
>>>>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
>>>>>   at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
>>>>>   at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
>>>>>   at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>>>>   at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
>>>>>   at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>>>>   at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
>>>>>   at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
>>>>>   at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
>>>>>   at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
>>>>>   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>>>>   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>>>>   at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>>>>   at java.lang.Thread.run(Thread.java:745)
>>>>>
>>>>> Jun 25, 2015 2:29:08 AM org.apache.catalina.core.StandardWrapperValve invoke
>>>>> SEVERE: Servlet.service() for servlet [action] in context with path [/wormmine] threw exception [javax.servlet.ServletException: javax.servlet.jsp.JspException: Problem accessing the absolute URL "http://im-dev.wormbase.org:8080/header?desktop=true". java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true] with root cause
>>>>> java.io.FileNotFoundException: http://im-dev.wormbase.org:8080/header?desktop=true
>>>>>   at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1625)
>>>>>   at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireReader(ImportSupport.java:331)
>>>>>   at org.apache.taglibs.standard.tag.common.core.ImportSupport.acquireString(ImportSupport.java:241)
>>>>>   at org.apache.taglibs.standard.tag.common.core.ImportSupport.doEndTag(ImportSupport.java:158)
>>>>>   at org.apache.jsp.layout_jsp._jspx_meth_c_005fimport_005f0(layout_jsp.java:864)
>>>>>   at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:212)
>>>>>   at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>>>>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>>   at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439)
>>>>>   at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395)
>>>>>   at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339)
>>>>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
>>>>>   at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
>>>>>   at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
>>>>>   at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
>>>>>   at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1083)
>>>>>   at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:295)
>>>>>   at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:271)
>>>>>   at org.apache.struts.tiles.TilesRequestProcessor.processForwardConfig(TilesRequestProcessor.java:332)
>>>>>   at org.intermine.web.struts.InterMineRequestProcessor.processForwardConfig(InterMineRequestProcessor.java:214)
>>>>>   at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:232)
>>>>>   at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>>>>>   at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:449)
>>>>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
>>>>>   at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>>   at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>>   at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
>>>>>   at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
>>>>>   at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
>>>>>   at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>>>>   at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
>>>>>   at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>>>>   at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
>>>>>   at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
>>>>>   at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
>>>>>   at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
>>>>>   at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>>>>   at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>>>>   at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>>>>   at java.lang.Thread.run(Thread.java:745)
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