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Report error

Vallejos, Andrew

Not sure if I missed a step or what… I got 0.97 working locally, but for some reason the dev server throws the following error when going to a report page.

 

-Andrew

 

SEVERE: Servlet.service() for servlet action threw exception

javax.servlet.jsp.JspException: ServletException in '/report.jsp': javax.servlet.jsp.JspException: ServletException in '/reportAspect.jsp': javax.servlet.jsp.JspException: ServletException in '/reportRefsCols.jsp': javax.servlet.jsp.JspException: ServletException in '/reportCollectionTable.jsp': /reportCollectionTable.jsp(34,16) "${!empty(resultElementRow.items)}" contains invalid expression(s): javax.el.ELException: Function ':empty' not found

        at org.apache.struts.taglib.tiles.InsertTag$InsertHandler.doEndTag(InsertTag.java:921)

        at org.apache.struts.taglib.tiles.InsertTag.doEndTag(InsertTag.java:460)

        at org.apache.jsp.layout_jsp._jspx_meth_tiles_005fget_005f1(layout_jsp.java:860)

        at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:204)

        at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)

       at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

        at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:374)

        at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)

        at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

        at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:630)

        at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:436)

        at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:374)

        at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:302)

        at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1056)

        at org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProcessor.java:261)

        at org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(TilesRequestProcessor.java:237)

        at org.apache.struts.tiles.TilesRequestProcessor.internalModuleRelativeForward(TilesRequestProcessor.java:339)

        at org.apache.struts.action.RequestProcessor.processForward(RequestProcessor.java:553)

        at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:211)

        at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1164)

        at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:397)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

        at com.planetj.servlet.filter.compression.CompressingFilter.doFilter(CompressingFilter.java:270)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)

        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)

        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:286)

        at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)

        at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)

        at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:767)

        at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:697)

        at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:889)

        at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690)

        at java.lang.Thread.run(Thread.java:636)

 

======================

Andrew Vallejos

Web Developer II

Biotechnology and Bioengineering Center

Medical College of Wisconsin

414-955-4104

[hidden email]


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Re: Report error

Julie Sullivan
Hi Andrew,

Is your dev server using Tomcat 6.0.29?

http://www.europheus.com/?p=68

On 07/13/2011 02:55 PM, Vallejos, Andrew wrote:

> Not sure if I missed a step or what... I got 0.97 working locally, but
> for some reason the dev server throws the following error when going to
> a report page.
>
>
>
> -Andrew
>
>
>
> SEVERE: Servlet.service() for servlet action threw exception
>
> javax.servlet.jsp.JspException: ServletException in '/report.jsp':
> javax.servlet.jsp.JspException: ServletException in '/reportAspect.jsp':
> javax.servlet.jsp.JspException: ServletException in
> '/reportRefsCols.jsp': javax.servlet.jsp.JspException: ServletException
> in '/reportCollectionTable.jsp': /reportCollectionTable.jsp(34,16)
> "${!empty(resultElementRow.items)}" contains invalid expression(s):
> javax.el.ELException: Function ':empty' not found
>
>          at
> org.apache.struts.taglib.tiles.InsertTag$InsertHandler.doEndTag(InsertTa
> g.java:921)
>
>          at
> org.apache.struts.taglib.tiles.InsertTag.doEndTag(InsertTag.java:460)
>
>          at
> org.apache.jsp.layout_jsp._jspx_meth_tiles_005fget_005f1(layout_jsp.java
> :860)
>
>          at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:204)
>
>          at
> org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>
>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>
>          at
> org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
> va:374)
>
>          at
> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
>
>          at
> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
>
>          at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>
>          at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
> tionFilterChain.java:290)
>
>          at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
> erChain.java:206)
>
>          at
> org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatc
> her.java:630)
>
>          at
> org.apache.catalina.core.ApplicationDispatcher.processRequest(Applicatio
> nDispatcher.java:436)
>
>          at
> org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDisp
> atcher.java:374)
>
>          at
> org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispat
> cher.java:302)
>
>          at
> org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.jav
> a:1056)
>
>          at
> org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProc
> essor.java:261)
>
>          at
> org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(Til
> esRequestProcessor.java:237)
>
>          at
> org.apache.struts.tiles.TilesRequestProcessor.internalModuleRelativeForw
> ard(TilesRequestProcessor.java:339)
>
>          at
> org.apache.struts.action.RequestProcessor.processForward(RequestProcesso
> r.java:553)
>
>          at
> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:
> 211)
>
>          at
> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1164)
>
>          at
> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:397)
>
>          at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
>
>          at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>
>          at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
> tionFilterChain.java:290)
>
>          at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
> erChain.java:206)
>
>          at
> com.planetj.servlet.filter.compression.CompressingFilter.doFilter(Compre
> ssingFilter.java:270)
>
>          at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
> tionFilterChain.java:235)
>
>          at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
> erChain.java:206)
>
>          at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
> e.java:233)
>
>          at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
> e.java:191)
>
>          at
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
> :128)
>
>          at
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
> :102)
>
>          at
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
> java:109)
>
>          at
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:2
> 86)
>
>          at
> org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)
>
>          at
> org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
>
>          at
> org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:767)
>
>          at
> org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:
> 697)
>
>          at
> org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.
> java:889)
>
>          at
> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
> .java:690)
>
>          at java.lang.Thread.run(Thread.java:636)
>
>
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: Report error

Vallejos, Andrew
No, 6.0.18

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On
Behalf Of Julie Sullivan
Sent: Wednesday, July 13, 2011 9:12 AM
To: [hidden email]
Subject: Re: [InterMine Dev] Report error

Hi Andrew,

Is your dev server using Tomcat 6.0.29?

http://www.europheus.com/?p=68

On 07/13/2011 02:55 PM, Vallejos, Andrew wrote:
> Not sure if I missed a step or what... I got 0.97 working locally, but
> for some reason the dev server throws the following error when going
to

> a report page.
>
>
>
> -Andrew
>
>
>
> SEVERE: Servlet.service() for servlet action threw exception
>
> javax.servlet.jsp.JspException: ServletException in '/report.jsp':
> javax.servlet.jsp.JspException: ServletException in
'/reportAspect.jsp':
> javax.servlet.jsp.JspException: ServletException in
> '/reportRefsCols.jsp': javax.servlet.jsp.JspException:
ServletException
> in '/reportCollectionTable.jsp': /reportCollectionTable.jsp(34,16)
> "${!empty(resultElementRow.items)}" contains invalid expression(s):
> javax.el.ELException: Function ':empty' not found
>
>          at
>
org.apache.struts.taglib.tiles.InsertTag$InsertHandler.doEndTag(InsertTa
> g.java:921)
>
>          at
> org.apache.struts.taglib.tiles.InsertTag.doEndTag(InsertTag.java:460)
>
>          at
>
org.apache.jsp.layout_jsp._jspx_meth_tiles_005fget_005f1(layout_jsp.java
> :860)
>
>          at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:204)
>
>          at
> org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>
>         at
javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>
>          at
>
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
> va:374)
>
>          at
>
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
>
>          at
> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
>
>          at
javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>
>          at
>
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
> tionFilterChain.java:290)
>
>          at
>
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
> erChain.java:206)
>
>          at
>
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatc
> her.java:630)
>
>          at
>
org.apache.catalina.core.ApplicationDispatcher.processRequest(Applicatio
> nDispatcher.java:436)
>
>          at
>
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDisp
> atcher.java:374)
>
>          at
>
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispat
> cher.java:302)
>
>          at
>
org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.jav
> a:1056)
>
>          at
>
org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProc
> essor.java:261)
>
>          at
>
org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(Til
> esRequestProcessor.java:237)
>
>          at
>
org.apache.struts.tiles.TilesRequestProcessor.internalModuleRelativeForw
> ard(TilesRequestProcessor.java:339)
>
>          at
>
org.apache.struts.action.RequestProcessor.processForward(RequestProcesso
> r.java:553)
>
>          at
>
org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:
> 211)
>
>          at
>
org.apache.struts.action.ActionServlet.process(ActionServlet.java:1164)
>
>          at
> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:397)
>
>          at
javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
>
>          at
javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>
>          at
>
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
> tionFilterChain.java:290)
>
>          at
>
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
> erChain.java:206)
>
>          at
>
com.planetj.servlet.filter.compression.CompressingFilter.doFilter(Compre
> ssingFilter.java:270)
>
>          at
>
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
> tionFilterChain.java:235)
>
>          at
>
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
> erChain.java:206)
>
>          at
>
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
> e.java:233)
>
>          at
>
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
> e.java:191)
>
>          at
>
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
> :128)
>
>          at
>
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
> :102)
>
>          at
>
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
> java:109)
>
>          at
>
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:2

> 86)
>
>          at
> org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)
>
>          at
> org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
>
>          at
> org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:767)
>
>          at
>
org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:
> 697)
>
>          at
>
org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.
> java:889)
>
>          at
>
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool

> .java:690)
>
>          at java.lang.Thread.run(Thread.java:636)
>
>
>
> ======================
>
> Andrew Vallejos
>
> Web Developer II
>
> Biotechnology and Bioengineering Center
>
> Medical College of Wisconsin
>
> 414-955-4104
>
> [hidden email]
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
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Re: Report error

Julie Sullivan
I've fixed the problem (I think).  Do an svn update and then re-release your
webapp, and let me know if that works.

Tomcat 6.0.18 introduced a bug where `empty (value)` is valid but `empty(value)`
is not valid.  I've added the space.

Cheers,
Julie

On 07/13/2011 03:12 PM, Vallejos, Andrew wrote:

> No, 6.0.18
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On
> Behalf Of Julie Sullivan
> Sent: Wednesday, July 13, 2011 9:12 AM
> To: [hidden email]
> Subject: Re: [InterMine Dev] Report error
>
> Hi Andrew,
>
> Is your dev server using Tomcat 6.0.29?
>
> http://www.europheus.com/?p=68
>
> On 07/13/2011 02:55 PM, Vallejos, Andrew wrote:
>> Not sure if I missed a step or what... I got 0.97 working locally, but
>> for some reason the dev server throws the following error when going
> to
>> a report page.
>>
>>
>>
>> -Andrew
>>
>>
>>
>> SEVERE: Servlet.service() for servlet action threw exception
>>
>> javax.servlet.jsp.JspException: ServletException in '/report.jsp':
>> javax.servlet.jsp.JspException: ServletException in
> '/reportAspect.jsp':
>> javax.servlet.jsp.JspException: ServletException in
>> '/reportRefsCols.jsp': javax.servlet.jsp.JspException:
> ServletException
>> in '/reportCollectionTable.jsp': /reportCollectionTable.jsp(34,16)
>> "${!empty(resultElementRow.items)}" contains invalid expression(s):
>> javax.el.ELException: Function ':empty' not found
>>
>>           at
>>
> org.apache.struts.taglib.tiles.InsertTag$InsertHandler.doEndTag(InsertTa
>> g.java:921)
>>
>>           at
>> org.apache.struts.taglib.tiles.InsertTag.doEndTag(InsertTag.java:460)
>>
>>           at
>>
> org.apache.jsp.layout_jsp._jspx_meth_tiles_005fget_005f1(layout_jsp.java
>> :860)
>>
>>           at org.apache.jsp.layout_jsp._jspService(layout_jsp.java:204)
>>
>>           at
>> org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>>
>>          at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>>
>>           at
>>
> org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.ja
>> va:374)
>>
>>           at
>>
> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:342)
>>
>>           at
>> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:267)
>>
>>           at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>>
>>           at
>>
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
>> tionFilterChain.java:290)
>>
>>           at
>>
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
>> erChain.java:206)
>>
>>           at
>>
> org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatc
>> her.java:630)
>>
>>           at
>>
> org.apache.catalina.core.ApplicationDispatcher.processRequest(Applicatio
>> nDispatcher.java:436)
>>
>>           at
>>
> org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDisp
>> atcher.java:374)
>>
>>           at
>>
> org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispat
>> cher.java:302)
>>
>>           at
>>
> org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.jav
>> a:1056)
>>
>>           at
>>
> org.apache.struts.tiles.TilesRequestProcessor.doForward(TilesRequestProc
>> essor.java:261)
>>
>>           at
>>
> org.apache.struts.tiles.TilesRequestProcessor.processTilesDefinition(Til
>> esRequestProcessor.java:237)
>>
>>           at
>>
> org.apache.struts.tiles.TilesRequestProcessor.internalModuleRelativeForw
>> ard(TilesRequestProcessor.java:339)
>>
>>           at
>>
> org.apache.struts.action.RequestProcessor.processForward(RequestProcesso
>> r.java:553)
>>
>>           at
>>
> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:
>> 211)
>>
>>           at
>>
> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1164)
>>
>>           at
>> org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:397)
>>
>>           at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
>>
>>           at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>>
>>           at
>>
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
>> tionFilterChain.java:290)
>>
>>           at
>>
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
>> erChain.java:206)
>>
>>           at
>>
> com.planetj.servlet.filter.compression.CompressingFilter.doFilter(Compre
>> ssingFilter.java:270)
>>
>>           at
>>
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
>> tionFilterChain.java:235)
>>
>>           at
>>
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
>> erChain.java:206)
>>
>>           at
>>
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
>> e.java:233)
>>
>>           at
>>
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
>> e.java:191)
>>
>>           at
>>
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
>> :128)
>>
>>           at
>>
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
>> :102)
>>
>>           at
>>
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
>> java:109)
>>
>>           at
>>
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:2
>> 86)
>>
>>           at
>> org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)
>>
>>           at
>> org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:283)
>>
>>           at
>> org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:767)
>>
>>           at
>>
> org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:
>> 697)
>>
>>           at
>>
> org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.
>> java:889)
>>
>>           at
>>
> org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
>> .java:690)
>>
>>           at java.lang.Thread.run(Thread.java:636)
>>
>>
>>
>> ======================
>>
>> Andrew Vallejos
>>
>> Web Developer II
>>
>> Biotechnology and Bioengineering Center
>>
>> Medical College of Wisconsin
>>
>> 414-955-4104
>>
>> [hidden email]
>>
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
> _______________________________________________
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Underscores in attribute names

James Blackshaw
Hi,

In the previous version of Intermine that MitoMiner used, it was
possible to use underscores in attribute names, but now the attribute
names are enforced to not allow it despite Java generally accepting the
character. Asking around some possible users in the Unit, we decided
that underscores made for more easily readable names in our query
builder. For the next version of InterMine onwards, could PathQuery.java
and the other files be changed to allow underscores like before please?
Right now we're chaging the regular expression ourselves.

-James

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Re: Underscores in attribute names

Julie Sullivan
Hi James,

Readability of names is certainly an issue!  We hear a lot about this and most
users do not want to see the database column names as data labels, which is what
InterMine does now.

To address this, we've updated how the labels are displayed.  Take a look at the
beta version QueryBuilder built using the latest InterMine code:

        http://beta.flymine.org/beta/customQuery.do

We've updated the code to make the variable names human-readable by default.
The code takes the Java-name (eg. OntologyTerm) and splits it via the case (eg
Ontology Term).

There is a configuration file that overrides this default for when:

  1. the case isn't enough to know where to split the name
     * eg. CDSs
  2. the attribute name in the database isn't people-friendly
     * eg. we have relabeled primaryIdentifier to be DB identifier

Do you think this may address your readability issue?

InterMine 0.98 is going to be released in a few weeks.

Cheers,
Julie

On 07/15/2011 12:56 PM, James Blackshaw wrote:

> Hi,
>
> In the previous version of Intermine that MitoMiner used, it was possible to use
> underscores in attribute names, but now the attribute names are enforced to not
> allow it despite Java generally accepting the character. Asking around some
> possible users in the Unit, we decided that underscores made for more easily
> readable names in our query builder. For the next version of InterMine onwards,
> could PathQuery.java and the other files be changed to allow underscores like
> before please? Right now we're chaging the regular expression ourselves.
>
> -James
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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[hidden email]
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