Template Query webservice URL error

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Template Query webservice URL error

Michael O'Keefe
Hello everyone,

I've got an error in my Mine with the template query webservice URL not displaying. When I go to a template query and click on the "web service URL" link, I get a message that begins with the following in intermine.log:

org.intermine.web.struts.InterMineExceptionHandler     - org.intermine.api.template.TemplatePopulatorException: No value provided for required constraint Gene.goAnnotation.ontologyTerm.parents.name = DNA Binding
at org.intermine.api.template.TemplatePopulator.getPopulatedTemplate(TemplatePopulator.java:99)
 
(the full stacktrace is included at the bottom of the email)

And the URL field contains the HTML for an InterMine error webpage displaying the same error.

The template query I checked this on does have a required field Gene.goAnnotation.ontologyTerm.parents.name, but as the error message suggests, the value "DNA Binding" is provided. Does anyone know why the webapp would be doing this?

Thank you very much for your help once again everyone. I tried Googling the message but couldn't find anything useful.

Thanks,
Michael O'Keefe
[hidden email]

ERROR org.intermine.web.struts.InterMineExceptionHandler     - org.intermine.api.template.TemplatePopulatorException: No value provided for required constraint Gene.goAnnotation.ontologyTerm.parents.name = DNA Binding
    at org.intermine.api.template.TemplatePopulator.getPopulatedTemplate(TemplatePopulator.java:99)
    at org.intermine.web.struts.TemplateAction.execute(TemplateAction.java:150)
    at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:421)
    at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:226)
    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:127)
    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:298)
    at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
    at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
    at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
    at java.lang.Thread.run(Thread.java:680)

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Re: Template Query webservice URL error

Richard Smith
Hi Michael,
Could you export the XML for the template and send it to us please?

The export XML link is in the bottom right of the form.  Though there
is a chance that will fail as well if there is a TemplatePopulator
issue.

Cheers,
Richard.



On 05/08/2011 17:07, Michael O'Keefe wrote:

> Hello everyone,
>
> I've got an error in my Mine with the template query webservice URL not
> displaying. When I go to a template query and click on the "web service URL"
> link, I get a message that begins with the following in intermine.log:
>
> org.intermine.web.struts.InterMineExceptionHandler     -
> org.intermine.api.template.TemplatePopulatorException: No value provided for
> required constraint Gene.goAnnotation.ontologyTerm.parents.name = DNA
> Binding
> at
> org.intermine.api.template.TemplatePopulator.getPopulatedTemplate(TemplatePopulator.java:99)
>
> (the full stacktrace is included at the bottom of the email)
>
> And the URL field contains the HTML for an InterMine error webpage
> displaying the same error.
>
> The template query I checked this on does have a required field
> Gene.goAnnotation.ontologyTerm.parents.name, but as the error message
> suggests, the value "DNA Binding" is provided. Does anyone know why the
> webapp would be doing this?
>
> Thank you very much for your help once again everyone. I tried Googling the
> message but couldn't find anything useful.
>
> Thanks,
> Michael O'Keefe
> [hidden email]
>
> ERROR org.intermine.web.struts.InterMineExceptionHandler     -
> org.intermine.api.template.TemplatePopulatorException: No value provided for
> required constraint Gene.goAnnotation.ontologyTerm.parents.name = DNA
> Binding
>      at
> org.intermine.api.template.TemplatePopulator.getPopulatedTemplate(TemplatePopulator.java:99)
>      at
> org.intermine.web.struts.TemplateAction.execute(TemplateAction.java:150)
>      at
> org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:421)
>      at
> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:226)
>      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:127)
>      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:298)
>      at
> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
>      at
> org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
>      at
> org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
>      at java.lang.Thread.run(Thread.java:680)
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: Template Query webservice URL error

Michael O'Keefe
Hello Richard,

Here is the XML for the selected query:
<template name="GOTerm_genes" title="GO Term --&gt; Genes" longDescription="For a given GO Term (and descendants of that term), return associated genes." comment="">
  <query name="GOTerm_genes" model="genomic" view="Gene.primaryIdentifier Gene.symbol Gene.goAnnotation.ontologyTerm.identifier Gene.goAnnotation.ontologyTerm.name Gene.goAnnotation.ontologyTerm.parents.identifier Gene.goAnnotation.ontologyTerm.parents.name" longDescription="For a given GO Term (and descendants of that term), return associated genes." sortOrder="Gene.primaryIdentifier asc">
    <constraint path="Gene.goAnnotation.ontologyTerm" editable="false" type="GOTerm"/>
    <constraint path="Gene.goAnnotation.ontologyTerm.parents" editable="false" type="GOTerm"/>
    <constraint path="Gene.goAnnotation.ontologyTerm.parents.name" editable="true" description="" op="=" value="DNA Binding"/>
  </query>
</template>
As a note, the error is occurring in Intermine 0.97.

Thank you very much,
Michael O'Keefe

On Fri, Aug 5, 2011 at 12:26 PM, Richard Smith <[hidden email]> wrote:
Hi Michael,
Could you export the XML for the template and send it to us please?

The export XML link is in the bottom right of the form.  Though there
is a chance that will fail as well if there is a TemplatePopulator
issue.

Cheers,
Richard.




On 05/08/2011 17:07, Michael O'Keefe wrote:
Hello everyone,

I've got an error in my Mine with the template query webservice URL not
displaying. When I go to a template query and click on the "web service URL"
link, I get a message that begins with the following in intermine.log:

org.intermine.web.struts.InterMineExceptionHandler     -
org.intermine.api.template.TemplatePopulatorException: No value provided for
required constraint Gene.goAnnotation.ontologyTerm.parents.name = DNA
Binding
at
org.intermine.api.template.TemplatePopulator.getPopulatedTemplate(TemplatePopulator.java:99)

(the full stacktrace is included at the bottom of the email)

And the URL field contains the HTML for an InterMine error webpage
displaying the same error.

The template query I checked this on does have a required field
Gene.goAnnotation.ontologyTerm.parents.name, but as the error message
suggests, the value "DNA Binding" is provided. Does anyone know why the
webapp would be doing this?

Thank you very much for your help once again everyone. I tried Googling the
message but couldn't find anything useful.

Thanks,
Michael O'Keefe
[hidden email]

ERROR org.intermine.web.struts.InterMineExceptionHandler     -
org.intermine.api.template.TemplatePopulatorException: No value provided for
required constraint Gene.goAnnotation.ontologyTerm.parents.name = DNA
Binding
    at
org.intermine.api.template.TemplatePopulator.getPopulatedTemplate(TemplatePopulator.java:99)
    at
org.intermine.web.struts.TemplateAction.execute(TemplateAction.java:150)
    at
org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:421)
    at
org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:226)
    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:127)
    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:298)
    at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
    at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
    at
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
    at java.lang.Thread.run(Thread.java:680)




_______________________________________________
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: Template Query webservice URL error

Julie Sullivan
Hi Michael,

Thanks for the XML, that looks correct to me.

  1. Do the "code generation links" work for you?  (next to the XML link: "Perl
| Python | Java")
  2. Is this template tagged with "im:public"?
  3. You get a message in the log, what happens in the webapp?  eg. what happens
when you click on the link?  Do you get an error message or does nothing happen?
  4. Does that template query run correctly for you in the webapp?  What if you
delete "DNA Binding" from the GO term form field so that that field is empty?
  5. Do you have "autocomplete" on for GO term?  eg. when you type suggestions
pop up - like in the FlyMine template:
        http://www.flymine.org/release-30.0/template.do?name=GOTerm_Gene
  6. This is the URL that should have been generated for you, does this work?
(replacing http://localhost:8080/preview with your URL)

http://localhost:8080/preview/service/template/results?name=GOTerm_genes&constraint1=Gene.goAnnotation.ontologyTerm.parents.name&op1=eq&value1=DNA+Binding&format=tab&size=10

  7. Does the web service URL link work for other templates?

I wasn't able to reproduce the error locally using the 0.97 branch so I am
hoping your answers may help me figure what's going on.

Thanks!
Julie

On 05/08/11 17:45, Michael O'Keefe wrote:

> Hello Richard,
>
> Here is the XML for the selected query:
>
> <template name="GOTerm_genes" title="GO Term --&gt; Genes"
> longDescription="For a given GO Term (and descendants of that term),
> return associated genes." comment="">
>    <query name="GOTerm_genes" model="genomic"
> view="Gene.primaryIdentifier Gene.symbol
> Gene.goAnnotation.ontologyTerm.identifier
> Gene.goAnnotation.ontologyTerm.name
> Gene.goAnnotation.ontologyTerm.parents.identifier
> Gene.goAnnotation.ontologyTerm.parents.name" longDescription="For a
> given GO Term (and descendants of that term), return associated
> genes." sortOrder="Gene.primaryIdentifier asc">
>      <constraint path="Gene.goAnnotation.ontologyTerm" editable="false"
> type="GOTerm"/>
>      <constraint path="Gene.goAnnotation.ontologyTerm.parents"
> editable="false" type="GOTerm"/>
>      <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
> editable="true" description="" op="=" value="DNA Binding"/>
>    </query>
> </template>
>
> As a note, the error is occurring in Intermine 0.97.
>
> Thank you very much,
> Michael O'Keefe
>
> On Fri, Aug 5, 2011 at 12:26 PM, Richard Smith<[hidden email]>  wrote:
>
>> Hi Michael,
>> Could you export the XML for the template and send it to us please?
>>
>> The export XML link is in the bottom right of the form.  Though there
>> is a chance that will fail as well if there is a TemplatePopulator
>> issue.
>>
>> Cheers,
>> Richard.
>>
>>
>>
>>
>> On 05/08/2011 17:07, Michael O'Keefe wrote:
>>
>>> Hello everyone,
>>>
>>> I've got an error in my Mine with the template query webservice URL not
>>> displaying. When I go to a template query and click on the "web service
>>> URL"
>>> link, I get a message that begins with the following in intermine.log:
>>>
>>> org.intermine.web.struts.**InterMineExceptionHandler     -
>>> org.intermine.api.template.**TemplatePopulatorException: No value
>>> provided for
>>> required constraint Gene.goAnnotation.**ontologyTerm.parents.name<http://Gene.goAnnotation.ontologyTerm.parents.name>= DNA
>>> Binding
>>> at
>>> org.intermine.api.template.**TemplatePopulator.**getPopulatedTemplate(**
>>> TemplatePopulator.java:99)
>>>
>>> (the full stacktrace is included at the bottom of the email)
>>>
>>> And the URL field contains the HTML for an InterMine error webpage
>>> displaying the same error.
>>>
>>> The template query I checked this on does have a required field
>>> Gene.goAnnotation.**ontologyTerm.parents.name<http://Gene.goAnnotation.ontologyTerm.parents.name>,
>>> but as the error message
>>> suggests, the value "DNA Binding" is provided. Does anyone know why the
>>> webapp would be doing this?
>>>
>>> Thank you very much for your help once again everyone. I tried Googling
>>> the
>>> message but couldn't find anything useful.
>>>
>>> Thanks,
>>> Michael O'Keefe
>>> [hidden email]
>>>
>>> ERROR org.intermine.web.struts.**InterMineExceptionHandler     -
>>> org.intermine.api.template.**TemplatePopulatorException: No value
>>> provided for
>>> required constraint Gene.goAnnotation.**ontologyTerm.parents.name<http://Gene.goAnnotation.ontologyTerm.parents.name>= DNA
>>> Binding
>>>      at
>>> org.intermine.api.template.**TemplatePopulator.**getPopulatedTemplate(**
>>> TemplatePopulator.java:99)
>>>      at
>>> org.intermine.web.struts.**TemplateAction.execute(**
>>> TemplateAction.java:150)
>>>      at
>>> org.apache.struts.action.**RequestProcessor.**processActionPerform(**
>>> RequestProcessor.java:421)
>>>      at
>>> org.apache.struts.action.**RequestProcessor.process(**
>>> RequestProcessor.java:226)
>>>      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:127)
>>>      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:298)
>>>      at
>>> org.apache.coyote.http11.**Http11Processor.process(**
>>> Http11Processor.java:859)
>>>      at
>>> org.apache.coyote.http11.**Http11Protocol$**Http11ConnectionHandler.**
>>> process(Http11Protocol.java:**588)
>>>      at
>>> org.apache.tomcat.util.net.**JIoEndpoint$Worker.run(**
>>> JIoEndpoint.java:489)
>>>      at java.lang.Thread.run(Thread.**java:680)
>>>
>>>
>>>
>>>
>>> ______________________________**_________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-**bin/mailman/listinfo/dev<http://mail.intermine.org/cgi-bin/mailman/listinfo/dev>
>>>
>>
>>
>> ______________________________**_________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-**bin/mailman/listinfo/dev<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: Template Query webservice URL error

Michael O'Keefe
Hello, and thank you very much for taking the time to sort out this error.

1. The code generation links don't do anything currently. If you click on any of the links, nothing happens.

2. The template is tagged with "im:public".

3. The webapp doesn't display an error message, but the link isn't a link; it's the HTML for an error page. The HTML appears to be for an error page displaying the same message as in the log file; I've attached a text file with the raw HTML included (it was a lot to paste into the email, but let me know if you'd rather I pasted it in.)

4. The template query runs correctly with "DNA Binding" included in the term field. If you delete the text so the field is empty, the webapp still runs the query, but returns an empty results table. If you click on the webservice URL link, you get the same HTML error message, including the "DNA Binding" message still being there.

5. I do have autocomplete turned on for GO terms.

6. Running that query does return a .tsv file as a result, with the first 10 rows of the query included in the file (as I gather it's supposed to from the "size=10" option).

7. I get a similar error when I try to get the webservice URL for any other template. Same thing with the code generation links.

I hope this information helps debug the issue, and again I really appreciate the help.

Thank you very much,
Michael O'Keefe

On Mon, Aug 8, 2011 at 9:29 AM, Julie Sullivan <[hidden email]> wrote:
Hi Michael,

Thanks for the XML, that looks correct to me.

 1. Do the "code generation links" work for you?  (next to the XML link: "Perl | Python | Java")
 2. Is this template tagged with "im:public"?
 3. You get a message in the log, what happens in the webapp?  eg. what happens when you click on the link?  Do you get an error message or does nothing happen?
 4. Does that template query run correctly for you in the webapp?  What if you delete "DNA Binding" from the GO term form field so that that field is empty?
 5. Do you have "autocomplete" on for GO term?  eg. when you type suggestions pop up - like in the FlyMine template:
       http://www.flymine.org/release-30.0/template.do?name=GOTerm_Gene
 6. This is the URL that should have been generated for you, does this work? (replacing http://localhost:8080/preview with your URL)

http://localhost:8080/preview/service/template/results?name=GOTerm_genes&constraint1=Gene.goAnnotation.ontologyTerm.parents.name&op1=eq&value1=DNA+Binding&format=tab&size=10

 7. Does the web service URL link work for other templates?

I wasn't able to reproduce the error locally using the 0.97 branch so I am hoping your answers may help me figure what's going on.

Thanks!
Julie


On 05/08/11 17:45, Michael O'Keefe wrote:
Hello Richard,

Here is the XML for the selected query:

<template name="GOTerm_genes" title="GO Term --&gt; Genes"
longDescription="For a given GO Term (and descendants of that term),
return associated genes." comment="">
  <query name="GOTerm_genes" model="genomic"
view="Gene.primaryIdentifier Gene.symbol
Gene.goAnnotation.ontologyTerm.identifier
Gene.goAnnotation.ontologyTerm.name
Gene.goAnnotation.ontologyTerm.parents.identifier
Gene.goAnnotation.ontologyTerm.parents.name" longDescription="For a
given GO Term (and descendants of that term), return associated
genes." sortOrder="Gene.primaryIdentifier asc">
    <constraint path="Gene.goAnnotation.ontologyTerm" editable="false"
type="GOTerm"/>
    <constraint path="Gene.goAnnotation.ontologyTerm.parents"
editable="false" type="GOTerm"/>
    <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
editable="true" description="" op="=" value="DNA Binding"/>
  </query>
</template>

As a note, the error is occurring in Intermine 0.97.

Thank you very much,
Michael O'Keefe

On Fri, Aug 5, 2011 at 12:26 PM, Richard Smith<[hidden email]>  wrote:

Hi Michael,
Could you export the XML for the template and send it to us please?

The export XML link is in the bottom right of the form.  Though there
is a chance that will fail as well if there is a TemplatePopulator
issue.

Cheers,
Richard.




On 05/08/2011 17:07, Michael O'Keefe wrote:

Hello everyone,

I've got an error in my Mine with the template query webservice URL not
displaying. When I go to a template query and click on the "web service
URL"
link, I get a message that begins with the following in intermine.log:

org.intermine.web.struts.**InterMineExceptionHandler     -
org.intermine.api.template.**TemplatePopulatorException: No value
provided for
required constraint Gene.goAnnotation.**ontologyTerm.parents.name<http://Gene.goAnnotation.ontologyTerm.parents.name>= DNA

Binding
at
org.intermine.api.template.**TemplatePopulator.**getPopulatedTemplate(**
TemplatePopulator.java:99)

(the full stacktrace is included at the bottom of the email)

And the URL field contains the HTML for an InterMine error webpage
displaying the same error.

The template query I checked this on does have a required field
Gene.goAnnotation.**ontologyTerm.parents.name<http://Gene.goAnnotation.ontologyTerm.parents.name>,

but as the error message
suggests, the value "DNA Binding" is provided. Does anyone know why the
webapp would be doing this?

Thank you very much for your help once again everyone. I tried Googling
the
message but couldn't find anything useful.

Thanks,
Michael O'Keefe
[hidden email]

ERROR org.intermine.web.struts.**InterMineExceptionHandler     -
org.intermine.api.template.**TemplatePopulatorException: No value
provided for
required constraint Gene.goAnnotation.**ontologyTerm.parents.name<http://Gene.goAnnotation.ontologyTerm.parents.name>= DNA

Binding
    at
org.intermine.api.template.**TemplatePopulator.**getPopulatedTemplate(**
TemplatePopulator.java:99)
    at
org.intermine.web.struts.**TemplateAction.execute(**
TemplateAction.java:150)
    at
org.apache.struts.action.**RequestProcessor.**processActionPerform(**
RequestProcessor.java:421)
    at
org.apache.struts.action.**RequestProcessor.process(**
RequestProcessor.java:226)
    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:127)
    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:298)
    at
org.apache.coyote.http11.**Http11Processor.process(**
Http11Processor.java:859)
    at
org.apache.coyote.http11.**Http11Protocol$**Http11ConnectionHandler.**
process(Http11Protocol.java:**588)
    at
org.apache.tomcat.util.net.**JIoEndpoint$Worker.run(**
JIoEndpoint.java:489)
    at java.lang.Thread.run(Thread.**java:680)




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template_query_error_goterm_gene.txt (22K) Download Attachment
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Re: Template Query webservice URL error

Michael O'Keefe
Hello,

I have one additional piece of information about this error. The URL generation link on the template query itself does not work, as stated before, but if you choose to edit the query, and click on the webservice URL link in the template preview, the link works as it should. In addition, the code generation links work within the edit query page.

Thank you very much for helping, and I hope this further information proves useful.

Michael O'Keefe

On Mon, Aug 8, 2011 at 12:06 PM, Michael O'Keefe <[hidden email]> wrote:
Hello, and thank you very much for taking the time to sort out this error.

1. The code generation links don't do anything currently. If you click on any of the links, nothing happens.

2. The template is tagged with "im:public".

3. The webapp doesn't display an error message, but the link isn't a link; it's the HTML for an error page. The HTML appears to be for an error page displaying the same message as in the log file; I've attached a text file with the raw HTML included (it was a lot to paste into the email, but let me know if you'd rather I pasted it in.)

4. The template query runs correctly with "DNA Binding" included in the term field. If you delete the text so the field is empty, the webapp still runs the query, but returns an empty results table. If you click on the webservice URL link, you get the same HTML error message, including the "DNA Binding" message still being there.

5. I do have autocomplete turned on for GO terms.

6. Running that query does return a .tsv file as a result, with the first 10 rows of the query included in the file (as I gather it's supposed to from the "size=10" option).

7. I get a similar error when I try to get the webservice URL for any other template. Same thing with the code generation links.

I hope this information helps debug the issue, and again I really appreciate the help.


Thank you very much,
Michael O'Keefe

On Mon, Aug 8, 2011 at 9:29 AM, Julie Sullivan <[hidden email]> wrote:
Hi Michael,

Thanks for the XML, that looks correct to me.

 1. Do the "code generation links" work for you?  (next to the XML link: "Perl | Python | Java")
 2. Is this template tagged with "im:public"?
 3. You get a message in the log, what happens in the webapp?  eg. what happens when you click on the link?  Do you get an error message or does nothing happen?
 4. Does that template query run correctly for you in the webapp?  What if you delete "DNA Binding" from the GO term form field so that that field is empty?
 5. Do you have "autocomplete" on for GO term?  eg. when you type suggestions pop up - like in the FlyMine template:
       http://www.flymine.org/release-30.0/template.do?name=GOTerm_Gene
 6. This is the URL that should have been generated for you, does this work? (replacing http://localhost:8080/preview with your URL)

http://localhost:8080/preview/service/template/results?name=GOTerm_genes&constraint1=Gene.goAnnotation.ontologyTerm.parents.name&op1=eq&value1=DNA+Binding&format=tab&size=10

 7. Does the web service URL link work for other templates?

I wasn't able to reproduce the error locally using the 0.97 branch so I am hoping your answers may help me figure what's going on.

Thanks!
Julie


On 05/08/11 17:45, Michael O'Keefe wrote:
Hello Richard,

Here is the XML for the selected query:

<template name="GOTerm_genes" title="GO Term --&gt; Genes"
longDescription="For a given GO Term (and descendants of that term),
return associated genes." comment="">
  <query name="GOTerm_genes" model="genomic"
view="Gene.primaryIdentifier Gene.symbol
Gene.goAnnotation.ontologyTerm.identifier
Gene.goAnnotation.ontologyTerm.name
Gene.goAnnotation.ontologyTerm.parents.identifier
Gene.goAnnotation.ontologyTerm.parents.name" longDescription="For a
given GO Term (and descendants of that term), return associated
genes." sortOrder="Gene.primaryIdentifier asc">
    <constraint path="Gene.goAnnotation.ontologyTerm" editable="false"
type="GOTerm"/>
    <constraint path="Gene.goAnnotation.ontologyTerm.parents"
editable="false" type="GOTerm"/>
    <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
editable="true" description="" op="=" value="DNA Binding"/>
  </query>
</template>

As a note, the error is occurring in Intermine 0.97.

Thank you very much,
Michael O'Keefe

On Fri, Aug 5, 2011 at 12:26 PM, Richard Smith<[hidden email]>  wrote:

Hi Michael,
Could you export the XML for the template and send it to us please?

The export XML link is in the bottom right of the form.  Though there
is a chance that will fail as well if there is a TemplatePopulator
issue.

Cheers,
Richard.




On 05/08/2011 17:07, Michael O'Keefe wrote:

Hello everyone,

I've got an error in my Mine with the template query webservice URL not
displaying. When I go to a template query and click on the "web service
URL"
link, I get a message that begins with the following in intermine.log:

org.intermine.web.struts.**InterMineExceptionHandler     -
org.intermine.api.template.**TemplatePopulatorException: No value
provided for
required constraint Gene.goAnnotation.**ontologyTerm.parents.name<http://Gene.goAnnotation.ontologyTerm.parents.name>= DNA

Binding
at
org.intermine.api.template.**TemplatePopulator.**getPopulatedTemplate(**
TemplatePopulator.java:99)

(the full stacktrace is included at the bottom of the email)

And the URL field contains the HTML for an InterMine error webpage
displaying the same error.

The template query I checked this on does have a required field
Gene.goAnnotation.**ontologyTerm.parents.name<http://Gene.goAnnotation.ontologyTerm.parents.name>,

but as the error message
suggests, the value "DNA Binding" is provided. Does anyone know why the
webapp would be doing this?

Thank you very much for your help once again everyone. I tried Googling
the
message but couldn't find anything useful.

Thanks,
Michael O'Keefe
[hidden email]

ERROR org.intermine.web.struts.**InterMineExceptionHandler     -
org.intermine.api.template.**TemplatePopulatorException: No value
provided for
required constraint Gene.goAnnotation.**ontologyTerm.parents.name<http://Gene.goAnnotation.ontologyTerm.parents.name>= DNA

Binding
    at
org.intermine.api.template.**TemplatePopulator.**getPopulatedTemplate(**
TemplatePopulator.java:99)
    at
org.intermine.web.struts.**TemplateAction.execute(**
TemplateAction.java:150)
    at
org.apache.struts.action.**RequestProcessor.**processActionPerform(**
RequestProcessor.java:421)
    at
org.apache.struts.action.**RequestProcessor.process(**
RequestProcessor.java:226)
    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:127)
    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:298)
    at
org.apache.coyote.http11.**Http11Processor.process(**
Http11Processor.java:859)
    at
org.apache.coyote.http11.**Http11Protocol$**Http11ConnectionHandler.**
process(Http11Protocol.java:**588)
    at
org.apache.tomcat.util.net.**JIoEndpoint$Worker.run(**
JIoEndpoint.java:489)
    at java.lang.Thread.run(Thread.**java:680)




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dev mailing list
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dev mailing list
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