gene ontology failed display

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gene ontology failed display

Pengcheng Yang

Hi Miners,

This questions has been discussed previously: http://gmod.827538.n3.nabble.com/gene-ontology-display-problem-td4050690.html.  But now have new problem.

1. What the problem is:

The page without gene ontology display:

The project.xml file is:

    <source name="go" type="go" dump="true">
      <property name="src.data.file" location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
                        <property name="createrelations" value="false"/>
    </source>

    <source name="go-annotation" type="go-annotation" dump="true">
      <property name="ontologyfile" location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
      <property name="src.data.dir" location="/home/pengchy/Project/LocustMine/testdata/go-annotation/"/>
    </source>

2. I have tried to test the query provided by Julie Sullivan

<query name="" model="genomic"
view="Gene.goAnnotation.ontologyTerm.parents.name
Gene.goAnnotation.ontologyTerm.name
Gene.goAnnotation.evidence.code.code" longDescription=""
sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
constraintLogic="(A or B or C) and D">
   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
code="A" op="=" value="biological_process"/>
   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
code="B" op="=" value="molecular_function"/>
   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
code="C" op="=" value="cellular_component"/>
   <constraint path="Gene" code="D" op="LOOKUP" value="Ehbp1" extraValue=""/>
</query>

After click the "show" button for Symbol and DB identifier, the result page was as follow:

it is clear that this gene's GO annotation has been successfully loaded.

After clicking on the Ontology Term Name "protein binding", I got the collection of the gene ids that were annotated to this term:

So, this further support the GO annotation has been successfully loaded.

But, why it could not be displayed on the gene report page?

3. I try to remove the Gene Ontology displayer from the file webapp/resources/webapp/WEB-INF/webconfig-model.xml by comment the following lines:

   <reportdisplayer javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"
                     jspName="model/geneOntologyDisplayer.jsp"
                     replacesFields="goAnnotation,ontologyAnnotations"
                     placement="Genomics"
                     types="Gene"/>

I have successfully displayed the Gene Ontology annotation information, but there were two sections: "GO Annotation" and "Ontology Annotation", listed as follow:

How to merge these two sections?

Best,

Pengcheng Yang





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Re: gene ontology failed display

Julie Sullivan-2
Hi!

I have no idea what's wrong! Everything you show looks correct to me.

Is there a message in your log files? This should be in
$TOMCAT/logs/catalina.out. Can you send that to me? Maybe I can see
what's going on.

Julie

On 04/04/2018 05:22 PM, Pengcheng Yang wrote:

> Hi Miners,
>
> This questions has been discussed previously:
> http://gmod.827538.n3.nabble.com/gene-ontology-display-problem-td4050690.html.
> But now have new problem.
>
> 1. What the problem is:
>
> The page without gene ontology display:
>
> The project.xml file is:
>
>      <source name="go" type="go" dump="true">
>        <property name="src.data.file"
> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>                          <property name="createrelations" value="false"/>
>      </source>
>
>      <source name="go-annotation" type="go-annotation" dump="true">
>        <property name="ontologyfile"
> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>        <property name="src.data.dir"
> location="/home/pengchy/Project/LocustMine/testdata/go-annotation/"/>
>      </source>
>
> 2. I have tried to test the query provided by Julie Sullivan
>
> <query name="" model="genomic"
> view="Gene.goAnnotation.ontologyTerm.parents.name
> Gene.goAnnotation.ontologyTerm.name
> Gene.goAnnotation.evidence.code.code" longDescription=""
> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
> constraintLogic="(A or B or C) and D">
>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
> code="A" op="=" value="biological_process"/>
>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
> code="B" op="=" value="molecular_function"/>
>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
> code="C" op="=" value="cellular_component"/>
>     <constraint path="Gene" code="D" op="LOOKUP" value="Ehbp1"
> extraValue=""/>
> </query>
>
> After click the "show" button for Symbol and DB identifier, the result
> page was as follow:
>
> it is clear that this gene's GO annotation has been successfully loaded.
>
> After clicking on the Ontology Term Name "protein binding", I got the
> collection of the gene ids that were annotated to this term:
>
> So, this further support the GO annotation has been successfully loaded.
>
> But, why it could not be displayed on the gene report page?
>
> 3. I try to remove the Gene Ontology displayer from the file
> webapp/resources/webapp/WEB-INF/webconfig-model.xml by comment the
> following lines:
>
>     <reportdisplayer
> javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"
>                       jspName="model/geneOntologyDisplayer.jsp"
> replacesFields="goAnnotation,ontologyAnnotations"
>                       placement="Genomics"
>                       types="Gene"/>
>
> I have successfully displayed the Gene Ontology annotation information,
> but there were two sections: "GO Annotation" and "Ontology Annotation",
> listed as follow:
>
> How to merge these two sections?
>
> Best,
>
> Pengcheng Yang
>
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
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Re: gene ontology failed display

Pengcheng Yang
Hi Julie,

Following your suggestion, I have checked the message in
logs/catalina.out. But nothing related to GO displayer was found. The
latest 100 lines of the logs/catalina.out file after I visiting the gene
entry are pasted as follow. The error message maybe about another problem.


=========================== error message===========================

84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
84797 [http-apr-10.4.0.17-8080-exec-12] WARN
org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring: batchId[2]
message[java.lang.IllegalArgumentException: query is not valid: [Path
Gene.homologues.homologue.primaryIdentifier in view list is not in the
model, Path Gene.homologues.homologue.symbol in view list is not in the
model, Path Gene.homologues.homologue.organism.shortName in view list is
not in the model, Path Gene.homologues.type in constraint is not in the
model, Path Gene.homologues.homologue.organism.shortName in order by
list is not in the model]]
89921 [http-apr-10.4.0.17-8080-exec-14] WARN
org.directwebremoting.impl.DefaultRemoter  - Method execution failed:
java.lang.IllegalArgumentException: query is not valid: [Path
Gene.homologues.homologue.primaryIdentifier in view list is not in the
model, Path Gene.homologues.homologue.symbol in view list is not in the
model, Path Gene.homologues.homologue.organism.shortName in view list is
not in the model, Path Gene.homologues.type in constraint is not in the
model, Path Gene.homologues.homologue.organism.shortName in order by
list is not in the model]
         at org.intermine.api.mines.LocalMine.getRows(LocalMine.java:143)
         at
org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.runQuery(FriendlyMineLinkGenerator.java:166)
         at
org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.localHomologueStrategy(FriendlyMineLinkGenerator.java:138)
         at
org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.fetch(FriendlyMineLinkGenerator.java:106)
         at
org.intermine.bio.web.displayer.FriendlyMineLinkGenerator.getLinks(FriendlyMineLinkGenerator.java:85)
         at
org.intermine.dwr.AjaxServices.getFriendlyMineLinks(AjaxServices.java:730)
         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
         at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
         at java.lang.reflect.Method.invoke(Method.java:498)
         at
org.directwebremoting.impl.ExecuteAjaxFilter.doFilter(ExecuteAjaxFilter.java:34)
         at
org.directwebremoting.impl.DefaultRemoter$1.doFilter(DefaultRemoter.java:428)
         at
org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:431)
         at
org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:283)
         at
org.directwebremoting.servlet.PlainCallHandler.handle(PlainCallHandler.java:52)
         at
org.directwebremoting.servlet.UrlProcessor.handle(UrlProcessor.java:101)
         at
org.directwebremoting.servlet.DwrServlet.doPost(DwrServlet.java:146)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
         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.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:219)
         at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
         at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
         at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
         at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
         at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
         at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
         at
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
         at
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
         at
org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
         at
org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
         at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
         at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
         at
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
         at java.lang.Thread.run(Thread.java:748)
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
for 'java.lang.StackTraceElement'
89925 [http-apr-10.4.0.17-8080-exec-14] WARN
org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring: batchId[5]
message[java.lang.IllegalArgumentException: query is not valid: [Path
Gene.homologues.homologue.primaryIdentifier in view list is not in the
model, Path Gene.homologues.homologue.symbol in view list is not in the
model, Path Gene.homologues.homologue.organism.shortName in view list is
not in the model, Path Gene.homologues.type in constraint is not in the
model, Path Gene.homologues.homologue.organism.shortName in order by
list is not in the model]]


Best,

Pengcheng


On 2018-4-5 23:45, Julie Sullivan wrote:

> Hi!
>
> I have no idea what's wrong! Everything you show looks correct to me.
>
> Is there a message in your log files? This should be in
> $TOMCAT/logs/catalina.out. Can you send that to me? Maybe I can see
> what's going on.
>
> Julie
>
> On 04/04/2018 05:22 PM, Pengcheng Yang wrote:
>> Hi Miners,
>>
>> This questions has been discussed previously:
>> http://gmod.827538.n3.nabble.com/gene-ontology-display-problem-td4050690.html.
>> But now have new problem.
>>
>> 1. What the problem is:
>>
>> The page without gene ontology display:
>>
>> The project.xml file is:
>>
>>      <source name="go" type="go" dump="true">
>>        <property name="src.data.file"
>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>                          <property name="createrelations"
>> value="false"/>
>>      </source>
>>
>>      <source name="go-annotation" type="go-annotation" dump="true">
>>        <property name="ontologyfile"
>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>        <property name="src.data.dir"
>> location="/home/pengchy/Project/LocustMine/testdata/go-annotation/"/>
>>      </source>
>>
>> 2. I have tried to test the query provided by Julie Sullivan
>>
>> <query name="" model="genomic"
>> view="Gene.goAnnotation.ontologyTerm.parents.name
>> Gene.goAnnotation.ontologyTerm.name
>> Gene.goAnnotation.evidence.code.code" longDescription=""
>> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
>> constraintLogic="(A or B or C) and D">
>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>> code="A" op="=" value="biological_process"/>
>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>> code="B" op="=" value="molecular_function"/>
>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>> code="C" op="=" value="cellular_component"/>
>>     <constraint path="Gene" code="D" op="LOOKUP" value="Ehbp1"
>> extraValue=""/>
>> </query>
>>
>> After click the "show" button for Symbol and DB identifier, the
>> result page was as follow:
>>
>> it is clear that this gene's GO annotation has been successfully loaded.
>>
>> After clicking on the Ontology Term Name "protein binding", I got the
>> collection of the gene ids that were annotated to this term:
>>
>> So, this further support the GO annotation has been successfully loaded.
>>
>> But, why it could not be displayed on the gene report page?
>>
>> 3. I try to remove the Gene Ontology displayer from the file
>> webapp/resources/webapp/WEB-INF/webconfig-model.xml by comment the
>> following lines:
>>
>>     <reportdisplayer
>> javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"
>>                       jspName="model/geneOntologyDisplayer.jsp"
>> replacesFields="goAnnotation,ontologyAnnotations"
>>                       placement="Genomics"
>>                       types="Gene"/>
>>
>> I have successfully displayed the Gene Ontology annotation
>> information, but there were two sections: "GO Annotation" and
>> "Ontology Annotation", listed as follow:
>>
>> How to merge these two sections?
>>
>> Best,
>>
>> Pengcheng Yang
>>
>>
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Re: gene ontology failed display

Julie Sullivan-2
This query is returning no results for your mine:

https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/bio/web/displayer/GeneOntologyDisplayer.java#L170

Why? Because it looks like the data is there!

Try this query, it's exactly what the displayer is doing:

<query name="" model="genomic"
view="Gene.goAnnotation.ontologyTerm.parents.name
Gene.goAnnotation.ontologyTerm.name
Gene.goAnnotation.evidence.code.code" longDescription=""
sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
constraintLogic="(A or B or C) and D and E">
   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
code="A" op="=" value="biological_process"/>
   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
code="B" op="=" value="molecular_function"/>
   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
code="C" op="=" value="cellular_component"/>
   <constraint path="Gene.id" code="D" op="=" value="1"/>
   <constraint path="Gene.goAnnotation.qualifier" code="E" op="IS NULL"/>
</query>

It's the same one you ran before but with ID instead of symbol and I
added the qualifier. Change ID to be the id of the gene. To get the ID
look at the URL on the gene report page, e.g. report.do?id=1007180. The
id is what the displayer uses, so let's try that because I am running
out of ideas.

Try that?

On 04/06/2018 01:15 AM, Pengcheng Yang wrote:

> Hi Julie,
>
> Following your suggestion, I have checked the message in
> logs/catalina.out. But nothing related to GO displayer was found. The
> latest 100 lines of the logs/catalina.out file after I visiting the gene
> entry are pasted as follow. The error message maybe about another problem.
>
>
> =========================== error message===========================
>
> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 84797 [http-apr-10.4.0.17-8080-exec-12] WARN
> org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring: batchId[2]
> message[java.lang.IllegalArgumentException: query is not valid: [Path
> Gene.homologues.homologue.primaryIdentifier in view list is not in the
> model, Path Gene.homologues.homologue.symbol in view list is not in the
> model, Path Gene.homologues.homologue.organism.shortName in view list is
> not in the model, Path Gene.homologues.type in constraint is not in the
> model, Path Gene.homologues.homologue.organism.shortName in order by
> list is not in the model]]
> 89921 [http-apr-10.4.0.17-8080-exec-14] WARN
> org.directwebremoting.impl.DefaultRemoter  - Method execution failed:
> java.lang.IllegalArgumentException: query is not valid: [Path
> Gene.homologues.homologue.primaryIdentifier in view list is not in the
> model, Path Gene.homologues.homologue.symbol in view list is not in the
> model, Path Gene.homologues.homologue.organism.shortName in view list is
> not in the model, Path Gene.homologues.type in constraint is not in the
> model, Path Gene.homologues.homologue.organism.shortName in order by
> list is not in the model]
>          at org.intermine.api.mines.LocalMine.getRows(LocalMine.java:143)
>          at
> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.runQuery(FriendlyMineLinkGenerator.java:166)
>
>          at
> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.localHomologueStrategy(FriendlyMineLinkGenerator.java:138)
>
>          at
> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.fetch(FriendlyMineLinkGenerator.java:106)
>
>          at
> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator.getLinks(FriendlyMineLinkGenerator.java:85)
>
>          at
> org.intermine.dwr.AjaxServices.getFriendlyMineLinks(AjaxServices.java:730)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>
>          at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>
>          at java.lang.reflect.Method.invoke(Method.java:498)
>          at
> org.directwebremoting.impl.ExecuteAjaxFilter.doFilter(ExecuteAjaxFilter.java:34)
>
>          at
> org.directwebremoting.impl.DefaultRemoter$1.doFilter(DefaultRemoter.java:428)
>
>          at
> org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:431)
>          at
> org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:283)
>          at
> org.directwebremoting.servlet.PlainCallHandler.handle(PlainCallHandler.java:52)
>
>          at
> org.directwebremoting.servlet.UrlProcessor.handle(UrlProcessor.java:101)
>          at
> org.directwebremoting.servlet.DwrServlet.doPost(DwrServlet.java:146)
>          at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>          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.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:219)
>
>          at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
>
>          at
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
>
>          at
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>
>          at
> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
>          at
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>
>          at
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
>          at
> org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
>
>          at
> org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
>
>          at
> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
>
>          at
> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
>
>          at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>
>          at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>
>          at
> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>
>          at java.lang.Thread.run(Thread.java:748)
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
> org.directwebremoting.dwrp.DefaultConverterManager  - No converter found
> for 'java.lang.StackTraceElement'
> 89925 [http-apr-10.4.0.17-8080-exec-14] WARN
> org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring: batchId[5]
> message[java.lang.IllegalArgumentException: query is not valid: [Path
> Gene.homologues.homologue.primaryIdentifier in view list is not in the
> model, Path Gene.homologues.homologue.symbol in view list is not in the
> model, Path Gene.homologues.homologue.organism.shortName in view list is
> not in the model, Path Gene.homologues.type in constraint is not in the
> model, Path Gene.homologues.homologue.organism.shortName in order by
> list is not in the model]]
>
>
> Best,
>
> Pengcheng
>
>
> On 2018-4-5 23:45, Julie Sullivan wrote:
>> Hi!
>>
>> I have no idea what's wrong! Everything you show looks correct to me.
>>
>> Is there a message in your log files? This should be in
>> $TOMCAT/logs/catalina.out. Can you send that to me? Maybe I can see
>> what's going on.
>>
>> Julie
>>
>> On 04/04/2018 05:22 PM, Pengcheng Yang wrote:
>>> Hi Miners,
>>>
>>> This questions has been discussed previously:
>>> http://gmod.827538.n3.nabble.com/gene-ontology-display-problem-td4050690.html.
>>> But now have new problem.
>>>
>>> 1. What the problem is:
>>>
>>> The page without gene ontology display:
>>>
>>> The project.xml file is:
>>>
>>>      <source name="go" type="go" dump="true">
>>>        <property name="src.data.file"
>>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>>                          <property name="createrelations"
>>> value="false"/>
>>>      </source>
>>>
>>>      <source name="go-annotation" type="go-annotation" dump="true">
>>>        <property name="ontologyfile"
>>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>>        <property name="src.data.dir"
>>> location="/home/pengchy/Project/LocustMine/testdata/go-annotation/"/>
>>>      </source>
>>>
>>> 2. I have tried to test the query provided by Julie Sullivan
>>>
>>> <query name="" model="genomic"
>>> view="Gene.goAnnotation.ontologyTerm.parents.name
>>> Gene.goAnnotation.ontologyTerm.name
>>> Gene.goAnnotation.evidence.code.code" longDescription=""
>>> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
>>> constraintLogic="(A or B or C) and D">
>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>> code="A" op="=" value="biological_process"/>
>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>> code="B" op="=" value="molecular_function"/>
>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>> code="C" op="=" value="cellular_component"/>
>>>     <constraint path="Gene" code="D" op="LOOKUP" value="Ehbp1"
>>> extraValue=""/>
>>> </query>
>>>
>>> After click the "show" button for Symbol and DB identifier, the
>>> result page was as follow:
>>>
>>> it is clear that this gene's GO annotation has been successfully loaded.
>>>
>>> After clicking on the Ontology Term Name "protein binding", I got the
>>> collection of the gene ids that were annotated to this term:
>>>
>>> So, this further support the GO annotation has been successfully loaded.
>>>
>>> But, why it could not be displayed on the gene report page?
>>>
>>> 3. I try to remove the Gene Ontology displayer from the file
>>> webapp/resources/webapp/WEB-INF/webconfig-model.xml by comment the
>>> following lines:
>>>
>>>     <reportdisplayer
>>> javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"
>>>                       jspName="model/geneOntologyDisplayer.jsp"
>>> replacesFields="goAnnotation,ontologyAnnotations"
>>>                       placement="Genomics"
>>>                       types="Gene"/>
>>>
>>> I have successfully displayed the Gene Ontology annotation
>>> information, but there were two sections: "GO Annotation" and
>>> "Ontology Annotation", listed as follow:
>>>
>>> How to merge these two sections?
>>>
>>> Best,
>>>
>>> Pengcheng Yang
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
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Re: gene ontology failed display

Pengcheng Yang
Hi Julie,

No result was output using your new query (without any modification). 
Our Mine address is: http://www.locustmine.org:8080/testmine/begin.do.

Thank you and best,

Pengcheng


On 2018-4-6 16:01, Julie Sullivan wrote:

> This query is returning no results for your mine:
>
> https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/bio/web/displayer/GeneOntologyDisplayer.java#L170 
>
>
> Why? Because it looks like the data is there!
>
> Try this query, it's exactly what the displayer is doing:
>
> <query name="" model="genomic"
> view="Gene.goAnnotation.ontologyTerm.parents.name
> Gene.goAnnotation.ontologyTerm.name
> Gene.goAnnotation.evidence.code.code" longDescription=""
> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
> constraintLogic="(A or B or C) and D and E">
>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
> code="A" op="=" value="biological_process"/>
>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
> code="B" op="=" value="molecular_function"/>
>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
> code="C" op="=" value="cellular_component"/>
>   <constraint path="Gene.id" code="D" op="=" value="1"/>
>   <constraint path="Gene.goAnnotation.qualifier" code="E" op="IS NULL"/>
> </query>
>
> It's the same one you ran before but with ID instead of symbol and I
> added the qualifier. Change ID to be the id of the gene. To get the ID
> look at the URL on the gene report page, e.g. report.do?id=1007180.
> The id is what the displayer uses, so let's try that because I am
> running out of ideas.
>
> Try that?
>
> On 04/06/2018 01:15 AM, Pengcheng Yang wrote:
>> Hi Julie,
>>
>> Following your suggestion, I have checked the message in
>> logs/catalina.out. But nothing related to GO displayer was found. The
>> latest 100 lines of the logs/catalina.out file after I visiting the
>> gene entry are pasted as follow. The error message maybe about
>> another problem.
>>
>>
>> =========================== error message===========================
>>
>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 84797 [http-apr-10.4.0.17-8080-exec-12] WARN
>> org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring:
>> batchId[2] message[java.lang.IllegalArgumentException: query is not
>> valid: [Path Gene.homologues.homologue.primaryIdentifier in view list
>> is not in the model, Path Gene.homologues.homologue.symbol in view
>> list is not in the model, Path
>> Gene.homologues.homologue.organism.shortName in view list is not in
>> the model, Path Gene.homologues.type in constraint is not in the
>> model, Path Gene.homologues.homologue.organism.shortName in order by
>> list is not in the model]]
>> 89921 [http-apr-10.4.0.17-8080-exec-14] WARN
>> org.directwebremoting.impl.DefaultRemoter  - Method execution failed:
>> java.lang.IllegalArgumentException: query is not valid: [Path
>> Gene.homologues.homologue.primaryIdentifier in view list is not in
>> the model, Path Gene.homologues.homologue.symbol in view list is not
>> in the model, Path Gene.homologues.homologue.organism.shortName in
>> view list is not in the model, Path Gene.homologues.type in
>> constraint is not in the model, Path
>> Gene.homologues.homologue.organism.shortName in order by list is not
>> in the model]
>>          at
>> org.intermine.api.mines.LocalMine.getRows(LocalMine.java:143)
>>          at
>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.runQuery(FriendlyMineLinkGenerator.java:166)
>>
>>          at
>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.localHomologueStrategy(FriendlyMineLinkGenerator.java:138)
>>
>>          at
>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.fetch(FriendlyMineLinkGenerator.java:106)
>>
>>          at
>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator.getLinks(FriendlyMineLinkGenerator.java:85)
>>
>>          at
>> org.intermine.dwr.AjaxServices.getFriendlyMineLinks(AjaxServices.java:730)
>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>          at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>>
>>          at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>
>>          at java.lang.reflect.Method.invoke(Method.java:498)
>>          at
>> org.directwebremoting.impl.ExecuteAjaxFilter.doFilter(ExecuteAjaxFilter.java:34)
>>
>>          at
>> org.directwebremoting.impl.DefaultRemoter$1.doFilter(DefaultRemoter.java:428)
>>
>>          at
>> org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:431)
>>          at
>> org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:283)
>>          at
>> org.directwebremoting.servlet.PlainCallHandler.handle(PlainCallHandler.java:52)
>>
>>          at
>> org.directwebremoting.servlet.UrlProcessor.handle(UrlProcessor.java:101)
>>          at
>> org.directwebremoting.servlet.DwrServlet.doPost(DwrServlet.java:146)
>>          at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>>          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.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:219)
>>
>>          at
>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
>>
>>          at
>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
>>
>>          at
>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>
>>          at
>> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
>>          at
>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>
>>          at
>> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
>>          at
>> org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
>>
>>          at
>> org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
>>
>>          at
>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
>>
>>          at
>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
>>
>>          at
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>
>>          at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>
>>          at
>> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>
>>          at java.lang.Thread.run(Thread.java:748)
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>> found for 'java.lang.StackTraceElement'
>> 89925 [http-apr-10.4.0.17-8080-exec-14] WARN
>> org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring:
>> batchId[5] message[java.lang.IllegalArgumentException: query is not
>> valid: [Path Gene.homologues.homologue.primaryIdentifier in view list
>> is not in the model, Path Gene.homologues.homologue.symbol in view
>> list is not in the model, Path
>> Gene.homologues.homologue.organism.shortName in view list is not in
>> the model, Path Gene.homologues.type in constraint is not in the
>> model, Path Gene.homologues.homologue.organism.shortName in order by
>> list is not in the model]]
>>
>>
>> Best,
>>
>> Pengcheng
>>
>>
>> On 2018-4-5 23:45, Julie Sullivan wrote:
>>> Hi!
>>>
>>> I have no idea what's wrong! Everything you show looks correct to me.
>>>
>>> Is there a message in your log files? This should be in
>>> $TOMCAT/logs/catalina.out. Can you send that to me? Maybe I can see
>>> what's going on.
>>>
>>> Julie
>>>
>>> On 04/04/2018 05:22 PM, Pengcheng Yang wrote:
>>>> Hi Miners,
>>>>
>>>> This questions has been discussed previously:
>>>> http://gmod.827538.n3.nabble.com/gene-ontology-display-problem-td4050690.html.
>>>> But now have new problem.
>>>>
>>>> 1. What the problem is:
>>>>
>>>> The page without gene ontology display:
>>>>
>>>> The project.xml file is:
>>>>
>>>>      <source name="go" type="go" dump="true">
>>>>        <property name="src.data.file"
>>>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>>>                          <property name="createrelations"
>>>> value="false"/>
>>>>      </source>
>>>>
>>>>      <source name="go-annotation" type="go-annotation" dump="true">
>>>>        <property name="ontologyfile"
>>>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>>>        <property name="src.data.dir"
>>>> location="/home/pengchy/Project/LocustMine/testdata/go-annotation/"/>
>>>>      </source>
>>>>
>>>> 2. I have tried to test the query provided by Julie Sullivan
>>>>
>>>> <query name="" model="genomic"
>>>> view="Gene.goAnnotation.ontologyTerm.parents.name
>>>> Gene.goAnnotation.ontologyTerm.name
>>>> Gene.goAnnotation.evidence.code.code" longDescription=""
>>>> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
>>>> constraintLogic="(A or B or C) and D">
>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>> code="A" op="=" value="biological_process"/>
>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>> code="B" op="=" value="molecular_function"/>
>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>> code="C" op="=" value="cellular_component"/>
>>>>     <constraint path="Gene" code="D" op="LOOKUP" value="Ehbp1"
>>>> extraValue=""/>
>>>> </query>
>>>>
>>>> After click the "show" button for Symbol and DB identifier, the
>>>> result page was as follow:
>>>>
>>>> it is clear that this gene's GO annotation has been successfully
>>>> loaded.
>>>>
>>>> After clicking on the Ontology Term Name "protein binding", I got
>>>> the collection of the gene ids that were annotated to this term:
>>>>
>>>> So, this further support the GO annotation has been successfully
>>>> loaded.
>>>>
>>>> But, why it could not be displayed on the gene report page?
>>>>
>>>> 3. I try to remove the Gene Ontology displayer from the file
>>>> webapp/resources/webapp/WEB-INF/webconfig-model.xml by comment the
>>>> following lines:
>>>>
>>>>     <reportdisplayer
>>>> javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"
>>>> jspName="model/geneOntologyDisplayer.jsp"
>>>> replacesFields="goAnnotation,ontologyAnnotations"
>>>>                       placement="Genomics"
>>>>                       types="Gene"/>
>>>>
>>>> I have successfully displayed the Gene Ontology annotation
>>>> information, but there were two sections: "GO Annotation" and
>>>> "Ontology Annotation", listed as follow:
>>>>
>>>> How to merge these two sections?
>>>>
>>>> Best,
>>>>
>>>> Pengcheng Yang
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
> _______________________________________________
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> [hidden email]
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Re: gene ontology failed display

Julie Sullivan-2
Hi Pengcheng!

Your qualifier for that GO annotation is 0, whereas the displayer
expects it to be NULL.

Here's the docs on that qualifier column:

        http://geneontology.org/page/go-annotation-conventions#qual

"Allowable values are NOT, contributes_to, and colocalizes_with. "

We make this assumption (qualifier should be NULL) a lot of places so
this will cause you problems!

Julie

On 04/06/2018 11:15 AM, Pengcheng Yang wrote:

> Hi Julie,
>
> No result was output using your new query (without any modification).
> Our Mine address is: http://www.locustmine.org:8080/testmine/begin.do.
>
> Thank you and best,
>
> Pengcheng
>
>
> On 2018-4-6 16:01, Julie Sullivan wrote:
>> This query is returning no results for your mine:
>>
>> https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/bio/web/displayer/GeneOntologyDisplayer.java#L170 
>>
>>
>> Why? Because it looks like the data is there!
>>
>> Try this query, it's exactly what the displayer is doing:
>>
>> <query name="" model="genomic"
>> view="Gene.goAnnotation.ontologyTerm.parents.name
>> Gene.goAnnotation.ontologyTerm.name
>> Gene.goAnnotation.evidence.code.code" longDescription=""
>> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
>> constraintLogic="(A or B or C) and D and E">
>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>> code="A" op="=" value="biological_process"/>
>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>> code="B" op="=" value="molecular_function"/>
>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>> code="C" op="=" value="cellular_component"/>
>>   <constraint path="Gene.id" code="D" op="=" value="1"/>
>>   <constraint path="Gene.goAnnotation.qualifier" code="E" op="IS NULL"/>
>> </query>
>>
>> It's the same one you ran before but with ID instead of symbol and I
>> added the qualifier. Change ID to be the id of the gene. To get the ID
>> look at the URL on the gene report page, e.g. report.do?id=1007180.
>> The id is what the displayer uses, so let's try that because I am
>> running out of ideas.
>>
>> Try that?
>>
>> On 04/06/2018 01:15 AM, Pengcheng Yang wrote:
>>> Hi Julie,
>>>
>>> Following your suggestion, I have checked the message in
>>> logs/catalina.out. But nothing related to GO displayer was found. The
>>> latest 100 lines of the logs/catalina.out file after I visiting the
>>> gene entry are pasted as follow. The error message maybe about
>>> another problem.
>>>
>>>
>>> =========================== error message===========================
>>>
>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 84797 [http-apr-10.4.0.17-8080-exec-12] WARN
>>> org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring:
>>> batchId[2] message[java.lang.IllegalArgumentException: query is not
>>> valid: [Path Gene.homologues.homologue.primaryIdentifier in view list
>>> is not in the model, Path Gene.homologues.homologue.symbol in view
>>> list is not in the model, Path
>>> Gene.homologues.homologue.organism.shortName in view list is not in
>>> the model, Path Gene.homologues.type in constraint is not in the
>>> model, Path Gene.homologues.homologue.organism.shortName in order by
>>> list is not in the model]]
>>> 89921 [http-apr-10.4.0.17-8080-exec-14] WARN
>>> org.directwebremoting.impl.DefaultRemoter  - Method execution failed:
>>> java.lang.IllegalArgumentException: query is not valid: [Path
>>> Gene.homologues.homologue.primaryIdentifier in view list is not in
>>> the model, Path Gene.homologues.homologue.symbol in view list is not
>>> in the model, Path Gene.homologues.homologue.organism.shortName in
>>> view list is not in the model, Path Gene.homologues.type in
>>> constraint is not in the model, Path
>>> Gene.homologues.homologue.organism.shortName in order by list is not
>>> in the model]
>>>          at
>>> org.intermine.api.mines.LocalMine.getRows(LocalMine.java:143)
>>>          at
>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.runQuery(FriendlyMineLinkGenerator.java:166)
>>>
>>>          at
>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.localHomologueStrategy(FriendlyMineLinkGenerator.java:138)
>>>
>>>          at
>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.fetch(FriendlyMineLinkGenerator.java:106)
>>>
>>>          at
>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator.getLinks(FriendlyMineLinkGenerator.java:85)
>>>
>>>          at
>>> org.intermine.dwr.AjaxServices.getFriendlyMineLinks(AjaxServices.java:730)
>>>
>>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>          at
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>>>
>>>          at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>
>>>          at java.lang.reflect.Method.invoke(Method.java:498)
>>>          at
>>> org.directwebremoting.impl.ExecuteAjaxFilter.doFilter(ExecuteAjaxFilter.java:34)
>>>
>>>          at
>>> org.directwebremoting.impl.DefaultRemoter$1.doFilter(DefaultRemoter.java:428)
>>>
>>>          at
>>> org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:431)
>>>
>>>          at
>>> org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:283)
>>>
>>>          at
>>> org.directwebremoting.servlet.PlainCallHandler.handle(PlainCallHandler.java:52)
>>>
>>>          at
>>> org.directwebremoting.servlet.UrlProcessor.handle(UrlProcessor.java:101)
>>>          at
>>> org.directwebremoting.servlet.DwrServlet.doPost(DwrServlet.java:146)
>>>          at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>>>          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.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:219)
>>>
>>>          at
>>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
>>>
>>>          at
>>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
>>>
>>>          at
>>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>>
>>>          at
>>> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
>>>
>>>          at
>>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>>
>>>          at
>>> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
>>>
>>>          at
>>> org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
>>>
>>>          at
>>> org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
>>>
>>>          at
>>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
>>>
>>>          at
>>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
>>>
>>>          at
>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>>
>>>          at
>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>>
>>>          at
>>> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>>
>>>          at java.lang.Thread.run(Thread.java:748)
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>> found for 'java.lang.StackTraceElement'
>>> 89925 [http-apr-10.4.0.17-8080-exec-14] WARN
>>> org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring:
>>> batchId[5] message[java.lang.IllegalArgumentException: query is not
>>> valid: [Path Gene.homologues.homologue.primaryIdentifier in view list
>>> is not in the model, Path Gene.homologues.homologue.symbol in view
>>> list is not in the model, Path
>>> Gene.homologues.homologue.organism.shortName in view list is not in
>>> the model, Path Gene.homologues.type in constraint is not in the
>>> model, Path Gene.homologues.homologue.organism.shortName in order by
>>> list is not in the model]]
>>>
>>>
>>> Best,
>>>
>>> Pengcheng
>>>
>>>
>>> On 2018-4-5 23:45, Julie Sullivan wrote:
>>>> Hi!
>>>>
>>>> I have no idea what's wrong! Everything you show looks correct to me.
>>>>
>>>> Is there a message in your log files? This should be in
>>>> $TOMCAT/logs/catalina.out. Can you send that to me? Maybe I can see
>>>> what's going on.
>>>>
>>>> Julie
>>>>
>>>> On 04/04/2018 05:22 PM, Pengcheng Yang wrote:
>>>>> Hi Miners,
>>>>>
>>>>> This questions has been discussed previously:
>>>>> http://gmod.827538.n3.nabble.com/gene-ontology-display-problem-td4050690.html.
>>>>> But now have new problem.
>>>>>
>>>>> 1. What the problem is:
>>>>>
>>>>> The page without gene ontology display:
>>>>>
>>>>> The project.xml file is:
>>>>>
>>>>>      <source name="go" type="go" dump="true">
>>>>>        <property name="src.data.file"
>>>>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>>>>                          <property name="createrelations"
>>>>> value="false"/>
>>>>>      </source>
>>>>>
>>>>>      <source name="go-annotation" type="go-annotation" dump="true">
>>>>>        <property name="ontologyfile"
>>>>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>>>>        <property name="src.data.dir"
>>>>> location="/home/pengchy/Project/LocustMine/testdata/go-annotation/"/>
>>>>>      </source>
>>>>>
>>>>> 2. I have tried to test the query provided by Julie Sullivan
>>>>>
>>>>> <query name="" model="genomic"
>>>>> view="Gene.goAnnotation.ontologyTerm.parents.name
>>>>> Gene.goAnnotation.ontologyTerm.name
>>>>> Gene.goAnnotation.evidence.code.code" longDescription=""
>>>>> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
>>>>> constraintLogic="(A or B or C) and D">
>>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>> code="A" op="=" value="biological_process"/>
>>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>> code="B" op="=" value="molecular_function"/>
>>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>> code="C" op="=" value="cellular_component"/>
>>>>>     <constraint path="Gene" code="D" op="LOOKUP" value="Ehbp1"
>>>>> extraValue=""/>
>>>>> </query>
>>>>>
>>>>> After click the "show" button for Symbol and DB identifier, the
>>>>> result page was as follow:
>>>>>
>>>>> it is clear that this gene's GO annotation has been successfully
>>>>> loaded.
>>>>>
>>>>> After clicking on the Ontology Term Name "protein binding", I got
>>>>> the collection of the gene ids that were annotated to this term:
>>>>>
>>>>> So, this further support the GO annotation has been successfully
>>>>> loaded.
>>>>>
>>>>> But, why it could not be displayed on the gene report page?
>>>>>
>>>>> 3. I try to remove the Gene Ontology displayer from the file
>>>>> webapp/resources/webapp/WEB-INF/webconfig-model.xml by comment the
>>>>> following lines:
>>>>>
>>>>>     <reportdisplayer
>>>>> javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"
>>>>> jspName="model/geneOntologyDisplayer.jsp"
>>>>> replacesFields="goAnnotation,ontologyAnnotations"
>>>>>                       placement="Genomics"
>>>>>                       types="Gene"/>
>>>>>
>>>>> I have successfully displayed the Gene Ontology annotation
>>>>> information, but there were two sections: "GO Annotation" and
>>>>> "Ontology Annotation", listed as follow:
>>>>>
>>>>> How to merge these two sections?
>>>>>
>>>>> Best,
>>>>>
>>>>> Pengcheng Yang
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
> _______________________________________________
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> [hidden email]
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Re: gene ontology failed display

Pengcheng Yang
Hi Julie,

Thank you for your suggestions. Because the GO annotation information of
my data was obtained using InterProScan, it is not easy to set the value
of the fourth column. Further, according to the definition of GAF 2.0,
the fourth column is not mandatory, and can be cardinality 0, 1, >1.
Indeed, the fourth column of the gaf data from the example maliramine
"go-annotation/gene_association.GeneDB_Pfalciparum" is also empty
(NULL), i.e cardinality 0. So, I set this column as empty. But the
Ontology Annotation and GO Annotation still displayed as before.

Best,

Pengcheng


On 2018-4-6 18:23, Julie Sullivan wrote:

> Hi Pengcheng!
>
> Your qualifier for that GO annotation is 0, whereas the displayer
> expects it to be NULL.
>
> Here's the docs on that qualifier column:
>
>     http://geneontology.org/page/go-annotation-conventions#qual
>
> "Allowable values are NOT, contributes_to, and colocalizes_with. "
>
> We make this assumption (qualifier should be NULL) a lot of places so
> this will cause you problems!
>
> Julie
>
> On 04/06/2018 11:15 AM, Pengcheng Yang wrote:
>> Hi Julie,
>>
>> No result was output using your new query (without any modification).
>> Our Mine address is: http://www.locustmine.org:8080/testmine/begin.do.
>>
>> Thank you and best,
>>
>> Pengcheng
>>
>>
>> On 2018-4-6 16:01, Julie Sullivan wrote:
>>> This query is returning no results for your mine:
>>>
>>> https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/bio/web/displayer/GeneOntologyDisplayer.java#L170 
>>>
>>>
>>> Why? Because it looks like the data is there!
>>>
>>> Try this query, it's exactly what the displayer is doing:
>>>
>>> <query name="" model="genomic"
>>> view="Gene.goAnnotation.ontologyTerm.parents.name
>>> Gene.goAnnotation.ontologyTerm.name
>>> Gene.goAnnotation.evidence.code.code" longDescription=""
>>> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
>>> constraintLogic="(A or B or C) and D and E">
>>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>> code="A" op="=" value="biological_process"/>
>>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>> code="B" op="=" value="molecular_function"/>
>>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>> code="C" op="=" value="cellular_component"/>
>>>   <constraint path="Gene.id" code="D" op="=" value="1"/>
>>>   <constraint path="Gene.goAnnotation.qualifier" code="E" op="IS
>>> NULL"/>
>>> </query>
>>>
>>> It's the same one you ran before but with ID instead of symbol and I
>>> added the qualifier. Change ID to be the id of the gene. To get the
>>> ID look at the URL on the gene report page, e.g.
>>> report.do?id=1007180. The id is what the displayer uses, so let's
>>> try that because I am running out of ideas.
>>>
>>> Try that?
>>>
>>> On 04/06/2018 01:15 AM, Pengcheng Yang wrote:
>>>> Hi Julie,
>>>>
>>>> Following your suggestion, I have checked the message in
>>>> logs/catalina.out. But nothing related to GO displayer was found.
>>>> The latest 100 lines of the logs/catalina.out file after I visiting
>>>> the gene entry are pasted as follow. The error message maybe about
>>>> another problem.
>>>>
>>>>
>>>> =========================== error message===========================
>>>>
>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] WARN
>>>> org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring:
>>>> batchId[2] message[java.lang.IllegalArgumentException: query is not
>>>> valid: [Path Gene.homologues.homologue.primaryIdentifier in view
>>>> list is not in the model, Path Gene.homologues.homologue.symbol in
>>>> view list is not in the model, Path
>>>> Gene.homologues.homologue.organism.shortName in view list is not in
>>>> the model, Path Gene.homologues.type in constraint is not in the
>>>> model, Path Gene.homologues.homologue.organism.shortName in order
>>>> by list is not in the model]]
>>>> 89921 [http-apr-10.4.0.17-8080-exec-14] WARN
>>>> org.directwebremoting.impl.DefaultRemoter  - Method execution failed:
>>>> java.lang.IllegalArgumentException: query is not valid: [Path
>>>> Gene.homologues.homologue.primaryIdentifier in view list is not in
>>>> the model, Path Gene.homologues.homologue.symbol in view list is
>>>> not in the model, Path Gene.homologues.homologue.organism.shortName
>>>> in view list is not in the model, Path Gene.homologues.type in
>>>> constraint is not in the model, Path
>>>> Gene.homologues.homologue.organism.shortName in order by list is
>>>> not in the model]
>>>>          at
>>>> org.intermine.api.mines.LocalMine.getRows(LocalMine.java:143)
>>>>          at
>>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.runQuery(FriendlyMineLinkGenerator.java:166)
>>>>
>>>>          at
>>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.localHomologueStrategy(FriendlyMineLinkGenerator.java:138)
>>>>
>>>>          at
>>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.fetch(FriendlyMineLinkGenerator.java:106)
>>>>
>>>>          at
>>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator.getLinks(FriendlyMineLinkGenerator.java:85)
>>>>
>>>>          at
>>>> org.intermine.dwr.AjaxServices.getFriendlyMineLinks(AjaxServices.java:730)
>>>>
>>>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
>>>> Method)
>>>>          at
>>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>>>>
>>>>          at
>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>>
>>>>          at java.lang.reflect.Method.invoke(Method.java:498)
>>>>          at
>>>> org.directwebremoting.impl.ExecuteAjaxFilter.doFilter(ExecuteAjaxFilter.java:34)
>>>>
>>>>          at
>>>> org.directwebremoting.impl.DefaultRemoter$1.doFilter(DefaultRemoter.java:428)
>>>>
>>>>          at
>>>> org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:431)
>>>>
>>>>          at
>>>> org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:283)
>>>>
>>>>          at
>>>> org.directwebremoting.servlet.PlainCallHandler.handle(PlainCallHandler.java:52)
>>>>
>>>>          at
>>>> org.directwebremoting.servlet.UrlProcessor.handle(UrlProcessor.java:101)
>>>>
>>>>          at
>>>> org.directwebremoting.servlet.DwrServlet.doPost(DwrServlet.java:146)
>>>>          at
>>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>>>>          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.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:219)
>>>>
>>>>          at
>>>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
>>>>
>>>>          at
>>>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
>>>>
>>>>          at
>>>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>>>
>>>>          at
>>>> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
>>>>
>>>>          at
>>>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>>>
>>>>          at
>>>> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
>>>>
>>>>          at
>>>> org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
>>>>
>>>>          at
>>>> org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
>>>>
>>>>          at
>>>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
>>>>
>>>>          at
>>>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
>>>>
>>>>          at
>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>>>
>>>>          at
>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>>>
>>>>          at
>>>> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>>>
>>>>          at java.lang.Thread.run(Thread.java:748)
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No converter
>>>> found for 'java.lang.StackTraceElement'
>>>> 89925 [http-apr-10.4.0.17-8080-exec-14] WARN
>>>> org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring:
>>>> batchId[5] message[java.lang.IllegalArgumentException: query is not
>>>> valid: [Path Gene.homologues.homologue.primaryIdentifier in view
>>>> list is not in the model, Path Gene.homologues.homologue.symbol in
>>>> view list is not in the model, Path
>>>> Gene.homologues.homologue.organism.shortName in view list is not in
>>>> the model, Path Gene.homologues.type in constraint is not in the
>>>> model, Path Gene.homologues.homologue.organism.shortName in order
>>>> by list is not in the model]]
>>>>
>>>>
>>>> Best,
>>>>
>>>> Pengcheng
>>>>
>>>>
>>>> On 2018-4-5 23:45, Julie Sullivan wrote:
>>>>> Hi!
>>>>>
>>>>> I have no idea what's wrong! Everything you show looks correct to me.
>>>>>
>>>>> Is there a message in your log files? This should be in
>>>>> $TOMCAT/logs/catalina.out. Can you send that to me? Maybe I can
>>>>> see what's going on.
>>>>>
>>>>> Julie
>>>>>
>>>>> On 04/04/2018 05:22 PM, Pengcheng Yang wrote:
>>>>>> Hi Miners,
>>>>>>
>>>>>> This questions has been discussed previously:
>>>>>> http://gmod.827538.n3.nabble.com/gene-ontology-display-problem-td4050690.html.
>>>>>> But now have new problem.
>>>>>>
>>>>>> 1. What the problem is:
>>>>>>
>>>>>> The page without gene ontology display:
>>>>>>
>>>>>> The project.xml file is:
>>>>>>
>>>>>>      <source name="go" type="go" dump="true">
>>>>>>        <property name="src.data.file"
>>>>>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>>>>>                          <property name="createrelations"
>>>>>> value="false"/>
>>>>>>      </source>
>>>>>>
>>>>>>      <source name="go-annotation" type="go-annotation" dump="true">
>>>>>>        <property name="ontologyfile"
>>>>>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>>>>>        <property name="src.data.dir"
>>>>>> location="/home/pengchy/Project/LocustMine/testdata/go-annotation/"/>
>>>>>>
>>>>>>      </source>
>>>>>>
>>>>>> 2. I have tried to test the query provided by Julie Sullivan
>>>>>>
>>>>>> <query name="" model="genomic"
>>>>>> view="Gene.goAnnotation.ontologyTerm.parents.name
>>>>>> Gene.goAnnotation.ontologyTerm.name
>>>>>> Gene.goAnnotation.evidence.code.code" longDescription=""
>>>>>> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
>>>>>> constraintLogic="(A or B or C) and D">
>>>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>>> code="A" op="=" value="biological_process"/>
>>>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>>> code="B" op="=" value="molecular_function"/>
>>>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>>> code="C" op="=" value="cellular_component"/>
>>>>>>     <constraint path="Gene" code="D" op="LOOKUP" value="Ehbp1"
>>>>>> extraValue=""/>
>>>>>> </query>
>>>>>>
>>>>>> After click the "show" button for Symbol and DB identifier, the
>>>>>> result page was as follow:
>>>>>>
>>>>>> it is clear that this gene's GO annotation has been successfully
>>>>>> loaded.
>>>>>>
>>>>>> After clicking on the Ontology Term Name "protein binding", I got
>>>>>> the collection of the gene ids that were annotated to this term:
>>>>>>
>>>>>> So, this further support the GO annotation has been successfully
>>>>>> loaded.
>>>>>>
>>>>>> But, why it could not be displayed on the gene report page?
>>>>>>
>>>>>> 3. I try to remove the Gene Ontology displayer from the file
>>>>>> webapp/resources/webapp/WEB-INF/webconfig-model.xml by comment
>>>>>> the following lines:
>>>>>>
>>>>>>     <reportdisplayer
>>>>>> javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"
>>>>>> jspName="model/geneOntologyDisplayer.jsp"
>>>>>> replacesFields="goAnnotation,ontologyAnnotations"
>>>>>>                       placement="Genomics"
>>>>>>                       types="Gene"/>
>>>>>>
>>>>>> I have successfully displayed the Gene Ontology annotation
>>>>>> information, but there were two sections: "GO Annotation" and
>>>>>> "Ontology Annotation", listed as follow:
>>>>>>
>>>>>> How to merge these two sections?
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Pengcheng Yang
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email]
>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
> _______________________________________________
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> [hidden email]
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Re: gene ontology failed display

Julie Sullivan-2
I am glad you got it working! :D

On 04/09/2018 09:16 AM, Pengcheng Yang wrote:

> Hi Julie,
>
> Thank you a lot! I have put the GO displayer back and It works!
>
> Best,
>
> Pengcheng
>
>
>
> On 2018-4-9 15:27, Julie Sullivan wrote:
>> Can you put the GO displayer back so I can see what it's doing?
>>
>> The query works for me now:
>>
>> <query name="" model="genomic"
>> view="Gene.goAnnotation.ontologyTerm.parents.name
>> Gene.goAnnotation.ontologyTerm.name
>> Gene.goAnnotation.evidence.code.code" longDescription=""
>> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
>> constraintLogic="(A or B or C) and D">
>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>> code="A" op="=" value="biological_process"/>
>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>> code="B" op="=" value="molecular_function"/>
>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>> code="C" op="=" value="cellular_component"/>
>>   <constraint path="Gene.id" code="D" op="=" value="1000041"/>
>> </query>
>>
>>
>> On 04/09/2018 06:46 AM, Pengcheng Yang wrote:
>>> Hi Julie,
>>>
>>> Thank you for your suggestions. Because the GO annotation information
>>> of my data was obtained using InterProScan, it is not easy to set the
>>> value of the fourth column. Further, according to the definition of
>>> GAF 2.0, the fourth column is not mandatory, and can be cardinality
>>> 0, 1, >1. Indeed, the fourth column of the gaf data from the example
>>> maliramine "go-annotation/gene_association.GeneDB_Pfalciparum" is
>>> also empty (NULL), i.e cardinality 0. So, I set this column as empty.
>>> But the Ontology Annotation and GO Annotation still displayed as before.
>>>
>>> Best,
>>>
>>> Pengcheng
>>>
>>>
>>> On 2018-4-6 18:23, Julie Sullivan wrote:
>>>> Hi Pengcheng!
>>>>
>>>> Your qualifier for that GO annotation is 0, whereas the displayer
>>>> expects it to be NULL.
>>>>
>>>> Here's the docs on that qualifier column:
>>>>
>>>> http://geneontology.org/page/go-annotation-conventions#qual
>>>>
>>>> "Allowable values are NOT, contributes_to, and colocalizes_with. "
>>>>
>>>> We make this assumption (qualifier should be NULL) a lot of places
>>>> so this will cause you problems!
>>>>
>>>> Julie
>>>>
>>>> On 04/06/2018 11:15 AM, Pengcheng Yang wrote:
>>>>> Hi Julie,
>>>>>
>>>>> No result was output using your new query (without any
>>>>> modification). Our Mine address is:
>>>>> http://www.locustmine.org:8080/testmine/begin.do.
>>>>>
>>>>> Thank you and best,
>>>>>
>>>>> Pengcheng
>>>>>
>>>>>
>>>>> On 2018-4-6 16:01, Julie Sullivan wrote:
>>>>>> This query is returning no results for your mine:
>>>>>>
>>>>>> https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/bio/web/displayer/GeneOntologyDisplayer.java#L170 
>>>>>>
>>>>>>
>>>>>> Why? Because it looks like the data is there!
>>>>>>
>>>>>> Try this query, it's exactly what the displayer is doing:
>>>>>>
>>>>>> <query name="" model="genomic"
>>>>>> view="Gene.goAnnotation.ontologyTerm.parents.name
>>>>>> Gene.goAnnotation.ontologyTerm.name
>>>>>> Gene.goAnnotation.evidence.code.code" longDescription=""
>>>>>> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
>>>>>> constraintLogic="(A or B or C) and D and E">
>>>>>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>>> code="A" op="=" value="biological_process"/>
>>>>>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>>> code="B" op="=" value="molecular_function"/>
>>>>>>   <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>>> code="C" op="=" value="cellular_component"/>
>>>>>>   <constraint path="Gene.id" code="D" op="=" value="1"/>
>>>>>>   <constraint path="Gene.goAnnotation.qualifier" code="E" op="IS
>>>>>> NULL"/>
>>>>>> </query>
>>>>>>
>>>>>> It's the same one you ran before but with ID instead of symbol and
>>>>>> I added the qualifier. Change ID to be the id of the gene. To get
>>>>>> the ID look at the URL on the gene report page, e.g.
>>>>>> report.do?id=1007180. The id is what the displayer uses, so let's
>>>>>> try that because I am running out of ideas.
>>>>>>
>>>>>> Try that?
>>>>>>
>>>>>> On 04/06/2018 01:15 AM, Pengcheng Yang wrote:
>>>>>>> Hi Julie,
>>>>>>>
>>>>>>> Following your suggestion, I have checked the message in
>>>>>>> logs/catalina.out. But nothing related to GO displayer was found.
>>>>>>> The latest 100 lines of the logs/catalina.out file after I
>>>>>>> visiting the gene entry are pasted as follow. The error message
>>>>>>> maybe about another problem.
>>>>>>>
>>>>>>>
>>>>>>> =========================== error message===========================
>>>>>>>
>>>>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84796 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 84797 [http-apr-10.4.0.17-8080-exec-12] WARN
>>>>>>> org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring:
>>>>>>> batchId[2] message[java.lang.IllegalArgumentException: query is
>>>>>>> not valid: [Path Gene.homologues.homologue.primaryIdentifier in
>>>>>>> view list is not in the model, Path
>>>>>>> Gene.homologues.homologue.symbol in view list is not in the
>>>>>>> model, Path Gene.homologues.homologue.organism.shortName in view
>>>>>>> list is not in the model, Path Gene.homologues.type in constraint
>>>>>>> is not in the model, Path
>>>>>>> Gene.homologues.homologue.organism.shortName in order by list is
>>>>>>> not in the model]]
>>>>>>> 89921 [http-apr-10.4.0.17-8080-exec-14] WARN
>>>>>>> org.directwebremoting.impl.DefaultRemoter  - Method execution
>>>>>>> failed:
>>>>>>> java.lang.IllegalArgumentException: query is not valid: [Path
>>>>>>> Gene.homologues.homologue.primaryIdentifier in view list is not
>>>>>>> in the model, Path Gene.homologues.homologue.symbol in view list
>>>>>>> is not in the model, Path
>>>>>>> Gene.homologues.homologue.organism.shortName in view list is not
>>>>>>> in the model, Path Gene.homologues.type in constraint is not in
>>>>>>> the model, Path Gene.homologues.homologue.organism.shortName in
>>>>>>> order by list is not in the model]
>>>>>>>          at
>>>>>>> org.intermine.api.mines.LocalMine.getRows(LocalMine.java:143)
>>>>>>>          at
>>>>>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.runQuery(FriendlyMineLinkGenerator.java:166)
>>>>>>>
>>>>>>>          at
>>>>>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.localHomologueStrategy(FriendlyMineLinkGenerator.java:138)
>>>>>>>
>>>>>>>          at
>>>>>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator$LinkFetcher.fetch(FriendlyMineLinkGenerator.java:106)
>>>>>>>
>>>>>>>          at
>>>>>>> org.intermine.bio.web.displayer.FriendlyMineLinkGenerator.getLinks(FriendlyMineLinkGenerator.java:85)
>>>>>>>
>>>>>>>          at
>>>>>>> org.intermine.dwr.AjaxServices.getFriendlyMineLinks(AjaxServices.java:730)
>>>>>>>
>>>>>>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
>>>>>>> Method)
>>>>>>>          at
>>>>>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>>>>>>>
>>>>>>>          at
>>>>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>>>>>
>>>>>>>          at java.lang.reflect.Method.invoke(Method.java:498)
>>>>>>>          at
>>>>>>> org.directwebremoting.impl.ExecuteAjaxFilter.doFilter(ExecuteAjaxFilter.java:34)
>>>>>>>
>>>>>>>          at
>>>>>>> org.directwebremoting.impl.DefaultRemoter$1.doFilter(DefaultRemoter.java:428)
>>>>>>>
>>>>>>>          at
>>>>>>> org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:431)
>>>>>>>
>>>>>>>          at
>>>>>>> org.directwebremoting.impl.DefaultRemoter.execute(DefaultRemoter.java:283)
>>>>>>>
>>>>>>>          at
>>>>>>> org.directwebremoting.servlet.PlainCallHandler.handle(PlainCallHandler.java:52)
>>>>>>>
>>>>>>>          at
>>>>>>> org.directwebremoting.servlet.UrlProcessor.handle(UrlProcessor.java:101)
>>>>>>>
>>>>>>>          at
>>>>>>> org.directwebremoting.servlet.DwrServlet.doPost(DwrServlet.java:146)
>>>>>>>          at
>>>>>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>>>>>>>          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.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:219)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
>>>>>>>
>>>>>>>          at
>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>>>>>>
>>>>>>>          at
>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>>>>>>
>>>>>>>          at
>>>>>>> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>>>>>>
>>>>>>>          at java.lang.Thread.run(Thread.java:748)
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89923 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89924 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89925 [http-apr-10.4.0.17-8080-exec-14] ERROR
>>>>>>> org.directwebremoting.dwrp.DefaultConverterManager  - No
>>>>>>> converter found for 'java.lang.StackTraceElement'
>>>>>>> 89925 [http-apr-10.4.0.17-8080-exec-14] WARN
>>>>>>> org.directwebremoting.dwrp.BaseCallMarshaller  - --Erroring:
>>>>>>> batchId[5] message[java.lang.IllegalArgumentException: query is
>>>>>>> not valid: [Path Gene.homologues.homologue.primaryIdentifier in
>>>>>>> view list is not in the model, Path
>>>>>>> Gene.homologues.homologue.symbol in view list is not in the
>>>>>>> model, Path Gene.homologues.homologue.organism.shortName in view
>>>>>>> list is not in the model, Path Gene.homologues.type in constraint
>>>>>>> is not in the model, Path
>>>>>>> Gene.homologues.homologue.organism.shortName in order by list is
>>>>>>> not in the model]]
>>>>>>>
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Pengcheng
>>>>>>>
>>>>>>>
>>>>>>> On 2018-4-5 23:45, Julie Sullivan wrote:
>>>>>>>> Hi!
>>>>>>>>
>>>>>>>> I have no idea what's wrong! Everything you show looks correct
>>>>>>>> to me.
>>>>>>>>
>>>>>>>> Is there a message in your log files? This should be in
>>>>>>>> $TOMCAT/logs/catalina.out. Can you send that to me? Maybe I can
>>>>>>>> see what's going on.
>>>>>>>>
>>>>>>>> Julie
>>>>>>>>
>>>>>>>> On 04/04/2018 05:22 PM, Pengcheng Yang wrote:
>>>>>>>>> Hi Miners,
>>>>>>>>>
>>>>>>>>> This questions has been discussed previously:
>>>>>>>>> http://gmod.827538.n3.nabble.com/gene-ontology-display-problem-td4050690.html.
>>>>>>>>> But now have new problem.
>>>>>>>>>
>>>>>>>>> 1. What the problem is:
>>>>>>>>>
>>>>>>>>> The page without gene ontology display:
>>>>>>>>>
>>>>>>>>> The project.xml file is:
>>>>>>>>>
>>>>>>>>>      <source name="go" type="go" dump="true">
>>>>>>>>>        <property name="src.data.file"
>>>>>>>>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>>>>>>>>
>>>>>>>>>                          <property name="createrelations"
>>>>>>>>> value="false"/>
>>>>>>>>>      </source>
>>>>>>>>>
>>>>>>>>>      <source name="go-annotation" type="go-annotation"
>>>>>>>>> dump="true">
>>>>>>>>>        <property name="ontologyfile"
>>>>>>>>> location="/home/pengchy/Project/LocustMine/testdata/go/go-basic.obo"/>
>>>>>>>>>
>>>>>>>>>        <property name="src.data.dir"
>>>>>>>>> location="/home/pengchy/Project/LocustMine/testdata/go-annotation/"/>
>>>>>>>>>
>>>>>>>>>      </source>
>>>>>>>>>
>>>>>>>>> 2. I have tried to test the query provided by Julie Sullivan
>>>>>>>>>
>>>>>>>>> <query name="" model="genomic"
>>>>>>>>> view="Gene.goAnnotation.ontologyTerm.parents.name
>>>>>>>>> Gene.goAnnotation.ontologyTerm.name
>>>>>>>>> Gene.goAnnotation.evidence.code.code" longDescription=""
>>>>>>>>> sortOrder="Gene.goAnnotation.ontologyTerm.parents.name asc"
>>>>>>>>> constraintLogic="(A or B or C) and D">
>>>>>>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>>>>>> code="A" op="=" value="biological_process"/>
>>>>>>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>>>>>> code="B" op="=" value="molecular_function"/>
>>>>>>>>>     <constraint path="Gene.goAnnotation.ontologyTerm.parents.name"
>>>>>>>>> code="C" op="=" value="cellular_component"/>
>>>>>>>>>     <constraint path="Gene" code="D" op="LOOKUP" value="Ehbp1"
>>>>>>>>> extraValue=""/>
>>>>>>>>> </query>
>>>>>>>>>
>>>>>>>>> After click the "show" button for Symbol and DB identifier, the
>>>>>>>>> result page was as follow:
>>>>>>>>>
>>>>>>>>> it is clear that this gene's GO annotation has been
>>>>>>>>> successfully loaded.
>>>>>>>>>
>>>>>>>>> After clicking on the Ontology Term Name "protein binding", I
>>>>>>>>> got the collection of the gene ids that were annotated to this
>>>>>>>>> term:
>>>>>>>>>
>>>>>>>>> So, this further support the GO annotation has been
>>>>>>>>> successfully loaded.
>>>>>>>>>
>>>>>>>>> But, why it could not be displayed on the gene report page?
>>>>>>>>>
>>>>>>>>> 3. I try to remove the Gene Ontology displayer from the file
>>>>>>>>> webapp/resources/webapp/WEB-INF/webconfig-model.xml by comment
>>>>>>>>> the following lines:
>>>>>>>>>
>>>>>>>>>     <reportdisplayer
>>>>>>>>> javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer"
>>>>>>>>> jspName="model/geneOntologyDisplayer.jsp"
>>>>>>>>> replacesFields="goAnnotation,ontologyAnnotations"
>>>>>>>>>                       placement="Genomics"
>>>>>>>>>                       types="Gene"/>
>>>>>>>>>
>>>>>>>>> I have successfully displayed the Gene Ontology annotation
>>>>>>>>> information, but there were two sections: "GO Annotation" and
>>>>>>>>> "Ontology Annotation", listed as follow:
>>>>>>>>>
>>>>>>>>> How to merge these two sections?
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>>
>>>>>>>>> Pengcheng Yang
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> dev mailing list
>>>>>>>>> [hidden email]
>>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> dev mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> dev mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email]
>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>
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