post process error

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post process error

Sierra Moxon
BUILD FAILED
/home/intermine/intermine_0_94/imbuild/postprocess.xml:31: error  
running PostProcessTask (action: transfer-sequences)
         at  
org
.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:
148)
         at  
org.intermine.task.PostProcessTask.execute(PostProcessTask.java:112)
         at  
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
         at  
sun
.reflect
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at  
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
106)
         at org.apache.tools.ant.Task.perform(Task.java:348)
         at org.apache.tools.ant.Target.execute(Target.java:390)
         at org.apache.tools.ant.Target.performTasks(Target.java:411)
         at  
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
         at org.apache.tools.ant.Project.executeTarget(Project.java:
1366)
         at  
org
.apache
.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:
41)
         at org.apache.tools.ant.Project.executeTargets(Project.java:
1249)
         at org.apache.tools.ant.Main.runBuild(Main.java:801)
         at org.apache.tools.ant.Main.startAnt(Main.java:218)
         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.reflect.InvocationTargetException
         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
         at  
sun
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
39)
         at  
sun
.reflect
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
         at java.lang.reflect.Method.invoke(Method.java:597)
         at  
org
.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:
146)
         ... 17 more
Caused by: Operation was:transfer-sequences
         at  
org
.intermine
.bio
.postprocess
.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:291)
         ... 22 more
Caused by: java.lang.IllegalArgumentException: Field exons not found  
in interface org.intermine.model.bio.Transcript
         at  
org
.intermine
.objectstore
.query.QueryCollectionReference.<init>(QueryCollectionReference.java:46)
         at  
org
.intermine
.bio
.postprocess
.TransferSequences.transferToTranscripts(TransferSequences.java:336)
         at  
org
.intermine
.bio
.postprocess
.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:138)
         ... 22 more


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Re: post process error

Richard Smith
Hi Sierra,
Sorry, I thought I'd fixed all these.  The easy fix is to change your
project.xml:

Replace:
     <post-process name="transfer-sequences"/>

With:
     <post-process name="transfer-sequences-located-sequence-feature"/>
       
This shouldn't try to do anything with transcripts, it looks like you
don't have transcripts and exons in your model.

I've also checked in a fix and copied it to the branch so if you update
you hopefully won't get an error even if you don't change project.xml.

Cheers,
Richard.





Sierra Moxon wrote:

> BUILD FAILED
> /home/intermine/intermine_0_94/imbuild/postprocess.xml:31: error running
> PostProcessTask (action: transfer-sequences)
>         at
> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:148)
>
>         at
> org.intermine.task.PostProcessTask.execute(PostProcessTask.java:112)
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>         at org.apache.tools.ant.Task.perform(Task.java:348)
>         at org.apache.tools.ant.Target.execute(Target.java:390)
>         at org.apache.tools.ant.Target.performTasks(Target.java:411)
>         at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>         at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>         at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>
>         at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>         at org.apache.tools.ant.Main.runBuild(Main.java:801)
>         at org.apache.tools.ant.Main.startAnt(Main.java:218)
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> Caused by: java.lang.reflect.InvocationTargetException
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>
>         at java.lang.reflect.Method.invoke(Method.java:597)
>         at
> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:146)
>
>         ... 17 more
> Caused by: Operation was:transfer-sequences
>         at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:291)
>
>         ... 22 more
> Caused by: java.lang.IllegalArgumentException: Field exons not found in
> interface org.intermine.model.bio.Transcript
>         at
> org.intermine.objectstore.query.QueryCollectionReference.<init>(QueryCollectionReference.java:46)
>
>         at
> org.intermine.bio.postprocess.TransferSequences.transferToTranscripts(TransferSequences.java:336)
>
>         at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:138)
>
>         ... 22 more
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>


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Re: post process error

Sierra Moxon
Thanks! updating the code and changing project.xml worked.  I do have  
transcripts, but not exons (and not the sequence of either).

Got to another failure; probably because I had this line in my  
objectstoresummary.config.properties:
org.intermine.model.bio.Synonym.fields =
which used to say:
org.intermine.model.bio.Synonym.fields = type

same error with Chromosome, having '' in the  
objectstoresummary.config.properties file.

Maybe it was updated by the paths script? -- Removing these lines  
fixed the error.

/home/intermine/intermine_0_94/imbuild/postprocess.xml:31: error  
running PostProcessTask (action: summarise-objectstore)
        at  
org
.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:
148)
        at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:112)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at  
sun
.reflect
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at  
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
106)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:390)
        at org.apache.tools.ant.Target.performTasks(Target.java:411)
        at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
        at  
org
.apache
.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:
41)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
        at org.apache.tools.ant.Main.runBuild(Main.java:801)
        at org.apache.tools.ant.Main.startAnt(Main.java:218)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at  
sun
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
39)
        at  
sun
.reflect
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at  
org
.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:
146)
        ... 17 more
Caused by: Operation was:summarise-objectstore
        at  
org
.intermine
.bio
.postprocess
.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:291)
        ... 22 more
Caused by: java.lang.IllegalArgumentException: Field '' not found in  
interface org.intermine.model.bio.Synonym
        at org.intermine.objectstore.query.QueryField.<init>(QueryField.java:
58)
        at  
org
.intermine
.objectstore.ObjectStoreSummary.summariseField(ObjectStoreSummary.java:
258)
        at  
org
.intermine
.objectstore.ObjectStoreSummary.<init>(ObjectStoreSummary.java:109)
        at  
org
.intermine
.bio
.postprocess
.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:209)
        ... 22 more



On Oct 27, 2010, at 6:15 AM, Richard Smith wrote:

> Hi Sierra,
> Sorry, I thought I'd fixed all these.  The easy fix is to change your
> project.xml:
>
> Replace:
>    <post-process name="transfer-sequences"/>
>
> With:
>    <post-process name="transfer-sequences-located-sequence-feature"/>
>
> This shouldn't try to do anything with transcripts, it looks like you
> don't have transcripts and exons in your model.
>
> I've also checked in a fix and copied it to the branch so if you  
> update
> you hopefully won't get an error even if you don't change project.xml.
>
> Cheers,
> Richard.
>
>
>
>
>
> Sierra Moxon wrote:
>> BUILD FAILED
>> /home/intermine/intermine_0_94/imbuild/postprocess.xml:31: error  
>> running PostProcessTask (action: transfer-sequences)
>>        at  
>> org
>> .intermine
>> .task.PostProcessTask.doCorePostProcess(PostProcessTask.java:
>> 148)         at  
>> org.intermine.task.PostProcessTask.execute(PostProcessTask.java:112)
>>        at  
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>        at  
>> sun
>> .reflect
>> .DelegatingMethodAccessorImpl
>> .invoke(DelegatingMethodAccessorImpl.java:25)         at  
>> java.lang.reflect.Method.invoke(Method.java:597)
>>        at  
>> org
>> .apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:
>> 106)
>>        at org.apache.tools.ant.Task.perform(Task.java:348)
>>        at org.apache.tools.ant.Target.execute(Target.java:390)
>>        at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>        at  
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>        at org.apache.tools.ant.Project.executeTarget(Project.java:
>> 1366)
>>        at  
>> org
>> .apache
>> .tools
>> .ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:
>> 41)         at  
>> org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>        at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>        at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:
>> 109)
>> Caused by: java.lang.reflect.InvocationTargetException
>>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>        at  
>> sun
>> .reflect
>> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
>> 39)         at  
>> sun
>> .reflect
>> .DelegatingMethodAccessorImpl
>> .invoke(DelegatingMethodAccessorImpl.java:25)         at  
>> java.lang.reflect.Method.invoke(Method.java:597)
>>        at  
>> org
>> .intermine
>> .task.PostProcessTask.doCorePostProcess(PostProcessTask.java:
>> 146)         ... 17 more
>> Caused by: Operation was:transfer-sequences
>>        at  
>> org
>> .intermine
>> .bio
>> .postprocess
>> .PostProcessOperationsTask.execute(PostProcessOperationsTask.java:
>> 291)         ... 22 more
>> Caused by: java.lang.IllegalArgumentException: Field exons not  
>> found in interface org.intermine.model.bio.Transcript
>>        at  
>> org
>> .intermine
>> .objectstore
>> .query
>> .QueryCollectionReference.<init>(QueryCollectionReference.java:
>> 46)         at  
>> org
>> .intermine
>> .bio
>> .postprocess
>> .TransferSequences.transferToTranscripts(TransferSequences.java:
>> 336)         at  
>> org
>> .intermine
>> .bio
>> .postprocess
>> .PostProcessOperationsTask.execute(PostProcessOperationsTask.java:
>> 138)         ... 22 more
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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Re: post process error

Richard Smith
Yes, sounds like the update script left an empty value behind.  Deleting
it should be fine.

Cheers,
Richard.



Sierra Moxon wrote:

> Thanks! updating the code and changing project.xml worked.  I do have
> transcripts, but not exons (and not the sequence of either).
>
> Got to another failure; probably because I had this line in my
> objectstoresummary.config.properties:
> org.intermine.model.bio.Synonym.fields =
> which used to say:
> org.intermine.model.bio.Synonym.fields = type
>
> same error with Chromosome, having '' in the
> objectstoresummary.config.properties file.
>
> Maybe it was updated by the paths script? -- Removing these lines fixed
> the error.
>
> /home/intermine/intermine_0_94/imbuild/postprocess.xml:31: error running
> PostProcessTask (action: summarise-objectstore)
>     at
> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:148)
>
>     at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:112)
>     at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>     at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>     at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>
>     at java.lang.reflect.Method.invoke(Method.java:597)
>     at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>     at org.apache.tools.ant.Task.perform(Task.java:348)
>     at org.apache.tools.ant.Target.execute(Target.java:390)
>     at org.apache.tools.ant.Target.performTasks(Target.java:411)
>     at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>     at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>     at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>
>     at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>     at org.apache.tools.ant.Main.runBuild(Main.java:801)
>     at org.apache.tools.ant.Main.startAnt(Main.java:218)
>     at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>     at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> Caused by: java.lang.reflect.InvocationTargetException
>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>     at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>
>     at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>
>     at java.lang.reflect.Method.invoke(Method.java:597)
>     at
> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:146)
>
>     ... 17 more
> Caused by: Operation was:summarise-objectstore
>     at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:291)
>
>     ... 22 more
> Caused by: java.lang.IllegalArgumentException: Field '' not found in
> interface org.intermine.model.bio.Synonym
>     at
> org.intermine.objectstore.query.QueryField.<init>(QueryField.java:58)
>     at
> org.intermine.objectstore.ObjectStoreSummary.summariseField(ObjectStoreSummary.java:258)
>
>     at
> org.intermine.objectstore.ObjectStoreSummary.<init>(ObjectStoreSummary.java:109)
>
>     at
> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:209)
>
>     ... 22 more
>
>
>
> On Oct 27, 2010, at 6:15 AM, Richard Smith wrote:
>
>> Hi Sierra,
>> Sorry, I thought I'd fixed all these.  The easy fix is to change your
>> project.xml:
>>
>> Replace:
>>    <post-process name="transfer-sequences"/>
>>
>> With:
>>    <post-process name="transfer-sequences-located-sequence-feature"/>
>>    
>> This shouldn't try to do anything with transcripts, it looks like you
>> don't have transcripts and exons in your model.
>>
>> I've also checked in a fix and copied it to the branch so if you update
>> you hopefully won't get an error even if you don't change project.xml.
>>
>> Cheers,
>> Richard.
>>
>>
>>
>>
>>
>> Sierra Moxon wrote:
>>> BUILD FAILED
>>> /home/intermine/intermine_0_94/imbuild/postprocess.xml:31: error
>>> running PostProcessTask (action: transfer-sequences)
>>>        at
>>> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:148)        
>>> at org.intermine.task.PostProcessTask.execute(PostProcessTask.java:112)
>>>        at
>>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
>>>        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>>        at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)        
>>> at java.lang.reflect.Method.invoke(Method.java:597)
>>>        at
>>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>>>
>>>        at org.apache.tools.ant.Task.perform(Task.java:348)
>>>        at org.apache.tools.ant.Target.execute(Target.java:390)
>>>        at org.apache.tools.ant.Target.performTasks(Target.java:411)
>>>        at
>>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397)
>>>        at org.apache.tools.ant.Project.executeTarget(Project.java:1366)
>>>        at
>>> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)        
>>> at org.apache.tools.ant.Project.executeTargets(Project.java:1249)
>>>        at org.apache.tools.ant.Main.runBuild(Main.java:801)
>>>        at org.apache.tools.ant.Main.startAnt(Main.java:218)
>>>        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>>        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>> Caused by: java.lang.reflect.InvocationTargetException
>>>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>        at
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)        
>>> at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)        
>>> at java.lang.reflect.Method.invoke(Method.java:597)
>>>        at
>>> org.intermine.task.PostProcessTask.doCorePostProcess(PostProcessTask.java:146)        
>>> ... 17 more
>>> Caused by: Operation was:transfer-sequences
>>>        at
>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:291)        
>>> ... 22 more
>>> Caused by: java.lang.IllegalArgumentException: Field exons not found
>>> in interface org.intermine.model.bio.Transcript
>>>        at
>>> org.intermine.objectstore.query.QueryCollectionReference.<init>(QueryCollectionReference.java:46)        
>>> at
>>> org.intermine.bio.postprocess.TransferSequences.transferToTranscripts(TransferSequences.java:336)        
>>> at
>>> org.intermine.bio.postprocess.PostProcessOperationsTask.execute(PostProcessOperationsTask.java:138)        
>>> ... 22 more
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>


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