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[bioontology-support] error in R annotator client

Katie Planey ywrfc09 at stanford.edu
Tue Mar 19 15:43:02 PDT 2013


Thanks! Quite helpful.

Katie Planey, MBA
Stanford Biomedical Informatics

On Mar 19, 2013, at 9:22 AM, Andrew Su <asu at scripps.edu> wrote:

> Hi Katie,
> 
> Looks like there was a slight change in the XML format returned by the
> annotator.  You've successfully identified the line that is causing
> the error:
> 
>       localConceptId <-
> xmlValue(getNodeSet(result,"./term/localConceptId")[[1]])
> 
> If you update it to this:
> 
>       localConceptId <-
> xmlValue(getNodeSet(result,"./term/concept/localConceptId")[[1]])
> 
> the script should work.
> 
> NOTE TO NCBO -- I'm guessing that this change probably affects the
> other client examples.  For example, perhaps line 102 of the perl
> example (https://bmir-gforge.stanford.edu/gf/project/client_examples/scmsvn/?action=browse&path=%2Ftrunk%2FPerl%2FAnnotator-Perl%2Fannotator.pl&annotate=49)
> also needs updating?  Haven't tested it myself though...
> 
> Cheers,
> -andrew
> 
> 
> On Mon, Mar 18, 2013 at 5:46 PM, Trish Whetzel <whetzel at stanford.edu> wrote:
>> Hi Katie,
>> 
>> I have not seen this error reported previously. The Annotator R Client was
>> developed by Andrew Su,now included in this thread, and may be able to
>> provide more insight on this error.
>> 
>> Best,
>> Trish
>> 
>> 
>> Trish Whetzel, PhD
>> Outreach Coordinator
>> The National Center for Biomedical Ontology
>> Ph: 650-721-2378
>> http://www.bioontology.org
>> 
>> "Like" NCBO on Facebook: http://on.fb.me/bioontology
>> 
>> Follow NCBO on Twitter: http://twitter.com/#!/bioontology
>> 
>> Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
>> 
>> 
>> On Mar 18, 2013, at 6:28 AM, Katie Planey wrote:
>> 
>> Dear NCBO support,
>> 
>> I'm getting errors from the NCBO annotator R client running the simple
>> example given on the wiki page (I did input my own API key):
>> 
>> http://www.bioontology.org/wiki/index.php/Annotator_R_Client
>> 
>> 
>> It looks like
>> 
>> for( result in resultNodes ) {
>>    localConceptId <-
>> xmlValue(getNodeSet(resultNodes,"./term/localConceptId")[[1]])
>>    print( paste( "ID = ", localConceptId ) )
>> 
>> is causing error because the xmlValue() here returns a length of zero. Has
>> anyone else ever reported this error?
>> 
>> 
>> ___
>> Katie Planey, MBA
>> Stanford Biomedical Informatics
>> Butte Lab | http://buttelab.stanford.edu/
>> 
>> 
>> 
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
>> 
>> 


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