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[bioontology-support] error in R annotator client

Andrew Su asu at scripps.edu
Thu Mar 21 14:52:12 PDT 2013


Hi Trish,

My account request for the bioontology wiki was denied... :(  I was
going to make the change to the R client, but presumably someone will
have to make that for me then?

http://www.bioontology.org/wiki/index.php/Annotator_R_Client

-andrew

On Tue, Mar 19, 2013 at 3:43 PM, Katie Planey <ywrfc09 at stanford.edu> wrote:
> 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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