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[bioontology-support] error in R annotator client

Andrew Su asu at scripps.edu
Thu Mar 21 17:57:16 PDT 2013


All fixed now!

http://www.bioontology.org/wiki/index.php?title=Annotator_R_Client&action=historysubmit&diff=12593&oldid=12508

Cheers,
-andrew


On Thu, Mar 21, 2013 at 4:24 PM, Trish Whetzel <whetzel at stanford.edu> wrote:
> Hi Andrew,
>
> Ray manages wiki account requests and hopefully will be able to sort out the
> account request issue.
>
> Trish
>
>
>
>
> -------- Original message --------
> From: Andrew Su <asu at scripps.edu>
> Date:
> To: Trish Whetzel <whetzel at stanford.edu>,NCBO User Support
> <support at bioontology.org>
> Subject: Re: [bioontology-support] error in R annotator client
>
>
> 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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