[MOBY-l] MobyXMLObject.pm question...

[Ken Steube]

Michael,

I had meant to handle queryResponse identically to the way I handle
queryInput blocks, but forgot to put it in there.  It's in now so copy
the MobyXmlObject.pm file again from
http://plantgenome.sdsc.edu/mobyed2/Fasta_Service

What I do now is check for queryInput (and moby:queryInput) and if none is
found I check for queryResponse (and moby:queryResponse). Then from
whichever of those 4 blocks I found I return the Simples within.

As mentioned in the BUGs section I don't deal with Collections yet.
Will do this someday.

Lemme know if there are any further problems.

Ken

On Tue, 25 Nov 2003, Michael Jensen wrote:

> I have been trying to use the MobyXMLObject.pm as Ken suggested, but am
> having a few problems beyond the samples used. I am trying to combine
> the two pubmed services by piping the PMIDs from SearchPubmed to
> getting Medline output from getPubmed. I have been trying to get
> MobyXMLObject.pm to work with SearchPubmed but it doesn't want to work,
> returning nothing except for the webservice. I think the problem might
> be that the output has <Simple> tags instead of <moby:Simple> like so:
>
> <moby:queryResponse>
> 	<Simple>
> 		<moby:Object namespace='PMID' id="14607285">
>   		</moby:Object>
> 	</Simple>
> </moby:queryResponse>
>
> as opposed to the XML from the test xml found on Ken's learning site.
>
> <moby:queryInput>
> 	<moby:Simple>
> 		<moby:GenericSequence namespace='AGI_LocusCode' id='At3g19yyy'>
> 			<moby:Integer namespace='' id=''
> articleName='Length'>4</moby:Integer>
> 			<moby:String namespace='' id=''
> articleName='SequenceString'>MGGC</moby:String>
> 		</moby:GenericSequence>
> 	</moby:Simple>
> </moby:queryInput>
>
> I tried to slowly put in the results from SearchPubmed into the test
> xml script from Ken's site, and I can get a result as long as I keep a
> <moby:queryInput> from the example script along with a
> <moby:queryResponse> from the results of SearchPubmed (just copied and
> pasted). The mobyxmltest.pl file attached here is the one referred to
> just now, and the pubmed_combined.pl is my other attempt at using
> SearchPubmed to list the PMIDs (so next I can feed those into
> getPubmed).
>
> I am not sure if I am just missing something obvious or what, but I
> have tried a lot of different things to understand how to get the
> elements I need. Any help would be greatly appreciated! Thanks!
>
> (I tried posting this a few days ago, but never went through?)
>
>
>

-- 
-------------------------------------
Ken Steube            steube at sdsc.edu
San Diego Supercomputer Center @ UCSD
San Diego, California             USA