[MOBY-dev] Perl question

[Edward Kawas]

Hi Andreas,

So one of the problems is that getAttributeNS takes as argument a URI and
the attribute name.

However, that didn't fix the problem for you me.

So a quick hack would be to call getAttribute('moby:namespace');

Perhaps someone else knows why the 'right' way isn't working!

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: Friday, June 08, 2007 5:21 AM
> To: moby-dev at lists.open-bio.org
> Subject: [MOBY-dev] Perl question
> 
> Hiho,
> 
> because of the awesome perl hackers on the list.. I hope someone can help
> me....
> 
> I have the following Moby response
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
>   <moby:mobyContent>
>     <moby:mobyData moby:queryID="sip_1_">
>       <moby:Collection moby:articleName="pubmedID">
>         <moby:Simple>
>           <moby:Object moby:id="" moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="7743940   " moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="9090879   " moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="9090880   " moby:namespace="PMID_" />
>         </moby:Simple>
>       </moby:Collection>
>     </moby:mobyData>
>   </moby:mobyContent>
> </moby:MOBY>
> 
> and the following perl code
> 
> my $parser = XML::LibXML->new();
> $parser->clean_namespaces( 1 );
> my $doc = $parser->parse_string($resultXML);
> my $root = $doc->getDocumentElement;
> 
> my @objectNodes = ();
> # $outObjType = Object (!)
> @objectNodes = $root->findnodes("//moby:$outObjType");
> # deal with 'moby-less' xml tags:
> @objectNodes = $root->findnodes("//$outObjType") unless @objectNodes;
> my $resCnt = 0; # a result counter, used as default for file naming
> # iterate over all result objects
> foreach my $objectNode (@objectNodes) {
> # create a filename and write the object to the cache directory
> 
> # if provider uses other namespaces (that is other
> # than the start namespace of the application), get
> # this and use it for cache file name
> my ($ns,$id);
> if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
>      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> }
> # deal with 'moby-less' attributes
> elsif ( $objectNode->hasAttribute('namespace') ) {
>   $ns = $objectNode->getAttribute('namespace');
> }
> 
> as far as I understand this code (is from Dirks aggregator), it should
> parse
> the namespace of the element 'moby:Object'... but it doesnt.
> 
> I know nothing about LibXML and parsing xml in Perl.. so I was wondering,
> why
> 
> if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
>      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> }
> 
> is not working.
> 
> Any hints ?
> 
> Thanks
> Andreas
> 
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