[moby] Re: [MOBY-l] jMoby bug?

[Paul Gordon]

 From my experience, using more compliant parsers often 
counterintuitively leads to more parsing problems.  The problem is not 
usually the parser, but how the DOM query is formulated. This occurs, 
for example, when you ask for tag "Simple".  A non-namespace compliant 
or lax parser will give you the qualified Simple, whereas a proper 
parser will give you nothing, because there is no namespaceless Simple 
tag in the document, you must qualify your query with foo:Simple, where 
foo maps to the MOBY namespace, or otherwise somehow declare the moby 
namespace as the default for your queries. 

Mark Wilkinson wrote:

>On Wed, 2005-02-02 at 10:26, Paul Gordon wrote:
>
>  
>
>>I would be much more inclined to get the MOBY Central maintainers to 
>>accept namespaces (especially since it used to) than to reduce the XML 
>>to unqualified tags. Mark?
>>    
>>
>
>???  it should be even MORE accepting of XML namespaces now that we have
>switched to XML::LibXML.
>
>I'll pass this on to Eddie and see what he says.  If it is a problem
>with the underlying C libxml2 libraries then we are in big trouble!
>
>M
>
>  
>
>>In this case, the inputs part of the template service looked like
>><Input>
>><Simple xmlns="http://www.biomoby.org/moby">
>><objectType>AminoAcidSequence</objectType>
>><Namespace>NCBI_gi</Namespace>
>></Simple></Input>
>>
>>If I change it to look like this
>>
>><Input>
>><Simple>
>><objectType>AminoAcidSequence</objectType>
>><Namespace>NCBI_gi</Namespace>
>></Simple></Input>
>>
>>then it works.
>>
>>So basically moby central doesn't like to see the xml namespace in
>>    
>>
>there
>  
>
>>any more, though I'm pretty sure this worked last summer.
>>
>>    
>>
>
>  
>