[moby] [MOBY-l] Perl API: conversion of node content to and from XML

[Mark Wilkinson]

Thanks for the fix!  It is now committed to the CVS - let me know if it
still causes problems.

Cheers!

M


On Mon, 2005-03-07 at 03:48, Neerincx, Pieter wrote:
> Hi all,
> 
> I'm pretty new to BioMOBY and have a question about the Perl API. I have some problems with extracting text data from objects like for example the String object. I have something like this:
> 
> <String namespace='my.test.ns' id='0001' articleName='query'>some text &amp; more text</String>
> 
> The plain text contains for example "&" which has a special meaning in XML. Therefore I have to encode it using "&amp;". If I use the getNodeContentWithArticle sub from CommonSubs.pm it serializes the data resulting in raw XML. Hence the result contains the "&" still encoded as "&amp;". The same thing happens with encoded quotes. If I would be using the extractRawContent sub that would make sense to me. Off course I can convert the encoded stuff from and to raw XML manually, but wouldn't it be nicer if the API would take care of that? Or am I missing something here and is there a good reason the have for example the getNodeContentWithArticle sub return raw XML?
> 
> If I change the code like this:
> 
> sub getNodeContentWithArticle {
> 
>        ### lot's of other stuff ... ###
> 
> 					# Using ->toString results in raw XML and will
> 					# not map encoded chars like '&amp;' back to '&'.
> 					# Fetching node content using -> data will. 
> 					#$resp .= $_->toString;
> 					$resp .= $_->data;
> 
>        ### lot's of other stuff ... ###
> 
> }
> 
> decoding the raw XML is taken care of by the API. Any feedback would be appriciated.
> 
> Regards,
> 
> Pieter Neerincx
> 
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-- 
Mark Wilkinson
Assistant Professor (Bioinformatics)
Dept. Medical Genetics, UBC, Canada