RE: [R] xmlAttrs and problems with reading node attributes of XML file (b ug?)

[Tuszynski, Jaroslaw W.]

Duncan,

Thanks, that that make sense, I have never encountered namespaces so I did
not recognized them. So in my example xmlns=a xmlns:xsi=b are namespace
variables, and xsi:schemaLocation=c is a Schema-Related Markup
attribute. This last one seemed to be handled strangely, since it is listed
as attribute but its name got truncated from xsi:schemaLocation to
schemaLocation.

Jarek



-Original Message-
From: Duncan Temple Lang [mailto:[EMAIL PROTECTED] 
Sent: Tuesday, May 31, 2005 11:38 AM
To: Tuszynski, Jaroslaw W.
Cc: ([EMAIL PROTECTED]); '[EMAIL PROTECTED]'
Subject: Re: [R] xmlAttrs and problems with reading node attributes of XML
file (b ug?)


Hi Jarek.

Is the problem you are referring to simply that the xmlns=a and
xmlns:xsi=b are not appearing when your handler prints the attributes?  If
it is this the case, the explanation is quite simple - they are namespace
definitions, not attributes.
They are in the node object

x$namespaceDefinitions


names(unclass(x)) will help to see what is in the node.

HTH,
  D.


Tuszynski, Jaroslaw W. wrote:
 Hi,
 
 Consider the following code:
 
 require(XML)
 xmlFile = paste( ?xml version=\1.0\
 encoding=\ISO-8859-1\?\n, 
   mzXML xmlns=\a\ xmlns:xsi=\b\
 xsi:schemaLocation=\c\\n,
   parentFile a=\a\ b=\b\ /\n,
   /mzXML\n)
 cat(xmlFile)
 
 a = function(x,...){
   cat(Attributes of , xmlName(x), : ); 
   print(xmlAttrs(x));
   cat(\n); 
   NULL
 }
 
 xmlTreeParse(file=xmlFile, asText=TRUE,
 handlers=list(startElement=a) )
 
 And its output:
 
?xml version=1.0 encoding=ISO-8859-1?
mzXML xmlns=a xmlns:xsi=b xsi:schemaLocation=c
parentFile a=a b=b /
/mzXML
 
   Attributes of  parentFile :   a   b 
a b 
 
   Attributes of  mzXML : schemaLocation 
 c 
 It seems to me that XML parser was able to correctly list all the 
 attributes of the parentFile node but it failed on mzXML node.
 Am I missusing the functions somehow or is it a bug?
 Attribute names in mzXML node are part of mzXML file format and can 
 not be changed (removing all ':' would fix the problem) and I would 
 like to store than so whan I write mzXML file I have the same header.
 
 Jarek
 \===
 
  Jarek Tuszynski, PhD.   o / \ 
  Science Applications International Corporation  \__,|  
  (703) 676-4192  \
  [EMAIL PROTECTED] `\
 
 
 
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[R] xmlAttrs and problems with reading node attributes of XML file (b ug?)

[Tuszynski, Jaroslaw W.]

Hi,

Consider the following code:

  require(XML)
  xmlFile = paste( ?xml version=\1.0\
encoding=\ISO-8859-1\?\n, 
mzXML xmlns=\a\ xmlns:xsi=\b\
xsi:schemaLocation=\c\\n,
parentFile a=\a\ b=\b\ /\n,
/mzXML\n)
  cat(xmlFile)
  
  a = function(x,...){
cat(Attributes of , xmlName(x), : ); 
print(xmlAttrs(x));
cat(\n); 
NULL
  }
  
  xmlTreeParse(file=xmlFile, asText=TRUE,
handlers=list(startElement=a) )

And its output:

 ?xml version=1.0 encoding=ISO-8859-1?
 mzXML xmlns=a xmlns:xsi=b xsi:schemaLocation=c
 parentFile a=a b=b /
 /mzXML

Attributes of  parentFile :   a   b 
 a b 

Attributes of  mzXML : schemaLocation 
  c 
It seems to me that XML parser was able to correctly list all the attributes
of the parentFile node but it failed on mzXML node.
Am I missusing the functions somehow or is it a bug?
Attribute names in mzXML node are part of mzXML file format and can not be
changed (removing all ':' would fix the problem) and I would like to store
than so whan I write mzXML file I have the same header.

Jarek
\===

 Jarek Tuszynski, PhD.   o / \ 
 Science Applications International Corporation  \__,|  
 (703) 676-4192  \
 [EMAIL PROTECTED] `\



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