Re: XML parsing -- August 16, 2011 - 14:53

Hi,

Would you be able to create a bug report for this with a skeleton XML
file which reproduces this problem?  It looks like you could remove
everything between the tags:

<relax time="Wed Aug 10 19:02:16 2011" version="repository checkout">

and:

</relax>

This looks like an XML header issue.  I would like to see the XML
header in this file, because all relax save files should have is:

<?xml version="1.0" ?>
<relax time="Wed Aug 10 19:02:16 2011" version="repository checkout">
...
</relax>

The xml:lang="en_CA" looks like it has added something for Canadian
English, which is quite strange.  And the fact that this is line 8 of
the file suggests that there is quite a complex header in this file.
Has the XML file been pre-converted from one XML form to another?

Regards,

Edward


On 16 August 2011 14:37, Sébastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> Hi Ed,
>
> Here is what my colleague Jürgen (in CC) just sent me concerning the xml
> parsing problem:
>
> ==========
> ==========
> > conglomerate results
>
> Entity: line 8: parser error : Attribute xml:lang redefined
> <description xml:lang="en_CA" xml:lang="en">This is a document type
> associated
>                                                           ^
>
> ** (conglomerate:7470): WARNING **: Problem parsing xds file: readme.xds.
>
> ** Message: coverage of Conglomerate Release Notes = 0.000000
> ** Message: coverage of Apache Documentation DTD v1.2 = 0.028571
> ** Message: coverage of XHTML 1.0 (strict) = 0.000000
> ** Message: coverage of DocBook = 0.028571
> ** Message: coverage of Website Layout = 0.000000
> ** Message: coverage of TEI Lite = 0.000000
> ** Message: coverage of Webpage = 0.000000
> ** Message: coverage of "Kernel Traffic" Newsletter = 0.000000
> ** Message: coverage of Conglomerate Display Specification = 0.000000
> ** Message: coverage of Experimental "cnxml" format = 0.028571
> ** Message: coverage of RELAX NG = 0.000000
> ** Message: coverage of Experimental "opml" format = 0.000000
> ** Message: coverage of XSL stylesheet = 0.000000
>
>
> but it may be a special problem with 'conglomerate', now I tried
> 'xmlcopyeditor' and this one didn't complain.
> ==========
> ==========
>
> I checked a bit and found a discussion of this problem on the web at:
> http://lists.copyleft.no/pipermail/conglomerate-devel/2005-June/003682.html
>
> All the best,
>
>
> Séb  :)
>
>
> On 11-08-15 10:39 AM, Edward d'Auvergne wrote:
> > Hi,
> >
> > Would you have any information about which part he cannot parse?
> > relax is using the standard python XML module 'xml'
> > (http://docs.python.org/library/xml.dom.minidom.html).  This should
> > produce valid XML.  Do you know what he's using to parse the XML?  In
> > any case, if he can do a little programming, all the spin data is
> > reachable with something along the lines of:
> >
> > from generic_fns.mol_res_spin import spin_loop
> >
> > for spin in spin_loop():
> >     print spin.s2
> >
> > Regards,
> >
> > Edward
> >
> >
> >
> > On 15 August 2011 10:20, Sébastien Morin<sebastien.morin@xxxxxxxxx>
> >  wrote:
> > > Hi Edward,
> > >
> > > One colleague of mine has recently started using relax and told me he was
> > > unable to read the xml output of relax using an xml reader...
> > >
> > > I haven't verified this myself as I am really lacking time currently, but
> > > I
> > > thought you might know a bit about this.  ;)
> > >
> > > Cheers,
> > >
> > >
> > > Séb  :)
> > >
> > > P.S. As a compromise to using an external xml reader, I told him he could
> > > start from the "final_data_extraction.py" script and modify it to fit his
> > > needs...
> > >
> > > --
> > > Sébastien Morin, Ph.D.
> > > Postdoctoral Fellow, S. Grzesiek NMR Laboratory
> > > Department of Structural Biology
> > > Biozentrum, Universität Basel
> > > Klingelbergstrasse 70
> > > 4056 Basel
> > > Switzerland
> > >
> > >
> > > _______________________________________________
> > > relax (http://nmr-relax.com)
> > >
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> > > relax-devel@xxxxxxx
> > >
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>
> --
> Sébastien Morin, Ph.D.
> Postdoctoral Fellow, S. Grzesiek NMR Laboratory
> Department of Structural Biology
> Biozentrum, Universität Basel
> Klingelbergstrasse 70
> 4056 Basel
> Switzerland