Re: XML parsing -- August 22, 2011 - 09:56

Hi,

I actually use the XML parser in Python, as that is very stable and
robust.  For extracting parameters, I use either the value.write()
user function, or if I'd like to play with the data itself, I use some
of relax's internal methods.  For example to print the S2 values, I
would use a relax script such as:

-----
from generic_fns.mol_res_spin import spin_loop

for spin, spin_id in spin_loop(return_id=True):
    print("%-20s %20s" % (spin_id, spin.s2))
-----

I find that it is not necessary to play with the XML directly.  I
chose XML for the save files (a suggestion from Andrew Perry) as it
makes the files readable and portable.  The earlier relax save files
were using the Python pickle module which, unfortunately, is
completely unreadable and the files are often not compatible between
minor relax versions.  Therefore the XML is only used for portable
storage.

Regards,

Edward


On 22 August 2011 09:47, jurgen <juergen.sass@xxxxxxxxx> wrote:
> Hi Edward,
>
> thanks a lot for your help, I think your last suggestion is the best, I
> don't have to stick to coglomerate, it was just by chance that I used it.
> Which XML editor do you use ?
>
> Best wishes
>
> Jürgen
>
> On 08/22/2011 08:25 AM, Edward d'Auvergne wrote:
> > Hi Jürgen,
> >
> > I have been trying to work out what the problem here is, but it's
> > eluding me.  I have managed to compile the newest version of
> > conglomerate.  That was the trunk version from their SVN repository:
> >
> > $ svn co http://svn.gnome.org/svn/conglomerate/trunk
> >
> > I noticed that the dependencies are quite old.  The code is also quite
> > old, the last changes being in 2008, though there was only really
> > proper coding going on between 1999 to 2005.  So Conglomerate
> > unfortunately seems like a dead project (unless someone new takes
> > over).  Anyway, after compiling the program, I loaded the relax save
> > file into it and it gave no error messages and opened it perfectly.
> > The program did run incredibly slowly though, which is unrelated to
> > the relax save file - conglomerate really needs looking after to
> > properly support the newer Gnome infrastructure (libraries).
> > Therefore I would say that the problem you see is a bug in the
> > conglomerate program itself which has been fixed in the source code
> > repository, possibly at this position here:
> >
> > ------------------------------------------------------------------------
> > r2108 | michga | 2005-06-25 06:27:35 +0200 (Sat, 25 Jun 2005) | 2 lines
> > Changed paths:
> >    M /trunk/dispspecs/ChangeLog
> >    M /trunk/dispspecs/readme.xds.in
> >
> > michga@xxxxxxxxxxxxx
> >
> > ------------------------------------------------------------------------
> >
> > I would recommend looking at a newer version of Conglomerate, or at
> > another XML editor.
> >
> > Regards,
> >
> > Edward
> >
> >
> > On 19 August 2011 10:20, jurgen<juergen.sass@xxxxxxxxx>  wrote:
> > > Hi Jurgen,
> > >
> > > Would you be able to resend the message so that it reaches the
> > > relax-devel@xxxxxxx  mailing list?
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > >
> > > On 16 August 2011 17:03, jurgen<juergen.sass@xxxxxxxxx>    wrote:
> > >
> > > > >  Hi,
> > > > >
> > > > >  this is the short version of the file :
> > > > >
> > > > >  <?xml version="1.0" ?>
> > > > >  <relax time="Sun Aug 14 16:42:30 2011" version="1.3.11">
> > > > >
> > > > >  </relax>
> > > > >
> > > > >  producing the same error :
> > > > >
> > > > >
> > > > >  [jurgen@pake m4]$ conglomerate  results-cut.xml
> > > > >  Entity: line 8: parser error : Attribute xml:lang redefined
> > > > >  <description xml:lang="en_CA" xml:lang="en">This is a document type
> > > > >  associated
> > > > >                                                             ^
> > > > >
> > > > >  ** (conglomerate:12238): WARNING **: Problem parsing xds file:
> > > > > readme.xds.
> > > > >
> > > > >  ** Message: coverage of Conglomerate Release Notes = 0.000000
> > > > >  ** Message: coverage of Apache Documentation DTD v1.2 = 0.000000
> > > > >  ** Message: coverage of XHTML 1.0 (strict) = 0.000000
> > > > >  ** Message: coverage of DocBook = 0.000000
> > > > >  ** 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 = 0.000000
> > > > >  ** Message: coverage of RELAX NG = 0.000000
> > > > >  ** Message: coverage of Experimental "opml" format = 0.000000
> > > > >  ** Message: coverage of XSL stylesheet = 0.000000
> > > > >  ** Message: cong_document_finalize
> > > > >
> > > > >  best wishes
> > > > >
> > > > >  Jürgen
> > > _______________________________________________
> > > relax (http://nmr-relax.com)
> > >
> > > This is the relax-devel mailing list
> > > relax-devel@xxxxxxx
> > >
> > > To unsubscribe from this list, get a password
> > > reminder, or change your subscription options,
> > > visit the list information page at
> > > https://mail.gna.org/listinfo/relax-devel