Re: [bug #11913] Problems with reading Sparky formatted file -- July 03, 2008

On Mon, Jun 30, 2008 at 3:18 AM, RMB Hoffman <rmb.hoffman@xxxxxxxxx> wrote:

Hello,

these peak lists.  So would it be ok if I add the debug.xpk file to
the relax test-suite (in the data store)?


Yes, that's okay.


Thanks.

If so, would you have a
more descriptive name for the file I can rename it to for better
identification?


For the purpose of having an identifier, we can call it "cNTnC.xpk". I'm not
sure I understand the question...does that answer it?


Yes, that answers the question.  I just needed a more descriptive file
name so that it is more obvious what the file is.  I'll add the file
to relax and try to write a system test loading the peak heights.

Cheers,

Edward

ry

On 28-Jun-08, at 6:36 AM, Edward d'Auvergne wrote:

Hi,

Thank you for the report.  This is a hard one to decide were to post
it.  Ideally the feature request and discussion would be posted to the
relax-devel mailing list and then I would create a task for this
(https://gna.org/task/?group=relax).  The bug would then be placed in
the bug tracker separately.  But, anyway, this is too complex and it
really doesn't matter.

So, for the NMRView peak list support, this can easily be added.  I'm
happy to add support for any input data into relax, and anyone is free
to add this to relax themselves if they wish.  Outputting to any
format will also be accepted.  There's not much point spending effort
on converting data to one of the formats relax currently supports.
The effort may be better spent adding the support directly to relax
(and this would be less effort anyway), and then everyone using
NMRView will benefit.

For the addition of this feature, I would like to first add a system
test to the relax test suite for the reading of this data before the
support is implemented.  This will make the addition of the NMRView
support much easier, and will safeguard the introduction of
regressions in future relax versions causing bugs in the reading of
these peak lists.  So would it be ok if I add the debug.xpk file to
the relax test-suite (in the data store)?  If so, would you have a
more descriptive name for the file I can rename it to for better
identification?  I will implement NMRView support in relax-1.3 and if
it not too disruptive, and only if you need it in the 1.2 versions,
maybe I'll port it back to the 1.2 line.

I might start a second thread for the Sparkly peak list reading bug.

Regards,

Edward


On Sat, Jun 28, 2008 at 1:10 AM, Ryan MB Hoffman
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:


URL:
 <http://gna.org/bugs/?11913>

               Summary: Problems with reading Sparky formatted file
               Project: relax
          Submitted by: rydog
          Submitted on: Friday 06/27/2008 at 23:10
              Category: relax's source code
              Severity: 3 - Normal
              Priority: 5 - Normal
                Status: None
               Privacy: Public
           Assigned to: None
       Originator Name:
      Originator Email:
           Open/Closed: Open
       Discussion Lock: Any
               Release: 1.2.13
      Operating System: GNU/Linux

  _______________________________________________________

Details:

Hello,

First of all, I would like to request that relax support NMRView peak
lists.
I appreciate this is not the right location to request this, but the
community is still small, and I'm submitting a bug anyways. I have
attached
an example of this type of file (debug.xpk), and a Perl script that can
extract the volume lines (xpk2list.pl). They are attached as the tarball
"convert.tgz"

For the meantime, I have been converting the NMRView peaklists to Sparky
with
a script.

The actual session I/O looks like:


noe.read(name,file='cNTnC_noe0_3.list',spectrum_type='ref',format='sparky')
Reference spectrum.
Sparky formatted data file.

Opening the file 'cNTnC_noe0_3.list' for reading.
Number of header lines found: 2
RelaxError: Improperly formatted Sparky file.

I get the same error with a handful of .list files, generated either by
my
conversion scripts or from Sparky itself. Three files are attached. The
one
ending in '_2' was directly outputted from Sparky.




  _______________________________________________________

File Attachments:


-------------------------------------------------------
Date: Friday 06/27/2008 at 23:10  Name: cNTnC_noe0_2.list  Size: 8kB
By:
rydog

<http://gna.org/bugs/download.php?file_id=4485>
-------------------------------------------------------
Date: Friday 06/27/2008 at 23:10  Name: cNTnC_noe0_3.list  Size: 157B
By:
rydog

<http://gna.org/bugs/download.php?file_id=4486>
-------------------------------------------------------
Date: Friday 06/27/2008 at 23:10  Name: cNTnC_noe0-2.list  Size: 153B
By:
rydog

<http://gna.org/bugs/download.php?file_id=4487>
-------------------------------------------------------
Date: Friday 06/27/2008 at 23:10  Name: convert.tgz  Size: 776B   By:
rydog

<http://gna.org/bugs/download.php?file_id=4488>

  _______________________________________________________

Reply to this item at:

 <http://gna.org/bugs/?11913>

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Re: [bug #11913] Problems with reading Sparky formatted file

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