Hi Stephen,
Yes, I agree and I think it would be pretty easy to add in the
conversion of a CDL to netcdf.
I'm going to have to make one more release of the current incarnation of
the checker for CF-1.6 so I'll have a look at this at the same time.
The CGI script is indeed written in perl. Ag originally wrote the web
interface IIRC.
The interface on PUMA definitely started out life as the same as the
BADC one.
Again it was supposed to be making its way into the subversion
repository, but never made it.
netcdf4-python was what I was looking at for the replacement for CDAT.
So it's good that you recommend it too.
In terms of the web interface, that would also get redone and I have
some ideas on this too, which you'll be glad to hear would be python. :-)
Cheers,
Ros.
On 01/03/12 09:59, stephen.pascoe at stfc.ac.uk wrote:
>
> Great,
>
> I had further thoughts last night and the logical way forward is to
> get the CGI script to generate a dummy netcdf file from CDL submitted
> in the web form. An official headers-only option would definitely help.
>
> Ros, is the CGM CGI script written in perl? Ours is but I have no
> idea whether we share the same code. I think it makes sense to share
> the same codebase if we are going to add features to the CGI -- my
> preference is obviously Python.
>
> Remove CDAT: +1 from me. I would recommend netcdf4-python as a better
> binding. I believe the various Python tooling efforts happening in
> the UK (cf-python, IRIS) are using netcdf4-python so it would
> consolidate our toolset.
>
> Cheers,
>
> Stephen.
>
> ---
>
> Stephen Pascoe +44 (0)1235 445980
>
> Centre of Environmental Data Archival
>
> STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK
>
> *From:*Rosalyn Hatcher [mailto:r.s.hatcher at reading.ac.uk]
> *Sent:* 01 March 2012 08:32
> *To:* Pascoe, Stephen (STFC,RAL,RALSP)
> *Cc:* philip.bentley at metoffice.gov.uk; cf-metadata at cgd.ucar.edu
> *Subject:* Re: [CF-metadata] machine-accessible CF compliance checker?
>
> Hi Stephen,
>
> I've been out of the office the last couple of days and not seen this
> till now.
>
> #3 is already on my to-do list :-)
>
> #2 I actually do this quite a bit and just supply the "ncdump -c"
> ouput passed through ncgen and ignore the couple of
> errors for the checks that can't be performed. If this would be
> useful for others then it should be relatively easy to officially add
> a headers-only option.
> Off the top of my head I think there are 2 checks that require the
> variable data
> (1) That variable data lies within cell boundaries and
> (2) The check that coord data is monotonic
>
> I also plan in the next 6months to completely re-write the CF checker,
> it's developed a lot since I first wrote it and is now becoming rather
> unwieldy.
> One thing I'd like to do is remove the dependency on CDAT. So if
> anyone has any further suggestions for improvements or additional
> functionality
> they'd like to see please let me know.
>
> Regards,
> Ros.
>
>
>
> On 29/02/12 15:31, stephen.pascoe at stfc.ac.uk
> <mailto:stephen.pascoe at stfc.ac.uk> wrote:
>
> Hi Phil,
>
> So far my role has simply been to package and deploy Rosalyn's cfchecker code, therefore I really don't know to what extent it needs the real NetCDF.
>
> I think an alternative checker (i.e. codebase) is a bad idea because they might give contradictory results. I would suggest several options:
>
> 1. Work on making the cfchecker package easier to install so that users can run it on their real NetCDF. A user would have to know how to install python packages, compile UDUNITS and edit a config file.
> 2. Add a "headers-only" feature to Rosalyn's code so that user's can create dummy NetCDF with ncgen to upload to one of the online checkers.
> 3. As an addition to #2, add a feature to Rosalyn's code, or the CGI wrapper, to upload CDL.
>
> I am willing to do #1, if people think it would meet user's needs, but it would have to be added to my ever-expanding TODO list :-). Rosalyn, do you have any comments on #2&3?
>
> Cheers,
> Stephen.
>
> ---
> Stephen Pascoe +44 (0)1235 445980
> Centre of Environmental Data Archival
> STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, UK
>
>
> -----Original Message-----
> From: Bentley, Philip [mailto:philip.bentley at metoffice.gov.uk]
> Sent: 29 February 2012 14:56
> To: Pascoe, Stephen (STFC,RAL,RALSP);cf-metadata at cgd.ucar.edu <mailto:cf-metadata at cgd.ucar.edu>
> Subject: RE: [CF-metadata] machine-accessible CF compliance checker?
>
> Hi Stephen,
>
> I may well be wrong, but I suspect that one of the reasons - perhaps the
> main reason - why folks would like access to a stand-alone cfchecker
> utility is the large size of their netcdf files. (It's certainly the
> reason we use a local version.)
>
> As you know only too well (from CMIP5), most of the netcdf files we're
> dealing with these days run into the high 100s of MB or low GBs. It's
> not really practical to upload such files in order to perform a CF
> compliance check. At least not on more than a few files.
>
> I wonder, therefore, if a possible solution is to develop an alternative
> checker utility that operates not on the netcdf file itself, but rather
> on the header info output by the ncdump -h command. Generating and
> uploading those would be trivial by comparison.
>
> Off the top of my head (and having given it almost zero thought!) the
> only test that I can think of which examines the actual data values is
> the check for coord vars being monotonic. But I suspect there are others
> I'm unaware of.
>
> If nothing else, such a utility might have some value as a 'first pass'
> checker.
>
> Any mileage in this? Apologies if it's already done the rounds!
>
> Regards,
> Phil
>
>
>
> -----Original Message-----
>
> From:cf-metadata-bounces at cgd.ucar.edu <mailto:cf-metadata-bounces at cgd.ucar.edu>
>
> [mailto:cf-metadata-bounces at cgd.ucar.edu] On Behalf Of
>
> stephen.pascoe at stfc.ac.uk <mailto:stephen.pascoe at stfc.ac.uk>
>
> Sent: 29 February 2012 11:39
>
> To:christopher.s.lynnes at nasa.gov <mailto:christopher.s.lynnes at nasa.gov>;cf-metadata at cgd.ucar.edu <mailto:cf-metadata at cgd.ucar.edu>
>
> Subject: Re: [CF-metadata] machine-accessible CF compliance checker?
>
>
>
> Hi Christopher,
>
>
>
> Are you looking for a way to run the cfchecker locally or
>
> submit checking requests to one of the websites in a script?
>
>
>
> I think both would be possible with a little help. The
>
> cfchecker is now available on the Python Package Index at
>
> http://pypi.python.org/pypi/cfchecker. It needs a little
>
> help to work out of the box -- you need to configure UDUNITS
>
> and the location of several CF XML files. It's on my
>
> long-term TODO list to make this configuration easier.
>
>
>
> Also the CF-checker at BADC and NCAS-CMS has a very simple
>
> HTTP interface that could be scripted.
>
>
>
> Cheers,
>
> Stephen.
>
>
>
> ---
>
> Stephen Pascoe +44 (0)1235 445980
>
> Centre of Environmental Data Archival
>
> STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot
>
> OX11 0QX, UK
>
>
>
>
>
> -----Original Message-----
>
> From:cf-metadata-bounces at cgd.ucar.edu <mailto:cf-metadata-bounces at cgd.ucar.edu>
>
> [mailto:cf-metadata-bounces at cgd.ucar.edu] On Behalf Of
>
> Lynnes, Christopher S. (GSFC-6102)
>
> Sent: 28 February 2012 16:03
>
> To:cf-metadata at cgd.ucar.edu <mailto:cf-metadata at cgd.ucar.edu>
>
> Subject: [CF-metadata] machine-accessible CF compliance checker?
>
>
>
> I know about the web sites where you use a form to upload
>
> files to check CF compliance, but is there a service
>
> somewhere that can be accessed by a script?
>
> --
>
> Dr. Christopher Lynnes NASA/GSFC, Code 610.2 phone:
>
> 301-614-5185
>
>
>
>
>
> _______________________________________________
>
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>
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>
> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>
> --
>
> Scanned by iCritical.
>
> _______________________________________________
>
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>
> CF-metadata at cgd.ucar.edu <mailto:CF-metadata at cgd.ucar.edu>
>
> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>
>
>
>
>
> --
> Rosalyn Hatcher
> NCAS Computational Modelling Services
> Dept. of Meteorology, University of Reading,
> Earley Gate, Reading. RG6 6BB
> Email:r.s.hatcher at reading.ac.uk <mailto:r.s.hatcher at reading.ac.uk> Tel: +44 (0) 118 378 6016
>
> --
> Scanned by iCritical.
>
>
--
Rosalyn Hatcher
NCAS Computational Modelling Services
Dept. of Meteorology, University of Reading,
Earley Gate, Reading. RG6 6BB
Email: r.s.hatcher at reading.ac.uk Tel: +44 (0) 118 378 6016
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