[Nexus] nxvalidate example.zip file; NXplot

[freddie.akeroyd at stfc.ac.uk]

Hi Jeff,

the NXDL validation files are contained in the base_classes, applications and contributed_definitions directories of http://svn.nexusformat.org/definitions/trunk/  If you "build" the definitions tree, it also generates an "all.nxdl.xml" file that is a combination of all individual definitions - this  file is included in the nexus definitions install kit  at http://download.nexusformat.org/kits/definitions/ and is a convenient way to test against all base class definitions in one go (as opposed to just testing against an individual application definition, such as NXmonopd.nxdl.xml) 

The GUI NXvalidate program itself does not know about the location of the definitions, so needs to be told which NXDL file to use (this is partly because this tool is bundled with the nexus API, which is a separate distribution from the nexus definitions). NXvalidate internally converts this NXDL file into a set of schematron rules which are then used to validate the supplied NeXus file. I've recently added a simpler command line validation tool at http://svn.nexusformat.org/definitions/trunk/validate_cmdline/ which is currently "work in progress" and does the same validation as the GUI program - it is installed if you "build" from the definitions svn repository using cmake

Regards,

Freddie  

> -----Original Message-----
> From: teeters1 at gmail.com [mailto:teeters1 at gmail.com] On Behalf Of Jeff
> Teeters
> Sent: 07 March 2013 22:02
> To: Akeroyd, Freddie (STFC,RAL,ISIS)
> Cc: nexus at nexusformat.org
> Subject: Re: [Nexus] nxvalidate example.zip file; NXplot
> 
> Hi Freddie,
> Thanks for that information.  I have several followup questions.
> 
> The nxvalidate GUI Help screen (same as at:
> http://download.nexusformat.org/doc/nxvalidate/ch01s08.html
> ) says to load two files:
> 1. NXmonopd.hdf - the data file.
> 2. NXmonopd.nxdl.xml - the NXDL definition file.
> 
> I see the first file in the trunk/test directory, but not the second.
> Is the second file or a replacement available?
> 
> I'm a little uncertain about how the NXDL definition files work work
> in validation.  According to:
> http://download.nexusformat.org/doc/html/validation.html
> "All the NXDL files are converted into a single Schematron file" which
> is used for validation.  Is that single Schematron file built into the
> "nxvalidate" program?  If so, why does the validation program prompt
> for a NXDL definition file?
> 
> Thanks again,
> Jeff
> 
> 
> On Thu, Mar 7, 2013 at 10:40 AM,  <freddie.akeroyd at stfc.ac.uk> wrote:
> > Hi,
> >
> >
> >
> > nxvalidate used to be a command line tool, but was then replaced by a java
> > GUI application developed by a colleague, but I am working on reinstating a
> > command line version too - I will update you when this is complete. I am
> not
> > sure of the location of "example.zip", but some test data for nxvalidate is
> > at http://svn.nexusformat.org/definitions/trunk/test/
> >
> >
> >
> > NXplot was a utility started a few years ago and is available in the
> > "contrib/applications" directory, but is not installed as part of the build.
> > There is a README.build file there, but I have not used the utility myself.
> >
> >
> >
> > The README is indeed incorrect in your case - it should say that you only
> > need to run autogen.sh if you do not have a "configure" file, which is the
> > case if you obtain a copy directly from the subversion repository; as you
> > have a tar download kit, this includes a generated "configure" and hence
> > excludes autogen.sh
> >
> >
> >
> > Please share any definitions you develop for neuroscience data with us and
> > let us know if we can be of any further help
> >
> >
> >
> > Regards,
> >
> >
> >
> > Freddie
> >
> >
> >
> >
> >
> > From: nexus-bounces at nexusformat.org [mailto:nexus-
> bounces at nexusformat.org]
> > On Behalf Of Jeff Teeters
> > Sent: 06 March 2013 00:49
> > To: nexus at nexusformat.org
> > Subject: [Nexus] nxvalidate example.zip file; NXplot
> >
> >
> >
> > I'm trying to learn about the NeXus Format because I think some of it's
> > features may be useful for a project I'm working on, which is to help
> > develop a standard for sharing neuroscience data.
> >
> > I've installed NeXus on Linux from a recent source, file is:
> > nexus-4.3.0-20120814svn.tar.gz
> >
> > Now I'm trying to get the various utilities working, which are documented
> > at:
> > http://download.nexusformat.org/doc/html/utilities.html
> >
> > There are two validation utilities described in the documentation: a
> command
> > line tool (nxvalidate) and a Java GUI program (NXvalidate).
> >
> > After doing the installation, I found the following utilities in
> > /usr/local/bin:
> > nexpy  nexus-config  nxbrowse  nxbuild  nxconvert  nxdiff  nxdir  nxingest
> > nxsummary  nxtranslate  nxtraverse  nxvalidate
> >
> > The only validation utility is named "nxvalidate" (all lower case), but it's
> > a Java GUI application, not a command line utility as the documentation
> > states.
> >
> > When I run nxvalidate, inside the GUI, there is a Help menu which includes
> > the following page:
> > http://download.nexusformat.org/doc/nxvalidate/ch01s08.html
> >
> > That page states that there is a download available, "example.zip", which
> > contains an example that can be used with NXvalidate.  However, I was not
> > able to find the example.zip file at the location which is referenced:
> > http://www.nexusformat.org/Download
> >
> > Question 1) Is there another location where this example.zip file is
> > available, or are there some other sample files that can be downloaded and
> > used with with the utilities?
> >
> > Question 2) The page documenting the utilities also mentions a utility
> named
> > "NXplot".  I did not find that in the /usr/local/bin.  Is it, or a
> > replacement, available?
> >
> >
> > ----------
> >
> > One thing I noticed while doing the installation:  The README file inside
> > the source download directory states:  "2) At present it is necessary to run
> > the autogen shell script to produce the correct configure file.
> >    sh autogen.sh"
> >
> > But there is no "autogen.sh" file in the directory.  I assumed that this was
> > an error in the README file, since the autogen.sh file was missing and the
> > installation seemed to work OK without that step.
> >
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