[cellml-discussion] Review solicited for application/cellml+xml

[Matt Halstead]

There is nothing stopping anyone from storing the file with any  
extension, so my vote is ideally to have no extension at all since  
all we are doing is serving these files across a system that supports  
mime-types.

I would prefer mounting a webdav folder than a local folder so that  
mime-type is available.

People should be free to call it what they want. If they have more  
advanced file systems then various metadata frameworks can be  
employed automatically to determine file types and application  
installers can add their signatures to these local systems.

A useful summary of some concepts is here : http://en.wikipedia.org/ 
wiki/File_type

Lets just drop file extension altogether. They look ugly in RDF  
metadata URIs anyway :-)

cheers
Matt


On 10/05/2006, at 5:55 PM, Alan Garny wrote:

> Dear all,
>
> Please find my 2 cents worth of comments regarding Andrew's  
> Internet draft.
>
>> We have several reasons for not encouraging anything other
>> than .xml as the file
>> extension:
>> 1) We have used .cml (which conflicted with other markup
>> languages, like Chemical Markup Language) in the past, and
>> changed to .xml. Having a history of too many file extensions
>> makes it hard to encourage software vendors to stick with a
>> particular one.
>
> Just for accuracy, I believe to be the one who started using .cml  
> in my
> software (http://cor.physiol.ox.ac.uk/). Are there others who do so  
> too now?
>
> You mention that .cml conflicts with other markup languages, but I  
> would
> argue that .xml conflicts with even more markup languages.  
> Personally, .cml
> is not used on my system by anything else but for CellML files, so  
> I don't
> have that conflict you mention, while it wouldn't be the case if my  
> CellML
> files were to have the .xml extension.
>
> As for a history of file extensions, again, as far I can recall  
> (please
> correct me if I am wrong), .xml has been the extension chosen for  
> CellML
> files from day one. It's just me who has been some kind of a  
> dissident for
> going for .cml from day one too (more on the reasons below).
>
>> 2) There is currently repository software which uses .xml,
>> and changing this will likely create problems for (some)
>> client software using the repositories.
>
> You will always have problems of some sort or another. To go from  
> CellML 1.0
> to 1.1 is not a trivial thing either, be it for the software  
> developer or
> modeller. To change the file extension from .xml to whatever surely  
> is a
> very trivial problem, at least of the kind that I would be glad to  
> deal with
> on a daily basis, if they were to be the only problems I had to have!
>
>> 3) Many users of CellML like to edit their models as XML in a
>> text editor. Using the XML extension allows this to work on
>> systems which know nothing about CellML.
>
> Many CellML users like to edit their models as XML in a text  
> editor? Is that
> really true? I certainly don't want to start an argument here, but  
> I somehow
> think that my users would feel very strongly about having to modify  
> CellML
> files using a simple text editor. I am, personally, very glad that  
> I don't
> have to use a text editor, nothing worse than modifying a CellML  
> file than
> using such an editor (very much error prone!). Allow me another  
> quick plug
> in: have a look at COR and you might change your mind and never use  
> a text
> editor in the future (though you might still want to do that once  
> in a while
> for whatever reason).
>
> Also, it is very simple, on any operating system, to associate a  
> particular
> extension to a particular problem.
>
>> 4) Using a specific extension encourages software vendors to
>> rely on this file extension. Although all software developed
>> at the Bioengineering Institute does not rely on a specific
>> file extension, there is software developed elsewhere that
>> will not open files which do not have a .cml file extension
>> (even when the user specifically tries to open that file in
>> the program), and I have heard that this is creating problems
>> for users.
>
> I believe that it would have to be my software indeed... I have had  
> several
> email exchanges with David Nickerson about this over the last few  
> years. In
> a nutshell, the main reason I am rather reluctant about the idea of  
> using
> .xml for CellML files is that by having using .cml, I can associate  
> that
> extension to COR, while the same cannot really be done with .xml.
>
> My point is that COR has been designed from the beginning to be as  
> user
> friendly as possible. It is something that is very high on our  
> agenda and
> that has surely been very much appreciated by our users (from what I
> know/understand, there is no way they would use a text editor to  
> edit CellML
> files for instance).
>
> To make COR user friendly involved associating .cml files to COR,  
> because
> all the users have to do to open a CellML file is, for instance, to  
> double
> click on it rather than opening a program, then opening a CellML  
> file. It
> may not be too much to do the latter, but why not make the user's life
> easier if all that takes is associate an extension to a particular  
> program?
>
>> By having only a more generic file extension, we
>> encourage software developers not to use the file extension
>> to determine whether they should open a certain file, and
>> instead look at the MIME type (where available) and/or the
>> XML namespace.
>
> Yes, that could easily be done, but... :)
>
> 	Best regards, Alan.
>
> --
> University of Oxford, Department of Physiology, Anatomy and Genetics
> Sherrington Building, Parks Road, Oxford, OX1 3PT, England
> http://noble.physiol.ox.ac.uk/people/agarny/
>
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