[BioRuby] RFC Caching (was BioRuby standards)

[Pjotr Prins]

Hi Naohisa,

Thanks for comments. See below.

On Wed, Sep 10, 2008 at 10:48:20AM +0900, Naohisa GOTO wrote:
> Hi,
> 
> I think the most important thing for cache is data integrity.
> For example, timing for detecting updates of original data,
> controlling accesses and resolving race conditions
> (two or more processes or threads simultaneously want to
> use, update, create, and/or remove the same cache data).
> However, your code only contains directory name determination.

Well, caching is a universal term for storing stuff intermediately.
And what I need is a place to put files. With regard to race
conditions you are right - if two processes were to download the same
file it would get mangled. However, them being XML the program would
throw an error on parsing. For me that works well enough. For BioRuby
we may need to think of something more universal - and it is not that
hard to do. That is why I wrote my earlier mail. If you want to
support something universal it should be at a higher point in the
source tree.

But maybe leave it until someone gets an itch to scratch.

> line 24:
> >      def set directory, subdir = nil
> 
> In def lines, please use parentheses explicitly,
> e.g.   def set(directory, subdir = nil),
> because most of existing code in BioRuby does so.

I like the 'most'. But OK.

> line 28:
> >         dir = dir + '/' + subdir
> 
> File.join(dir, subdir) should be used, possibly to support
> non-UNIX systems like Windows.

OK

> lines 41 to 45:
> >          if cache==nil or cache==''
> >            cache = ENV['TMPDIR']
> >          end
> >          cache = '/tmp' if cache==nil or cache==''
> >          set cache, subdir
> 
> Using Dir.tmpdir defined in tempdir.rb is better.
> http://www.ruby-doc.org/stdlib/libdoc/tmpdir/rdoc/index.html

Thanks,

Pj.