[BioRuby] BioRuby standards

[Pjotr Prins]

Hi everyone,

I have been doing some work on microarray support for BioRuby, see

  http://github.com/pjotrp/bioruby/tree/bioruby-testing-pjotr

There are two questions I want to raise about standards, as I see
different solutions in the current tree. First is about error
handling. Second about caching.

1) Error handling ought to print to stderr, and we need a consistent
way of handling them, as well as a more fine grained approach towards
warnings, info, debug etc. messages. Can we come up with a standard
where a user can set these from outside Bioruby, e.g. through an
environment setting. And what classes can we use for consistent
messaging. Obviously a standard way for exceptions is part of that.

2) Web based tools often like to cache things on the local file
system. I suggest using BIORUBY_CACHE as a standard environment
variable. And, perhaps, BIORUBY_CACHE_SIZE, though that would require
a module to monitor that.

For (1) David Powers came up with a nice approach for the Cfruby
project - where modules can override behaviour of the error handling
(I wanted that for the Cfenjin application). See 

  http://rubyforge.org/projects/cfruby/

and the source code at:

  http://cfruby.rubyforge.org/svn/lib/libcfruby/flowmonitor.rb

with my usage:

	http://cfruby.rubyforge.org/svn/lib/libcfenjin/cfp_logger.rb
  http://cfruby.rubyforge.org/svn/lib/libcfenjin/cfp_flowmonitor.rb

In my case I wanted to override the standard single switch for WARN,
INFO, DEBUG etc., with a second switch for TRACING, VERBOSITY levels
and TESTING. For BioRuby it is simpler, as we have (perhaps) have no
such requirement at the library level.

Pj.