Bio::GMOD::Adaptor::FlyBase - Defaults for programmatically interacting with Wormbase

  my $adaptor = Bio::GMOD::Adaptor::FlyBase->new();

package Bio::GMOD::Adaptor::FlyBase;

use strict;
use vars qw/@ISA $AUTOLOAD/;
use Bio::GMOD::Adaptor;
use Bio::GMOD::Util::Rearrange;

@ISA = qw/Bio::GMOD::Adaptor/;

# Bio::GMOD::Adaptor::* can optionally read defaults and current versions
# from CGI scripts If not provided, the corresponding values can be
# overridden either as constants or as options passed to the new()
# method.

my %DEFAULTS = (		
		# DEFAULTS_CGI (optional)
		# A CGI script that provides these same values
		# Full URL to CGI that delivers key value pairs of these options This
		# is optional but lets you quickly change paths to system
		# resources. Moreover, these changes willl be invisible to end user.s
		# If not provided -- or if user is working offline -- these values
		# will be populated from this module.
		# DEFAULTS_CGI => 'http://dev.wormbase.org/db/gmod/defaults',
		
		# NAME (required)
		# Symbolic name of the MOD / Adaptor
		NAME             => 'FlyBase',

		# LIVE_NAME, LIVE_URL, LIVE_DESCRIPTION (required)
		# Live public server variables
		LIVE_NAME        => 'FlyBase live server',
		LIVE_URL         => 'http://www.flybase.org',
		LIVE_DESCRIPTION => 'The FlyBase public server',
		
		# DEVELOPMENT_NAME, DEVELOPMENT_URL, DEVELOPMENT_DESCRIPTION (optional)
		# Development server variables, if applicable
		#  DEVELOPMENT_NAME => 'FlyBase development server',
		#  DEVELOPMENT_URL  => 'http://dev.flybase.org',
		#  DEVELOPMENT_DESCRIPTION => 'The FlyBase semi-public development server',		
		
		# VERSION_LIVE, VERSION_DEV (optional, but recommended!)
		# If you would like to provide your users a convenient
		# mechanism for fetching versions specify one or both
		# of these variables. At FlyBase, the version cgi
		# checks the local verison of the database and returns
		# a string.  This script is available in the cgi-bin/
		# directory.

		# Where does the version XML file live?
		# This may be a file or generated by a CGI
		VERSION_LIVE => 'http://www.flybase.org/db/gmod/version',
		# VERSION_DEV  => 'http://dev.flybase.org/db/gmod/version',

		# Where does the Standard URLs XML file live?
		STANDARD_URLS_XML => 'http://www.flybase.org/standard_urls/standard_urls.xml',

		# The FlyBase data mining URL. Generic fetching of objects by name
		DATAMINING_URL => 'http://flybase.bio.indiana.edu/docs/lk/fbhelp/fbdatamine.pl',
		
		# Gene searches
		#  GENE_SEARCH_URL => 'http://www.flybase.org/genes/fbgquery.hform',
		GENE_SEARCH_URL => 'http://www.flybase.org/.bin/fbgenq.html',
	       );


sub defaults {
  my $self = shift;
  return (keys %DEFAULTS);
}


# Automatically create lc data accessor methods
# for each configuration variable
sub AUTOLOAD {
  my $self = shift;
  my $attr = $AUTOLOAD;
  $attr =~ s/.*:://;
  return unless $attr =~ /[^A-Z]/;  # skip DESTROY and all-cap methods
  return if $attr eq 'new'; # Provided by superclass
  #  die "invalid attribute method: ->$attr()" unless $DEFAULTS{uc($attr)};
  $self->{uc($attr)} = shift if @_;
  my $val = $self->{defaults}->{lc($attr)};  # Get what is already there
  $val ||= $DEFAULTS{uc($attr)};  # Perhaps it hasn't been defined yet.
  return $val;
}

__END__

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