File Coverage

blib/lib/Bio/GMOD/Adaptor/WormBase.pm

Criterion	Covered	Total	%
statement	7	9	77.7
branch			n/a
condition			n/a
subroutine	3	3	100.0
pod			n/a
total	10	12	83.3

package Bio::GMOD::Adaptor::WormBase;

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             => 'WormBase',

		# LIVE_NAME, LIVE_URL, LIVE_DESCRIPTION (required)
		# Live public server variables
		LIVE_NAME        => 'WormBase live server',
		LIVE_URL         => 'http://www.wormbase.org',
		LIVE_DESCRIPTION => 'The WormBase live public server',

		# DEVELOPMENT_NAME, DEVELOPMENT_URL, DEVELOPMENT_DESCRIPTION (optional)
		# Development server variables, if applicable
		DEVELOPMENT_NAME => 'WormBase development server',
		DEVELOPMENT_URL  => 'http://dev.wormbase.org',
		DEVELOPMENT_DESCRIPTION => 'The WormBase 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 WormBase, 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_DEV  => 'http://dev.wormbase.org/db/gmod/version',
		VERSION_LIVE => 'http://www.wormbase.org/db/gmod/version',

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

		# Suitable local paths for WormBase
		ACEDB_PATH     => '/usr/local/acedb/elegans',  # This will actually be a symlink
		MYSQL_PATH     => '/usr/local/mysql/data',
		TMP_PATH       => '/usr/local/gmod/wormbase/releases',
		INSTALL_ROOT   => '/usr/local/wormbase',

		# Remote paths:
		FTP_SITE      => 'dev.wormbase.org',
		FTP_ROOT      => '/usr/local/ftp',   # full local path
		FTP_PATH      => '/pub/wormbase/mirror/database_tarballs',  # Relative

                # Where to find prepackaged databases
                DATABASE_REPOSITORY => '/pub/wormbase/mirror/database_tarballs',
                DATABASE_REPOSITORY_STABLE => '/pub/wormbase/mirror/database_tarballs/stable',

                # Tarball filenames
                ACEDB_TARBALL        => 'elegans_%s.ace.tgz',
                ELEGANS_GFF_TARBALL  => 'elegans_%s.gff.tgz',
                BRIGGSAE_GFF_TARBALL => 'briggsae_%s.gff.tgz',
                BLAST_TARBALL        => 'blast_%s.tgz',

                # Disk space requirements (GB)
                ACEDB_DISK_SPACE        => '10',
                ELEGANS_GFF_DISK_SPACE  => '3.5',
                BRIGGSAE_GFF_DISK_SPACE => '5',
                BLAST_DISK_SPACE        => '0.5',

		# Software updating
		RSYNC_URL       => 'rsync://dev.wormbase.org',
		RSYNC_MODULE    => 'wormbase-live',
		CVS_ROOT        => ':pserver:[e-mail]:/usr/local/cvs',

		# DATA MINING CONSTANTS
		DATA_MINING_URL    => 'http://aceserver.cshl.org',
		DATA_MINING_SERVER => 'aceserver.cshl.org',
#		DATA_MINING_SERVER => 'localhost',
		DATA_MINING_PORT   => '2005',

		# GENERIC QUERIES
		GENE_FETCH_QUERY  => 'select a,a->Public_name,a->Concise_description from a in class Gene where a->Public_name="%s"',
		GENE_SEARCH_QUERY => '',

		PROTEIN_FETCH_QUERY  => 'find Protein $s',
		PROTEIN_SEARCH_QUERY => '',

		# PACKAGE PATHS (LOCAL) (NOT YET SYNCED WITH CGI)
		# Suitable constants for creating packages
		# PACKAGE_PATH   => (getpwnam('ftp'))[7]   . '/pub/wormbase/database_tarballs',
		# LOCAL_PACKAGE_PATH => (getpwnam('ftp'))[7]   . '/pub/wormbase/database_tarballs',
		# CURRENT_PACKAGE_SYMLINK => (getpwnam('ftp'))[7]   . '/pub/wormbase/database_tarballs/current_release',

		# Constants for archiving
		CURRENT_RELEASE => (getpwnam('ftp'))[7]   . '/pub/wormbase/elegans-current_release',

	       );



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__