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inc/Module/Install.pm  view on Meta::CPAN

# }

use 5.005;
use strict 'vars';
use Cwd        ();
use File::Find ();
use File::Path ();

use vars qw{$VERSION $MAIN};
BEGIN {
	# All Module::Install core packages now require synchronised versions.
	# This will be used to ensure we don't accidentally load old or
	# different versions of modules.
	# This is not enforced yet, but will be some time in the next few
	# releases once we can make sure it won't clash with custom
	# Module::Install extensions.
	$VERSION = '1.06';

	# Storage for the pseudo-singleton
	$MAIN    = undef;

lib/Bio/MAGETAB/Util/DBLoader.pm  view on Meta::CPAN

=head1 CAVEATS

Objects when modified are not automatically updated in the
database. You should use the C<update> method to do this (see
L<METHODS|Bio::MAGETAB::Util::Builder/METHODS> in the Builder class). In particular, it is
important to bear in mind that there are places in the Bio::MAGETAB
model where relationships between objects are being maintained behind
the scenes (this allows certain relationships to be navigable in both
directions). When modifying these objects, you must also call
C<update> on their target objects to ensure the database is kept
synchronized with the objects held in memory. For example:

 # SDRFRow to Nodes is a reciprocal relationship:
 my $row = $loader->create_sdrf_row({
    nodes => \@nodes,
 });
 
 # @nodes now know about $row, but the database doesn't know this:
 $loader->update( @nodes );

 # Similarly, with Edges and Nodes:

lib/Bio/MAGETAB/Util/Persistence.pm  view on Meta::CPAN

use MooseX::Types::Moose qw( Str HashRef ArrayRef );

# Uncomment these to print the SQL statements used to STDOUT.
#$Tangram::TRACE = \*STDOUT;
#$Tangram::DEBUG_LEVEL = 1;

sub class_config {

    my ( $class ) = @_;

    # This is where the magic happens. This needs to be kept synchronised
    # with any changes made to the core MAGETAB model.
    my $hashref = {

    classes => [

        'Bio::MAGETAB::ArrayDesign' => {
            bases  => [ 'Bio::MAGETAB::DatabaseEntry' ],
            fields => {
                string => { name             => {},
                            version          => {},