NAME

Bio::Chado::Schema::Util

SYNOPSIS

sub create_organismprops {
    my ($self, $props, $opts) = @_;

    # process opts
    $opts ||= {};
    $opts->{cv_name} = 'organism_property'
        unless defined $opts->{cv_name};

    return Bio::Chado::Schema::Util->create_props
        ( properties => $props,
          options    => $opts,
          row        => $self,
          prop_relation_name => 'organismprops',
        );
}

DESCRIPTION

Helper functions used by several schema classes.

Important Note: This package is located in the Schema.pm file as secondary package and it haven't a file for itself. Nevertheless, the use will be the same.

NAME

Bio::Chado::Schema::Util - utility functions shared by Bio::Chado::Schema objects

PACKAGE METHODS

create_properties

Usage: *::Util->create_properties( row => $self,
                                   properties => { baz => 2, foo => 'bar' },
                                   options => { cv_name => autocreate => 0, ...},
                                   prop_relation_name => 'organismprops',
                                 );

Desc : Chado has a number of <thing>prop tables with a similar
       structure.  This utility function is used by a number of
       modules to create properties in these kinds of tables.

Args : row => the DBIC row object to create properties for,
       prop_relation_name => the DBIC relation name for the
                             properties table to operate on,
                             e.g. 'featureprops',
       properties => hashref of { propname => value, ...},
       options => options hashref as:
           {
             autocreate => 0,
                (optional) boolean, if passed, automatically create cv,
                cvterm, and dbxref rows if one cannot be found for the
                given featureprop name.  Default false.

             cv_name => cv.name to use for the given featureprops.
                        Defaults to 'feature_property',

             db_name => db.name to use for autocreated dbxrefs,
                        default 'null',

             allow_duplicate_values => default false.
                 If true, allow duplicate instances of the same cvterm
                 and value in the properties of the feature.  Duplicate
                 values will have different ranks.

             dbxref_accession_prefix => optional, default
                                        'autocreated:',
             definitions => optional hashref of:
                 { cvterm_name => definition,
                 }
              to load into the cvterm table when autocreating cvterms
           }
Ret  : hashref of { propname => new row object in property table }

AUTHOR

Robert Buels, <rmb32@cornell.edu>

Naama Menda, <naama.menda@gmail.com>

COPYRIGHT & LICENSE

Copyright 2009 Boyce Thompson Institute for Plant Research

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

AUTHOR

Robert Buels <rbuels@cpan.org>

COPYRIGHT AND LICENSE

This software is copyright (c) 2011 by Robert Buels.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.