Bio::Chado::Schema::Result::Organism::Organism - Bio::Chado::Schema::Result::Organism::Organism documentation

  data_type: 'integer'
  is_auto_increment: 1
  is_nullable: 0
  sequence: 'organism_organism_id_seq'

  data_type: 'varchar'
  is_nullable: 1
  size: 255

  data_type: 'varchar'
  is_nullable: 0
  size: 255

  data_type: 'varchar'
  is_nullable: 0
  size: 255

  data_type: 'varchar'
  is_nullable: 1
  size: 255

  data_type: 'text'
  is_nullable: 1

  Usage: $set->create_organismprops({ baz => 2, foo => 'bar' });
  Desc : convenience method to create organism properties using cvterms
          from the ontology with the given name
  Args : hashref of { propname => value, ...},
         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 organismprops.
                       Defaults to 'organism_property',

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

            dbxref_accession_prefix => optional, default
                                       'autocreated:',
            definitions => optional hashref of:
                { cvterm_name => definition,
                }
             to load into the cvterm table when autocreating cvterms

            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.
          }
  Ret  : hashref of { propname => new organismprop object }

package Bio::Chado::Schema::Result::Organism::Organism;
BEGIN {
  $Bio::Chado::Schema::Result::Organism::Organism::AUTHORITY = 'cpan:RBUELS';
}
BEGIN {
  $Bio::Chado::Schema::Result::Organism::Organism::VERSION = '0.08100';
}

# Created by DBIx::Class::Schema::Loader
# DO NOT MODIFY THE FIRST PART OF THIS FILE

use strict;
use warnings;

use base 'DBIx::Class::Core';



__PACKAGE__->table("organism");


__PACKAGE__->add_columns(
  "organism_id",
  {
    data_type         => "integer",
    is_auto_increment => 1,
    is_nullable       => 0,
    sequence          => "organism_organism_id_seq",
  },
  "abbreviation",
  { data_type => "varchar", is_nullable => 1, size => 255 },
  "genus",
  { data_type => "varchar", is_nullable => 0, size => 255 },
  "species",
  { data_type => "varchar", is_nullable => 0, size => 255 },
  "common_name",
  { data_type => "varchar", is_nullable => 1, size => 255 },
  "comment",
  { data_type => "text", is_nullable => 1 },
);
__PACKAGE__->set_primary_key("organism_id");
__PACKAGE__->add_unique_constraint("organism_c1", ["genus", "species"]);


__PACKAGE__->has_many(
  "biomaterials",
  "Bio::Chado::Schema::Result::Mage::Biomaterial",
  { "foreign.taxon_id" => "self.organism_id" },
  { cascade_copy => 0, cascade_delete => 0 },
);


__PACKAGE__->has_many(
  "cell_lines",
  "Bio::Chado::Schema::Result::CellLine::CellLine",
  { "foreign.organism_id" => "self.organism_id" },
  { cascade_copy => 0, cascade_delete => 0 },
);


__PACKAGE__->has_many(
  "features",
  "Bio::Chado::Schema::Result::Sequence::Feature",
  { "foreign.organism_id" => "self.organism_id" },
  { cascade_copy => 0, cascade_delete => 0 },
);


__PACKAGE__->has_many(
  "libraries",
  "Bio::Chado::Schema::Result::Library::Library",
  { "foreign.organism_id" => "self.organism_id" },
  { cascade_copy => 0, cascade_delete => 0 },
);


__PACKAGE__->has_many(
  "organism_dbxrefs",
  "Bio::Chado::Schema::Result::Organism::OrganismDbxref",
  { "foreign.organism_id" => "self.organism_id" },
  { cascade_copy => 0, cascade_delete => 0 },
);


__PACKAGE__->has_many(
  "organismprops",
  "Bio::Chado::Schema::Result::Organism::Organismprop",
  { "foreign.organism_id" => "self.organism_id" },
  { cascade_copy => 0, cascade_delete => 0 },
);


__PACKAGE__->has_many(
  "phenotype_comparisons",
  "Bio::Chado::Schema::Result::Genetic::PhenotypeComparison",
  { "foreign.organism_id" => "self.organism_id" },
  { cascade_copy => 0, cascade_delete => 0 },
);


__PACKAGE__->has_many(
  "phylonode_organisms",
  "Bio::Chado::Schema::Result::Phylogeny::PhylonodeOrganism",
  { "foreign.organism_id" => "self.organism_id" },
  { cascade_copy => 0, cascade_delete => 0 },
);


__PACKAGE__->has_many(
  "stocks",
  "Bio::Chado::Schema::Result::Stock::Stock",
  { "foreign.organism_id" => "self.organism_id" },
  { cascade_copy => 0, cascade_delete => 0 },
);


# Created by DBIx::Class::Schema::Loader v0.07010 @ 2011-03-16 23:09:59
# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:/CHPcA8KHLuOon9UfLVglQ


__PACKAGE__->many_to_many
    (
     'phylonodes',
     'phylonode_organisms' => 'phylonode',
    );


__PACKAGE__->many_to_many
    (
     'dbxrefs',
     'organism_dbxrefs' => 'dbxref',
    );



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_properties
        ( properties => $props,
          options    => $opts,
          row        => $self,
          prop_relation_name => 'organismprops',
        );
}


1;

__END__