package Bio::Chado::Schema::Result::Stock::Stock;
BEGIN {
$Bio::Chado::Schema::Result::Stock::Stock::AUTHORITY = 'cpan:RBUELS';
}
BEGIN {
$Bio::Chado::Schema::Result::Stock::Stock::VERSION = '0.10010';
}
# Created by DBIx::Class::Schema::Loader
# DO NOT MODIFY THE FIRST PART OF THIS FILE
use strict;
use warnings;
use base 'DBIx::Class::Core';
=head1 NAME
Bio::Chado::Schema::Result::Stock::Stock
=head1 DESCRIPTION
Any stock can be globally identified by the
combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.
=cut
__PACKAGE__->table("stock");
=head1 ACCESSORS
=head2 stock_id
data_type: 'integer'
is_auto_increment: 1
is_nullable: 0
sequence: 'stock_stock_id_seq'
=head2 dbxref_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 1
The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref.
=head2 organism_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 1
The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined.
=head2 name
data_type: 'varchar'
is_nullable: 1
size: 255
The name is a human-readable local name for a stock.
=head2 uniquename
data_type: 'text'
is_nullable: 0
=head2 description
data_type: 'text'
is_nullable: 1
The description is the genetic description provided in the stock list.
=head2 type_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 0
The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm.
=head2 is_obsolete
data_type: 'boolean'
default_value: false
is_nullable: 0
=cut
__PACKAGE__->add_columns(
"stock_id",
{
data_type => "integer",
is_auto_increment => 1,
is_nullable => 0,
sequence => "stock_stock_id_seq",
},
"dbxref_id",
{ data_type => "integer", is_foreign_key => 1, is_nullable => 1 },
"organism_id",
{ data_type => "integer", is_foreign_key => 1, is_nullable => 1 },
"name",
{ data_type => "varchar", is_nullable => 1, size => 255 },
"uniquename",
{ data_type => "text", is_nullable => 0 },
"description",
{ data_type => "text", is_nullable => 1 },
"type_id",
{ data_type => "integer", is_foreign_key => 1, is_nullable => 0 },
"is_obsolete",
{ data_type => "boolean", default_value => \"false", is_nullable => 0 },
);
__PACKAGE__->set_primary_key("stock_id");
__PACKAGE__->add_unique_constraint("stock_c1", ["organism_id", "uniquename", "type_id"]);
=head1 RELATIONS
=head2 nd_experiment_stocks
Type: has_many
Related object: L<Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStock>
=cut
__PACKAGE__->has_many(
"nd_experiment_stocks",
"Bio::Chado::Schema::Result::NaturalDiversity::NdExperimentStock",
{ "foreign.stock_id" => "self.stock_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
=head2 dbxref
Type: belongs_to
Related object: L<Bio::Chado::Schema::Result::General::Dbxref>
=cut
__PACKAGE__->belongs_to(
"dbxref",
"Bio::Chado::Schema::Result::General::Dbxref",
{ dbxref_id => "dbxref_id" },
{
cascade_copy => 0,
cascade_delete => 0,
is_deferrable => 1,
join_type => "LEFT",
on_delete => "CASCADE",
on_update => "CASCADE",
},
);
=head2 type
Type: belongs_to
Related object: L<Bio::Chado::Schema::Result::Cv::Cvterm>
=cut
__PACKAGE__->belongs_to(
"type",
"Bio::Chado::Schema::Result::Cv::Cvterm",
{ cvterm_id => "type_id" },
{
cascade_copy => 0,
cascade_delete => 0,
is_deferrable => 1,
on_delete => "CASCADE",
on_update => "CASCADE",
},
);
=head2 organism
Type: belongs_to
Related object: L<Bio::Chado::Schema::Result::Organism::Organism>
=cut
__PACKAGE__->belongs_to(
"organism",
"Bio::Chado::Schema::Result::Organism::Organism",
{ organism_id => "organism_id" },
{
cascade_copy => 0,
cascade_delete => 0,
is_deferrable => 1,
join_type => "LEFT",
on_delete => "CASCADE",
on_update => "CASCADE",
},
);
=head2 stockcollection_stocks
Type: has_many
Related object: L<Bio::Chado::Schema::Result::Stock::StockcollectionStock>
=cut
__PACKAGE__->has_many(
"stockcollection_stocks",
"Bio::Chado::Schema::Result::Stock::StockcollectionStock",
{ "foreign.stock_id" => "self.stock_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
=head2 stock_cvterms
Type: has_many
Related object: L<Bio::Chado::Schema::Result::Stock::StockCvterm>
=cut
__PACKAGE__->has_many(
"stock_cvterms",
"Bio::Chado::Schema::Result::Stock::StockCvterm",
{ "foreign.stock_id" => "self.stock_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
=head2 stock_dbxrefs
Type: has_many
Related object: L<Bio::Chado::Schema::Result::Stock::StockDbxref>
=cut
__PACKAGE__->has_many(
"stock_dbxrefs",
"Bio::Chado::Schema::Result::Stock::StockDbxref",
{ "foreign.stock_id" => "self.stock_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
=head2 stock_genotypes
Type: has_many
Related object: L<Bio::Chado::Schema::Result::Stock::StockGenotype>
=cut
__PACKAGE__->has_many(
"stock_genotypes",
"Bio::Chado::Schema::Result::Stock::StockGenotype",
{ "foreign.stock_id" => "self.stock_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
=head2 stockprops
Type: has_many
Related object: L<Bio::Chado::Schema::Result::Stock::Stockprop>
=cut
__PACKAGE__->has_many(
"stockprops",
"Bio::Chado::Schema::Result::Stock::Stockprop",
{ "foreign.stock_id" => "self.stock_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
=head2 stock_pubs
Type: has_many
Related object: L<Bio::Chado::Schema::Result::Stock::StockPub>
=cut
__PACKAGE__->has_many(
"stock_pubs",
"Bio::Chado::Schema::Result::Stock::StockPub",
{ "foreign.stock_id" => "self.stock_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
=head2 stock_relationship_subjects
Type: has_many
Related object: L<Bio::Chado::Schema::Result::Stock::StockRelationship>
=cut
__PACKAGE__->has_many(
"stock_relationship_subjects",
"Bio::Chado::Schema::Result::Stock::StockRelationship",
{ "foreign.subject_id" => "self.stock_id" },
{ cascade_copy => 0, cascade_delete => 0 },
);
=head2 stock_relationship_objects
Type: has_many
Related object: L<Bio::Chado::Schema::Result::Stock::StockRelationship>
=cut
__PACKAGE__->has_many(
"stock_relationship_objects",
"Bio::Chado::Schema::Result::Stock::StockRelationship",
{ "foreign.object_id" => "self.stock_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:v+GluxMkFEC508znwinNsA
=head2 create_stockprops
Usage: $set->create_stockprops({ baz => 2, foo => 'bar' });
Desc : convenience method to create stock properties using cvterms
from the ontology with the given name
Args : hashref of { propname => value, ...},
options hashref as:
{
autocreate => 0,
(optional) boolean, if passed, automatically create cv,
cvterm, and dbxref rows if one cannot be found for the
given stockprop name. Default false.
cv_name => cv.name to use for the given stockprops.
Defaults to 'stock_property',
db_name => db.name to use for autocreated dbxrefs,
default 'null',
dbxref_accession_prefix => optional, default
'autocreated:',
definitions => optional hashref of:
{ cvterm_name => definition,
}
to load into the cvterm table when autocreating cvterms
rank => force numeric rank. Be careful not to pass ranks that already exist
for the property type. The function will die in such case.
allow_duplicate_values => default false.
If true, allow duplicate instances of the same stock
and value in the properties of the stock. Duplicate
values will have different ranks.
}
Ret : hashref of { propname => new stockprop object }
=cut
sub create_stockprops {
my ($self, $props, $opts) = @_;
# process opts
$opts->{cv_name} = 'stock_property'
unless defined $opts->{cv_name};
return Bio::Chado::Schema::Util->create_properties
( properties => $props,
options => $opts,
row => $self,
prop_relation_name => 'stockprops',
);
}
# You can replace this text with custom content, and it will be preserved on regeneration
1;