/usr/share/perl5/Bio/Chado/Schema/Result/Stock/Stock.pm is in libbio-chado-schema-perl 0.20000-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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BEGIN {
$Bio::Chado::Schema::Result::Stock::Stock::AUTHORITY = 'cpan:RBUELS';
}
{
$Bio::Chado::Schema::Result::Stock::Stock::VERSION = '0.20000';
}
# 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',
);
}
############ STOCK CUSTOM RESULTSET PACKAGE #############################
__PACKAGE__->resultset_class('Bio::Chado::Schema::Result::Stock::Stock::ResultSet');
package Bio::Chado::Schema::Result::Stock::Stock::ResultSet;
BEGIN {
$Bio::Chado::Schema::Result::Stock::Stock::ResultSet::AUTHORITY = 'cpan:RBUELS';
}
{
$Bio::Chado::Schema::Result::Stock::Stock::ResultSet::VERSION = '0.20000';
}
use base qw/ DBIx::Class::ResultSet /;
use Carp;
=head1 ADDITIONAL METHODS
=head2 stock_phenotypes_rs
Usage: $schema->resultset("Stock::Stock")->stock_phenotypes_rs($stock_rs);
Desc: retrieve a resultset for stock(s) with phenotyping experiments with the following values mapped to [column name]
stock_id [stock_id]
phenotype.value [value]
observable.name [observable] (the cvterm name for the phenotype.observable field)
observable_cvterm_id [observable_id]
observable.definition [definition]
unit_name (from phenotype_cvterm)
cv_name (the cv_name for the phenotype_cvterm)
type_name (the cvterm name for the phenotype_cvterm)
method_name (a phenotypeprop value)
dbxref.accession [accession] of the observable cvterm
db.name of the observable cvterm [db_name] (useful for constructing the ontology ID of the observable)
project.description [project_description] (useful for grouping phenotype values by projects)
Args: a L<Bio::Chado::Schema::Result::Stock::Stock> resultset
Ret: a resultset with the above columns. Access the data with e.g. $rs->get_column('stock_id')
=cut
sub stock_phenotypes_rs {
my $self = shift;
my $stock = shift;
my $rs = $stock->result_source->schema->resultset("Stock::Stock")->search_rs(
{
'observable.name' => { '!=', undef } ,
'me.stock_id' => { '-in' => $stock->get_column('stock_id')->as_query },
} , {
join => [
{ nd_experiment_stocks => {
nd_experiment => {
nd_experiment_phenotypes => {
phenotype => {
observable => { dbxref => 'db' },
phenotypeprops => 'type',
phenotype_cvterms => { cvterm => 'cv' }
},
},
nd_experiment_projects => 'project',
},
}
} ,
],
select => [ qw/ me.stock_id phenotype.value observable.name observable.cvterm_id observable.definition phenotypeprops.value type.name dbxref.accession db.name project.description cv.name cvterm.name / ],
as => [ qw/ stock_id value observable observable_id definition method_name type_name accession db_name project_description cv_name unit_name / ],
distinct => 1,
order_by => [ 'project.description' , 'observable.name' ],
} );
return $rs;
}
=head2 recursive_phenotypes_rs
Usage: $schema->resultset("Stock::Stock")->recursive_phenotypes_rs($stock_rs, \@results)
Desc: Retrieve recursively phenotypes of stock objects and their subjects
Args: Stock resultSet and an arrayref with the results
Ret: listref of stock_phenotypes_rs (see function stock_phenotypes_rs for columns fetched)
=cut
sub recursive_phenotypes_rs {
my $self = shift ;
my $stock_rs = shift;
my $results = shift;
my $rs = $self->stock_phenotypes_rs($stock_rs);
push @$results, $rs ;
my $subjects = $stock_rs->result_source->schema->resultset("Stock::Stock")->search(
{
'me.stock_id' => { '-in' => [ map { $_->subject_id } $stock_rs->search_related('stock_relationship_objects')->all ] }
} );
if ($subjects->count ) {
$self->recursive_phenotypes_rs($subjects, $results);
}
return $results;
}
=head2 stock_genotypes_rs
Usage: $schema->resultset("Stock::Stock")->stock_genotypes_rs($stock_rs);
Desc: retrieve a resultset for stock(s) with genotyping experiments
with the following values mapped to [column name]
stock_id [stock_id]
genotype.name [name]
genotype.uniquname [uniquename]
genotype.description [description]
genotype.type.name [type_name] (the cvterm name for the genotype type)
propvalue [propvalue] (a genotypeprop value)
Args: a L<Bio::Chado::Schema::Result::Stock::Stock> resultset
Ret: a resultset with the above columns. Access the data with e.g. $rs->get_column('stock_id')
=cut
sub stock_genotypes_rs {
my $self = shift;
my $stock = shift;
my $rs = $stock->result_source->schema->resultset("Stock::Stock")->search_rs(
{
'genotype.uniquename' => { '!=', undef } ,
'me.stock_id' => { '-in' => $stock->get_column('stock_id')->as_query },
} , {
join => [
{ nd_experiment_stocks => {
nd_experiment => {
nd_experiment_genotypes => {
genotype => {
genotypeprops => 'type',
},
'type',
},
},
}
} ,
],
select => [ qw/ stock_id genotype.name genotype.uniquename genotype.description type.name genotypeprops.value / ],
as => [ qw/ stock_id name uniquename description type_name propvalue / ],
distinct => 1,
order_by => [],
} );
return $rs;
}
=head2 stock_project_phenotypes
Usage: $schema->resultset("Stock::Stock")->stock_project_phenotypes($stock_rs);
Desc: retrieve a list of phenotype resultsets by project name
Args: a L<Bio::Chado::Schema::Result::Stock::Stock> object or a stock resultset
Ret: hashref key = project descriptions, values = hash ref of
{phenotypes} = phenotype resultset
{project} = L<Bio::Chado::Schema::Result::Project::Project> object
=cut
sub stock_project_phenotypes {
my $self = shift;
my $stock = shift;
my %phenotypes;
my $project_rs = $stock->search_related('nd_experiment_stocks')
->search_related('nd_experiment')
->search_related('nd_experiment_projects')
->search_related('project' , {} , { distinct =>1 } );
while (my $project = $project_rs->next) {
my $experiment_rs = $stock->search_related('nd_experiment_stocks')
->search_related('nd_experiment' ,
{ 'project.project_id' => $project->project_id },
{ prefetch => { 'nd_experiment_projects' => 'project' } },
);
$phenotypes{ $project->description }->{project} = $project;
my $nd_exp_phen_rs = $experiment_rs->search_related('nd_experiment_phenotypes');
my $phenotype_rs = $nd_exp_phen_rs->search_related('phenotype') if $nd_exp_phen_rs;
$phenotypes{ $project->description }->{phenotypes} = $phenotype_rs;
}
return \%phenotypes;
}
1;
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