Utility functions shared by bio::chado::schema objects
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',
);
}
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.
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 }
Robert Buels, <[email protected]>
Naama Menda, <[email protected]>