debian man page for bio::chado::schema::util

Bio::Chado::Schema::Util(3pm)				User Contributed Perl Documentation			     Bio::Chado::Schema::Util(3pm)

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

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.

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.

perl v5.14.2							    2011-11-08					     Bio::Chado::Schema::Util(3pm)