bio::chado::schema::test(3pm) [debian man page]

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

NAME

       Bio::Chado::Schema::Test - Library to be used by Bio::Chado::Schema test scripts.

SYNOPSIS

	 use lib qw(t/lib);
	 use Bio::Chado::Schema::Test;
	 use Test::More;

	 my $schema = Bio::Chado::Schema::Test->init_schema();

DESCRIPTION

       This module provides the basic utilities to write tests against Bio::Chado::Schema.

METHODS

   init_schema
	 my $schema = Bio::Chado::Schema::Test->init_schema(
	   deploy	     => 1,
	   populate	     => 1,
	   storage_type      => '::DBI::Replicated',
	   storage_type_args => {
	     balancer_type=>'DBIx::Class::Storage::DBI::Replicated::Balancer::Random'
	   },
	 );

       This method removes the test SQLite database in t/var/BCS.db and then creates a new, empty database.

       This method will call deploy_schema() by default, unless the deploy flag is set to 0.

       This method will call populate_schema() if the populate argument is set to a true value.

   has_custom_dsn
       Returns true if the BCS_TEST_DSN environment variable is set.

   deploy_schema
	 Bio::Chado::Schema::Test->deploy_schema( $schema );

       This method does one of two things to the schema.  It can either call the experimental $schema->deploy() if the BCSTEST_SQLT_DEPLOY
       environment variable is set, otherwise the default is to read in the t/lib/sqlite.sql file and execute the SQL within. Either way you end
       up with a fresh set of tables for testing.

   populate_schema
	 Bio::Chado::Schema::Test->populate_schema( $schema );

       After you deploy your schema you can use this method to populate the tables with test data.

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

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)