NAME

Test::Chado::Cvterm

VERSION

version v4.1.1

NAME

API for testing cvterm.

API

Exported method groups

There are three exported groups. As usual, all methods could be exported by the special all export group.

count

count_cvterm_ok

count_obsolete_cvterm_ok

count_relationship_cvterm_ok

count_alt_id_ok

count_comment_ok

count_object_ok

count_subject_ok

count_synonym_ok

check

has_synonym

has_alt_id

has_comment

has_relationship

is_obsolete_cvterm

has_xref

has_synonym

relationship

count_object_ok

count_subject_ok

has_relationship

count_relationship_cvterm_ok

Methods

Unless specified, all parameters are mandatory.

count_cvterm_ok(DBIx::Class::Schema, \%expected, [description])

Tests for numbers of cvterms in an ontology excluding obsolete and relationship terms.

parameters

cv: Name of the cv.

count: Expected number of cvterms in that cv

count_obsolete_cvterm_ok(DBIx::Class::Schema, \%expected, [description])

Tests for numbers of obsolete cvterms. Identical parameters as count_cvterm_ok

count_relationship_cvterm_ok(DBIx::Class::Schema, \%expected, [description])

Tests for numbers of relationship cvterms excluding the built-ins and obsoletes. Identical parameters as count_cvterm_ok

count_synonym_ok(DBIx::Class::Schema, \%expected, [description])

Identical parameters as count_cvterm_ok

count_comment_ok(DBIx::Class::Schema, \%expected, [description])

Identical parameters as count_cvterm_ok

count_alt_id_ok(DBIx::Class::Schema, \%expected, [description])

parameters

cv: Name of the cv.

count: Expected number of alt_ids

db: Database namespace in which the alternate ids belongs to. Both cv and db namespaces will be used for counting.

count_subject_ok(DBIx::Class::Schema, \%expected, [description])

Tests the number of children terms for a parent.

parameters

cv: Name of the cv.

object: Name of parent cvterm

count: Expected number of children

relationship: Name of relationship, optional

count_object_ok(DBIx::Class::Schema, \%expected, [description])

Tests the number of parent terms for a child.

parameters

cv: Name of the cv.

subject: Name of child cvterm

expected: Expected number of parent(s)

relationship: Name of relationship, optional

has_cvterm_synonym(DBIx::Class::Schema, \%expected, [description])

Tests if a cvterm has particular synonym.

parameters

cv: Name of the cv, optional.

term: Name of cvterm.

synonym: Name of synonym.

has_alt_id(DBIx::Class::Schema, \%expected, [description])

Tests if a cvterm has particular alternate id.

parameters

cv: Name of the cv, optional.

term: Name of cvterm.

alt_id: Name of alternate id.

has_xref(DBIx::Class::Schema, \%expected, [description])

Tests if a cvterm has a particular xref.

parameters

cv: Name of the cv, optional.

term: Name of cvterm.

xref: Name of alternate id.

has_comment(DBIx::Class::Schema, \%expected, [description])

Tests if a cvterm has particular comment.

parameters

cv: Name of the cv, optional.

term: Name of cvterm.

comment: Comment text.

has_relationship(DBIx::Class::Schema, \%expected, [description])

Tests if parent and child has a particular relationship

parameters

object: Name of the parent term.

subject: Name of the child term.

relationship: Name of the relationship term.

is_obsolete_cvterm(DBIx::Class::Schema, \%expected, [description])

Tests if an existing cvterm is obsolete

parameters

cv: Name of the cv.

term: Name of the obsolete term.

AUTHOR

Siddhartha Basu <biosidd@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2011 by Siddhartha Basu.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.