|CC:||"bug-onto-perl [...] rt.cpan.org" <bug-onto-perl [...] rt.cpan.org>|
|Subject:||OBO::Parser::OWLParser doesn't use XML::Parser|
|Date:||Wed, 8 Apr 2015 16:13:26 +0000|
|To:||"vladimir.n.mironov [...] gmail.com" <vladimir.n.mironov [...] gmail.com>|
|From:||Ben Hutton <bh7 [...] sanger.ac.uk>|
Hi Vladimir, I am trying to use your ONTO-PERL distribution of modules. It installed OK, but there is a problem (or two) with the OWL Parser. OWLParser.pm line 146 tries to create a new XML::Parser object, but the module never uses XML::Parser. This is not picked up by the tests, as the test skips the test if the module is not installed, and it checks if it is installed or not by using XML::Parser. After amending the module to use XML::Parser, I hit an undefined sub at line 640. subset_def_set is not defined in OBO::Core::Ontology. The file in question I am trying to use is an owl file converted from an obo file (. The Sequence Ontology claim that an owl file is available, but it hasn't been updated "nightly" since 2012. I'm willing to help fix this if I can. Thanks in advance. Ben -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.