[Bioperl-l] Re: [Gmod-schema] install problems, continued (fwd)

[Jason Stajich]

ignore this sorry -- wasn't thinking.  as hilmar replied on gmod-schema
list this was improper comparison with bioperl 1.2.x branch not bioperl
1.4.

--jason
On Fri, 27 Feb 2004, Jason Stajich wrote:

>
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
> ---------- Forwarded message ----------
> Date: Fri, 27 Feb 2004 14:30:57 -0500 (EST)
> From: Don Gilbert <gilbertd at bio.indiana.edu>
> To: cain at cshl.org, p.lijnzaad at med.uu.nl
> Cc: gmod-schema at lists.sourceforge.net
> Subject: Re: [Gmod-schema] install problems, continued
>
>
> THere is a problem with bioperl-1.4 related to ontology parsing.
> I'm assuming people in bioperl/ontology world know about this, but
> here is what I found -- Bio/Ontology/RelationshipType.pm
> has been reverted to remove some of Allen Day's necessary patches
> and now it won't parse SO and some of the other standard bio ontology data.
>
> - Don
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Found unknown type of relationship: [derived_from]
> Known types are: [IS_A], [PART_OF], [CONTAINS], [FOUND_IN]
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /bio/biodb/common/perl/lib/Bio/Root/Root.pm:328
> STACK: Bio::Ontology::RelationshipType::get_instance /bio/biodb/common/perl/lib/Bio/Ontology/RelationshipType.pm:143
> STACK: Bio::Ontology::SimpleGOEngine::add_relationship_type /bio/biodb/common/perl/lib/Bio/Ontology/SimpleGOEngine.pm:284
> STACK: Bio::OntologyIO::dagflat::_parse_flat_file /bio/biodb/common/perl/lib/Bio/OntologyIO/dagflat.pm:556
> STACK: Bio::OntologyIO::dagflat::parse /bio/biodb/common/perl/lib/Bio/OntologyIO/dagflat.pm:250
> STACK: Bio::OntologyIO::dagflat::next_ontology /bio/biodb/common/perl/lib/Bio/OntologyIO/dagflat.pm:284
> STACK: /bio/biodb/gmod/bin/gmod_load_ontology.pl:119
> -----------------------------------------------------------
> Problem loading ontology /bio/biodb/gmod/data/ontologies/song/so.ontology: 65280 at bin/
>
> -- reinstated below comment out, leading to lots of errors
> -- UC versus lc terms, and derived_from, other relations not in perl module.
>
>
> cricket.% diff
>   [bioperl-eariler]/Bio/Ontology/RelationshipType.pm
>   [bioperl-1.4]/Bio/Ontology/RelationshipType.pm
> 1c1
> < # $Id: RelationshipType.pm,v 1.11 2003/06/20 18:31:44 allenday Exp $
> ---
> > # $Id: RelationshipType.pm,v 1.5.2.5 2003/09/08 12:16:19 heikki Exp $
> 136,145c136,141
> <
> < #
> < #see the cell ontology.  this code is too strict, even for dag-edit files. -allen
> < #
> < #    if ( ! (($name eq IS_A) || ($name eq PART_OF) ||
> < #         ($name eq CONTAINS) || ( $name eq FOUND_IN ))) {
> < #        my $msg = "Found unknown type of relationship: [" . $name . "]\n";
> < #        $msg .= "Known types are: [" . IS_A . "], [" . PART_OF . "], [" . CONTAINS . "], [" . FOUND_IN . "]";
> < #        $class->throw( $msg );
> < #    }
> ---
> >     if ( ! (($name eq IS_A) || ($name eq PART_OF) ||
> >           ($name eq CONTAINS) || ( $name eq FOUND_IN ))) {
> >         my $msg = "Found unknown type of relationship: [" . $name . "]\n";
> >         $msg .= "Known types are: [" . IS_A . "], [" . PART_OF . "], [" . CONTAINS . "], [" . FOUND_IN . "]";
> >         $class->throw( $msg );
> >     }
> 364a361,363
> >
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu