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This queue is for tickets about the onto-perl CPAN distribution.

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The Basics
Id: 71505
Status: rejected
Priority: 0/
Queue: onto-perl
People
Owner: Nobody in particular
Requestors: perl [...] luther.ca
Cc:
AdminCc:
Bug Information
Severity: Normal
Broken in: 1.35
Fixed in: (no value)

History Show all quoted text
  Thu Oct 06 13:28:31 2011 perl [...] luther.ca - Ticket created
Subject: subset parsing error
The parser module doesn't seem to handle namespace subsets with spaces. An example can be found in the OBO file: http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mi/rel25/data/psi- mi25.obo The line: subset: PSI-MI slim Causes an error: The subset 'PSI-MI' is not defined in the header! Check your OBO file line '44' at /usr/local/pkg/perl- 5.8.8/lib/site_perl/5.8.8/OBO/Parser/OBOParser.pm line 302. Looking at old versions of this ontology file the space has been in that subset name for 2-3 years, so the fact it's existed that long without being changed makes me think spaces are valid in this tag in the OBO spec. Thanks.
  Wed Oct 19 05:34:07 2011 erick.antezana [...] gmail.com - Correspondence added
Hi, subset names cannot have a whitespace, c.f. http://sourceforge.net/mailarchive/forum.php?thread_name=A48C3367-874D-42E2-9120-C791D65D75AB%40lbl.gov&forum_name=obo-format http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html MI has to be fixed. cheers, Erick On Thu Oct 06 19:28:31 2011, LAIRDM wrote: Show quoted text
> The parser module doesn't seem to handle namespace subsets with spaces. > An example can be found in the OBO file: > > http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mi/rel25/data/psi- > mi25.obo > > The line: > > subset: PSI-MI slim > > Causes an error: > > The subset 'PSI-MI' is not defined in the header! Check your OBO file > line '44' at /usr/local/pkg/perl- > 5.8.8/lib/site_perl/5.8.8/OBO/Parser/OBOParser.pm line 302. > > Looking at old versions of this ontology file the space has been in that > subset name for 2-3 years, so the fact it's existed that long without > being changed makes me think spaces are valid in this tag in the OBO > spec. > > Thanks.
  Wed Oct 19 05:34:08 2011 The RT System itself - Status changed from 'new' to 'open'
  Wed Oct 19 05:34:09 2011 erick.antezana [...] gmail.com - Status changed from 'open' to 'rejected'