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rvosa / bio-phylo

Bio::Phylo - Phyloinformatic analysis using Perl
http://search.cpan.org/dist/Bio-Phylo
GNU General Public License v3.0
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Bio::Phylo fails to deal with polymorphic state symbols #44

Open hlapp opened 5 years ago

hlapp commented 5 years ago

The symbol attribute for AbstractState, which StandardPolymorphicStateSet inherits from, is defined as xs:anySimpleType, so presumably anything should go, including "1 and 0".

That's in contrast to StandardState, which also inherits from AbstractState but restricts the symbol attribute to StandardToken.

It seems the NeXML validator, which I think is based on running Bio::Phylo, confuses the symbol datatype restrictions.

See phenoscape/phenoscape-kb-services#149 for the original issue.

rvosa commented 5 years ago

Mmmm... the nexml validator is only partially based on Bio::Phylo, namely insofar as checking for complex referential integrity. Basic type validation is done using the schema. So if the type passes, I guess it's valid...?