Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Bio::Phylo fails to deal with polymorphic state symbols #44

Open
hlapp opened this issue Jul 12, 2019 · 1 comment
Open

Bio::Phylo fails to deal with polymorphic state symbols #44

hlapp opened this issue Jul 12, 2019 · 1 comment

Comments

@hlapp
Copy link

hlapp commented Jul 12, 2019

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.
@hlapp hlapp mentioned this issue Jul 12, 2019
Closed
@rvosa
Copy link
Owner

rvosa commented Aug 22, 2019

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...?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@hlapp @rvosa