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phenoscape / phenoscape-data

NeXML data files annotated by Phenoscape curators.
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Illegal ids in nexml #10

Open mtholder opened 10 years ago

mtholder commented 10 years ago

HI, I have the strong suspicion that I am reporting this issue to the wrong repo. Sorry about that, I'm not sure which repo stores the tool that creates these files...

For files like: https://raw.github.com/phenoscape/phenoscape-data/master/Curation%20Files/completed-phenex-files/Characiformes/Buckup_1998.xml

I am getting nexml validation errors:

Error validating [../phenoscape/nexml] against [../nexml/xsd/nexml.xsd]:

cvc-datatype-valid.1.2.1: '4341922c-a479-4088-b02e-42a0e248a825' is not a valid value for 'NCName'.

4341922c-a479-4088-b02e-42a0e248a825 is an otu ID. I think that IDs have to start with a letter or underscore. See http://www.w3.org/TR/1999/REC-xml-names-19990114/#NT-NCName

mtholder commented 10 years ago

Sorry. I should have pointed out that I was am using code from http://code.google.com/p/xml-validator/ to validate against the nexml schema from github (commit 47e35d14665ea921c170253879262bdf20a278ec), and that is what is giving the error

balhoff commented 10 years ago

Thanks @mtholder, the problem is with Phenex: issue phenoscape/phenex/issues/76

This hasn't been a practical problem for our toolchain so I've been slow to get to it.