kehh / biolink

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XML-IO cannot handle traits with special characters in their names #211

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago
What steps will reproduce the problem?
1. Create a trait category with a '#' sign in its name
2. Add a trait of that category to a taxa 
3. Attempt to export to XML

What is the expected output? What do you see instead?

Get an error box. Should export correctly with the special characters encoded 
so as to be XML safe

Original issue reported on code.google.com by david.ba...@gmail.com on 4 Dec 2013 at 4:02

GoogleCodeExporter commented 9 years ago
The previous routine in the XML export facility used a black list of illegal 
characters in trait names that where then mangled into XML entity names for 
each trait. Many illegal characters where actually not included in list black 
list, so to fix this issue the mangle routine has a white list of allowed 
characters, and all others are converted into underscores. It seems that the 
actual name of the entity is not actually significant, as the ALIAS attribute 
holds the true trait name. Perhaps in future trait elements should simply be 
stored in <trait/> elements?

Original comment by david.ba...@gmail.com on 4 Dec 2013 at 5:55