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Duplicated gene associations in a reaction (Previous issue #333) #547

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ehukim opened this issue Jul 19, 2017 · 2 comments
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Duplicated gene associations in a reaction (Previous issue #333) #547

ehukim opened this issue Jul 19, 2017 · 2 comments

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@ehukim
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ehukim commented Jul 19, 2017

Hi cobrapy team,

I found that your previous fix for the Issue #333 broke in recent releases of cobrapy: at least in 0.7.0 and 0.6.2. This problem was easy to identify as my work often involves repeated writing/reading of sbml files.

Thank you so much for your great work/support!
Hyun Uk
@Midnighter
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Thanks for reporting this again. In future we might move this from the notes field to annotations (see the somewhat long and derailed discussion in #534) with the help of some XML schema additions. Until then we'll try to fix the notes, of course. Did you discover this bug with the same model that you linked in the original issue #333?

@ehukim
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ehukim commented Jul 19, 2017

Thanks for the info. I used the same base model with a few additional set of reactions.
Thanks!

hredestig added a commit that referenced this issue Aug 6, 2017
@hredestig
fix: use internally consistent key w/o underscores
4f1c281 
Underscores in keys for KEY: value associations in the notes field are
replaced with spaces so internally use only underscore free keys or
key-values may get repeated in legacy sbml output. Tricky to create
meaningful test for this as the notes field as (mis)using
legacy/incomplete sbml specification for sake of backwards
compatibility.

Fix #547.
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@Midnighter @ehukim