Importing SBML not working like it used to

[lianamerk]

Hi bioscrape team,

I have an SBML model from class a few weeks ago that I used to be able to import fine. I updated bioscrape today to get inference, and now two methods of importing sbml files is failing. I've tried:

bioscrape.sbmlutil.import_sbml(filename) and bioscrape.types.Model(sbml_filename = filename)

Both are giving me: SBML File (filename) cannot be read without errors.

I can attach the file or test out more ways of importing if needed.

Thanks!!

[ayush9pandey]

I have had this error earlier when the SBML filename was invalid or not present in the directory. Either that or the SBML file is empty somehow? Can you check if one of these is the case for you?

[lianamerk]

The filename is valid and is present in the directory. I am able to read it in with other methods like "xmltodict" and "xml.etree.ElementTree"

[emlarsson]

Hi,

When I try to save my Bioscrape model using:
"M.write_sbml_model("name.xml")"
I get an error saying one of the species is not found. Saving like this worked about a month ago when I saved an earlier version of my model.

Thanks!

[WilliamIX]

@ayush9pandey do you think this bioscrape issue is related to the problems you just fixed in biocrnpyler?

[ayush9pandey]

I don't think so, I suspect this has something to do with latest commits to bioscrape? I haven't recreated the issue on my end yet.

[ayush9pandey]

Thanks to Liana, we tracked down this issue . The problem is with species names that are not allowed in SBML (such as those having colons, semicolons etc.). This is activated when such a species is added in a reaction.

[ayush9pandey]

Fixed with #50.

It should throw an error now saying that SBML does not allow names with colons, etc. @lianamerk whenever you have a chance can you check if that is the case?