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sys-bio / libOmexMeta

libOmexMeta is a library aimed at providing developer-level support for reading, writing, editing and managing semantic annotations for biosimulation models.
https://sys-bio.github.io/libOmexMeta/
Apache License 2.0
8 stars 6 forks source link

Segmentation fault/Exception error #139

Open luciansmith opened 2 years ago

luciansmith commented 2 years ago

When using pyomexmeta, the following code fails:

import pyomexmeta
rdf = pyomexmeta.RDF()
editor =rdf.to_editor("metadata0.xml.txt")
editor.get_xml()

metadata0.xml.txt

On linux, it fails with a segmentation fault; on Windows it fails with an OS error:

OSError: exception: access violation reading 0x0000000000000010

and about 5 million lines of warnings/info from threading.

The problem is probably that the SBML file in question has no 'model' child, but this should be caught before dying spectacularly.

jonrkarr commented 2 years ago

I can also replicate this with pyomexmeta 1.2.13

Here's the example file I tried -- very similar to Lucian's:

<sbml></sbml>
jonrkarr commented 2 years ago

For easy reference, here's the example Lucian tried

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4"/>