model load error

[brunorbqi]

I was testing the S. aureus rf122 GEM published in the work,doi: 10.1073/pnas.1523199113 , named SA_RF122_uid57661_273036_3.xml. The cobrapy failed in load the model returning the following error:

CobraSBMLError: Something went wrong reading the SBML model. Most likely the SBML model is not valid.

I tried to validate the SBML file using cobrapy and that is what it returns:

A = cobra.io.sbml.validate_sbml_model('SA_RF122_uid57661_273036_3.xml')
A

(None,
{'SBML_FATAL': [],
'SBML_ERROR': ['E0 (Error): XML content (core, L1); Missing XML declaration; Missing XML declaration at beginning of XML input.\n',
'E1 (Error): General SBML conformance (core, L3); No model definition found; An SBML document must contain a element. The element is optional in L3V2 and beyond.\nReference: L3V1 Section 4.1\n'],
'SBML_SCHEMA_ERROR': [],
'SBML_WARNING': [],
'COBRA_FATAL': [],
'COBRA_ERROR': ['No SBML model detected in file.'],
'COBRA_WARNING': [],
'COBRA_CHECK': []})

I wish to know if there is any way to convert a sbml lvl3 fbc 1 to sbml lvl3 fbc2. Because I suppose that is the issue of this model. Best regards.

[Midnighter]

I can't look at the model myself right now, but the error that stands out to me is:

Missing XML declaration; Missing XML declaration at beginning of XML input.

[cdiener]

Checked the ones from the publication and unfortunately those are not valid SBML models. If you add <?xml version="1.0" encoding="UTF-8"?> as the first line of the file you will get a bit further but there are still some invalid IDs.