Aquileo | Recent changes to 11: Conversion to SBML L3 results in SBML L2

Aquileo | #11 Conversion to SBML L3 results in SBML L2

Wed, 11 Mar 2020 10:20:54 -0000

status: accepted --> closed-fixed

Aquileo | #11 Conversion to SBML L3 results in SBML L2

Tue, 10 Mar 2020 14:34:33 -0000

status: open --> accepted
assigned_to: Nicolas Rodriguez

Aquileo | #11 Conversion to SBML L3 results in SBML L2

Tue, 10 Mar 2020 14:33:54 -0000

It is an old "feature" of the converter. If the convrsion fail, it does return the original model to the user, we need to change that so that it does fail and return the errors to the user directly.

Here are the error detected for the model:

line 50572: (21111 [Error]) The value of a <speciesreference> 'species' attribute must be the identifier of an existing <species> in the model.
Reference: L2V1 Section 4.9.5
The <speciesreference> in the <reaction> with id 'biomass_bulk_c0' references species 'cpd11312_c0', which is undefined.</reaction></speciesreference></species></speciesreference>

line 50576: (21111 [Error]) The value of a <speciesreference> 'species' attribute must be the identifier of an existing <species> in the model.
Reference: L2V1 Section 4.9.5
The <speciesreference> in the <reaction> with id 'biomass_bulk_c0' references species 'cpdPolyPn1_c0', which is undefined.</reaction></speciesreference></species></speciesreference>

line 50598: (21111 [Error]) The value of a <speciesreference> 'species' attribute must be the identifier of an existing <species> in the model.
Reference: L2V1 Section 4.9.5
The <speciesreference> in the <reaction> with id 'biomass_bulk_c0' references species 'cpdPolyPn_c0', which is undefined.</reaction></speciesreference></species></speciesreference>

If you correct those errors, you should be able to convert the model. There is a way to force the conversion even if there are some errors which in your case should produce a usable result but it is not supported at the moment.

Aquileo | Conversion to SBML L3 results in SBML L2

Wed, 26 Feb 2020 01:20:33 -0000

I selected input format SBML, then selected output format SBML Level 3 version 1, uploaded a Level 2 version 1 SBML file, hit convert. The resulting file has L3V1 suffix, however, the file header still says SBML Level 2 version 1.

I've attached the input file that I tried in case that helps.

Aquileo | Conversion to SBML L3 results in SBML L2

Wed, 26 Feb 2020 01:20:33 -0000

Ticket 11 has been modified: Conversion to SBML L3 results in SBML L2
Edited By: Nicolas Rodriguez (niko-rodrigue)
Status updated: u'open' => u'accepted'
Owner updated: None => u'niko-rodrigue'

Aquileo | Conversion to SBML L3 results in SBML L2

Wed, 26 Feb 2020 01:20:33 -0000

Ticket 11 has been modified: Conversion to SBML L3 results in SBML L2
Edited By: Nicolas Rodriguez (niko-rodrigue)
Status updated: u'accepted' => u'closed-fixed'