Model notes are not written to SBML

[Midnighter]

Did we already have an issue for this?

import logging

logging.basicConfig(level="INFO")

import cobra
from cobra.io import write_sbml_model

cobra.show_versions()

System Information
==================
OS                     Linux
OS-release 4.15.0-58-generic
Python                 3.6.8

Package Versions
================
cobra                       0.16.0
depinfo                      1.5.1
future                      0.17.1
numpy                       1.17.0
optlang                      1.4.4
pandas                      0.25.0
pip                         19.2.1
python-libsbml-experimental 5.18.0
ruamel.yaml                 0.16.1
setuptools                  41.0.1
six                         1.12.0
swiglpk                     4.65.0
wheel                       0.33.4

model = cobra.Model()

model.notes["Remark"] = "This is not written to SBML."

met = cobra.Metabolite("pyr_c", compartment="c")

model.add_metabolites([met])

met.notes["Remark"] = "I appear."

rxn = cobra.Reaction("GOLD")

model.add_reactions([rxn])

rxn.notes["Remark"] = "What about me?"

write_sbml_model(model, "bug.xml")

[akaviaLab]

Seems to be written on my development branch SBMLImprovments. Try testing after merging #901

[Hemant27031999]

This issue is still unresolved. Notes attached with models are still not written to SBML. Can I work on this?

[akaviaLab]

You're right. Reaction and metabolite notes are written, but model notes aren't.
The problem seems to be if hasattr(cobra_model, "_sbml"): in cobra.io.sbml._model_to_sbml

@matthiaskoenig Why does _sbase_notes_dict(sbase, notes) require the sbase to already exist?

As far as I'm concerned, you can work on it, but you might want to make sure you understand _sbase_notes_dict(sbase, notes).

[Hemant27031999]

I think problem is not with "hasattr(cobra_model, "_sbml")". The _sbml attribute store the notes and annotation corresponding to the main SBML document. Annotation and Notes of models (present inside the SBML) are stored in cobra_model.annotation and cobra_model.notes respectively. In the method "_model_to_sbml()" where parsing is done, only annotation is parsed from cobra_model to libsbml.SBMLDocument (in line 938). Here we need to parse the notes also corresponding to that model. I added this and now it is working fine.

[akaviaLab]

Great! Can you please add relevant tests to test_sbml.py? Thank you. Uri David On Fri, Mar 13, 2020 at 12:46 PM Hemant_Yadav <[email protected]<mailto:[email protected]>> wrote: I think problem is not with "hasattr(cobra_model, "_sbml")". The _sbml attribute store the notes and annotation corresponding to the main SBML document. Annotation and Notes of models (present inside the SBML) are stored in cobra_model.annotation and cobra_model.notes respectively. In the method "_model_to_sbml()" where parsing is done, only annotation is parsed from cobra_model to libsbml.SBMLDocument (in line 938). Here we need to parse the notes also corresponding to that model. I added this and now it is working fine. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#902 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACQYYZVVUI3SKC5QDETEH2DRHJPONANCNFSM4IOPH2MA>.

…

-- Uri David Akavia, Ph.D. Assistant Professor, Biochemistry Department Associate Member, Rosalind & Morris Goodman Cancer Research Centre Membre Associé, Centre de recherche sur le cancer Rosalind & Morris Goodman [email protected]<mailto:[email protected]> McIntyre Medical Sciences Building 3655 Promenade Sir William Osler, Room 815B Montreal, Quebec H3G 1Y6 Office tel: 514-398-8526 Facebook<https://www.facebook.com/GCRC.McGill/> | Twitter<https://twitter.com/McGillGCRC> | LinkedIn<https://www.linkedin.com/company/goodman-cancer-research-centre-mcgill-university/> | Instagram<http://www.instagram.com/goodmancancerresearchcentre> | Gala<http://mcgillgcrcgala.com/> | Défi Canderel<https://www.deficanderel.com/> [cid:[email protected]]

[cdiener]

Relevant prior discussions are here #695 (also see the schema link in there).

[Midnighter]

Resolved by #943