[BUG] Error loading model from BioModels repository

[abates20]

Is there an existing issue for this?

• I have searched the existing issues

Problem description

I am trying to use cobra.io.load_model to get models from the BioModels repository, but I keep getting a UnicodeDecodeError. My expectation is that using cobra.io.load_model should load the model from BioModels without raising an error.

Code sample

Code run:

import cobra
cobra.io.load_model("BIOMD0000001089")

Traceback:

Traceback (most recent call last):
  File "/Users/fbg3yp/repos/reconstructor/dev/test.py", line 2, in <module>
    cobra.io.load_model("BIOMD0000001089")
  File "/Users/fbg3yp/Library/Caches/pypoetry/virtualenvs/reconstructor-rVg7mL4q-py3.9/lib/python3.9/site-packages/cobra/io/web/load.py", line 94, in load_model
    return get_model_from_gzip_sbml(data)
  File "/Users/fbg3yp/Library/Caches/pypoetry/virtualenvs/reconstructor-rVg7mL4q-py3.9/lib/python3.9/site-packages/cobra/io/web/load.py", line 199, in get_model_from_gzip_sbml
    libsbml.readSBMLFromString(gzip.decompress(stream).decode("utf-8"))
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa1 in position 10: invalid start byte

Environment

Package Information

Package	Version
cobra	0.30.0

Dependency Information

Package	Version
appdirs~	missing
black	25.11.0
bumpversion	missing
depinfo~	missing
diskcache~	missing
future	1.0.0
httpx~	missing
isort	missing
numpy	1.24.4
optlang~	missing
pandas	2.3.3
pydantic	2.11.10
python-libsbml~	missing
rich	14.1.0
ruamel.yaml~	missing
scipy	missing
swiglpk	5.0.12
tox	missing

Build Tools Information

Package	Version
pip	25.3

Platform Information

Darwin	25.1.0-x86_64
CPython	3.9.24

Anything else?

It appears that the file downloaded from BioModels using BioModels.get_sbml is actually a gzipped zip archive. For example, if you decompress the file contents with gzip.decompress, you can then open the archive with zipfile.ZipFile:

import cobra
import gzip
import zipfile

biomodels = cobra.io.BioModels()
raw_contents = biomodels.get_sbml("BIOMD0000001089")
with open("model.sbml.zip", "wb") as file:
    file.write(gzip.decompress(raw_contents))

with zipfile.ZipFile("model.sbml.zip") as file:
    print(file.namelist())

Output from running the above code:

['manifest.xml', '253_2019_9630_MOESM3_ESM.xml', 'FROG/01_objective.tsv', 'FROG/02_fva.tsv', 'FROG/03_gene_deletion.tsv', 'FROG/04_reaction_deletion.tsv', 'FROG/metadata.json']

I haven't checked thoroughly but I would suspect that '253_2019_9630_MOESM3_ESM.xml' is the actual SBML file for the model.