sqlite3.OperationalError: disk I/O error

[Jamie Stankiewiz]

Hi there!!

I am new to cobrapy and tried to load a simple model to get started. Below is my code that I ran. Immediately, I got a sqlite3 disk error and I am wondering what the underlying issues is and how I can fix this? Thank you in advanced!!

 

Test.py:

 

import cobra

from cobra.io import load_model

model = load_model("textbook")

 

Traceback:

 

Traceback (most recent call last):

  File "/test.py", line 5, in <module>

    model = load_model("textbook")

  File "/.local/lib/python3.9/site-packages/cobra/io/web/load.py", line 88, in load_model

    data = _cached_load(

  File "/.local/lib/python3.9/site-packages/cobra/io/web/load.py", line 121, in _cached_load

    with diskcache.Cache(

  File "/.local/lib/python3.9/site-packages/diskcache/core.py", line 478, in __init__

    self.reset(key, value, update=False)

  File "/.local/lib/python3.9/site-packages/diskcache/core.py", line 2431, in reset

    ((old_value,),) = sql(

sqlite3.OperationalError: disk I/O error

 

 

 

Thank you for the help!
Jamie

 

[Joshua Lerman]

Hi Jamie,

Remember me?  I can confirm your code is absolutely fine. I think the error is more about where you are running the code and if there is some sort of permissions error.

From your desktop:

# Create a new virtual environment
python -m venv cobra_env

# Activate the virtual environment
# For Windows:
cobra_env\Scripts\activate
# For macOS/Linux:
source cobra_env/bin/activate

# Install cobrapy
pip install cobra

Then try running test.py on your desktop.

Please write back if you have difficulties. This page may also be useful for you https://github.com/opencobra/cobrapy/blob/devel/INSTALL.rst

Best,

Josh

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[Jamie Stankiewiz]

Wow, Josh Lerman - hi!!
Hope you are well!

Thanks for the feedback here. I suspected this has to be related to a vm issue that I'm running this code on. I'll reply back if there's more issues that come up.

Happy holidays!!
Jamie

[Matthias König]

Just try this in a clean virtual environment (e.g. created with uv). Also I recommend using a more up to date python version such as py3.12.

I had no issues loading the model in a clean test environment:

```

mkoenig@mklab:~/Downloads/test_cobrapy$ uv venv --python 3.12
Using CPython 3.12.8 interpreter at: /usr/bin/python3.12
Creating virtual environment at: .venv
Activate with: source .venv/bin/activate

mkoenig@mklab:~/Downloads/test_cobrapy$ uv pip install cobra
Resolved 34 packages in 553ms
Prepared 15 packages in 4.19s
Installed 34 packages in 44ms
 + annotated-types==0.7.0
 + anyio==4.8.0
 + appdirs==1.4.4
 + certifi==2024.12.14
 + cobra==0.29.1
 + depinfo==2.2.0
 + diskcache==5.6.3
 + future==1.0.0
 + h11==0.14.0
 + httpcore==1.0.7
 + httpx==0.28.1
 + idna==3.10
 + importlib-resources==6.5.2
 + markdown-it-py==3.0.0
 + mdurl==0.1.2
 + mpmath==1.3.0
 + numpy==2.2.1
 + optlang==1.8.2
 + pandas==2.2.3
 + pydantic==2.10.4
 + pydantic-core==2.27.2
 + pygments==2.19.1
 + python-dateutil==2.9.0.post0
 + python-libsbml==5.20.4
 + pytz==2024.2
 + rich==13.9.4
 + ruamel-yaml==0.18.10
 + ruamel-yaml-clib==0.2.12
 + six==1.17.0
 + sniffio==1.3.1
 + swiglpk==5.0.12
 + sympy==1.13.3
 + typing-extensions==4.12.2
 + tzdata==2024.2

mkoenig@mklab:~/Downloads/test_cobrapy$ source .venv/bin/activate

(test_cobrapy) mkoenig@mklab:~/Downloads/test_cobrapy$ python
Python 3.12.8 (main, Dec  4 2024, 08:54:13) [GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

>>> import cobra
>>> from cobra.io import load_model
>>> model = load_model("textbook")

>>> model
<Model e_coli_core at 0x7f59c07f6630>
```

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