Issue with omnipath and dc.translate_net(msigdb, target_organism = 'mouse', unique_by = ('geneset', 'genesymbol'))

[dantyrr]

Describe the bug I see this: Omnipath wrappers (get_resource, get_dorothea and get_progeny) now accept any organism name. so I tried to use this: msigdb = dc.get_resource('MSigDB', organism='Mus musculus') msigdb

I'm in a Jupyter notebook, and I get this: TypeError: object of type 'NoneType' has no len()

pypath-omnipath is not installed. Please install it with: pip install git+https://github.com/saezlab/pypath.git /Users/dtyrell/rosetta2/miniconda3/envs/viaenv/lib/python3.10/site-packages/decoupler/_misc.py:22: UserWarning: pypath-omnipath is not installed. Please install it with: pip install git+https://github.com/saezlab/pypath.git

I've ensured that omnipath is installed:

Name: pypath-omnipath Version: 0.16.15 Summary: Molecular signaling prior knowledge processing Home-page: https://omnipathdb.org/ Author: Denes Turei Author-email: turei.denes@gmail.com License: GPL-3.0-only Location: /Users/dtyrell/rosetta2/miniconda3/envs/viaenv/lib/python3.10/site-packages Requires: beautifulsoup4, certifi, cryptography, dill, future, glom, lxml, matplotlib, numpy, openpyxl, pandas, psutil, pycurl, pypath-common, pyreadr, pysftp, PyYAML, rdata, requests, scipy, sqlparse, tabulate, timeloop, toml, tornado, tqdm, typing_extensions, xlrd

"dc.get_collectri(organism='mouse')" works just fine. "msigdb = dc.get_resource('MSigDB', organism='human')" works just fine

if I download the human MSigDB and try to convert it to mouse, I get the same error: "mouse_msigdb = dc.translate_net(msigdb, target_organism = 'mouse', unique_by = ('geneset', 'genesymbol'))" TypeError: object of type 'NoneType' has no len()

pypath-omnipath is not installed. Please install it with: pip install git+https://github.com/saezlab/pypath.git /Users/dtyrell/rosetta2/miniconda3/envs/viaenv/lib/python3.10/site-packages/decoupler/_misc.py:22: UserWarning: pypath-omnipath is not installed. Please install it with: pip install git+https://github.com/saezlab/pypath.git

Curious if this is a known issue?

When I run this code all together: import omnipath as op

Check the version of the omnipath library

print("OmniPath version:", op.version)

msigdb = dc.get_resource('MSigDB', organism='mouse') msigdb

it confirms I have omnipath v 1.0.8

I am using: AnnData version: 0.10.5.post1 Python version: 3.10.13 (main, Sep 11 2023, 08:39:02) [Clang 14.0.6 ]

thanks for any assistance! Really love the package.

[deeenes]

Apparently it is indeed installed in the correct path. The exception handling can cover some errors. Try to import pypath and some submodules of it and if you see an exception, share it here:

import pypath
from pypath.utils import mapping
from pypath.utils import orthology
from pypath.internals import input_formats

[maltekuehl]

I am experiencing the same issue and it seems to be related with the function _check_if_pypath. If I remove the call to _check_if_pypath and just paste the code from translate_net directly into my code, it works as expected. My theory:

• If I run: import pypath followed by print(pypath.__version__) I get 0.1, which is lower than PYPATH_MIN_VERSION fixed in omnip.py
• The RuntimeError implementation here is faulty, since the Runtime Error will never be raised because it is caught by the except on line 96 and replaced with an ImportError: https://github.com/saezlab/decoupler-py/blob/main/decoupler/omnip.py#L96
• What I expect the origin of the error to be (at least in my case): I accidentally installed the PyPi package pypath before installing pypath-omnipath. For submodules, as required by decoupler, the imports seem to come from pypath-omnipath but for the version it seems to return the version of pypath, the other package. Adding a check that what get's imported at pypath has the correct submodules and warning about this other version might be a good solution for decoupler to help users find the problem.

[PauBadiaM]

Fixed in 06bae401f234e84359c959696ac9a758d55bdbfe