Error getting the Enrichr libraries

[talponer]

Setup

I am reporting a problem with GSEApy version, Python version, and operating
system as follows:

3.8.17 | packaged by conda-forge | (default, Jun 16 2023, 07:06:00) 
[GCC 11.4.0]
CPython
Linux-4.18.0-326.el8.x86_64-x86_64-with-glibc2.10
0.10.8

Expected behaviour

gp.get_library_name()[1:10]
['ARCHS4_Cell-lines',
 'ARCHS4_IDG_Coexp',
 'ARCHS4_Kinases_Coexp',
 'ARCHS4_TFs_Coexp',
 'ARCHS4_Tissues',
 'Achilles_fitness_decrease',
 'Achilles_fitness_increase',
 'Aging_Perturbations_from_GEO_down',
 'Aging_Perturbations_from_GEO_up',
 'Allen_Brain_Atlas_10x_scRNA_2021']

Actual behaviour

gp.get_library_name()[1:10]
Exception: Error getting the Enrichr libraries

The same problem arise when using the function enrichr:

smad3jun_reactome = gp.enrichr(
    gene_list = smad3jun,
    gene_sets = ['Reactome_2016'],
    organism = 'Human', 
    description = 'SMAD3 - JUN',
    background = None, 
    outdir = None,
    verbose = True
 )

2023-11-24 10:33:49,115 Connecting to Enrichr Server to get latest library names


Truncated Traceback (Use C-c C-$ to view full TB):
File /envs/scenicplus/lib/python3.8/site-packages/gseapy/enrichr.py:241, in Enrichr.get_libraries(self)
    239 response = requests.get(lib_url, verify=True)
    240 if not response.ok:
--> 241     raise Exception("Error getting the Enrichr libraries")
    242 libs_json = json.loads(response.text)
    243 libs = [lib['libraryName'] for lib in libs_json['statistics']]

Exception: Error getting the Enrichr libraries

Thank you for checking this!

[dpaysan]

I have the same problem

[romain-lopez]

Hi! I also have the same problem!

[dpaysan]

I recommend as a temporary workaround to download the respective .gmt files from MSigDB and running enrichr with providing the file location of the .gmt file as parameter for the genesets.

[romain-lopez]

Thanks! This is really useful!

[zqfang]

I'll try to connect to enrichr web service to see whether they can provide a more stable link

[zqfang]

@talponer , I just noticed that you've used a quite old version of GSEApy.

Pleaes update GSEApy to the latest version, which will solve your issue

The link to enrichr has expired since it uses a new web site address

[racng]

Upgrading from v1.0.4 to v1.1.0 has solved my issue.