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Arcadia-Science / ProteinCartography

a pipeline to build similarity maps of protein space
MIT License
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Fix ESMFold API requests - disable SSL to avoid certificate errors #81

Closed naailkhan28 closed 10 months ago

naailkhan28 commented 10 months ago

Fixes #80 - now ESMFold API requests work and don't fail SSL certificate checks.

ProteinCartography/esmfold_apiquery.py has been updated to disable SSL when making the API request, and suppress the warnings from the requests module.

Tested using python ProteinCartography/esmfold_apiquery.py -i 2PK8_monomer.fasta -o ./2PK8_esmfold.pdb - outputs a PDB file as expected.

naailkhan28 commented 10 months ago

I've added more commits - I've changed the warnings.simplefilter() to only include the SSL warning, and I've reformatted my files using the make format workflow as suggested. I've also added a comment indicating that this is (hopefully) a temporary fix.

Let me know if there's anything else :)

keithchev commented 10 months ago

Looks great! There's just one more tiny formatting issue - the comment on line 57 in esmfold_apiquery.py is too long (the max line length in 100 chars and unfortunately ruff doesn't automatically fix this). If you break that line into two lines, then that should get the CI checks passing. Thanks!

naailkhan28 commented 10 months ago

(PS: On Twitter, we saw that you were having issues regarding BLAST with the pipeline, if you share more details in a GitHub issue so we can replicate, we'd be happy to look into and try to issue a fix).

I'm currently having some issues replicating my own BLAST errors! Will investigate further.

I also had some ideas on avoiding BLAST searches but I'll post these in #67

naailkhan28 commented 10 months ago

Looks great! There's just one more tiny formatting issue - the comment on line 57 in esmfold_apiquery.py is too long (the max line length in 100 chars and unfortunately ruff doesn't automatically fix this). If you break that line into two lines, then that should get the CI checks passing. Thanks!

Should be fixed now :)