Re: [Biopython] BioPython URLError

Peter Cock <[email protected]> Wed, 15 Nov 2023 21:19:46 +0000

Newsgroups	gmane.comp.python.bio.general
Message-ID	<CAKVJ-_6uEec8h6iv6jy80jccCV1Wx-VwB3NZRfzqn-EnLst=6g@mail.gmail.com>

Hopefully just a one-off glitch at the NCBI, try:

print(handle.url)

And then test the URL in your browser?

Peter

On Wed, Nov 15, 2023 at 3:40 PM Jeffrey Posey <[email protected]> wrote:

> I've downloaded BioPython to my Jupyter notebook terminal, entered the
> code from BioPython notebook (below), and it results in a URLError. What
> might be the problem?
>
> from Bio import Entrez
> Entrez.email = " [email protected]".
> handle = Entrez.esearch(db ="protein", retmax = 100, term=" COVID-19
> surface glycoprotein")
> record = Entrez.read(handle)
>
> URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:1002)>
>
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