[Biopython-dev] Fwd: [Fwd: missing NCBI DTDs]

[Peter Cock]

Three more NCBI Entrez DTD files added:

https://github.com/biopython/biopython/commit/58e024f7704c3b7d3694fda42be6fa47808dad7d

The downside of the new Entrez code is it silently downloads
and caches missing DTD files, so we may want to add something
to the manual release process to check what missing DTD files
have been cached locally... e.g.

$ ls ~/.config/biopython/Bio/Entrez/DTDs/

Regards,

Peter

---------- Forwarded message ----------
From: Peter Cock <p.j.a.cock at googlemail.com>
Date: Mon, Mar 24, 2014 at 4:19 PM
Subject: Re: [Fwd: missing NCBI DTDs]
To: xxx at uci.edu
Cc: "biopython-owner at lists.open-bio.org" <biopython-owner at lists.open-bio.org>


Thanks for getting in touch.

Sadly back when anyone could email the list we had far too
much spam. Unfortunately the only practical solution was to
insist people join the mailing list before posting.

With hindsight the missing DTD message should have also
said please check the latest code / issue tracker - in this
case we've fixed the missing esummary-v1.dtd file:
https://github.com/biopython/biopython/commit/cb560e79def4b24c831725308f17123af4e8eeff

We do seem to be missing the other three through,

bookdoc_140101.dtd
nlmmedlinecitationset_140101.dtd
pubmed_140101.dtd

The sample code you provided makes testing this easier,
thank you.

Peter

---------- Forwarded message ----------
On Mon, Mar 24, 2014 at 4:04 PM,  <xxx at uci.edu> wrote:

When I attempted to run the following python script:

from Bio import Entrez
Entrez.email = "esharman at uci.edu"
handle = Entrez.efetch(db="pubmed", id="24653700", retmode="xml")
record = Entrez.read(handle)
handle.close()
print record[0]["ArticleTitle"]

the following DTDs were reported missing:

bookdoc_140101.dtd
nlmmedlinecitationset_140101.dtd
pubmed_140101.dtd

When I ran a similar script to access the SNP database, the following DTD
was reported missing:

esummary-v1.dtd

Downloading and saving these files to the requested python directory
eliminated the error messages.

Biopython is an absolutely super package! Hope this helps.