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

[Michiel de Hoon]

We could consider to not include any DTDs with Biopython, and rely on downloading them automatically.
This seems a better test case than what we currently have, because as NCBI updates their DTDs, Bio.Entrez depends on this automatic download capability.

Best,
-Michiel.

--------------------------------------------
On Mon, 3/24/14, Peter Cock <p.j.a.cock at googlemail.com> wrote:

 Subject: [Biopython-dev] Fwd: [Fwd: missing NCBI DTDs]
 To: "Biopython-Dev Mailing List" <biopython-dev at biopython.org>
 Date: Monday, March 24, 2014, 12:42 PM
 
 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.
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