missing DTD's for esearch and esummary

[norling]

Warning about missing DTD's to be downloaded.

to replicate:

Python 2.7.5 (default, Aug 25 2013, 00:04:04) 
[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio import Entrez
>>> import Bio
>>> Bio.__version__
'1.63'
>>> Entrez.email = "my-email@slu.se"
>>> data = Entrez.read(Entrez.esearch("nucleotide", "48165[BioProject]"))
/Library/Python/2.7/site-packages/Bio/Entrez/Parser.py:525: UserWarning: Unable to load 
DTD file esearch.dtd.
[...]
>>> summary = Entrez.read(Entrez.esummary(db="nucleotide", id=data['IdList'][0]))
/Library/Python/2.7/site-packages/Bio/Entrez/Parser.py:525: UserWarning: Unable to load 
DTD file esummary-v1.dtd.
[...]

Keep up the good work! =)

[peterjc]

The missing esearch.dtd file was handled on issue #287 6c2e7db

Strangely I'm not seeing the warning about esummary-v1.dtd here (perhaps already cached locally?):

$ python
Python 2.7.5 (default, Aug 25 2013, 00:04:04) 
[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio import Entrez
>>> Entrez.email = "p.j.a.cock@googlemail.com"
>>> Entrez.read(Entrez.esummary(db="nucleotide", id="295413968"))
[{'Status': 'live', 'Comment': '  ', 'Caption': 'NC_014083', 'Title': 'Torque teno virus 25, complete genome', 'CreateDate': '2010/04/29', 'Extra': 'gi|295413968|ref|NC_014083.1||gnl|NCBI_GENOMES|26054[295413968]', 'TaxId': 687364, 'ReplacedBy': '', u'Item': [], 'Length': 3763, 'Flags': 768, 'UpdateDate': '2010/04/29', u'Id': '295413968', 'Gi': 295413968}]
>>> quit()

The raw XML (which GitHub tries to render if I paste it in full) includes:

<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary v1 20060131//EN" "http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060131/esummary-v1.dtd">

[peterjc]

The missing DTD file will be bundled with the next release (which through prior work will also download and cache missing DTD files automatically).

Thanks for reporting this.