<div dir="ltr">Michiel, Peter,<div><br></div><div>Thanks, for the feedback. Updating <span style="font-family:arial,sans-serif;font-size:12.7272720336914px">startNamespaceDeclHandler </span>seems to be the logical way to go. I don't have much experience with XML schemas, but I will give it a try and make a pull request if I get something decent working.</div><div><br></div><div>Ivan</div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Nov 20, 2014 at 8:20 PM, Michiel de Hoon <span dir="ltr"><<a href="mailto:mjldehoon@yahoo.com" target="_blank">mjldehoon@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Ivan,<br>
<br>
I am the original author of Bio.Entrez.<br>
The parser in Bio.Entrez consists of two parts: The XML parser and the DTD parser.<br>
The DTD parser is used to determine how the elements in the XML file should be represented in Python.<br>
To allow schemas, all that is needed is to write a parser for the schema; the XML parser is unchanged.<br>
In Bio/Entrez/Parser.py, you will find the method startNamespaceDeclHandler;<br>
currently it just raises a NotImplementedError.<br>
If you try the Bio.Entrez parser on your XML file, you will see that this error gets raised.<br>
So all you would have to do is to implement startNamespaceDeclHandler;<br>
it should parallel externalEntityRefHandler, which parses DTD files, though the bulk of the work is done in elementDecl.<br>
Please let me know if you run into any problems.<br>
<br>
Best,<br>
-Michiel.<br>
<br>
<br>
<br>
<br>
--------------------------------------------<br>
On Fri, 11/21/14, Ivan Erill <<a href="mailto:ivan.erill@gmail.com" target="_blank">ivan.erill@gmail.com</a>> wrote:<br>
<br>
Subject: [Biopython] NCBI e-utils parser upgrade<br>
To: <a href="mailto:biopython@mailman.open-bio.org" target="_blank">biopython@mailman.open-bio.org</a><br>
Date: Friday, November 21, 2014, 2:42 AM<br>
<div><div><br>
Hi all,<br>
As part of my<br>
work, I need to deal with the new WP protein records at NCBI<br>
and, specifically, with the information on their coding<br>
sequences. This information is returned by E-utils through a<br>
an integrated protein report type of view:<br>
<a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=231025&rettype=ipg" target="_blank">http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=231025&rettype=ipg</a><br>
<br>
which does not use<br>
a DTD for the XML, but rather a schema. Although there has<br>
been no formal announcement, I've been talking to NCBI<br>
people and they tell me that they will progressively be<br>
moving to schemas (which provide more fine grained<br>
validation specification). Specifically, all new XML exports<br>
from NCBI will be using schemas. I don't believe that<br>
existing DTDs are going to be replaced by schemas for<br>
now.<br>
My original<br>
through was to branch an update for the current XML parser<br>
in BioPython, but it looks like using schemas would be a<br>
major overhaul of the existing code-base and it might make<br>
more sense to develop a parallel parser, so I first wanted<br>
to check on what approach you guys would prefer to do<br>
code-wise.<br>
Regards,<br>
Ivan<br>
<br>
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