<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10px"><div id="yui_3_16_0_ym19_1_1482206854351_13850"><span>Entrez.read works for me for the example shown.</span></div><div id="yui_3_16_0_ym19_1_1482206854351_13898"><br><span></span></div><div id="yui_3_16_0_ym19_1_1482206854351_13899"><span>Best,</span></div><div id="yui_3_16_0_ym19_1_1482206854351_13900"><span>-Michiel</span></div> <div class="qtdSeparateBR"><br><br></div><div style="display: block;" class="yahoo_quoted"> <div style="font-family: HelveticaNeue-Light, Helvetica Neue Light, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font face="Arial" size="2"> On Sunday, December 18, 2016 11:57 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:<br></font></div> <br><br> <div class="y_msg_container">On Sun, Dec 18, 2016 at 2:50 AM, Peter Cock <<a shape="rect" ymailto="mailto:p.j.a.cock@googlemail.com" href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br clear="none">> On Thu, Dec 15, 2016 at 7:37 PM, Konrad Koehler <<a shape="rect" ymailto="mailto:konrad.koehler@mac.com" href="mailto:konrad.koehler@mac.com">konrad.koehler@mac.com</a>> wrote:<br clear="none">>> Hello everyone,<br clear="none">>><br clear="none">>> I have been using Entrez.parse for years without any errors. However just<br clear="none">>> in the last day or two, it stopped working. I have been able to reproduce<br clear="none">>> the error using the following example from the biopython Package Entrez<br clear="none">>> documentation:<br clear="none">>><br clear="none">><br clear="none">> I can reproduce this. The XML looks sensible, two <PubmedArticle><br clear="none">> tags:<br clear="none">><br clear="none">> <?xml version="1.0" ?><br clear="none">> <!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st<br clear="none">> January 2017//EN"<br clear="none">> "<a shape="rect" href="https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd" target="_blank">https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd</a>"><br clear="none">> <PubmedArticleSet><br clear="none">> <PubmedArticle><br clear="none">> <MedlineCitation Status="MEDLINE" Owner="NLM"><br clear="none">> <PMID Version="1">19304878</PMID><br clear="none">> ...<br clear="none">> </MedlineCitation><br clear="none">> <PubmedData><br clear="none">> ...<br clear="none">> </PubmedData><br clear="none">> </PubmedArticle><br clear="none">> <PubmedArticle><br clear="none">> <MedlineCitation Status="MEDLINE" Owner="NLM"><br clear="none">> <PMID Version="1">14630660</PMID><br clear="none">> ...<br clear="none">> </MedlineCitation><br clear="none">> <PubmedData><br clear="none">> ...<br clear="none">> </PubmedData><br clear="none">> </PubmedArticle><br clear="none">> </PubmedArticleSet><br clear="none">><br clear="none">> Note however it is using a new DTD file for Jan 2017,<br clear="none">><br clear="none">> <a shape="rect" href="https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd" target="_blank">https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd</a><br clear="none">><br clear="none">><br clear="none">>> Does anyone have any suggestions on how to get Entrez.parse working again? I<br clear="none">>> am also curious why this stopped working. Has the NCBI server changed?<br clear="none">>><br clear="none">><br clear="none">> I would guess that the NCBI changed something subtly. Michiel?<br clear="none">><br clear="none">> Peter<br clear="none"><br clear="none">Logged on GitHub,<br clear="none"><br clear="none"><a shape="rect" href="https://github.com/biopython/biopython/issues/1027" target="_blank">https://github.com/biopython/biopython/issues/1027</a><div class="yqt5514597011" id="yqtfd52192"><br clear="none"><br clear="none">Peter<br clear="none"></div><br><br></div> </div> </div> </div></div></body></html>