<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hello everyone,<div class=""><br class=""></div><div class="">I have been using Entrez.parse for years without any errors. However just in the last day or two, it stopped working. I have been able to reproduce the error using the following example from the biopython <a href="http://biopython.org/DIST/docs/api/Bio.Entrez-module.html" class="">Package Entrez</a> documentation:</div><div class=""><br class=""></div><div class=""><span class="" style="font-family: Courier; font-size: 11px;">from Bio import Entrez</span></div><font face="Courier" class=""><div class=""><span class="" style="font-size: 11px;">print Bio.__version__ # to verify the that latest version of biopython is installed</span></div><div class=""><span class="" style="font-size: 11px;">>>> 1.68</span></div><div class="" style="font-size: 11px;"><font face="Courier" class=""><br class=""></font></div><span class="" style="font-size: 11px;">Entrez.email = "<a href="mailto:Your.Name.Here@example.org" class="">Your.Name.Here@example.org</a>”</span></font><div class=""><font face="Courier" class="" style="font-size: 11px;"><br class=""></font></div><div class=""><font face="Courier" class="" style="font-size: 11px;">handle = Entrez.efetch("pubmed", id="19304878,14630660", retmode="xml")</font><div class=""><font face="Courier" class="" style="font-size: 11px;">records = Entrez.parse(handle)<br class=""><br class="Apple-interchange-newline">for record in records:<br class=""> print(record['MedlineCitation']['Article']['ArticleTitle’])</font></div><div class=""><div class=""><br class=""></div></div><div class="">The above generates the following error message:</div><div class=""><br class=""></div><div class=""><span class="" style="font-size: 11px;"><font face="Courier" class="">Traceback (most recent call last):</font></span></div><div class=""><div class="" style="margin: 0px; font-size: 11px; line-height: normal;"><span class="" style="font-variant-ligatures: no-common-ligatures;"><font face="Courier" class=""> File "<stdin>", line 1, in <module></font></span></div><div class="" style="margin: 0px; font-size: 11px; line-height: normal;"><span class="" style="font-variant-ligatures: no-common-ligatures;"><font face="Courier" class=""> File "/Users/username/anaconda/lib/python2.7/site-packages/Bio/Entrez/Parser.py", line 304, in parse</font></span></div><div class="" style="margin: 0px; font-size: 11px; line-height: normal;"><span class="" style="font-variant-ligatures: no-common-ligatures;"><font face="Courier" class=""> raise ValueError("The XML file does not represent a list. Please use Entrez.read instead of Entrez.parse")</font></span></div><div class="" style="margin: 0px; font-size: 11px; line-height: normal;"><span class="" style="font-variant-ligatures: no-common-ligatures;"><font face="Courier" class="">ValueError: The XML file does not represent a list. Please use Entrez.read instead of Entrez.parse</font></span></div><div class=""><br class=""></div>records = Entrez.read(handle), does work, but the output is xml that would take some work to parse.<br class=""></div></div><div class=""><br class=""></div><div class="">Does anyone have any suggestions on how to get Entrez.parse working again? I am also curious why this stopped working. Has the NCBI server changed?</div><div class=""><br class=""></div><div class="">Thanks, Konrad</div></body></html>