[Biopython] Entrez.parse error

[Peter Cock]

On Thu, Dec 15, 2016 at 7:37 PM, Konrad Koehler <konrad.koehler at mac.com> wrote:
> Hello everyone,
>
> 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 Package Entrez
> documentation:
>

I can reproduce this. The XML looks sensible, two <PubmedArticle>
tags:

<?xml version="1.0" ?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st
January 2017//EN"
"https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd">
<PubmedArticleSet>
<PubmedArticle>
    <MedlineCitation Status="MEDLINE" Owner="NLM">
        <PMID Version="1">19304878</PMID>
        ...
    </MedlineCitation>
    <PubmedData>
       ...
    </PubmedData>
</PubmedArticle>
<PubmedArticle>
    <MedlineCitation Status="MEDLINE" Owner="NLM">
        <PMID Version="1">14630660</PMID>
        ...
    </MedlineCitation>
    <PubmedData>
        ...
    </PubmedData>
</PubmedArticle>
</PubmedArticleSet>

Note however it is using a new DTD file for Jan 2017,

https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd


> 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?
>

I would guess that the NCBI changed something subtly. Michiel?

Peter