[Biopython] Entrez.parse error

[Michiel de Hoon]

In what sense is the current result from Entrez.read more difficult to parse than the previous result from Entrez.parse?As far as I can tell, Entrez.read and Entrez.parse are both working correctly.Best,-Michiel


    On Tuesday, December 20, 2016 1:43 PM, Konrad Koehler <konrad.koehler at mac.com> wrote:
 

 Then how does one parse the output? Entrez.parse used to work, but no longer. Apparently NCBI has made changes to their xml that has broken Entrez.parse. Entrez.read returns a complex data structure that is difficult to parse.If one adds "['PubmedArticle']" to line 302 of /Bio/Entrez/Parse.py so that it reads:records = self.stack[0]['PubmedArticle']this suppresses the error message, but it mysteriously returns only the strings "PubmedArticle" and "PubmedBookArticle" and not the citation. Any ideas?
Konrad

On 20 Dec 2016, at 05:16, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
Entrez.read works for me for the example shown.
Best,-Michiel 

    On Sunday, December 18, 2016 11:57 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
 

 On Sun, Dec 18, 2016 at 2:50 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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

Logged on GitHub,

https://github.com/biopython/biopython/issues/1027

Peter


   



   
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