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[EP-tech] Antwort: Antwort: Re: Antwort: Re: fail to import PubMedID

Somewhat related is the announcement by NCBI:

https://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml

Greetings,

Martin

Inactive hide details for martin.braendle---07/11/2016 15:50:16---Also the bin/metadata_update script is affected (line 327, whmartin.braendle---07/11/2016 15:50:16---Also the bin/metadata_update script is affected (line 327, which uses EPrints::XML::parse_url( $url

Von: martin.braendle@id.uzh.ch
An: eprints-tech@ecs.soton.ac.uk
Datum: 07/11/2016 15:50
Betreff: [EP-tech] Antwort: Re:  Antwort: Re:  fail to import PubMedID
Gesendet von: eprints-tech-bounces@ecs.soton.ac.uk




Also the bin/metadata_update script is affected (line 327, which uses EPrints::XML::parse_url( $url )).

Probably all instances of EPrints::XML::parse_url / LibXML::parse_{something} must be rewritten to be able to handle https.

Best regards,

Martin

--
Dr. Martin Brändle
Zentrale Informatik
Universität Zürich
Stampfenbachstr. 73
CH-8006 Zürich

Inactive hide details for Adam Field ---07/11/2016 14:37:17---….on, incidentally, it’s this line: https://github.com/eprints/Adam Field ---07/11/2016 14:37:17---….on, incidentally, it’s this line: https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plu

Von: Adam Field <Adam.Field@jisc.ac.uk>
An: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk>
Datum: 07/11/2016 14:37
Betreff: Re: [EP-tech] Antwort: Re:  fail to import PubMedID
Gesendet von: eprints-tech-bounces@ecs.soton.ac.uk



….on, incidentally, it’s this line:

https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plugin/Import/PubMedID.pm#L58

 

    Adam Field
    SHERPA services analyst developer
 

From: Adam Field <Adam.Field@jisc.ac.uk>
Date: Monday, 7 November 2016 13:32
To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk>
Subject: Re: [EP-tech] Antwort: Re: fail to import PubMedID

I can confirm this – I can also download the metadata via https using curl.

Jens’ suggestions are good.  We should be able to respond to this kind of thing as a community – it’s a non-core, simple bug.  I’m happy to offer advice, code review and testing if anyone wants to give it a stab.  Alternatively, is there anyone out there who can offer me the same if I take a stab?

Best
 

    Adam Field
    SHERPA services analyst developer
 

From: <eprints-tech-bounces@ecs.soton.ac.uk> on behalf of "jens.vieler@id.uzh.ch" <jens.vieler@id.uzh.ch>
Reply-To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk>
Date: Monday, 7 November 2016 10:45
To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk>
Subject: [EP-tech] Antwort: Re: fail to import PubMedID
 

Dear Adam, Hiroshi, List

Watching the same since this morning #-) ...they changed to https this weekend.

wget'ing https works fine, but we canot simply change the protocol in our script, because it seems LibXML can't handle it. So what about getting the https from out of the script and change parse_url into parse_file on that local file. Or change to LWP::Protocol::https?

Jens


--
Jens Vieler
Zentrale Informatik
Universität Zürich
Stampfenbachstrasse 73
CH-8006 Zürich

mail:  jens.vieler@id.uzh.ch
phone: +41 44 63 56777
http://www.id.uzh.ch

active hide details for Adam Field ---07.11.2016 11:30:30---Visiting theAdam Field ---07.11.2016 11:30:30---Visiting the URL, I get: <eFetchResult>

Von: Adam Field <Adam.Field@jisc.ac.uk>
An: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk>
Datum: 07.11.2016 11:30
Betreff: Re: [EP-tech] fail to import PubMedID
Gesendet von: eprints-tech-bounces@ecs.soton.ac.uk





Visiting the URL, I get:

<eFetchResult>
<ERROR>WebEnv parameter is required</ERROR>
</eFetchResult>

If I add a dummy WebEnb parameter, I get:

<eFetchResult>
<ERROR>query_key parameter is required</ERROR>
</eFetchResult>

…it looks like the API the plugin is using has changed L  It’s unlikely to be a local problem.

 

    Adam Field
    SHERPA services analyst developer
 

From: <eprints-tech-bounces@ecs.soton.ac.uk> on behalf of Hiroshi Watabe <hwatabe@m.tohoku.ac.jp>
Organization: CYRIC
Reply-To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk>
Date: Monday, 7 November 2016 01:27
To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk>
Subject: [EP-tech] fail to import PubMedID

Dear all,

It seems PubMed only accepts https now and I cannot import PubMed ID
anymore. I got the following warning message.
Unhandled warning in Import::PubMedID: http error : Unknown IO error

I modified PubMedID.pm as follows but no success.
27c27
<       $self->{EFETCH_URL} =
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=full';
---    
Error message is as follows;
Unhandled exception in Import::PubMedID: Could not create file parser
context for file

Could you help me?

Hiroshi
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