….on, incidentally, it’s this line:

 

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

 

 

 

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

 

 

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

Adam 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';
---

       $self->{EFETCH_URL} =
'https://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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