<html><body bgcolor="#FFFFFF">
<p><font size="2" face="sans-serif">Somewhat related is the announcement by NCBI:</font><br>
<br>
<a href="https://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml"><font size="2" face="sans-serif">https://www.ncbi.nlm.nih.gov/home/develop/https-guidance.shtml</font></a><br>
<br>
<font size="2" face="sans-serif">Greetings,</font><br>
<br>
<font size="2" face="sans-serif">Martin</font><br>
<br>
<img width="16" height="16" src="cid:1__=4EBB0AF7DFC1B2328f9e8a93df9@lotus.uzh.ch" border="0" alt="Inactive hide details for martin.braendle---07/11/2016 15:50:16---Also the bin/metadata_update script is affected (line 327, wh"><font size="2" color="#424282" face="sans-serif">martin.braendle---07/11/2016 15:50:16---Also the bin/metadata_update script is affected (line 327, which uses EPrints::XML::parse_url( $url</font><br>
<br>
<font size="1" color="#5F5F5F" face="sans-serif">Von: </font><font size="1" face="sans-serif">martin.braendle@id.uzh.ch</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">An: </font><font size="1" face="sans-serif">eprints-tech@ecs.soton.ac.uk</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Datum: </font><font size="1" face="sans-serif">07/11/2016 15:50</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Betreff: </font><font size="1" face="sans-serif">[EP-tech] Antwort: Re: Antwort: Re: fail to import PubMedID</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Gesendet von: </font><font size="1" face="sans-serif">eprints-tech-bounces@ecs.soton.ac.uk</font><br>
<hr width="100%" size="2" align="left" noshade style="color:#8091A5; "><br>
<br>
<br>
<font size="2" face="sans-serif">Also the bin/metadata_update script is affected (line 327, which uses EPrints::XML::parse_url( $url )).</font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
Probably all instances of EPrints::XML::parse_url / LibXML::parse_{something} must be rewritten to be able to handle https.<br>
<br>
Best regards,</font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
Martin</font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
--<br>
Dr. Martin Brändle<br>
Zentrale Informatik<br>
Universität Zürich<br>
Stampfenbachstr. 73<br>
CH-8006 Zürich</font><font size="3" face="serif"><br>
<br>
</font><img src="cid:1__=4EBB0AF7DFC1B2328f9e8a93df9@lotus.uzh.ch" width="16" height="16" alt="Inactive hide details for Adam Field ---07/11/2016 14:37:17---….on, incidentally, it’s this line: https://github.com/eprints/"><font size="2" color="#424282" face="sans-serif">Adam Field ---07/11/2016 14:37:17---….on, incidentally, it’s this line: </font><a href="https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plu"><font size="2" color="#0000FF" face="sans-serif"><u>https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plu</u></font></a><font size="3" face="serif"><br>
</font><font size="1" color="#5F5F5F" face="sans-serif"><br>
Von: </font><font size="1" face="sans-serif">Adam Field <Adam.Field@jisc.ac.uk></font><font size="1" color="#5F5F5F" face="sans-serif"><br>
An: </font><font size="1" face="sans-serif">"eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk></font><font size="1" color="#5F5F5F" face="sans-serif"><br>
Datum: </font><font size="1" face="sans-serif">07/11/2016 14:37</font><font size="1" color="#5F5F5F" face="sans-serif"><br>
Betreff: </font><font size="1" face="sans-serif">Re: [EP-tech] Antwort: Re: fail to import PubMedID</font><font size="1" color="#5F5F5F" face="sans-serif"><br>
Gesendet von: </font><font size="1" face="sans-serif">eprints-tech-bounces@ecs.soton.ac.uk</font><font size="3" face="serif"><br>
</font><hr width="100%" size="2" align="left" noshade><font size="3" face="serif"><br>
<br>
</font><font size="2" face="Calibri"><br>
….on, incidentally, it’s this line:<br>
</font><font size="3" color="#0000FF" face="serif"><u><br>
</u></font><a href="https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plugin/Import/PubMedID.pm#L58"><font size="2" color="#0000FF" face="Calibri"><u>https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plugin/Import/PubMedID.pm#L58</u></font></a><font size="2" face="Calibri"><br>
</font><font size="2" face="Times New Roman"><br>
</font><font size="3" face="serif"> </font>
<p>
<table class="MsoNormalTable" border="1">
<tr valign="top"><td width="217">
<ul style="padding-left: 2pt"><a href="http://www.jisc.ac.uk/"><img src="cid:2__=4EBB0AF7DFC1B2328f9e8a93df9@lotus.uzh.ch" width="60" height="35" align="bottom" border="0"></a></ul>
</td></tr>
<tr valign="top"><td width="217">
<ul style="padding-left: 2pt"><font size="3" color="#2C3841" face="Corbel"><b>Adam Field</b></font><font size="3" color="#2C3841" face="Corbel"><br>
SHERPA services analyst developer</font></ul>
</td></tr>
</table>
<font size="2" face="Calibri"> <br>
</font><font size="3" face="Calibri"><b><br>
From: </b></font><font size="3" face="Calibri">Adam Field <Adam.Field@jisc.ac.uk></font><font size="3" face="Calibri"><b><br>
Date: </b></font><font size="3" face="Calibri">Monday, 7 November 2016 13:32</font><font size="3" face="Calibri"><b><br>
To: </b></font><font size="3" face="Calibri">"eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk></font><font size="3" face="Calibri"><b><br>
Subject: </b></font><font size="3" face="Calibri">Re: [EP-tech] Antwort: Re: fail to import PubMedID</font><font size="3" face="Times New Roman"><br>
</font><font size="2" face="Calibri"><br>
I can confirm this – I can also download the metadata via https using curl.<br>
<br>
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?<br>
<br>
Best</font><font size="2" face="Times New Roman"><br>
</font><font size="3" face="serif"> </font>
<p>
<table class="MsoNormalTable" border="1">
<tr valign="top"><td width="217">
<ul style="padding-left: 2pt"><a href="http://www.jisc.ac.uk/"><img src="cid:3__=4EBB0AF7DFC1B2328f9e8a93df9@lotus.uzh.ch" width="60" height="35" align="bottom" border="0"></a></ul>
</td></tr>
<tr valign="top"><td width="217">
<ul style="padding-left: 2pt"><font size="3" color="#2C3841" face="Corbel"><b>Adam Field</b></font><font size="3" color="#2C3841" face="Corbel"><br>
SHERPA services analyst developer</font></ul>
</td></tr>
</table>
<font size="2" face="Calibri"> <br>
</font><font size="3" face="Calibri"><b><br>
From: </b></font><font size="3" face="Calibri"><eprints-tech-bounces@ecs.soton.ac.uk> on behalf of "jens.vieler@id.uzh.ch" <jens.vieler@id.uzh.ch></font><font size="3" face="Calibri"><b><br>
Reply-To: </b></font><font size="3" face="Calibri">"eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk></font><font size="3" face="Calibri"><b><br>
Date: </b></font><font size="3" face="Calibri">Monday, 7 November 2016 10:45</font><font size="3" face="Calibri"><b><br>
To: </b></font><font size="3" face="Calibri">"eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk></font><font size="3" face="Calibri"><b><br>
Subject: </b></font><font size="3" face="Calibri">[EP-tech] Antwort: Re: fail to import PubMedID</font><font size="3" face="Times New Roman"><br>
</font><font size="3" face="serif"> </font>
<p><font size="2" face="Helvetica">Dear Adam, </font><font size="2" face="Consolas">Hiroshi</font><font size="2" face="Helvetica">, List<br>
<br>
Watching the same since this morning #-) ...they changed to https this weekend. <br>
<br>
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 </font><font size="3" face="serif">LWP::Protocol::https</font><font size="2" face="Helvetica">?<br>
<br>
Jens</font><font size="3" face="Times New Roman"><br>
</font><font size="2" face="Helvetica"><br>
<br>
-- <br>
Jens Vieler<br>
Zentrale Informatik<br>
Universität Zürich<br>
Stampfenbachstrasse 73<br>
CH-8006 Zürich<br>
<br>
mail: jens.vieler@id.uzh.ch<br>
phone: +41 44 63 56777</font><font size="3" color="#0000FF" face="serif"><u><br>
</u></font><a href="http://www.id.uzh.ch/"><font size="2" color="#0000FF" face="Helvetica"><u>http://www.id.uzh.ch</u></font></a><font size="3" face="Times New Roman"><br>
</font><font size="3" face="serif"><br>
</font><img src="cid:4__=4EBB0AF7DFC1B2328f9e8a93df9@lotus.uzh.ch" width="16" height="16" alt="active hide details for Adam Field ---07.11.2016 11:30:30---Visiting the"><font size="2" color="#424282" face="Helvetica">Adam Field ---07.11.2016 11:30:30---Visiting the URL, I get: <eFetchResult></font><font size="1" color="#5F5F5F" face="Helvetica"><br>
<br>
Von: </font><font size="1" face="Helvetica">Adam Field <Adam.Field@jisc.ac.uk></font><font size="1" color="#5F5F5F" face="Helvetica"><br>
An: </font><font size="1" face="Helvetica">"eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk></font><font size="1" color="#5F5F5F" face="Helvetica"><br>
Datum: </font><font size="1" face="Helvetica">07.11.2016 11:30</font><font size="1" color="#5F5F5F" face="Helvetica"><br>
Betreff: </font><font size="1" face="Helvetica">Re: [EP-tech] fail to import PubMedID</font><font size="1" color="#5F5F5F" face="Helvetica"><br>
Gesendet von: </font><font size="1" face="Helvetica">eprints-tech-bounces@ecs.soton.ac.uk</font><font size="3" face="serif"><br>
</font><hr width="100%" size="2" align="left" noshade><font size="3" face="Times New Roman"><br>
<br>
</font><font size="2" face="Calibri"><br>
<br>
Visiting the URL, I get:<br>
<br>
<eFetchResult><br>
<ERROR>WebEnv parameter is required</ERROR><br>
</eFetchResult><br>
<br>
If I add a dummy WebEnb parameter, I get:<br>
<br>
<eFetchResult><br>
<ERROR>query_key parameter is required</ERROR><br>
</eFetchResult><br>
<br>
…it looks like the API the plugin is using has changed </font><font size="2" face="Wingdings">L</font><font size="2" face="Calibri"> It’s unlikely to be a local problem.</font><font size="2" face="Times New Roman"><br>
</font><font size="3" face="Times New Roman"><br>
</font><font size="3" face="serif"> </font>
<p>
<table class="MsoNormalTable" border="1">
<tr valign="top"><td width="235">
<ul style="padding-left: 38pt"><a href="http://www.jisc.ac.uk/"><img src="cid:5__=4EBB0AF7DFC1B2328f9e8a93df9@lotus.uzh.ch" width="60" height="35" align="bottom" border="0"></a></ul>
</td></tr>
<tr valign="top"><td width="235">
<ul style="padding-left: 38pt"><font size="3" color="#2C3841" face="Corbel"><b>Adam Field</b></font><font size="3" color="#2C3841" face="Corbel"><br>
SHERPA services analyst developer</font></ul>
</td></tr>
</table>
<font size="2" face="Calibri"> </font><font size="3" face="Calibri"><b><br>
<br>
From: </b></font><font size="3" face="Calibri"><eprints-tech-bounces@ecs.soton.ac.uk> on behalf of Hiroshi Watabe <hwatabe@m.tohoku.ac.jp></font><font size="3" face="Calibri"><b><br>
Organization: </b></font><font size="3" face="Calibri">CYRIC</font><font size="3" face="Calibri"><b><br>
Reply-To: </b></font><font size="3" face="Calibri">"eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk></font><font size="3" face="Calibri"><b><br>
Date: </b></font><font size="3" face="Calibri">Monday, 7 November 2016 01:27</font><font size="3" face="Calibri"><b><br>
To: </b></font><font size="3" face="Calibri">"eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk></font><font size="3" face="Calibri"><b><br>
Subject: </b></font><font size="3" face="Calibri">[EP-tech] fail to import PubMedID</font><font size="2" face="Consolas"><br>
<br>
Dear all,<br>
<br>
It seems PubMed only accepts https now and I cannot import PubMed ID<br>
anymore. I got the following warning message.<br>
Unhandled warning in Import::PubMedID: http error : Unknown IO error <br>
<br>
I modified PubMedID.pm as follows but no success.<br>
27c27<br>
< $self->{EFETCH_URL} =<br>
'</font><a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=full"><font size="2" color="#0000FF" face="Consolas"><u>http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=full</u></font></a><font size="2" face="Consolas">';<br>
---</font><font size="3" face="Times New Roman"> </font><font size="3" face="serif"> </font>
<ul style="padding-left: 36pt"><font size="2" face="Consolas"> $self->{EFETCH_URL} =<br>
'</font><a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=full"><font size="2" color="#0000FF" face="Consolas"><u>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=full</u></font></a><font size="2" face="Consolas">'; </font></ul>
<font size="2" face="Consolas"> <br>
Error message is as follows;<br>
Unhandled exception in Import::PubMedID: Could not create file parser<br>
context for file <br>
<br>
Could you help me?<br>
<br>
Hiroshi<br>
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