<html><body bgcolor="#FFFFFF">
<p><font size="2" face="sans-serif">I have published our version of the PubMedID Import plugin to </font><br>
<br>
<a href="https://github.com/eprintsug/PubMedID-Import"><font size="2" face="sans-serif">https://github.com/eprintsug/PubMedID-Import</font></a><br>
<br>
<font size="2" face="sans-serif">It has been updated to cope with the https protocol that NCBI uses and also contains some code that does a duplicate check in the EPrints repo. See also attached phrases files (English and German).</font><br>
<br>
<font size="2" face="sans-serif">Feel free to use from this code whatever you think is useful for your implementation.</font><br>
<br>
<font size="2" face="sans-serif">Best regards,</font><br>
<br>
<font size="2" face="sans-serif">Martin</font><br>
<br>
<font size="2" face="sans-serif">--</font><br>
<font size="2" face="sans-serif">Dr. Martin Brändle</font><br>
<font size="2" face="sans-serif">Zentrale Informatik</font><br>
<font size="2" face="sans-serif">Universität Zürich</font><br>
<font size="2" face="sans-serif">Stampfenbachstr. 73</font><br>
<font size="2" face="sans-serif">CH-8006 Zürich</font><br>
<br>
<font size="2" face="sans-serif">mail: martin.braendle@id.uzh.ch</font><br>
<font size="2" face="sans-serif">phone: +41 44 63 56705</font><br>
<font size="2" face="sans-serif">fax: +41 44 63 54505</font><br>
<font size="2" face="sans-serif"><a href="http://www.zi.uzh.ch">http://www.zi.uzh.ch</a></font><br>
<br>
<img width="16" height="16" src="cid:1__=4EBB0AF6DFD363698f9e8a93df9@lotus.uzh.ch" border="0" alt="Inactive hide details for jens.vieler---07/11/2016 16:05:41---...i think, it is more general if XML::LibXML can't deal with htt"><font size="2" color="#424282" face="sans-serif">jens.vieler---07/11/2016 16:05:41---...i think, it is more general if XML::LibXML can't deal with https. So it's here: perl_lib/EPrints/</font><br>
<br>
<font size="1" color="#5F5F5F" face="sans-serif">Von: </font><font size="1" face="sans-serif">jens.vieler@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 16:05</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">...i think, it is more general if XML::LibXML can't deal with https. So it's here: perl_lib/EPrints/XML/LibXML.pm (Line 69) and 'XML::LibXML->new();' is the wrong parser for our needs.</font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
What would you suggest? Changing Import/PubMedID.pm and bin/metadata_update from anything like</font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
EPrints::XML::parse_url( $url );</font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
to something like </font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
- using LWP to retrieve it<br>
- then LibXML to decode it to xml</font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
or create a more general and new EPrints::XML module?</font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
Workarounds or other quick & dirtys are also welcome</font><font size="3" face="serif"><br>
</font><font size="2" face="sans-serif"><br>
Jens</font><font size="3" face="serif"><br>
<br>
<br>
</font><font size="2" face="sans-serif"><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="2" color="#0000FF" face="sans-serif"><u><br>
</u></font><a href="http://www.id.uzh.ch/"><font size="2" color="#0000FF" face="sans-serif"><u>http://www.id.uzh.ch</u></font></a><font size="3" face="serif"><br>
<br>
</font><img src="cid:1__=4EBB0AF6DFD363698f9e8a93df9@lotus.uzh.ch" width="16" height="16" alt="Inactive hide details for Adam Field ---07.11.2016 14:39:46---….on, incidentally, it’s this line: https://github.com/eprints/"><font size="2" color="#424282" face="sans-serif">Adam Field ---07.11.2016 14:39:46---….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 14:39</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="235">
<ul style="padding-left: 2pt"><a href="http://www.jisc.ac.uk/"><img src="cid:2__=4EBB0AF6DFD363698f9e8a93df9@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: 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="235">
<ul style="padding-left: 2pt"><a href="http://www.jisc.ac.uk/"><img src="cid:3__=4EBB0AF6DFD363698f9e8a93df9@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: 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="serif">Dear Adam, </font><font size="2" face="Consolas">Hiroshi</font><font size="2" face="serif">, 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="serif">?<br>
<br>
Jens</font><font size="3" face="Times New Roman"><br>
</font><font size="2" face="serif"><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="serif"><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__=4EBB0AF6DFD363698f9e8a93df9@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="serif">Adam Field ---07.11.2016 11:30:30---Visiting the URL, I get: <eFetchResult></font><font size="1" color="#5F5F5F" face="serif"><br>
<br>
Von: </font><font size="1" face="serif">Adam Field <Adam.Field@jisc.ac.uk></font><font size="1" color="#5F5F5F" face="serif"><br>
An: </font><font size="1" face="serif">"eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk></font><font size="1" color="#5F5F5F" face="serif"><br>
Datum: </font><font size="1" face="serif">07.11.2016 11:30</font><font size="1" color="#5F5F5F" face="serif"><br>
Betreff: </font><font size="1" face="serif">Re: [EP-tech] fail to import PubMedID</font><font size="1" color="#5F5F5F" face="serif"><br>
Gesendet von: </font><font size="1" face="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="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="188">
<ul style="padding-left: 38pt"><a href="http://www.jisc.ac.uk/"><img src="cid:5__=4EBB0AF6DFD363698f9e8a93df9@lotus.uzh.ch" width="60" height="35" align="bottom" border="0"></a></ul>
</td></tr>
<tr valign="top"><td width="188">
<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>
*** Options: </font><a href="http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech"><font size="2" color="#0000FF" face="Consolas"><u>http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech</u></font></a><font size="2" face="Consolas"><br>
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<p><font size="1" face="Corbel"><br>
Jisc is a registered charity (number 1149740) and a company limited by guarantee which is registered in England under Company No. 5747339, VAT No. GB 197 0632 86. Jisc’s registered office is: One Castlepark, Tower Hill, Bristol, BS2 0JA. T 0203 697 5800.<br>
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Jisc Services Limited is a wholly owned Jisc subsidiary and a company limited by guarantee which is registered in England under company number 2881024, VAT number GB 197 0632 86. The registered office is: One Castle Park, Tower Hill, Bristol BS2 0JA. T 0203 697 5800. </font><font size="2" face="Courier New">*** Options: </font><a href="http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech"><font size="2" color="#0000FF" face="Courier New"><u>http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech</u></font></a><font size="2" face="Courier New"><br>
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