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<p><font size="2" face="sans-serif">Hi,</font><br>
<br>
<font size="2" face="sans-serif">thanks also to Adam Field who reviewed my code and provided useful suggestions.</font><br>
<br>
<font size="2" face="sans-serif">If you have not done yet, you should get the latest revision which returns an XML error code if the NCBI server fails from </font><a href="https://github.com/eprintsug/PubMedID-Import"><font size="2" face="sans-serif">https://github.com/eprintsug/PubMedID-Import</font></a><font size="2" face="sans-serif"> .</font><br>
<br>
<font size="2" face="sans-serif">Also, Jens had updated the metadata_update script that uses PubMed too and provides it at the URL above.</font><br>
<br>
<font size="2" face="sans-serif">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>
<br>
<img width="16" height="16" src="cid:1__=4EBB0AF5DFB91FB88f9e8a93df9@lotus.uzh.ch" border="0" alt="Inactive hide details for Hiroshi Watabe ---09/11/2016 01:03:35---Dear Martin, Thank you for your code. Now it works for me (al"><font size="2" color="#424282" face="sans-serif">Hiroshi Watabe ---09/11/2016 01:03:35---Dear Martin, Thank you for your code. Now it works for me (although I must skip</font><br>
<br>
<font size="1" color="#5F5F5F" face="sans-serif">Von: </font><font size="1" face="sans-serif">Hiroshi Watabe <hwatabe@m.tohoku.ac.jp></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">09/11/2016 01:03</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Betreff: </font><font size="1" face="sans-serif">Re: [EP-tech] Antwort: 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>
<tt><font size="2">Dear Martin,<br>
<br>
Thank you for your code. Now it works for me (although I must skip<br>
duplication check because my table does not have eprint.pubmedid).<br>
<br>
Regards,<br>
<br>
Hiroshi<br>
On Tue, 8 Nov 2016<br>
12:52:43 +0100 martin.braendle@id.uzh.ch wrote:<br>
<br>
> I have published our version of the PubMedID Import plugin to<br>
> <br>
> </font></tt><tt><font size="2"><a href="https://github.com/eprintsug/PubMedID-Import">https://github.com/eprintsug/PubMedID-Import</a></font></tt><tt><font size="2"><br>
> <br>
> It has been updated to cope with the https protocol that NCBI uses<br>
> and also contains some code that does a duplicate check in the<br>
> EPrints repo. See also attached phrases files (English and German).<br>
> <br>
> Feel free to use from this code whatever you think is useful for your<br>
> implementation.<br>
> <br>
> Best regards,<br>
> <br>
> Martin<br>
> <br>
> --<br>
> Dr. Martin Brändle<br>
> Zentrale Informatik<br>
> Universität Zürich<br>
> Stampfenbachstr. 73<br>
> CH-8006 Zürich<br>
> <br>
> mail: martin.braendle@id.uzh.ch<br>
> phone: +41 44 63 56705<br>
> fax: +41 44 63 54505<br>
> </font></tt><tt><font size="2"><a href="http://www.zi.uzh.ch">http://www.zi.uzh.ch</a></font></tt><tt><font size="2"><br>
> <br>
> <br>
> <br>
> Von: jens.vieler@id.uzh.ch<br>
> An: eprints-tech@ecs.soton.ac.uk<br>
> Datum: 07/11/2016 16:05<br>
> Betreff: [EP-tech] Antwort: Re: Antwort: Re: fail to import<br>
> PubMedID Gesendet von: eprints-tech-bounces@ecs.soton.ac.uk<br>
> <br>
> <br>
> <br>
> ...i think, it is more general if XML::LibXML can't deal with https.<br>
> So it's here: perl_lib/EPrints/XML/LibXML.pm (Line 69) and<br>
> 'XML::LibXML->new ();' is the wrong parser for our needs.<br>
> <br>
> What would you suggest? Changing Import/PubMedID.pm and<br>
> bin/metadata_update from anything like<br>
> <br>
> EPrints::XML::parse_url( $url );<br>
> <br>
> to something like<br>
> <br>
> - using LWP to retrieve it<br>
> - then LibXML to decode it to xml<br>
> <br>
> or create a more general and new EPrints::XML module?<br>
> <br>
> Workarounds or other quick & dirtys are also welcome<br>
> <br>
> Jens<br>
> <br>
> <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<br>
> </font></tt><tt><font size="2"><a href="http://www.id.uzh.ch">http://www.id.uzh.ch</a></font></tt><tt><font size="2"><br>
> <br>
> Inactive hide details for Adam Field ---07.11.2016 14:39:46---….on,<br>
> incidentally, it’s this line: </font></tt><tt><font size="2"><a href="https://github.com/eprints/Adam">https://github.com/eprints/Adam</a></font></tt><tt><font size="2"> Field<br>
> ---07.11.2016 14:39:46---….on, incidentally, it’s this line:<br>
> </font></tt><tt><font size="2"><a href="https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plu">https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plu</a></font></tt><tt><font size="2"><br>
> <br>
> Von: Adam Field <Adam.Field@jisc.ac.uk><br>
> An: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk><br>
> Datum: 07.11.2016 14:39<br>
> Betreff: Re: [EP-tech] Antwort: Re: fail to import PubMedID<br>
> Gesendet von: eprints-tech-bounces@ecs.soton.ac.uk<br>
> <br>
> <br>
> <br>
> ….on, incidentally, it’s this line:<br>
> <br>
> </font></tt><tt><font size="2"><a href="https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plugin/Import/PubMedID.pm#L58">https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plugin/Import/PubMedID.pm#L58</a></font></tt><tt><font size="2"><br>
> <br>
> <br>
> <br>
> <br>
> <br>
> |-----------------------------|<br>
> | |<br>
> |-----------------------------|<br>
> |Adam Field |<br>
> |SHERPA services analyst |<br>
> |developer |<br>
> |-----------------------------|<br>
> <br>
> <br>
> <br>
> <br>
> From: Adam Field <Adam.Field@jisc.ac.uk><br>
> Date: Monday, 7 November 2016 13:32<br>
> To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk><br>
> Subject: Re: [EP-tech] Antwort: Re: fail to import PubMedID<br>
> <br>
> I can confirm this – I can also download the metadata via https using<br>
> curl.<br>
> <br>
> Jens’ suggestions are good. We should be able to respond to this<br>
> kind of thing as a community – it’s a non-core, simple bug. I’m<br>
> happy to offer advice, code review and testing if anyone wants to<br>
> give it a stab. Alternatively, is there anyone out there who can<br>
> offer me the same if I take a stab?<br>
> <br>
> Best<br>
> <br>
> <br>
> <br>
> |-----------------------------|<br>
> | |<br>
> |-----------------------------|<br>
> |Adam Field |<br>
> |SHERPA services analyst |<br>
> |developer |<br>
> |-----------------------------|<br>
> <br>
> <br>
> <br>
> <br>
> From: <eprints-tech-bounces@ecs.soton.ac.uk> on behalf of<br>
> "jens.vieler@id.uzh.ch" <jens.vieler@id.uzh.ch><br>
> Reply-To: "eprints-tech@ecs.soton.ac.uk"<br>
> <eprints-tech@ecs.soton.ac.uk> Date: Monday, 7 November 2016 10:45<br>
> To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk><br>
> Subject: [EP-tech] Antwort: Re: fail to import PubMedID<br>
> <br>
> <br>
> <br>
> Dear Adam, Hiroshi, List<br>
> <br>
> Watching the same since this morning #-) ...they changed to https this<br>
> weekend.<br>
> <br>
> wget'ing https works fine, but we canot simply change the protocol in<br>
> our script, because it seems LibXML can't handle it. So what about<br>
> getting the https from out of the script and change parse_url into<br>
> parse_file on that local file. Or change to LWP::Protocol::https?<br>
> <br>
> Jens<br>
> <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<br>
> </font></tt><tt><font size="2"><a href="http://www.id.uzh.ch">http://www.id.uzh.ch</a></font></tt><tt><font size="2"><br>
> <br>
> active hide details for Adam Field ---07.11.2016 11:30:30---Visiting<br>
> the Adam Field ---07.11.2016 11:30:30---Visiting the URL, I get:<br>
> <eFetchResult><br>
> <br>
> Von: Adam Field <Adam.Field@jisc.ac.uk><br>
> An: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk><br>
> Datum: 07.11.2016 11:30<br>
> Betreff: Re: [EP-tech] fail to import PubMedID<br>
> Gesendet von: eprints-tech-bounces@ecs.soton.ac.uk<br>
> <br>
> <br>
> <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 L It’s<br>
> unlikely to be a local problem.<br>
> <br>
> <br>
> <br>
> <br>
> |-----------------------|<br>
> | |<br>
> |-----------------------|<br>
> | Adam Field |<br>
> | SHERPA services |<br>
> | analyst developer|<br>
> |-----------------------|<br>
> <br>
> <br>
> <br>
> <br>
> From: <eprints-tech-bounces@ecs.soton.ac.uk> on behalf of Hiroshi<br>
> Watabe <hwatabe@m.tohoku.ac.jp><br>
> Organization: CYRIC<br>
> Reply-To: "eprints-tech@ecs.soton.ac.uk"<br>
> <eprints-tech@ecs.soton.ac.uk> Date: Monday, 7 November 2016 01:27<br>
> To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk><br>
> Subject: [EP-tech] fail to import PubMedID<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>
> '<br>
> </font></tt><tt><font size="2"><a href="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=full">http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=full</a></font></tt><tt><font size="2"><br>
> ';<br>
> ---<br>
> $self->{EFETCH_URL} =<br>
> '<br>
> </font></tt><tt><font size="2"><a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=full">https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&rettype=full</a></font></tt><tt><font size="2"><br>
> ';<br>
> <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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