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



Thanks Martin.
I was just starting to look into this too.  But I?ll look to use yours instead.

Just to double check while we are looking.  Should we still be using the same end point, or should we move over to something more like:
	https://www.ncbi.nlm.nih.gov/pubmed/?term=(26686599[PMID])&report=xml&format=xml

Regards,
	Justin

> On 8 Nov 2016, at 11:52, martin.braendle at id.uzh.ch wrote:
> 
> I have published our version of the PubMedID Import plugin to 
> 
> https://github.com/eprintsug/PubMedID-Import <https://github.com/eprintsug/PubMedID-Import>
> 
> 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).
> 
> Feel free to use from this code whatever you think is useful for your implementation.
> 
> Best regards,
> 
> Martin
> 
> --
> Dr. Martin Br?ndle
> Zentrale Informatik
> Universit?t Z?rich
> Stampfenbachstr. 73
> CH-8006 Z?rich
> 
> mail: martin.braendle at id.uzh.ch
> phone: +41 44 63 56705
> fax: +41 44 63 54505
> http://www.zi.uzh.ch <http://www.zi.uzh.ch/>
> 
> <graycol.gif>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/
> 
> Von:	jens.vieler at id.uzh.ch
> An:	eprints-tech at ecs.soton.ac.uk
> Datum:	07/11/2016 16:05
> Betreff:	[EP-tech] Antwort: Re:  Antwort: Re:  fail to import PubMedID
> Gesendet von:	eprints-tech-bounces at ecs.soton.ac.uk
> 
> 
> 
> ...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.
> 
> What would you suggest? Changing Import/PubMedID.pm and bin/metadata_update from anything like
> 
> EPrints::XML::parse_url( $url );
> 
> to something like 
> 
> - using LWP to retrieve it
> - then LibXML to decode it to xml
> 
> or create a more general and new EPrints::XML module?
> 
> Workarounds or other quick & dirtys are also welcome
> 
> Jens
> 
> 
> 
> -- 
> Jens Vieler
> Zentrale Informatik
> Universit?t Z?rich
> Stampfenbachstrasse 73
> CH-8006 Z?rich
> 
> mail:  jens.vieler at id.uzh.ch
> phone: +41 44 63 56777
> http://www.id.uzh.ch <http://www.id.uzh.ch/>
> 
> <graycol.gif>Adam Field ---07.11.2016 14:39:46---?.on, incidentally, it?s this line: https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plu <https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plu>
> 
> Von: Adam Field <Adam.Field at jisc.ac.uk>
> An: "eprints-tech at ecs.soton.ac.uk" <eprints-tech at ecs.soton.ac.uk>
> Datum: 07.11.2016 14:39
> Betreff: Re: [EP-tech] Antwort: Re:  fail to import PubMedID
> Gesendet von: eprints-tech-bounces at 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 <https://github.com/eprints/eprints/blob/3.3/perl_lib/EPrints/Plugin/Import/PubMedID.pm#L58>
> 
>  
> <35553429.gif> <http://www.jisc.ac.uk/>
> Adam Field
> SHERPA services analyst developer
>  
> 
> From: Adam Field <Adam.Field at jisc.ac.uk>
> Date: Monday, 7 November 2016 13:32
> To: "eprints-tech at ecs.soton.ac.uk" <eprints-tech at 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
>  
> 
> <35669103.gif> <http://www.jisc.ac.uk/>
> Adam Field
> SHERPA services analyst developer
>  
> 
> From: <eprints-tech-bounces at ecs.soton.ac.uk> on behalf of "jens.vieler at id.uzh.ch" <jens.vieler at id.uzh.ch>
> Reply-To: "eprints-tech at ecs.soton.ac.uk" <eprints-tech at ecs.soton.ac.uk>
> Date: Monday, 7 November 2016 10:45
> To: "eprints-tech at ecs.soton.ac.uk" <eprints-tech at 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
> Universit?t Z?rich
> Stampfenbachstrasse 73
> CH-8006 Z?rich
> 
> mail:  jens.vieler at id.uzh.ch
> phone: +41 44 63 56777
> http://www.id.uzh.ch <http://www.id.uzh.ch/>
> 
> <35252086.gif>Adam Field ---07.11.2016 11:30:30---Visiting the URL, I get: <eFetchResult>
> 
> Von: Adam Field <Adam.Field at jisc.ac.uk>
> An: "eprints-tech at ecs.soton.ac.uk" <eprints-tech at ecs.soton.ac.uk>
> Datum: 07.11.2016 11:30
> Betreff: Re: [EP-tech] fail to import PubMedID
> Gesendet von: eprints-tech-bounces at 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.
> 
>  
> <35386694.gif> <http://www.jisc.ac.uk/>
> Adam Field
> SHERPA services analyst developer
>  
> 
> From: <eprints-tech-bounces at ecs.soton.ac.uk> on behalf of Hiroshi Watabe <hwatabe at m.tohoku.ac.jp>
> Organization: CYRIC
> Reply-To: "eprints-tech at ecs.soton.ac.uk" <eprints-tech at ecs.soton.ac.uk>
> Date: Monday, 7 November 2016 01:27
> To: "eprints-tech at ecs.soton.ac.uk" <eprints-tech at 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 <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 <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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>  
> 
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> 
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--
Justin Bradley
Strategy & Technical Lead
EPrints Services
University of Southampton

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