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

Hiroshi Watabe hwatabe at m.tohoku.ac.jp
Tue Nov 8 23:59:59 GMT 2016


Dear Martin,

Thank you for your code. Now it works for me (although I must skip
duplication check because my table does not have eprint.pubmedid).

Regards,

Hiroshi
 On Tue, 8 Nov 2016
12:52:43 +0100 martin.braendle at id.uzh.ch wrote:

> I have published our version of the PubMedID Import plugin to
> 
> 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 Brändle
> Zentrale Informatik
> Universität Zürich
> Stampfenbachstr. 73
> CH-8006 Zürich
> 
> mail: martin.braendle at id.uzh.ch
> phone: +41 44 63 56705
> fax: +41 44 63 54505
> http://www.zi.uzh.ch
> 
> 
> 
> 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
> Universität Zürich
> Stampfenbachstrasse 73
> CH-8006 Zürich
> 
> mail:  jens.vieler at id.uzh.ch
> phone: +41 44 63 56777
> http://www.id.uzh.ch
> 
> Inactive hide details for Adam Field ---07.11.2016 14:39:46---….on,
> incidentally, it’s this line: https://github.com/eprints/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
> 
> 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
> 
> 
> 
> 
> 
> |-----------------------------|
> |                             |
> |-----------------------------|
> |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
> 
> 
> 
> |-----------------------------|
> |                             |
> |-----------------------------|
> |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
> Universität Zürich
> Stampfenbachstrasse 73
> CH-8006 Zürich
> 
> mail:  jens.vieler at id.uzh.ch
> phone: +41 44 63 56777
> http://www.id.uzh.ch
> 
> active hide details for Adam Field ---07.11.2016 11:30:30---Visiting
> the 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.
> 
> 
> 
> 
> |-----------------------|
> |                       |
> |-----------------------|
> |      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
> ';
> ---
>              $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
> *** Options:
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> 
> 
> 
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> 



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