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Re: [EP-tech] Antwort: Antwort: Re: Antwort: Re: fail to import PubMedID
- To: eprints-tech@ecs.soton.ac.uk
- Subject: Re: [EP-tech] Antwort: Antwort: Re: Antwort: Re: fail to import PubMedID
- From: Hiroshi Watabe <hwatabe@m.tohoku.ac.jp>
- Date: Wed, 9 Nov 2016 08:59:59 +0900
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@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@id.uzh.ch > phone: +41 44 63 56705 > fax: +41 44 63 54505 > http://www.zi.uzh.ch > > > > Von: jens.vieler@id.uzh.ch > An: eprints-tech@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@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@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@jisc.ac.uk> > An: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@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@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@jisc.ac.uk> > Date: Monday, 7 November 2016 13:32 > To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@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@ecs.soton.ac.uk> on behalf of > "jens.vieler@id.uzh.ch" <jens.vieler@id.uzh.ch> > Reply-To: "eprints-tech@ecs.soton.ac.uk" > <eprints-tech@ecs.soton.ac.uk> Date: Monday, 7 November 2016 10:45 > To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@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@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@jisc.ac.uk> > An: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@ecs.soton.ac.uk> > Datum: 07.11.2016 11:30 > Betreff: Re: [EP-tech] fail to import PubMedID > Gesendet von: eprints-tech-bounces@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@ecs.soton.ac.uk> on behalf of Hiroshi > Watabe <hwatabe@m.tohoku.ac.jp> > Organization: CYRIC > Reply-To: "eprints-tech@ecs.soton.ac.uk" > <eprints-tech@ecs.soton.ac.uk> Date: Monday, 7 November 2016 01:27 > To: "eprints-tech@ecs.soton.ac.uk" <eprints-tech@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: > http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech *** > Archive: http://www.eprints.org/tech.php/ *** EPrints community wiki: > http://wiki.eprints.org/ *** EPrints developers Forum: > http://forum.eprints.org/ > > > > > > 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. > > 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. *** > Options: http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech > *** Archive: http://www.eprints.org/tech.php/ > *** EPrints community wiki: http://wiki.eprints.org/ > *** EPrints developers Forum: http://forum.eprints.org/*** Options: > http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech > *** Archive: http://www.eprints.org/tech.php/ > *** EPrints community wiki: http://wiki.eprints.org/ > *** EPrints developers Forum: http://forum.eprints.org/*** Options: > http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech > *** Archive: http://www.eprints.org/tech.php/ > *** EPrints community wiki: http://wiki.eprints.org/ > *** EPrints developers Forum: http://forum.eprints.org/ > > > > >
- References:
- [EP-tech] fail to import PubMedID
- From: Hiroshi Watabe <hwatabe@m.tohoku.ac.jp>
- [EP-tech] Antwort: Re: fail to import PubMedID
- From: jens.vieler@id.uzh.ch
- Re: [EP-tech] Antwort: Re: fail to import PubMedID
- From: Adam Field <Adam.Field@jisc.ac.uk>
- Re: [EP-tech] Antwort: Re: fail to import PubMedID
- From: Adam Field <Adam.Field@jisc.ac.uk>
- [EP-tech] Antwort: Antwort: Re: Antwort: Re: fail to import PubMedID
- From: martin.braendle@id.uzh.ch
- [EP-tech] fail to import PubMedID
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