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



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 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



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

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
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

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
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