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Re: [EP-tech] PubMed ID import Plugin

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Hi David!

 Replacing the file with the fixed one worked OOTB. Thanks!

Il 25/10/23 09:38, David R Newman ha scritto:

Hi Yuri,

This issues looks to be fixed in 3.3 by this buxfix back in November
2017:

https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Feprints%2Feprints%2Fcommit%2F5874d48aca85cda6703b3880b8c366926a59ce6c&data=05%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Ca16c92a7d7614b6ebb9108dbd5342b64%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638338192264694890%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=icfM%2FaSJ%2BMAeAue3l%2FoyBTtizX%2FhtU%2F0uULRTAq8hAQ%3D&reserved=0


This looks to be part of the 3.3.16 release.  I think maybe 3.3.15
already has the HTTPS URL but the code that uses this URL cannot
properly do HTTPS requests, so the import plugin was updated so it
can.  There is info in the bugfix which explains what you need to do,
beyond the code change in the commit, to make it work. (I.e. install
Perl module LWP::Protocol::https if not already installed).

Regards

David Newman

On 25/10/2023 8:19 am, Yuri wrote:

CAUTION: This e-mail originated outside the University of Southampton.

CAUTION: This e-mail originated outside the University of Southampton.

Hi!

 Eprins 3.3.15.

 Is the PubMed ID import plugin working? The url is ok but something in
the plugin make the data disappear, I get this error (I've added the url
in the debug):

url:
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fefetch.fcgi%3Fdb%3Dpubmed%26retmode%3Dxml%26rettype%3Dfull%26id%3D37863056&data=05%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Ca16c92a7d7614b6ebb9108dbd5342b64%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638338192264694890%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=rS0xBDcWt5fBl0uiO%2B4u3rn7S6y6B4dc83Vm6e5vRqo%3D&reserved=0


"Error

Unhandled exception in Import::PubMedID: Empty String at
/usr/lib/x86_64-linux-↲
gnu/perl5/5.28/XML/LibXML.pm line 836.
XML::LibXML::parse_string(XML::LibXML=HA↲
SH(0x5563bf0e8a68), undef) called at
/usr/share/eprints3/perl_lib/EPrints/XML/L↲
ibXML.pm line 101 EPrints::XML::parse_xml_string(undef) called at
/usr/share/ep↲
rints3/perl_lib/EPrints/XML.pm line 129
EPrints::XML::parse_string(undef) calle↲
d at /usr/share/eprints3/perl_lib/EPrints/Plugin/Import/PubMedID.pm line
62 EPr↲
ints::Plugin::Import::PubMedID::input_fh(EPrints::Plugin::Import::PubMedID=HASH↲

(0x5563c3b809b0), "dataset", EPrints::DataSet=HASH(0x5563bede14e0),
"fh", File:↲
:Temp=GLOB(0x5563c3b874e8), "user",
EPrints::DataObj::User=HASH(0x5563c3b90c08)↲
, "filename", ...) called at
/usr/share/eprints3/perl_lib/EPrints/Plugin/Screen↲
/Import.pm line 312 eval {...} called at
/usr/share/eprints3/perl_lib/EPrints/P↲
lugin/Screen/Import.pm line 303
EPrints::Plugin::Screen::Import::run_import(EPr↲
ints::Plugin::Screen::Import=HASH(0x5563c0936ed8), 1, 0,
File::Temp=GLOB(0x5 ..."

I've tried also to import from a file with the id but the error is
the same.

From command line:

eprints@xxx:~$ ./bin/import --user admin repo eprint PubMedID
/tmp/id.txt
Warning!
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Feutils.ncbi.nlm.nih.gov%2Fentrez%2Feutils%2Fefetch.fcgi%3Fdb%3Dpubmed%26retmode%3Dxml%26rettype%3Dfull%26id%3D37863056&data=05%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Ca16c92a7d7614b6ebb9108dbd5342b64%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638338192264694890%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=rS0xBDcWt5fBl0uiO%2B4u3rn7S6y6B4dc83Vm6e5vRqo%3D&reserved=0

Warning!
Error! Unhandled exception in Import::PubMedID: Empty String at
/usr/share/eprints3/bin/../perl_lib/EPrints/XML/LibXML.pm line 101.

 How should this work?


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--
Yuri Carrer

 CAB - Centro di Ateneo per le Biblioteche, Università di Padova
 Tel: 049/827 9712 - Via Beato Pellegrino, 28 - Padova