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Re: [EP-tech] PubMed ID import Plugin

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%7C0d8159b09fc3457363e508dbd52d6c06%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638338163281088773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=L9QB7sW2Mk9EdoX41UZBmer1iVyON9vYmB7SchwioOc%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%7C0d8159b09fc3457363e508dbd52d6c06%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638338163281088773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Vp82ZjKy8VRlftmFHyQgrjtG0aRmDO0mOrVw0mgv%2Fms%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%7C0d8159b09fc3457363e508dbd52d6c06%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638338163281088773%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Vp82ZjKy8VRlftmFHyQgrjtG0aRmDO0mOrVw0mgv%2Fms%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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