EPrints Technical Mailing List Archive

Message: #09462


< Previous (by date) | Next (by date) > | < Previous (in thread) | Next (in thread) > | Messages - Most Recent First | Threads - Most Recent First

[EP-tech] PubMed ID import Plugin


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%7C833890423d864812e54008dbd52ac698%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638338151912470816%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WY0VKmDC5BjPZBdnHIPJ9uvf9J1zrlaxR8IUSMqzif8%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%7C833890423d864812e54008dbd52ac698%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638338151912470816%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WY0VKmDC5BjPZBdnHIPJ9uvf9J1zrlaxR8IUSMqzif8%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?