[EP-tech] Re: Import Items error - Pubmed XML

Tim Brody tdb2 at ecs.soton.ac.uk
Fri Mar 16 17:51:04 GMT 2012


Hi,

Definitely some problems here ...

I've written a fix for this regression:
http://trac.eprints.org/eprints/changeset/7512

It also fixes a seg fault to do with non-ASCII characters (but that may
just be my version of libxml).

/Tim.

On Fri, 2012-03-16 at 16:04 +0100, Ulf Laube wrote:
> Hi all,
> 
> if I try to import a pubmed xml  paste data and uploading file occurs same 
> error:
> unexpected tag: expected <> found <PubmedArticleSet>
> 
> xml sample file attached.
> 
> 
> settings: 
> eprints r7487
> opensuse 12.1 x86
> kernel 3.2.9
> apache2-prefork-2.2.21
> apache2-mod_perl-2.0.5
> mysql-community-server-5.5.16
> perl-5.14.2
> libxml2 2.7.8
> perl-XML-LibXML 1.95
> perl-libxml-perl 0.08
> 
> 
> error_log:
>  at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/XML/LibXML.pm 
> line 877
>     
> XML::LibXML::parse_fh('XML::LibXML=HASH(0xba1043f8)', 'File::Temp=GLOB(0xba122d38)') 
> called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/XML/LibXML/SAX.pm 
> line 99
>     eval {...} called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/XML/LibXML/SAX.pm 
> line 98
>     XML::LibXML::SAX::_parse('XML::LibXML::SAX=HASH(0xba12ed30)') called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/XML/LibXML/SAX.pm 
> line 54
>     
> XML::LibXML::SAX::_parse_bytestream('XML::LibXML::SAX=HASH(0xba12ed30)', 'File::Temp=GLOB(0xba122d38)') 
> called at /opt/eprints3/perl_lib/XML/SAX/Base.pm line 2602
>     
> XML::SAX::Base::parse('XML::LibXML::SAX=HASH(0xba12ed30)', 'HASH(0xba130008)') 
> called at /opt/eprints3/perl_lib/XML/SAX/Base.pm line 2631
>     
> XML::SAX::Base::parse_file('XML::LibXML::SAX=HASH(0xba12ed30)', 'File::Temp=GLOB(0xba122d38)') 
> called at /opt/eprints3/perl_lib/EPrints/XML/LibXML.pm line 131
>     
> EPrints::XML::event_parse('File::Temp=GLOB(0xba122d38)', 'EPrints::Plugin::Import::DefaultXML::DOMHandler=HASH(0xb7f0f5b0)') 
> called at /opt/eprints3/perl_lib/EPrints/Plugin/Import/DefaultXML.pm line 81
>     eval {...} called 
> at /opt/eprints3/perl_lib/EPrints/Plugin/Import/DefaultXML.pm line 81
>     
> EPrints::Plugin::Import::DefaultXML::input_fh('EPrints::Plugin::Import::PubMedXML=HASH(0xba1306b8)', 'dataset', 'EPrints::DataSet=HASH(0xb8b91860)', 'fh', 'File::Temp=GLOB(0xba122d38)', 'user', 'EPrints::DataObj::User=HASH(0xba128c20)', 'filename', 
> undef, ...) called at /opt/eprints3/perl_lib/EPrints/Plugin/Screen/Import.pm 
> line 298
>     eval {...} called 
> at /opt/eprints3/perl_lib/EPrints/Plugin/Screen/Import.pm line 297
>     
> EPrints::Plugin::Screen::Import::run_import('EPrints::Plugin::Screen::Import=HASH(0xba11ed80)', 
> 1, 0, 'File::Temp=GLOB(0xba122d38)') called 
> at /opt/eprints3/perl_lib/EPrints/Plugin/Screen/Import.pm line 146
>     
> EPrints::Plugin::Screen::Import::action_test_data('EPrints::Plugin::Screen::Import=HASH(0xba11ed80)') 
> called at /opt/eprints3/perl_lib/EPrints/Plugin/Screen.pm line 240
>     
> EPrints::Plugin::Screen::from('EPrints::Plugin::Screen::Import=HASH(0xba11ed80)') 
> called at /opt/eprints3/perl_lib/EPrints/ScreenProcessor.pm line 310
>     
> EPrints::ScreenProcessor::process('EPrints::ScreenProcessor', 'session', 'EPrints::Repository=HASH(0xb9dfcef0)', 'template', 
> undef, 'url', '/cgi/users/home') called at /opt/eprints3/cgi/users/home line 
> 40
>     
> ModPerl::ROOT::ModPerl::Registry::opt_eprints3_cgi_users_home::handler('Apache2::RequestRec=SCALAR(0xb9ba57a8)') 
> called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/RegistryCooker.pm 
> line 204
>     eval {...} called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/RegistryCooker.pm 
> line 204
>     ModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0xb9acc980)') called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/RegistryCooker.pm 
> line 170
>     
> ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0xb9acc980)') 
> called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/Registry.pm 
> line 31
>     
> ModPerl::Registry::handler('ModPerl::Registry', 'Apache2::RequestRec=SCALAR(0xb9ba57a8)') 
> called at -e line 0
>     eval {...} called at -e line 0
>  
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/XML/LibXML/SAX.pm 
> line 109
>     XML::LibXML::SAX::_parse('XML::LibXML::SAX=HASH(0xba12ed30)') called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/XML/LibXML/SAX.pm 
> line 54
>     
> XML::LibXML::SAX::_parse_bytestream('XML::LibXML::SAX=HASH(0xba12ed30)', 'File::Temp=GLOB(0xba122d38)') 
> called at /opt/eprints3/perl_lib/XML/SAX/Base.pm line 2602
>     
> XML::SAX::Base::parse('XML::LibXML::SAX=HASH(0xba12ed30)', 'HASH(0xba130008)') 
> called at /opt/eprints3/perl_lib/XML/SAX/Base.pm line 2631
>     
> XML::SAX::Base::parse_file('XML::LibXML::SAX=HASH(0xba12ed30)', 'File::Temp=GLOB(0xba122d38)') 
> called at /opt/eprints3/perl_lib/EPrints/XML/LibXML.pm line 131
>     
> EPrints::XML::event_parse('File::Temp=GLOB(0xba122d38)', 'EPrints::Plugin::Import::DefaultXML::DOMHandler=HASH(0xb7f0f5b0)') 
> called at /opt/eprints3/perl_lib/EPrints/Plugin/Import/DefaultXML.pm line 81
>     eval {...} called 
> at /opt/eprints3/perl_lib/EPrints/Plugin/Import/DefaultXML.pm line 81
>     
> EPrints::Plugin::Import::DefaultXML::input_fh('EPrints::Plugin::Import::PubMedXML=HASH(0xba1306b8)', 'dataset', 'EPrints::DataSet=HASH(0xb8b91860)', 'fh', 'File::Temp=GLOB(0xba122d38)', 'user', 'EPrints::DataObj::User=HASH(0xba128c20)', 'filename', 
> undef, ...) called at /opt/eprints3/perl_lib/EPrints/Plugin/Screen/Import.pm 
> line 298
>     eval {...} called 
> at /opt/eprints3/perl_lib/EPrints/Plugin/Screen/Import.pm line 297
>     
> EPrints::Plugin::Screen::Import::run_import('EPrints::Plugin::Screen::Import=HASH(0xba11ed80)', 
> 1, 0, 'File::Temp=GLOB(0xba122d38)') called 
> at /opt/eprints3/perl_lib/EPrints/Plugin/Screen/Import.pm line 146
>     
> EPrints::Plugin::Screen::Import::action_test_data('EPrints::Plugin::Screen::Import=HASH(0xba11ed80)') 
> called at /opt/eprints3/perl_lib/EPrints/Plugin/Screen.pm line 240
>     
> EPrints::Plugin::Screen::from('EPrints::Plugin::Screen::Import=HASH(0xba11ed80)') 
> called at /opt/eprints3/perl_lib/EPrints/ScreenProcessor.pm line 310
>     
> EPrints::ScreenProcessor::process('EPrints::ScreenProcessor', 'session', 'EPrints::Repository=HASH(0xb9dfcef0)', 'template', 
> undef, 'url', '/cgi/users/home') called at /opt/eprints3/cgi/users/home line 
> 40
>     
> ModPerl::ROOT::ModPerl::Registry::opt_eprints3_cgi_users_home::handler('Apache2::RequestRec=SCALAR(0xb9ba57a8)') 
> called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/RegistryCooker.pm 
> line 204
>     eval {...} called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/RegistryCooker.pm 
> line 204
>     ModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0xb9acc980)') called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/RegistryCooker.pm 
> line 170
>     
> ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0xb9acc980)') 
> called 
> at /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/Registry.pm 
> line 31
>     
> ModPerl::Registry::handler('ModPerl::Registry', 'Apache2::RequestRec=SCALAR(0xb9ba57a8)') 
> called at -e line 0
>     eval {...} called at -e line 0
> 
> 
> 
> best regards
> ulf
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