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

Ulf Laube ulf.laube at ontochem.com
Mon Mar 19 16:10:08 GMT 2012


I've installed and tested r7513 today. Import works well. Great job!
Thanks,
ulf


Am Freitag 16 März 2012 18:51:04 schrieb Tim Brody:
> 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::P
> >ubMedXML=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::Imp
> >ort=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::Scree
> >n::Import=HASH(0xba11ed80)') called at
> > /opt/eprints3/perl_lib/EPrints/Plugin/Screen.pm line 240
> >
> > EPrints::Plugin::Screen::from('EPrints::Plugin::Screen::Import=HASH(0xba1
> >1ed80)') 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('A
> >pache2::RequestRec=SCALAR(0xb9ba57a8)') called
> > at
> > /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/Registr
> >yCooker.pm line 204
> >     eval {...} called
> > at
> > /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/Registr
> >yCooker.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/Registr
> >yCooker.pm line 170
> >
> > ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0xb9acc9
> >80)') called
> > at
> > /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/Registr
> >y.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::P
> >ubMedXML=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::Imp
> >ort=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::Scree
> >n::Import=HASH(0xba11ed80)') called at
> > /opt/eprints3/perl_lib/EPrints/Plugin/Screen.pm line 240
> >
> > EPrints::Plugin::Screen::from('EPrints::Plugin::Screen::Import=HASH(0xba1
> >1ed80)') 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('A
> >pache2::RequestRec=SCALAR(0xb9ba57a8)') called
> > at
> > /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/Registr
> >yCooker.pm line 204
> >     eval {...} called
> > at
> > /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/Registr
> >yCooker.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/Registr
> >yCooker.pm line 170
> >
> > ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0xb9acc9
> >80)') called
> > at
> > /usr/lib/perl5/vendor_perl/5.14.2/i586-linux-thread-multi/ModPerl/Registr
> >y.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
> > *** Options: http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech
> > *** Archive: http://www.eprints.org/tech.php/
> > *** EPrints community wiki: http://wiki.eprints.org/



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