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[EP-tech] Import Items error - Pubmed XML
- To: eprints-tech@ecs.soton.ac.uk
- Subject: [EP-tech] Import Items error - Pubmed XML
- From: Ulf Laube <ulf.laube@ontochem.com>
- Date: Fri, 16 Mar 2012 16:04:43 +0100
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
--
OntoChem GmbH
Heinrich-Damerow-Str. 4
06120 Halle (Saale)
Germany
<?xml version="1.0"?> <!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2012//EN" "http://www.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_120101.dtd";> <PubmedArticleSet> <PubmedArticle> <MedlineCitation Owner="NLM" Status="In-Data-Review"> <PMID Version="1">22400019</PMID> <DateCreated> <Year>2012</Year> <Month>03</Month> <Day>08</Day> </DateCreated> <Article PubModel="Print-Electronic"> <Journal> <ISSN IssnType="Electronic">1687-6377</ISSN> <JournalIssue CitedMedium="Internet"> <Volume>2012</Volume> <PubDate> <Year>2012</Year> </PubDate> </JournalIssue> <Title>Advances in urology</Title> <ISOAbbreviation>Adv Urol</ISOAbbreviation> </Journal> <ArticleTitle>Radical prostatectomy and intraoperative radiation therapy in high-risk prostate cancer.</ArticleTitle> <Pagination> <MedlinePgn>687230</MedlinePgn> </Pagination> <Abstract> <AbstractText>Intraoperative electron beam radiotherapy (IOERT) for prostate cancer (PC) is a radiotherapeutic technique, giving high doses of radiation during radical prostatectomy (RP). This paper presents the published treatment approaches for intraoperative radiotherapy analyzing functional outcome, morbidity, and oncological outcome in patients with clinical intermediate-high-risk prostate cancer. A systematic review of the literature was performed, searching PubMed and Web of Science. A "free text" protocol using the term intraoperative radiotherapy and prostate cancer was applied. Ten records were retrieved and analyzed including more than 150 prostate cancer patients treated with IOERT. IOERT represents a feasible technique with acceptable surgical time and minimal toxicity. A greater number of cases and longer follow-up time are needed in order to assess the long-term side effects and oncological outcome.</AbstractText> </Abstract> <Affiliation>Division of Urology, University of Eastern Piedmont, Maggiore della Carità Hospital, Novara, Italy.</Affiliation> <AuthorList CompleteYN="Y"> <Author ValidYN="Y"> <LastName>Marchioro</LastName> <ForeName>Giansilvio</ForeName> <Initials>G</Initials> </Author> <Author ValidYN="Y"> <LastName>Volpe</LastName> <ForeName>Alessandro</ForeName> <Initials>A</Initials> </Author> <Author ValidYN="Y"> <LastName>Tarabuzzi</LastName> <ForeName>Roberto</ForeName> <Initials>R</Initials> </Author> <Author ValidYN="Y"> <LastName>Apicella</LastName> <ForeName>Giuseppina</ForeName> <Initials>G</Initials> </Author> <Author ValidYN="Y"> <LastName>Krengli</LastName> <ForeName>Marco</ForeName> <Initials>M</Initials> </Author> <Author ValidYN="Y"> <LastName>Terrone</LastName> <ForeName>Carlo</ForeName> <Initials>C</Initials> </Author> </AuthorList> <Language>eng</Language> <PublicationTypeList> <PublicationType>Journal Article</PublicationType> </PublicationTypeList> <ArticleDate DateType="Electronic"> <Year>2012</Year> <Month>01</Month> <Day>30</Day> </ArticleDate> </Article> <MedlineJournalInfo> <Country>Egypt</Country> <MedlineTA>Adv Urol</MedlineTA> <NlmUniqueID>101476240</NlmUniqueID> <ISSNLinking>1687-6369</ISSNLinking> </MedlineJournalInfo> </MedlineCitation> <PubmedData> <History> <PubMedPubDate PubStatus="received"> <Year>2011</Year> <Month>6</Month> <Day>14</Day> </PubMedPubDate> <PubMedPubDate PubStatus="revised"> <Year>2011</Year> <Month>9</Month> <Day>12</Day> </PubMedPubDate> <PubMedPubDate PubStatus="accepted"> <Year>2011</Year> <Month>9</Month> <Day>30</Day> </PubMedPubDate> <PubMedPubDate PubStatus="epublish"> <Year>2012</Year> <Month>1</Month> <Day>30</Day> </PubMedPubDate> <PubMedPubDate PubStatus="entrez"> <Year>2012</Year> <Month>3</Month> <Day>9</Day> <Hour>6</Hour> <Minute>0</Minute> </PubMedPubDate> <PubMedPubDate PubStatus="pubmed"> <Year>2012</Year> <Month>3</Month> <Day>9</Day> <Hour>6</Hour> <Minute>0</Minute> </PubMedPubDate> <PubMedPubDate PubStatus="medline"> <Year>2012</Year> <Month>3</Month> <Day>9</Day> <Hour>6</Hour> <Minute>0</Minute> </PubMedPubDate> </History> <PublicationStatus>ppublish</PublicationStatus> <ArticleIdList> <ArticleId IdType="doi">10.1155/2012/687230</ArticleId> <ArticleId IdType="pubmed">22400019</ArticleId> </ArticleIdList> </PubmedData> </PubmedArticle> </PubmedArticleSet>
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