diff options
Diffstat (limited to 'src/webquerypubmed.cpp')
| -rw-r--r-- | src/webquerypubmed.cpp | 535 |
1 files changed, 535 insertions, 0 deletions
diff --git a/src/webquerypubmed.cpp b/src/webquerypubmed.cpp new file mode 100644 index 0000000..f3dcb82 --- /dev/null +++ b/src/webquerypubmed.cpp @@ -0,0 +1,535 @@ +/*************************************************************************** +* Copyright (C) 2004-2009 by Thomas Fischer * +* [email protected] * +* * +* This program is free software; you can redistribute it and/or modify * +* it under the terms of the GNU General Public License as published by * +* the Free Software Foundation; either version 2 of the License, or * +* (at your option) any later version. * +* * +* This program is distributed in the hope that it will be useful, * +* but WITHOUT ANY WARRANTY; without even the implied warranty of * +* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * +* GNU General Public License for more details. * +* * +* You should have received a copy of the GNU General Public License * +* along with this program; if not, write to the * +* Free Software Foundation, Inc., * +* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * +***************************************************************************/ +#include <qwidget.h> +#include <qdom.h> +#include <qapplication.h> +#include <qstringlist.h> +#include <qbuffer.h> +#include <qcstring.h> +#include <qregexp.h> +#include <qspinbox.h> + +#include <klineedit.h> +#include <kdialog.h> +#include <klocale.h> +#include <kurl.h> +#include <kmessagebox.h> +#include <kio/netaccess.h> + +#include <entryfield.h> +#include <value.h> +#include <settings.h> +#include "webquerypubmed.h" + +namespace KBibTeX +{ + WebQueryPubMedWidget::WebQueryPubMedWidget( QWidget *parent, const char *name ) + : WebQueryWidget( parent, name ) + { + init(); + + Settings *settings = Settings::self(); + QString value = settings->getWebQueryDefault( "PubMed" ); + value = value == QString::null ? "" : value; + lineEditQuery->setText( value ); + slotTextChanged( value, true ); + } + + WebQueryPubMed::WebQueryPubMed( QWidget *parent ) : WebQuery( parent ) + { + m_widget = new WebQueryPubMedWidget( parent ); + } + + WebQueryPubMed::~WebQueryPubMed() + { + delete m_widget; + } + + QString WebQueryPubMed::title() + { + return i18n( "NCBI (PubMed)" ); + } + + QString WebQueryPubMed::disclaimer() + { + return i18n( "NCBI's Disclaimer and Copyright" ); + } + + QString WebQueryPubMed::disclaimerURL() + { + return "http://eutils.ncbi.nlm.nih.gov/About/disclaimer.html"; + } + + WebQueryWidget *WebQueryPubMed::widget() + { + return m_widget; + } + + void WebQueryPubMed::query() + { + WebQuery::query(); + Settings *settings = Settings::self(); + settings->setWebQueryDefault( "PubMed", m_widget->lineEditQuery->text() ); + + setNumStages( 2 ); + int numberOfResults = m_widget->spinBoxMaxHits->value(); + + QString searchTerm = m_widget->lineEditQuery->text().stripWhiteSpace().replace( '$', "" ); + if ( searchTerm.isEmpty() ) + { + setEndSearch( WebQuery::statusInvalidQuery ); + return; + } + + searchTerm = searchTerm.replace( "%", "%25" ).replace( "+", "%2B" ).replace( " ", "%20" ).replace( "#", "%23" ).replace( "&", "%26" ).replace( "?", "%3F" ); + KURL url = KURL( QString( "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=%2&retmax=%1&tool=KBibTeX&[email protected]" ).arg( numberOfResults ).arg( searchTerm ) ); + + QString data = downloadHTML( url ); + if ( data != QString::null && !m_aborted ) + { + QBuffer buffer; + buffer.open( IO_WriteOnly ); + QTextStream ts( &buffer ); + ts.setEncoding( QTextStream::UnicodeUTF8 ); + ts << data << endl; + buffer.close(); + + buffer.open( IO_ReadOnly ); + QValueList<int> intList; + QXmlInputSource inputSource( &buffer ); + QXmlSimpleReader reader; + WebQueryPubMedStructureParserQuery handler( &intList ); + reader.setContentHandler( &handler ); + reader.parse( &inputSource ); + buffer.close(); + + QString ids; + QValueList<int>::iterator it = intList.begin(); + if ( it != intList.end() ) + { + ids.append( QString::number( *it ) ); + ++it; + for ( ; it != intList.end(); ++it ) + { + ids.append( "," ); + ids.append( QString::number( *it ) ); + } + } + + url = KURL( QString( "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id=%1&tool=KBibTeX&[email protected]" ).arg( ids ) ); + data = downloadHTML( url ); + if ( data != QString::null && !m_aborted ) + { + buffer.open( IO_WriteOnly ); + QTextStream ts( &buffer ); + ts.setEncoding( QTextStream::UnicodeUTF8 ); + ts << data << endl; + buffer.close(); + + buffer.open( IO_ReadOnly ); + QDomDocument doc( "efetch'ed" ); + doc.setContent( &buffer ); + QDomElement docElem = doc.documentElement(); + WebQueryPubMedResultParser resultParser; + connect( &resultParser, SIGNAL( foundEntry( BibTeX::Entry*, bool ) ), this, SIGNAL( foundEntry( BibTeX::Entry*, bool ) ) ); + resultParser.parse( docElem ); + buffer.close(); + setEndSearch( WebQuery::statusSuccess ); + } + else if ( !m_aborted ) + { + QString message = KIO::NetAccess::lastErrorString(); + message.prepend( QString( i18n( "Querying database '%1' failed." ) ).arg( title() ) ); + KMessageBox::error( m_parent, message ); + setEndSearch( WebQuery::statusError ); + } + else + setEndSearch( WebQuery::statusAborted ); + } + else if ( !m_aborted ) + { + QString message = KIO::NetAccess::lastErrorString(); + if ( message.isEmpty() ) + message.prepend( '\n' ); + message.prepend( QString( i18n( "Querying database '%1' failed." ) ).arg( title() ) ); + KMessageBox::error( m_parent, message ); + setEndSearch( WebQuery::statusError ); + } + else + setEndSearch( WebQuery::statusAborted ); + } + + WebQueryPubMedStructureParserQuery::WebQueryPubMedStructureParserQuery( QValueList<int> *intList ) : QXmlDefaultHandler(), m_intList( intList ) + { + m_intList->clear(); + } + + WebQueryPubMedStructureParserQuery::~WebQueryPubMedStructureParserQuery( ) + { + // nothing + } + + bool WebQueryPubMedStructureParserQuery::startElement( const QString & /*namespaceURI*/, const QString & /*localName*/, const QString & /*qName*/, const QXmlAttributes & /*atts*/ ) + { + concatString = QString(); + return TRUE; + } + + bool WebQueryPubMedStructureParserQuery::endElement( const QString & /*namespaceURI*/, const QString & /*localName*/, const QString & qName ) + { + if ( qName == "Id" ) + { + bool ok; + int id = concatString.toInt( &ok ); + if ( ok && id > 0 && m_intList != NULL ) + m_intList->append( id ); + } + + return TRUE; + } + + bool WebQueryPubMedStructureParserQuery::characters( const QString & ch ) + { + concatString.append( ch ); + return TRUE; + } + + WebQueryPubMedResultParser::WebQueryPubMedResultParser( ) : QObject() + { + // nothing + } + + void WebQueryPubMedResultParser::parse( const QDomElement& rootElement ) + { + if ( rootElement.tagName() == "PubmedArticleSet" ) + for ( QDomNode n = rootElement.firstChild(); !n.isNull(); n = n.nextSibling() ) + { + QDomElement e = n.toElement(); + if ( !e.isNull() && e.tagName() == "PubmedArticle" ) + { + BibTeX::Entry * entry = new BibTeX::Entry( BibTeX::Entry::etMisc, "PubMed" ); + parsePubmedArticle( e, entry ); + emit foundEntry( entry, false ); + } + } + } + + WebQueryPubMedResultParser::~WebQueryPubMedResultParser() + { + // nothing + } + + void WebQueryPubMedResultParser::parsePubmedArticle( const QDomElement& element, BibTeX::Entry *entry ) + { + for ( QDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() ) + { + QDomElement e = n.toElement(); + if ( !e.isNull() && e.tagName() == "MedlineCitation" ) + parseMedlineCitation( e, entry ); + } + } + + void WebQueryPubMedResultParser::parseMedlineCitation( const QDomElement& element, BibTeX::Entry *entry ) + { + for ( QDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() ) + { + QDomElement e = n.toElement(); + if ( !e.isNull() ) + { + if ( e.tagName() == "PMID" ) + { + entry->setId( QString( "PubMed_%1" ).arg( e.text() ) ); + + /** add url to pubmed website */ + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftURL ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftURL ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( QString( "http://www.ncbi.nlm.nih.gov/pubmed/" ).append( e.text() ) ) ); + } + else if ( e.tagName() == "Article" ) + parseArticle( e, entry ); + else if ( e.tagName() == "MedlineJournalInfo" ) + { + for ( QDomNode n2 = e.firstChild(); !n2.isNull(); n2 = n2.nextSibling() ) + { + QDomElement e2 = n2.toElement(); + if ( e2.tagName() == "MedlineTA" ) + { + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftJournal ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftJournal ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( e2.text() ) ); + } + } + } + } + } + + } + + void WebQueryPubMedResultParser::parseArticle( const QDomElement& element, BibTeX::Entry *entry ) + { + for ( QDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() ) + { + QDomElement e = n.toElement(); + + if ( e.tagName() == "Journal" ) + { + parseJournal( e, entry ); + entry->setEntryType( BibTeX::Entry::etArticle ); + } + else if ( e.tagName() == "ArticleTitle" ) + { + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftTitle ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftTitle ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( e.text() ) ); + } + else if ( e.tagName() == "Pagination" ) + { + QDomElement medlinePgn = e.firstChild().toElement(); // may fail? + if ( !medlinePgn.text().isEmpty() ) + { + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftPages ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftPages ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( medlinePgn.text() ) ); + } + } + else if ( e.tagName() == "Abstract" ) + { + QDomElement abstractText = e.firstChild().toElement(); + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftAbstract ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftAbstract ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( abstractText.text() ) ); + } + else if ( e.tagName() == "Affiliation" ) + { + BibTeX::EntryField * field = entry->getField( "affiliation" ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( "affiliation" ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( e.text() ) ); + } + else if ( e.tagName() == "AuthorList" ) + parseAuthorList( e, entry ); + } + } + + void WebQueryPubMedResultParser::parseJournal( const QDomElement& element, BibTeX::Entry *entry ) + { + for ( QDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() ) + { + QDomElement e = n.toElement(); + + if ( e.tagName() == "ISSN" ) + { + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftISSN ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftISSN ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( e.text() ) ); + } + else if ( e.tagName() == "JournalIssue" ) + parseJournalIssue( e, entry ); + else if ( e.tagName() == "Title" ) + { + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftJournal ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftJournal ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( e.text() ) ); + } + } + } + + void WebQueryPubMedResultParser::parseJournalIssue( const QDomElement& element, BibTeX::Entry *entry ) + { + for ( QDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() ) + { + QDomElement e = n.toElement(); + + if ( e.tagName() == "Volume" ) + { + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftVolume ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftVolume ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( e.text() ) ); + } + else if ( e.tagName() == "Issue" ) + { + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftNumber ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftNumber ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( e.text() ) ); + } + else if ( e.tagName() == "PubDate" ) + parsePubDate( e, entry ); + } + } + + void WebQueryPubMedResultParser::parsePubDate( const QDomElement& element, BibTeX::Entry *entry ) + { + for ( QDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() ) + { + QDomElement e = n.toElement(); + + if ( e.tagName() == "Year" ) + { + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftYear ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftYear ); + entry->addField( field ); + } + field->setValue( new BibTeX::Value( e.text() ) ); + } + else if ( e.tagName() == "Month" ) + { + QString month = e.text().lower(); + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftMonth ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftMonth ); + entry->addField( field ); + } + BibTeX::Value *value = new BibTeX::Value(); + value->items.append( new BibTeX::MacroKey( month ) ); + field->setValue( value ); + } + else if ( e.tagName() == "MedlineDate" ) + { + QStringList frags = QStringList::split( QRegExp( "\\s+" ), e.text() ); + for ( QStringList::Iterator it = frags.begin(); it != frags.end(); ++it ) + { + bool ok; + int num = ( *it ).toInt( &ok ); + if ( ok && num > 1000 && num < 3000 ) + { + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftYear ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftYear ); + entry->addField( field ); + } + BibTeX::Value *value = new BibTeX::Value(); + value->items.append( new BibTeX::MacroKey( QString::number( num ) ) ); + field->setValue( value ); + } + else if ( !ok && ( *it ).length() == 3 ) + { + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftMonth ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftMonth ); + entry->addField( field ); + } + BibTeX::Value *value = new BibTeX::Value(); + value->items.append( new BibTeX::MacroKey(( *it ).lower() ) ); + field->setValue( value ); + } + } + } + } + } + + void WebQueryPubMedResultParser::parseAuthorList( const QDomElement& element, BibTeX::Entry *entry ) + { + if ( element.attribute( "CompleteYN", "Y" ) == "Y" ) + { + QStringList authorList; + for ( QDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() ) + { + QDomElement e = n.toElement(); + if ( e.tagName() == "Author" && e.attribute( "ValidYN", "Y" ) == "Y" ) + { + QString lastName = QString::null, firstName = QString::null; + for ( QDomNode n2 = e.firstChild(); !n2.isNull(); n2 = n2.nextSibling() ) + { + QDomElement e2 = n2.toElement(); + if ( e2.tagName() == "LastName" ) + lastName = e2.text(); + else if ( e2.tagName() == "CollectiveName" ) + lastName = e2.text(); + else if ( e2.tagName() == "FirstName" || e2.tagName() == "ForeName" ) + firstName = e2.text(); + } + QString name = lastName; + if ( !firstName.isNull() && !firstName.isEmpty() ) + { + if ( name.isNull() ) name = "UNSET"; + name.prepend( "|" ).prepend( firstName ); + } + if ( !name.isNull() ) + authorList.append( name ); + } + } + + BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftAuthor ); + if ( field == NULL ) + { + field = new BibTeX::EntryField( BibTeX::EntryField::ftAuthor ); + entry->addField( field ); + } + BibTeX::Value *value = new BibTeX::Value(); + Settings *settings = Settings::self(); + BibTeX::PersonContainer *personContainer = new BibTeX::PersonContainer( settings->editing_FirstNameFirst ); + value->items.append( personContainer ); + for ( QStringList::Iterator sli = authorList.begin(); sli != authorList.end(); ++sli ) + { + QStringList nameParts = QStringList::split( '|', *sli ); + QString firstName = nameParts.count() > 1 ? nameParts[0] : ""; + QString lastName = nameParts[nameParts.count() - 1]; + personContainer->persons.append( new BibTeX::Person( firstName, lastName, settings->editing_FirstNameFirst ) ); + } + field->setValue( value ); + } + } + +} +#include "webquerypubmed.moc" |