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536 lines
21 KiB
536 lines
21 KiB
/***************************************************************************
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* Copyright (C) 2004-2009 by Thomas Fischer *
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* fischer@unix-ag.uni-kl.de *
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* *
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* This program is free software; you can redistribute it and/or modify *
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* it under the terms of the GNU General Public License as published by *
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* the Free Software Foundation; either version 2 of the License, or *
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* (at your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, *
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* but WITHOUT ANY WARRANTY; without even the implied warranty of *
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
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* GNU General Public License for more details. *
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* *
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* You should have received a copy of the GNU General Public License *
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* along with this program; if not, write to the *
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* Free Software Foundation, Inc., *
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* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
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***************************************************************************/
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#include <ntqwidget.h>
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#include <ntqdom.h>
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#include <ntqapplication.h>
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#include <ntqstringlist.h>
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#include <ntqbuffer.h>
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#include <ntqcstring.h>
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#include <ntqregexp.h>
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#include <ntqspinbox.h>
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#include <klineedit.h>
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#include <kdialog.h>
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#include <tdelocale.h>
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#include <kurl.h>
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#include <tdemessagebox.h>
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#include <tdeio/netaccess.h>
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#include <entryfield.h>
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#include <value.h>
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#include <settings.h>
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#include "webquerypubmed.h"
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namespace KBibTeX
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{
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WebQueryPubMedWidget::WebQueryPubMedWidget( TQWidget *parent, const char *name )
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: WebQueryWidget( parent, name )
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{
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init();
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Settings *settings = Settings::self();
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TQString value = settings->getWebQueryDefault( "PubMed" );
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value = value == TQString::null ? "" : value;
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lineEditQuery->setText( value );
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slotTextChanged( value, true );
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}
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WebQueryPubMed::WebQueryPubMed( TQWidget *parent ) : WebQuery( parent )
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{
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m_widget = new WebQueryPubMedWidget( parent );
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}
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WebQueryPubMed::~WebQueryPubMed()
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{
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delete m_widget;
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}
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TQString WebQueryPubMed::title()
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{
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return i18n( "NCBI (PubMed)" );
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}
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TQString WebQueryPubMed::disclaimer()
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{
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return i18n( "NCBI's Disclaimer and Copyright" );
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}
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TQString WebQueryPubMed::disclaimerURL()
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{
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return "http://eutils.ncbi.nlm.nih.gov/About/disclaimer.html";
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}
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WebQueryWidget *WebQueryPubMed::widget()
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{
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return m_widget;
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}
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void WebQueryPubMed::query()
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{
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WebQuery::query();
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Settings *settings = Settings::self();
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settings->setWebQueryDefault( "PubMed", m_widget->lineEditQuery->text() );
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setNumStages( 2 );
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int numberOfResults = m_widget->spinBoxMaxHits->value();
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TQString searchTerm = m_widget->lineEditQuery->text().stripWhiteSpace().replace( '$', "" );
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if ( searchTerm.isEmpty() )
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{
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setEndSearch( WebQuery::statusInvalidQuery );
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return;
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}
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searchTerm = searchTerm.replace( "%", "%25" ).replace( "+", "%2B" ).replace( " ", "%20" ).replace( "#", "%23" ).replace( "&", "%26" ).replace( "?", "%3F" );
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KURL url = KURL( TQString( "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=%2&retmax=%1&tool=KBibTeX&email=kbibtex@unix-ag.uni-kl.de" ).arg( numberOfResults ).arg( searchTerm ) );
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TQString data = downloadHTML( url );
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if ( data != TQString::null && !m_aborted )
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{
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TQBuffer buffer;
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buffer.open( IO_WriteOnly );
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TQTextStream ts( &buffer );
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ts.setEncoding( TQTextStream::UnicodeUTF8 );
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ts << data << endl;
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buffer.close();
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buffer.open( IO_ReadOnly );
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TQValueList<int> intList;
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TQXmlInputSource inputSource( &buffer );
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TQXmlSimpleReader reader;
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WebQueryPubMedStructureParserQuery handler( &intList );
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reader.setContentHandler( &handler );
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reader.parse( &inputSource );
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buffer.close();
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TQString ids;
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TQValueList<int>::iterator it = intList.begin();
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if ( it != intList.end() )
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{
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ids.append( TQString::number( *it ) );
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++it;
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for ( ; it != intList.end(); ++it )
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{
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ids.append( "," );
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ids.append( TQString::number( *it ) );
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}
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}
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url = KURL( TQString( "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id=%1&tool=KBibTeX&email=kbibtex@unix-ag.uni-kl.de" ).arg( ids ) );
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data = downloadHTML( url );
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if ( data != TQString::null && !m_aborted )
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{
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buffer.open( IO_WriteOnly );
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TQTextStream ts( &buffer );
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ts.setEncoding( TQTextStream::UnicodeUTF8 );
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ts << data << endl;
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buffer.close();
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buffer.open( IO_ReadOnly );
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TQDomDocument doc( "efetch'ed" );
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doc.setContent( &buffer );
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TQDomElement docElem = doc.documentElement();
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WebQueryPubMedResultParser resultParser;
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connect( &resultParser, SIGNAL( foundEntry( BibTeX::Entry*, bool ) ), this, SIGNAL( foundEntry( BibTeX::Entry*, bool ) ) );
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resultParser.parse( docElem );
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buffer.close();
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setEndSearch( WebQuery::statusSuccess );
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}
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else if ( !m_aborted )
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{
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TQString message = TDEIO::NetAccess::lastErrorString();
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message.prepend( TQString( i18n( "Querying database '%1' failed." ) ).arg( title() ) );
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KMessageBox::error( m_parent, message );
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setEndSearch( WebQuery::statusError );
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}
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else
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setEndSearch( WebQuery::statusAborted );
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}
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else if ( !m_aborted )
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{
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TQString message = TDEIO::NetAccess::lastErrorString();
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if ( message.isEmpty() )
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message.prepend( '\n' );
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message.prepend( TQString( i18n( "Querying database '%1' failed." ) ).arg( title() ) );
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KMessageBox::error( m_parent, message );
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setEndSearch( WebQuery::statusError );
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}
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else
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setEndSearch( WebQuery::statusAborted );
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}
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WebQueryPubMedStructureParserQuery::WebQueryPubMedStructureParserQuery( TQValueList<int> *intList ) : TQXmlDefaultHandler(), m_intList( intList )
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{
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m_intList->clear();
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}
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WebQueryPubMedStructureParserQuery::~WebQueryPubMedStructureParserQuery( )
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{
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// nothing
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}
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bool WebQueryPubMedStructureParserQuery::startElement( const TQString & /*namespaceURI*/, const TQString & /*localName*/, const TQString & /*qName*/, const TQXmlAttributes & /*atts*/ )
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{
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concatString = TQString();
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return TRUE;
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}
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bool WebQueryPubMedStructureParserQuery::endElement( const TQString & /*namespaceURI*/, const TQString & /*localName*/, const TQString & qName )
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{
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if ( qName == "Id" )
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{
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bool ok;
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int id = concatString.toInt( &ok );
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if ( ok && id > 0 && m_intList != NULL )
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m_intList->append( id );
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}
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return TRUE;
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}
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bool WebQueryPubMedStructureParserQuery::characters( const TQString & ch )
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{
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concatString.append( ch );
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return TRUE;
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}
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WebQueryPubMedResultParser::WebQueryPubMedResultParser( ) : TQObject()
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{
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// nothing
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}
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void WebQueryPubMedResultParser::parse( const TQDomElement& rootElement )
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{
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if ( rootElement.tagName() == "PubmedArticleSet" )
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for ( TQDomNode n = rootElement.firstChild(); !n.isNull(); n = n.nextSibling() )
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{
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TQDomElement e = n.toElement();
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if ( !e.isNull() && e.tagName() == "PubmedArticle" )
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{
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BibTeX::Entry * entry = new BibTeX::Entry( BibTeX::Entry::etMisc, "PubMed" );
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parsePubmedArticle( e, entry );
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emit foundEntry( entry, false );
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}
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}
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}
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WebQueryPubMedResultParser::~WebQueryPubMedResultParser()
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{
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// nothing
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}
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void WebQueryPubMedResultParser::parsePubmedArticle( const TQDomElement& element, BibTeX::Entry *entry )
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{
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for ( TQDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() )
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{
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TQDomElement e = n.toElement();
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if ( !e.isNull() && e.tagName() == "MedlineCitation" )
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parseMedlineCitation( e, entry );
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}
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}
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void WebQueryPubMedResultParser::parseMedlineCitation( const TQDomElement& element, BibTeX::Entry *entry )
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{
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for ( TQDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() )
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{
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TQDomElement e = n.toElement();
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if ( !e.isNull() )
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{
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if ( e.tagName() == "PMID" )
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{
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entry->setId( TQString( "PubMed_%1" ).arg( e.text() ) );
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/** add url to pubmed website */
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftURL );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftURL );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( TQString( "http://www.ncbi.nlm.nih.gov/pubmed/" ).append( e.text() ) ) );
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}
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else if ( e.tagName() == "Article" )
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parseArticle( e, entry );
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else if ( e.tagName() == "MedlineJournalInfo" )
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{
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for ( TQDomNode n2 = e.firstChild(); !n2.isNull(); n2 = n2.nextSibling() )
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{
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TQDomElement e2 = n2.toElement();
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if ( e2.tagName() == "MedlineTA" )
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{
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftJournal );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftJournal );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( e2.text() ) );
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}
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}
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}
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}
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}
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}
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void WebQueryPubMedResultParser::parseArticle( const TQDomElement& element, BibTeX::Entry *entry )
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{
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for ( TQDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() )
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{
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TQDomElement e = n.toElement();
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if ( e.tagName() == "Journal" )
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{
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parseJournal( e, entry );
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entry->setEntryType( BibTeX::Entry::etArticle );
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}
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else if ( e.tagName() == "ArticleTitle" )
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{
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftTitle );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftTitle );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( e.text() ) );
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}
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else if ( e.tagName() == "Pagination" )
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{
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TQDomElement medlinePgn = e.firstChild().toElement(); // may fail?
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if ( !medlinePgn.text().isEmpty() )
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{
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftPages );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftPages );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( medlinePgn.text() ) );
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}
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}
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else if ( e.tagName() == "Abstract" )
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{
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TQDomElement abstractText = e.firstChild().toElement();
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftAbstract );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftAbstract );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( abstractText.text() ) );
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}
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else if ( e.tagName() == "Affiliation" )
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{
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BibTeX::EntryField * field = entry->getField( "affiliation" );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( "affiliation" );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( e.text() ) );
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}
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else if ( e.tagName() == "AuthorList" )
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parseAuthorList( e, entry );
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}
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}
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void WebQueryPubMedResultParser::parseJournal( const TQDomElement& element, BibTeX::Entry *entry )
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{
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for ( TQDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() )
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{
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TQDomElement e = n.toElement();
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if ( e.tagName() == "ISSN" )
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{
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftISSN );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftISSN );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( e.text() ) );
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}
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else if ( e.tagName() == "JournalIssue" )
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parseJournalIssue( e, entry );
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else if ( e.tagName() == "Title" )
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{
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftJournal );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftJournal );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( e.text() ) );
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}
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}
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}
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void WebQueryPubMedResultParser::parseJournalIssue( const TQDomElement& element, BibTeX::Entry *entry )
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{
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for ( TQDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() )
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{
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TQDomElement e = n.toElement();
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if ( e.tagName() == "Volume" )
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{
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftVolume );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftVolume );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( e.text() ) );
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}
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else if ( e.tagName() == "Issue" )
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{
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftNumber );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftNumber );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( e.text() ) );
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}
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else if ( e.tagName() == "PubDate" )
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parsePubDate( e, entry );
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}
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}
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void WebQueryPubMedResultParser::parsePubDate( const TQDomElement& element, BibTeX::Entry *entry )
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{
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for ( TQDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() )
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{
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TQDomElement e = n.toElement();
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if ( e.tagName() == "Year" )
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{
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftYear );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftYear );
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entry->addField( field );
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}
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field->setValue( new BibTeX::Value( e.text() ) );
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}
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else if ( e.tagName() == "Month" )
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{
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TQString month = e.text().lower();
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftMonth );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftMonth );
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entry->addField( field );
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}
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BibTeX::Value *value = new BibTeX::Value();
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value->items.append( new BibTeX::MacroKey( month ) );
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field->setValue( value );
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}
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else if ( e.tagName() == "MedlineDate" )
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{
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TQStringList frags = TQStringList::split( TQRegExp( "\\s+" ), e.text() );
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for ( TQStringList::Iterator it = frags.begin(); it != frags.end(); ++it )
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{
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bool ok;
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int num = ( *it ).toInt( &ok );
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if ( ok && num > 1000 && num < 3000 )
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{
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftYear );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftYear );
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entry->addField( field );
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}
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BibTeX::Value *value = new BibTeX::Value();
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value->items.append( new BibTeX::MacroKey( TQString::number( num ) ) );
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field->setValue( value );
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}
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else if ( !ok && ( *it ).length() == 3 )
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{
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BibTeX::EntryField * field = entry->getField( BibTeX::EntryField::ftMonth );
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if ( field == NULL )
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{
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field = new BibTeX::EntryField( BibTeX::EntryField::ftMonth );
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entry->addField( field );
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}
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BibTeX::Value *value = new BibTeX::Value();
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value->items.append( new BibTeX::MacroKey(( *it ).lower() ) );
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field->setValue( value );
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}
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}
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}
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}
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}
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void WebQueryPubMedResultParser::parseAuthorList( const TQDomElement& element, BibTeX::Entry *entry )
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{
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if ( element.attribute( "CompleteYN", "Y" ) == "Y" )
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{
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TQStringList authorList;
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for ( TQDomNode n = element.firstChild(); !n.isNull(); n = n.nextSibling() )
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{
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TQDomElement e = n.toElement();
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if ( e.tagName() == "Author" && e.attribute( "ValidYN", "Y" ) == "Y" )
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{
|
|
TQString lastName = TQString::null, firstName = TQString::null;
|
|
for ( TQDomNode n2 = e.firstChild(); !n2.isNull(); n2 = n2.nextSibling() )
|
|
{
|
|
TQDomElement 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();
|
|
}
|
|
TQString 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 ( TQStringList::Iterator sli = authorList.begin(); sli != authorList.end(); ++sli )
|
|
{
|
|
TQStringList nameParts = TQStringList::split( '|', *sli );
|
|
TQString firstName = nameParts.count() > 1 ? nameParts[0] : "";
|
|
TQString lastName = nameParts[nameParts.count() - 1];
|
|
personContainer->persons.append( new BibTeX::Person( firstName, lastName, settings->editing_FirstNameFirst ) );
|
|
}
|
|
field->setValue( value );
|
|
}
|
|
}
|
|
|
|
}
|
|
#include "webquerypubmed.moc"
|