Initial import

1 files changed, 535 insertions, 0 deletions

diff --git a/src/webquerypubmed.cpp b/src/webquerypubmed.cpp
new file mode 100644
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--- /dev/null
+++ b/src/webquerypubmed.cpp
@@ -0,0 +1,535 @@
+/***************************************************************************
+*   Copyright (C) 2004-2009 by Thomas Fischer                             *
+*   fischer@unix-ag.uni-kl.de                                             *
+*                                                                         *
+*   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=kbibtex@unix-ag.uni-kl.de" ).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=kbibtex@unix-ag.uni-kl.de" ).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"