File indexing completed on 2024-05-12 05:09:31

 /***************************************************************************
     Copyright (C) 2005-2020 Robby Stephenson <robby@periapsis.org>
  ***************************************************************************/
 
 /***************************************************************************
  *                                                                         *
  *   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) version 3 or any later version        *
  *   accepted by the membership of KDE e.V. (or its successor approved     *
  *   by the membership of KDE e.V.), which shall act as a proxy            *
  *   defined in Section 14 of version 3 of the license.                    *
  *                                                                         *
  *   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, see <http://www.gnu.org/licenses/>. *
  *                                                                         *
  ***************************************************************************/
 
 #include "entrezfetcher.h"
 #include "../utils/guiproxy.h"
 #include "../collection.h"
 #include "../entry.h"
 #include "../fieldformat.h"
 #include "../core/filehandler.h"
 #include "../translators/xslthandler.h"
 #include "../translators/tellicoimporter.h"
 #include "../utils/datafileregistry.h"
 #include "../tellico_debug.h"
 
 #include <KLocalizedString>
 #include <KIO/Job>
 #include <KIO/JobUiDelegate>
 #include <KConfigGroup>
 #include <KJobWidgets/KJobWidgets>
 
 #include <QDomDocument>
 #include <QLabel>
 #include <QFile>
 #include <QTextStream>
 #include <QGridLayout>
 #include <QLineEdit>
 #include <QUrlQuery>
 #include <QThread>
 #include <QJsonDocument>
 #include <QJsonObject>
 
 namespace {
   static const int ENTREZ_MAX_RETURNS_TOTAL = 25;
   static const char* ENTREZ_BASE_URL = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/";
   static const char* ENTREZ_SEARCH_CGI = "esearch.fcgi";
   static const char* ENTREZ_SUMMARY_CGI = "esummary.fcgi";
   static const char* ENTREZ_FETCH_CGI = "efetch.fcgi";
   static const char* ENTREZ_LINK_CGI = "elink.fcgi";
   static const char* ENTREZ_DEFAULT_DATABASE = "pubmed";
 }
 
 using namespace Tellico;
 using namespace Tellico::Fetch;
 using Tellico::Fetch::EntrezFetcher;
 
 EntrezFetcher::EntrezFetcher(QObject* parent_) : Fetcher(parent_), m_xsltHandler(nullptr),
     m_start(1), m_total(-1), m_step(Step::Begin), m_started(false) {
   m_idleTime.start();
 }
 
 EntrezFetcher::~EntrezFetcher() {
 }
 
 QString EntrezFetcher::source() const {
   return m_name.isEmpty() ? defaultName() : m_name;
 }
 
 bool EntrezFetcher::canSearch(Fetch::FetchKey k) const {
   return k == Title || k == Person || k == Keyword || k == Raw || k == PubmedID || k == DOI;
 }
 
 bool EntrezFetcher::canFetch(int type) const {
   return type == Data::Collection::Bibtex;
 }
 
 void EntrezFetcher::readConfigHook(const KConfigGroup& config_) {
   QString s = config_.readEntry("Database", ENTREZ_DEFAULT_DATABASE); // default to pubmed
   if(!s.isEmpty()) {
     m_dbname = s;
   }
   QString k = config_.readEntry("API Key");
   if(!k.isEmpty()) {
     m_apiKey = k;
   }
 }
 
 void EntrezFetcher::search() {
   m_started = true;
   m_start = 1;
   m_total = -1;
 
   if(m_dbname.isEmpty()) {
     m_dbname = QLatin1String(ENTREZ_DEFAULT_DATABASE);
   }
 
   QUrl u(QString::fromLatin1(ENTREZ_BASE_URL));
   u.setPath(u.path() + QLatin1String(ENTREZ_SEARCH_CGI));
   QUrlQuery q;
   q.addQueryItem(QStringLiteral("tool"),       QStringLiteral("Tellico"));
   q.addQueryItem(QStringLiteral("retmode"),    QStringLiteral("xml"));
   q.addQueryItem(QStringLiteral("usehistory"), QStringLiteral("y"));
   q.addQueryItem(QStringLiteral("retmax"),     QStringLiteral("1")); // we're just getting the count
   q.addQueryItem(QStringLiteral("db"),         m_dbname);
   q.addQueryItem(QStringLiteral("term"),       request().value());
   switch(request().key()) {
     case Title:
       q.addQueryItem(QStringLiteral("field"), QStringLiteral("titl"));
       break;
 
     case Person:
       q.addQueryItem(QStringLiteral("field"), QStringLiteral("auth"));
       break;
 
     case Keyword:
       // for Tellico Keyword searches basically mean search for any field matching
 //      q.addQueryItem(QLatin1String("field"), QLatin1String("word"));
       break;
 
     case PubmedID:
       q.addQueryItem(QStringLiteral("field"), QStringLiteral("pmid"));
       break;
 
     case DOI:
     case Raw:
       // for DOI, enough to match any field to DOI value
       //q.setQuery(u.query() + QLatin1Char('&') + request().value());
       break;
 
     default:
       myWarning() << source() << "- key not recognized:" << request().key();
       stop();
       return;
   }
   if(!m_apiKey.isEmpty()) {
     q.addQueryItem(QStringLiteral("api_key"), m_apiKey);
   }
   u.setQuery(q);
 
   m_step = Step::Search;
 //  myLog() << "search url: " << u.url();
   m_job = KIO::storedGet(u, KIO::NoReload, KIO::HideProgressInfo);
   KJobWidgets::setWindow(m_job, GUI::Proxy::widget());
   connect(m_job.data(), &KJob::result,
           this, &EntrezFetcher::slotComplete);
   markTime();
 }
 
 void EntrezFetcher::continueSearch() {
   m_started = true;
   doSummary();
 }
 
 void EntrezFetcher::stop() {
   if(!m_started) {
     return;
   }
   if(m_job) {
     m_job->kill();
     m_job = nullptr;
   }
   m_started = false;
   m_step = Step::Begin;
   emit signalDone(this);
 }
 
 void EntrezFetcher::slotComplete(KJob*) {
   Q_ASSERT(m_job);
   if(m_job->error()) {
     m_job->uiDelegate()->showErrorMessage();
     stop();
     return;
   }
 
   QByteArray data = m_job->data();
   if(data.isEmpty()) {
     myDebug() << "no data";
     stop();
     return;
   }
   // see bug 319662. If fetcher is cancelled, job is killed
   // if the pointer is retained, it gets double-deleted
   m_job = nullptr;
 
 #if 0
   myWarning() << "Remove debug from entrezfetcher.cpp: " << __LINE__;
   QFile f(QLatin1String("/tmp/test.xml"));
   if(f.open(QIODevice::WriteOnly)) {
     QTextStream t(&f);
     t.setCodec("UTF-8");
     t << data;
   }
   f.close();
 #endif
 
   switch(m_step) {
     case Step::Search:
       searchResults(data);
       break;
     case Step::Summary:
       summaryResults(data);
       break;
     case Step::Begin:
     case Step::Fetch:
     default:
       myLog() << "wrong step =" << int(m_step);
       stop();
       break;
   }
 }
 
 void EntrezFetcher::searchResults(const QByteArray& data_) {
   QDomDocument dom;
   if(!dom.setContent(data_, false)) {
     myWarning() << "server did not return valid XML.";
     stop();
     return;
   }
   // find Count, QueryKey, and WebEnv elements
   int count = 0;
   for(QDomNode n = dom.documentElement().firstChild(); !n.isNull(); n = n.nextSibling()) {
     QDomElement e = n.toElement();
     if(e.isNull()) {
       continue;
     }
     if(e.tagName() == QLatin1String("Count")) {
       m_total = e.text().toInt();
       ++count;
     } else if(e.tagName() == QLatin1String("QueryKey")) {
       m_queryKey = e.text();
       ++count;
     } else if(e.tagName() == QLatin1String("WebEnv")) {
       m_webEnv = e.text();
       ++count;
     }
     if(count >= 3) {
       break; // found them all
     }
   }
 
   doSummary();
 }
 
 void EntrezFetcher::doSummary() {
   QUrl u(QString::fromLatin1(ENTREZ_BASE_URL));
   u.setPath(u.path() + QLatin1String(ENTREZ_SUMMARY_CGI));
   QUrlQuery q;
   q.addQueryItem(QStringLiteral("tool"),       QStringLiteral("Tellico"));
   q.addQueryItem(QStringLiteral("retmode"),    QStringLiteral("xml"));
   if(m_start > 1) {
     q.addQueryItem(QStringLiteral("retstart"),   QString::number(m_start));
   }
   q.addQueryItem(QStringLiteral("retmax"),     QString::number(qMin(m_total-m_start-1, ENTREZ_MAX_RETURNS_TOTAL)));
   q.addQueryItem(QStringLiteral("usehistory"), QStringLiteral("y"));
   q.addQueryItem(QStringLiteral("db"),         m_dbname);
   q.addQueryItem(QStringLiteral("query_key"),  m_queryKey);
   q.addQueryItem(QStringLiteral("WebEnv"),     m_webEnv);
   if(!m_apiKey.isEmpty()) {
     q.addQueryItem(QStringLiteral("api_key"), m_apiKey);
   }
   u.setQuery(q);
 
   m_step = Step::Summary;
 //  myLog() << "summary url:" << u.url();
   m_job = KIO::storedGet(u, KIO::NoReload, KIO::HideProgressInfo);
   KJobWidgets::setWindow(m_job, GUI::Proxy::widget());
   connect(m_job.data(), &KJob::result,
           this, &EntrezFetcher::slotComplete);
   markTime();
 }
 
 void EntrezFetcher::summaryResults(const QByteArray& data_) {
   QDomDocument dom;
   if(!dom.setContent(data_, false)) {
     myWarning() << "server did not return valid XML.";
     stop();
     return;
   }
   // top child is eSummaryResult
   // all children are DocSum
   for(QDomNode n = dom.documentElement().firstChild(); !n.isNull(); n = n.nextSibling()) {
     QDomElement e = n.toElement();
     if(e.isNull() || e.tagName() != QLatin1String("DocSum")) {
       continue;
     }
     QDomNodeList nodes = e.elementsByTagName(QStringLiteral("Id"));
     if(nodes.count() == 0) {
       myDebug() << "no Id elements";
       continue;
     }
     int id = nodes.item(0).toElement().text().toInt();
     QString title, pubdate, authors;
     nodes = e.elementsByTagName(QStringLiteral("Item"));
     for(int j = 0; j < nodes.count(); ++j) {
       const auto elem = nodes.item(j).toElement();
       if(elem.attribute(QStringLiteral("Name")) == QLatin1String("Title")) {
         title = elem.text();
       } else if(elem.attribute(QStringLiteral("Name")) == QLatin1String("PubDate")) {
         pubdate = elem.text();
       } else if(elem.attribute(QStringLiteral("Name")) == QLatin1String("AuthorList")) {
         QStringList list;
         for(QDomNode aNode = nodes.item(j).firstChild(); !aNode.isNull(); aNode = aNode.nextSibling()) {
           // lazy, assume all children Items are authors
           if(aNode.nodeName() == QLatin1String("Item")) {
             list << aNode.toElement().text();
           }
         }
         authors = list.join(FieldFormat::delimiterString());
       }
       if(!title.isEmpty() && !pubdate.isEmpty() && !authors.isEmpty()) {
         break; // done now
       }
     }
     FetchResult* r = new FetchResult(this, title, pubdate + QLatin1Char('/') + authors);
     m_matches.insert(r->uid, id);
     emit signalResultFound(r);
   }
   m_start = m_matches.count() + 1;
   m_hasMoreResults = m_start <= m_total;
   stop(); // done searching
 }
 
 Tellico::Data::EntryPtr EntrezFetcher::fetchEntryHook(uint uid_) {
   // if we already grabbed this one, then just pull it out of the dict
   Data::EntryPtr entry = m_entries[uid_];
   if(entry) {
     return entry;
   }
 
   if(!m_matches.contains(uid_)) {
     return Data::EntryPtr();
   }
 
   if(!m_xsltHandler) {
     initXSLTHandler();
     if(!m_xsltHandler) { // probably an error somewhere in the stylesheet loading
       stop();
       return Data::EntryPtr();
     }
   }
 
   int id = m_matches[uid_];
 
   QUrl u(QString::fromLatin1(ENTREZ_BASE_URL));
   u.setPath(u.path() + QLatin1String(ENTREZ_FETCH_CGI));
   QUrlQuery q;
   q.addQueryItem(QStringLiteral("tool"),       QStringLiteral("Tellico"));
   q.addQueryItem(QStringLiteral("retmode"),    QStringLiteral("xml"));
   q.addQueryItem(QStringLiteral("rettype"),    QStringLiteral("abstract"));
   q.addQueryItem(QStringLiteral("db"),         m_dbname);
   q.addQueryItem(QStringLiteral("id"),         QString::number(id));
   if(!m_apiKey.isEmpty()) {
     q.addQueryItem(QStringLiteral("api_key"), m_apiKey);
   }
   u.setQuery(q);
 
   // now it's synchronous
 //  myDebug() << "id url:" << u.url();
   markTime();
   QString xmlOutput = FileHandler::readXMLFile(u, true /*quiet*/);
   if(xmlOutput.isEmpty()) {
     myWarning() << "unable to download " << u;
     return Data::EntryPtr();
   }
 #if 0
   myWarning() << "turn me off in entrezfetcher.cpp!";
   QFile f1(QLatin1String("/tmp/test-entry.xml"));
   if(f1.open(QIODevice::WriteOnly)) {
     QTextStream t(&f1);
     t.setCodec("UTF-8");
     t << xmlOutput;
   }
   f1.close();
 #endif
   QString str = m_xsltHandler->applyStylesheet(xmlOutput);
   if(str.isEmpty()) {
     // might be an API error, and message is in JSON
     QJsonDocument doc = QJsonDocument::fromJson(xmlOutput.toUtf8());
     if(!doc.isNull() && doc.object().contains(QStringLiteral("error"))) {
       const QString error = doc.object().value(QStringLiteral("error")).toString();
       message(error, MessageHandler::Error);
       myLog() << "EntrezFetcher -" << error;
     }
     return Data::EntryPtr();
   }
   Import::TellicoImporter imp(str);
   Data::CollPtr coll = imp.collection();
   if(!coll) {
     myWarning() << "invalid collection";
     return Data::EntryPtr();
   }
   if(coll->entryCount() == 0) {
     myDebug() << "no entries in collection";
     return Data::EntryPtr();
   } else if(coll->entryCount() > 1) {
     myDebug() << "collection has multiple entries, taking first one";
   }
 
   Data::EntryPtr e = coll->entries().front();
 
   // try to get a link, but only if necessary
   if(optionalFields().contains(QStringLiteral("url"))) {
     QUrl link(QString::fromLatin1(ENTREZ_BASE_URL));
     link.setPath(link.path() + QLatin1String(ENTREZ_LINK_CGI));
     QUrlQuery q;
     q.addQueryItem(QStringLiteral("tool"),   QStringLiteral("Tellico"));
     q.addQueryItem(QStringLiteral("cmd"),    QStringLiteral("llinks"));
     q.addQueryItem(QStringLiteral("db"),     m_dbname);
     q.addQueryItem(QStringLiteral("dbfrom"), m_dbname);
     q.addQueryItem(QStringLiteral("id"),     QString::number(id));
     if(!m_apiKey.isEmpty()) {
       q.addQueryItem(QStringLiteral("api_key"), m_apiKey);
     }
     link.setQuery(q);
 
     markTime();
     QDomDocument linkDom = FileHandler::readXMLDocument(link, false /* namespace */, true /* quiet */);
     // need eLinkResult/LinkSet/IdUrlList/IdUrlSet/ObjUrl/Url
     QDomNode linkNode = linkDom.namedItem(QStringLiteral("eLinkResult"))
                                .namedItem(QStringLiteral("LinkSet"))
                                .namedItem(QStringLiteral("IdUrlList"))
                                .namedItem(QStringLiteral("IdUrlSet"))
                                .namedItem(QStringLiteral("ObjUrl"))
                                .namedItem(QStringLiteral("Url"));
     if(!linkNode.isNull()) {
       QString u = linkNode.toElement().text();
 //      myDebug() << u;
       if(!u.isEmpty()) {
         if(!coll->hasField(QStringLiteral("url"))) {
           Data::FieldPtr field(new Data::Field(QStringLiteral("url"), i18n("URL"), Data::Field::URL));
           field->setCategory(i18n("Miscellaneous"));
           coll->addField(field);
         }
         e->setField(QStringLiteral("url"), u);
       }
     }
   }
 
   m_entries.insert(uid_, e);
   return e;
 }
 
 void EntrezFetcher::initXSLTHandler() {
   QString xsltfile = DataFileRegistry::self()->locate(QStringLiteral("pubmed2tellico.xsl"));
   if(xsltfile.isEmpty()) {
     myWarning() << "can not locate pubmed2tellico.xsl.";
     return;
   }
 
   QUrl u = QUrl::fromLocalFile(xsltfile);
 
   if(!m_xsltHandler) {
     m_xsltHandler = new XSLTHandler(u);
   }
   if(!m_xsltHandler->isValid()) {
     myWarning() << "error in pubmed2tellico.xsl.";
     delete m_xsltHandler;
     m_xsltHandler = nullptr;
     return;
   }
 }
 
 // without an API key, limit is 3 searches per second
 // with a key, limit is 10
 // https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
 void EntrezFetcher::markTime() {
   // not exactly the way to monitor rate over 3 or 10 calls, just a constant rate
   const int wait = m_apiKey.isEmpty() ? 350 : 110;
   while(m_idleTime.elapsed() < wait) {
     QThread::msleep(100);
   }
   m_idleTime.restart();
 }
 
 Tellico::Fetch::FetchRequest EntrezFetcher::updateRequest(Data::EntryPtr entry_) {
   QString s = entry_->field(QStringLiteral("pmid"));
   if(!s.isEmpty()) {
     return FetchRequest(PubmedID, s);
   }
 
   s = entry_->field(QStringLiteral("doi"));
   if(!s.isEmpty()) {
     return FetchRequest(DOI, s);
   }
 
   s = entry_->field(QStringLiteral("title"));
   if(!s.isEmpty()) {
     return FetchRequest(Title, s);
   }
   return FetchRequest();
 }
 
 QString EntrezFetcher::defaultName() {
   return i18n("Entrez Database");
 }
 
 QString EntrezFetcher::defaultIcon() {
   return favIcon("http://www.ncbi.nlm.nih.gov");
 }
 
 //static
 Tellico::StringHash EntrezFetcher::allOptionalFields() {
   StringHash hash;
   hash[QStringLiteral("institution")] = i18n("Institution");
   hash[QStringLiteral("abstract")]    = i18n("Abstract");
   hash[QStringLiteral("url")]         = i18n("URL");
   return hash;
 }
 
 Tellico::Fetch::ConfigWidget* EntrezFetcher::configWidget(QWidget* parent_) const {
   return new EntrezFetcher::ConfigWidget(parent_, this);
 }
 
 EntrezFetcher::ConfigWidget::ConfigWidget(QWidget* parent_, const EntrezFetcher* fetcher_/*=0*/)
     : Fetch::ConfigWidget(parent_) {
   QGridLayout* l = new QGridLayout(optionsWidget());
   l->setSpacing(4);
   l->setColumnStretch(1, 10);
 
   int row = -1;
 
   QLabel* label = new QLabel(i18n("Access key: "), optionsWidget());
   l->addWidget(label, ++row, 0);
 
   m_apiKeyEdit = new QLineEdit(optionsWidget());
   connect(m_apiKeyEdit, &QLineEdit::textChanged, this, &ConfigWidget::slotSetModified);
   l->addWidget(m_apiKeyEdit, row, 1);
   QString w = i18n("The default Tellico key may be used, but searching may fail due to reaching access limits.");
   label->setWhatsThis(w);
   m_apiKeyEdit->setWhatsThis(w);
   label->setBuddy(m_apiKeyEdit);
 
   l->setRowStretch(++row, 10);
 
   // now add additional fields widget
   addFieldsWidget(EntrezFetcher::allOptionalFields(), fetcher_ ? fetcher_->optionalFields() : QStringList());
 
   if(fetcher_) {
     m_apiKeyEdit->setText(fetcher_->m_apiKey);
   }
 }
 
 void EntrezFetcher::ConfigWidget::saveConfigHook(KConfigGroup& config_) {
   QString apiKey = m_apiKeyEdit->text().trimmed();
   if(!apiKey.isEmpty()) {
     config_.writeEntry("API Key", apiKey);
   }
 }
 
 QString EntrezFetcher::ConfigWidget::preferredName() const {
   return EntrezFetcher::defaultName();
 }