Kick off network requests for molecule names

Signed-off-by: Geoff Hutchison <[email protected]>

avogadro/qtplugins/molecularproperties/molecularmodel.cpp

@@ -7,11 +7,20 @@
 
 #include <avogadro/core/elements.h>
 #include <avogadro/core/residue.h>
+#include <avogadro/io/fileformatmanager.h>
 #include <avogadro/qtgui/molecule.h>
 
 #include <QtCore/QDebug>
 #include <QtCore/QRegularExpression>
-#include <QtGui/QColor>
+#include <QtCore/QTimer>
+
+#include <QtCore/QJsonArray>
+#include <QtCore/QJsonDocument>
+#include <QtCore/QJsonObject>
+#include <QtCore/QJsonValue>
+
+#include <QtNetwork/QNetworkAccessManager>
+#include <QtNetwork/QNetworkReply>
 
 #include <limits>
 
@@ -23,11 +32,110 @@ using QtGui::Molecule;
 MolecularModel::MolecularModel(QObject* parent)
   : QAbstractTableModel(parent), m_molecule(nullptr)
 {
+  m_network = new QNetworkAccessManager(this);
+  connect(m_network, SIGNAL(finished(QNetworkReply*)), this,
+          SLOT(updateNameReady(QNetworkReply*)));
 }
 
 void MolecularModel::setMolecule(QtGui::Molecule* molecule)
 {
   m_molecule = molecule;
+  // check if it has a pre-defined name
+  if (molecule) {
+    if (m_molecule->data("name").toString().empty())
+      m_autoName = true;
+    else
+      m_autoName = false;
+    m_name = QString::fromStdString(molecule->data("name").toString());
+  }
+}
+
+QString MolecularModel::name() const
+{
+  // if we have a defined name
+  // or we're not ready to update
+  // then return the current name
+  if (!m_autoName || m_nameRequestPending)
+    return m_name;
+
+  if (!m_molecule || m_molecule->atomCount() == 0)
+    return m_name; // empty
+
+  // okay, kick off the update
+  m_name = tr("(pending)", "asking server for molecule name");
+  m_nameRequestPending = true;
+
+  std::string smiles;
+  Io::FileFormatManager::instance().writeString(*m_molecule, smiles, "smi");
+  QString smilesString = QString::fromStdString(smiles);
+  smilesString.remove(QRegularExpression("\\s+.*"));
+  QString requestURL =
+    QString("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/" +
+            QUrl::toPercentEncoding(smilesString) + "/json");
+  m_network->get(QNetworkRequest(QUrl(requestURL)));
+
+  // don't update again until we're ready - 5 seconds
+  QTimer::singleShot(5000, this, SLOT(canUpdateName()));
+
+  return m_name;
+}
+
+void MolecularModel::canUpdateName()
+{
+  m_nameRequestPending = false;
+}
+
+void MolecularModel::updateNameReady(QNetworkReply* reply)
+{
+  // Read in all the data
+  if (!reply->isReadable()) {
+    reply->deleteLater();
+    m_name = tr("unknown molecule");
+    return;
+  }
+
+  // check if the data came through
+  QByteArray data = reply->readAll();
+  if (data.contains("Error report") || data.contains("<h1>")) {
+    reply->deleteLater();
+    m_name = tr("unknown molecule");
+    return;
+  }
+
+  // parse the JSON
+  // https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/…/json
+
+  // PC_Compounds[0].props
+  // iterate // get "urn" / "name" == "Markup" and "Preferred"
+  //    ..       get "value" / "sval"
+
+  QJsonDocument doc = QJsonDocument::fromJson(data);
+  QJsonObject obj = doc.object();
+  QJsonArray array = obj["PC_Compounds"].toArray();
+  if (array.isEmpty()) {
+    reply->deleteLater();
+    m_name = tr("unknown molecule");
+    return;
+  }
+  obj = array.first().toObject();
+  array = obj["props"].toArray(); // props is an array of objects
+  for (const QJsonValue& value : array) {
+    obj = value.toObject();
+    QJsonObject urn = obj["urn"].toObject();
+
+    if (urn["name"].toString() == "Markup") {
+      // HTML version for dialog
+      QJsonObject nameValue = obj["value"].toObject();
+      m_name = nameValue["sval"].toString();
+    } else if (urn["name"].toString() == "Preferred") {
+      // save this text version for files and copy/paste
+      QJsonObject nameValue = obj["value"].toObject();
+      m_molecule->setData("name", nameValue["sval"].toString().toStdString());
+      m_name = nameValue["sval"].toString();
+    }
+  }
+
+  reply->deleteLater();
 }
 
 int MolecularModel::rowCount(const QModelIndex& parent) const
@@ -59,7 +167,7 @@ int MolecularModel::columnCount(const QModelIndex& parent) const
   return 1; // values
 }
 
-QString formatFormula(Molecule* m)
+QString formatFormula(Molecule* molecule)
 {
   QString formula = QString::fromStdString(molecule->formula());
   QRegularExpression digitParser("(\\d+)");
@@ -76,9 +184,11 @@ QString formatFormula(Molecule* m)
   }
 
   // add total charge as a superscript
-  int charge = m->totalCharge();
-  if (charge != 0)
+  int charge = molecule->totalCharge();
+  if (charge < 0)
     formula += QString("<sup>%1</sup>").arg(charge);
+  else if (charge > 0)
+    formula += QString("<sup>+%1</sup>").arg(charge);
 
   return formula;
 }
@@ -107,7 +217,7 @@ QVariant MolecularModel::data(const QModelIndex& index, int role) const
     return QVariant();
 
   if (row == Name) {
-    return QString::fromStdString(m_molecule->data("name").toString());
+    return this->name();
   } else if (row == Mass) {
     return m_molecule->mass();
   } else if (row == Formula) {

avogadro/qtplugins/molecularproperties/molecularmodel.h

@@ -11,6 +11,9 @@
 #include <QtCore/QObject>
 #include <QtCore/QString>
 
+class QNetworkAccessManager;
+class QNetworkReply;
+
 #include <avogadro/qtgui/rwmolecule.h>
 
 namespace Avogadro {
@@ -35,6 +38,8 @@ class MolecularModel : public QAbstractTableModel
 
 public slots:
   void updateTable(unsigned int flags);
+  void updateNameReady(QNetworkReply* reply); // reply from network
+  void canUpdateName();                       // don't do it too often
 
 public:
   explicit MolecularModel(QObject* parent = 0);
@@ -50,8 +55,15 @@ public slots:
 
   void setMolecule(QtGui::Molecule* molecule);
 
+  QString name() const;
+
 private:
-  QtGui::Molecule* m_molecule;
+  QtGui::Molecule* m_molecule = nullptr;
+  mutable QString m_name;
+  mutable bool m_autoName = true;
+  mutable bool m_nameRequestPending = false;
+
+  QNetworkAccessManager* m_network = nullptr;
 };
 
 } // end namespace Avogadro