Merge pull request #432 from psavery/mongochem-use-geometries

Utilize new geometry endpoints for MongoChem
OpenChemistry · Jan 14, 2020 · 41fe64e · 41fe64e
2 parents 22f1091 + b55a677
commit 41fe64e
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Showing 4 changed files with 87 additions and 1 deletion.
diff --git a/avogadro/qtplugins/mongochem/calculationsubmitter.cpp b/avogadro/qtplugins/mongochem/calculationsubmitter.cpp
@@ -90,6 +90,40 @@ void CalculationSubmitter::finishUploadMolecule(const QVariant& results)
     return;
   }
 
+  // Now, upload the particular geometry that we will use
+  uploadGeometry();
+}
+
+void CalculationSubmitter::uploadGeometry()
+{
+  QByteArray postData = m_moleculeCjson.toLatin1();
+
+  QString url =(m_girderUrl + "/molecules/%1/geometries").arg(m_moleculeId);
+
+  QList<QPair<QString, QString>> urlQueries = {
+    { "provenanceType", "Uploaded from Avogadro2" }
+  };
+
+  auto* request =
+    new GirderRequest(m_networkManager.data(), url, m_girderToken);
+  request->setHeader(QNetworkRequest::ContentTypeHeader, "application/json");
+  request->setUrlQueries(urlQueries);
+  request->post(postData);
+
+  connect(request, &GirderRequest::result, this,
+          &CalculationSubmitter::finishUploadGeometry);
+  connect(request, &GirderRequest::error, this, &CalculationSubmitter::error);
+  deleteRequestWhenFinished(request);
+}
+
+void CalculationSubmitter::finishUploadGeometry(const QVariant& results)
+{
+  m_geometryId = results.toMap()["_id"].toString();
+  if (m_geometryId.isEmpty()) {
+    emit error("Failed to upload geometry!");
+    return;
+  }
+
   // Now, make sure the calculation has not already been done before.
   fetchCalculation();
 }
@@ -105,6 +139,7 @@ void CalculationSubmitter::fetchCalculation()
 
   QList<QPair<QString, QString>> urlQueries = {
     { "moleculeId", m_moleculeId },
+    { "geometryId", m_geometryId },
     { "inputParameters", inputParams },
     { "imageName", QString("%1:%2").arg(repository).arg(tag) }
   };
@@ -272,6 +307,7 @@ void CalculationSubmitter::createPendingCalculation()
 
   QJsonObject json;
   json["moleculeId"] = m_moleculeId;
+  json["geometryId"] = m_geometryId;
   json["public"] = true;
   json["cjson"] = QJsonValue();
 

diff --git a/avogadro/qtplugins/mongochem/calculationsubmitter.h b/avogadro/qtplugins/mongochem/calculationsubmitter.h
@@ -56,6 +56,9 @@ private slots:
   void uploadMolecule();
   void finishUploadMolecule(const QVariant& results);
 
+  void uploadGeometry();
+  void finishUploadGeometry(const QVariant& results);
+
   void fetchCalculation();
   void finishFetchCalculation(const QVariant& results);
 
@@ -94,6 +97,7 @@ private slots:
 
   // These will be set during the process
   QString m_moleculeId;
+  QString m_geometryId;
   QString m_pendingCalculationId;
   QString m_clusterId;
   QString m_queueId;

diff --git a/avogadro/qtplugins/mongochem/mongochemwidget.cpp b/avogadro/qtplugins/mongochem/mongochemwidget.cpp
@@ -263,7 +263,51 @@ void MongoChemWidget::uploadMolecule()
 
 void MongoChemWidget::finishUploadMolecule(const QVariant& results)
 {
-  Q_UNUSED(results)
+  auto moleculeId = results.toMap()["_id"].toString();
+  if (moleculeId.isEmpty()) {
+    QString message = "Failed to upload molecule";
+    qDebug() << message;
+    QMessageBox::critical(this, "MongoChem", message);
+    return;
+  }
+
+  // Now, upload the particular geometry
+  uploadGeometry(moleculeId);
+}
+
+void MongoChemWidget::uploadGeometry(const QString& moleculeId)
+{
+  QByteArray postData = m_plugin->currentMoleculeCjson().toLatin1();
+
+  QString url =(m_girderUrl + "/molecules/%1/geometries").arg(moleculeId);
+
+  QList<QPair<QString, QString>> urlQueries = {
+    { "provenanceType", "Uploaded by Avogadro2 User" }
+  };
+
+  auto* request =
+    new GirderRequest(m_networkManager.data(), url, m_girderToken);
+  request->setHeader(QNetworkRequest::ContentTypeHeader, "application/json");
+  request->setUrlQueries(urlQueries);
+  request->post(postData);
+
+  connect(request, &GirderRequest::result, this,
+          &MongoChemWidget::finishUploadGeometry);
+  connect(request, &GirderRequest::error, this, &MongoChemWidget::error);
+  connect(request, &GirderRequest::result, request,
+          &GirderRequest::deleteLater);
+  connect(request, &GirderRequest::error, request, &GirderRequest::deleteLater);
+}
+
+void MongoChemWidget::finishUploadGeometry(const QVariant& results)
+{
+  auto geometryId = results.toMap()["_id"].toString();
+  if (geometryId.isEmpty()) {
+    QString message = "Failed to upload geometry";
+    qDebug() << message;
+    QMessageBox::critical(this, "MongoChem", message);
+    return;
+  }
 
   QString message = "Upload successful!";
   qDebug() << message;

diff --git a/avogadro/qtplugins/mongochem/mongochemwidget.h b/avogadro/qtplugins/mongochem/mongochemwidget.h
@@ -54,6 +54,8 @@ private slots:
   void finishDownloadMolecule(const QVariant& results);
   void uploadMolecule();
   void finishUploadMolecule(const QVariant& results);
+  void uploadGeometry(const QString& moleculeId);
+  void finishUploadGeometry(const QVariant& results);
   void submitCalculation();
   void finishSubmitCalculation(const QVariantMap& results);
   void finishWatchCalculation(const QByteArray& cjson);