try catch around mcqr step code

src/gui/mcqr_run_view/mcqr_sds_xic_widget/mcqrsdsxicwidget.cpp

@@ -371,8 +371,9 @@ McqrSdsXicWidget::runQualityCheckingXic()
       grantlee_context.insert("sds_page",
                               ui->sds_page_switch->getSwitchValue());
 
-      getMcqrRunParentView()->getRProcessRunning()->write(
-        msp_rscriptTemplate->render(&grantlee_context).toUtf8());
+
+      getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+        "quality_xic", msp_rscriptTemplate->render(&grantlee_context));
     }
   qDebug();
 }
@@ -700,8 +701,8 @@ McqrSdsXicWidget::runProteinClustering()
                           transformQStringListInRListFormat(factors_list));
   grantlee_context.insert("nb_cluster", ui->cluster_spin->value());
 
-  getMcqrRunParentView()->getRProcessRunning()->write(
-    msp_rscriptTemplate->render(&grantlee_context).toUtf8());
+  getMcqrRunParentView()->getRProcessRunning()->executeMcqrStep(
+    "protein_clustering", msp_rscriptTemplate->render(&grantlee_context));
   qDebug();
 }
 

src/gui/mcqr_run_view/mcqrqprocess.cpp

@@ -52,3 +52,32 @@ McqrQProcess::getRScriptRun()
 {
   return m_RscriptRun;
 }
+
+qint64
+McqrQProcess::executeOffTheRecord(const QString &mcqr_otr)
+{
+  QProcess::write(mcqr_otr.toUtf8());
+  return 0;
+}
+
+
+qint64
+McqrQProcess::executeMcqrStep(const QString &mcqr_step_name,
+                              const QString &mcqr_step)
+{
+
+  write(QString("message(\"MCQRBegin: %1\")\n").arg(mcqr_step_name).toUtf8());
+  
+  executeOffTheRecord("vl <- tryCatch({\n");
+  write(mcqr_step.toUtf8());
+  // write(mcqr_step.toUtf8());
+  executeOffTheRecord(
+    "\n},warning = function(warn) {\n print(paste(\"MY "
+    "WARNING: "
+    "\", warn))\n},error "
+    "= function(err) {\n print(paste(\"MY ERROR: \",err))\n},finally = "
+    "function(f) "
+    "{\n print(paste(\"e: \", e))\n})\n print(paste(\"Output: \", vl))\n");
+  
+  write(QString("message(\"MCQREnd: %1\")\n").arg(mcqr_step_name).toUtf8());
+}

src/gui/mcqr_run_view/mcqrqprocess.h

@@ -40,6 +40,9 @@ class McqrQProcess : public QProcess
 
 
   qint64 write(const QByteArray &byte_array);
+  qint64 executeOffTheRecord(const QString &mcqr_otr);
+  qint64 executeMcqrStep(const QString &mcqr_step_name,
+                         const QString &mcqr_step);
   QString getRScriptRun();
 
   private: