From 46a9e14b56700d4c0b4737653d63b59b1e6f9d2a Mon Sep 17 00:00:00 2001
From: Marc Sturm <marc.sturm@med.uni-tuebingen.de>
Date: Mon, 11 Dec 2023 10:59:20 +0100
Subject: [PATCH] GSvar: improved logging to find out why IGV is sometimes
 cleared

---
 src/GSvar/IGVSession.cpp | 27 +++++++++++++++++----------
 src/GSvar/MainWindow.cpp | 19 ++++++++++++++++++-
 src/GSvar/MainWindow.h   |  5 +++++
 src/GSvar/MainWindow.ui  | 13 +++++++++++++
 src/cppCORE              |  2 +-
 5 files changed, 54 insertions(+), 12 deletions(-)

diff --git a/src/GSvar/IGVSession.cpp b/src/GSvar/IGVSession.cpp
index ce5674129..54d3ff4f7 100644
--- a/src/GSvar/IGVSession.cpp
+++ b/src/GSvar/IGVSession.cpp
@@ -143,17 +143,24 @@ bool IGVSession::isIgvRunning()
 	QList<IgvWorkerCommand> commands;
 	commands << IgvWorkerCommand{-1, "echo running"};
 
-	//start command
-	IGVCommandWorker* command_worker = new IGVCommandWorker(igv_data_, commands, 2000);
-	command_worker->setAutoDelete(false);
-    execution_pool_.start(command_worker);
-
-	//get answer
-	execution_pool_.waitForDone();
-	QString answer = command_worker->answer();
-	command_worker->deleteLater();
+	//try up to four times
+	for (int i=0; i<4; ++i)
+	{
+		//start command
+		IGVCommandWorker* command_worker = new IGVCommandWorker(igv_data_, commands, 500);
+		command_worker->setAutoDelete(false);
+		execution_pool_.start(command_worker);
+
+		//get answer
+		execution_pool_.waitForDone();
+		QString answer = command_worker->answer();
+		command_worker->deleteLater();
+
+		if (answer=="running") return true;
+		else Log::info("No answer for 'echo running' from IGV (try " + QString::number(i+1) + " of 4)");
+	}
 
-	return answer=="running";
+	return false;
 }
 
 bool IGVSession::hasRunningCommands()
diff --git a/src/GSvar/MainWindow.cpp b/src/GSvar/MainWindow.cpp
index e68d8c201..81d4ddb85 100644
--- a/src/GSvar/MainWindow.cpp
+++ b/src/GSvar/MainWindow.cpp
@@ -1821,7 +1821,7 @@ void MainWindow::on_actionDeleteIgvFolder_triggered()
 	   return;
 	}
 
-	int res = QMessageBox::question(this, "Delete IGV folder", "Do you want to delete the IGV folder?\nLocation: "+path_canonical+"\n\nYou will use all settings (proxy, alignment options, ...)!");
+	int res = QMessageBox::question(this, title, "Do you want to delete the IGV folder?\nLocation: "+path_canonical+"\n\nYou will use all settings (proxy, alignment options, ...)!");
 	if (res==QMessageBox::Yes)
 	{
 		QDir(path_canonical).removeRecursively();
@@ -7046,6 +7046,23 @@ void MainWindow::on_actionBurdenTest_triggered()
 	addModelessDialog(dlg);
 }
 
+void MainWindow::on_actionOpenLogFile_triggered()
+{
+	QDesktopServices::openUrl("file:///"+ Log::fileName());
+}
+
+void MainWindow::on_actionClearLogFile_triggered()
+{
+	QString title = "Delete GSvar log file";
+	QString filename = Log::fileName();
+
+	int res = QMessageBox::question(this, title, "Do you want to delete the GSvar log file?\nLocation: "+filename);
+	if (res==QMessageBox::Yes)
+	{
+		QFile::remove(filename);
+	}
+ }
+
 
 void MainWindow::editVariantClassification(VariantList& variants, int index, bool is_somatic)
 {
diff --git a/src/GSvar/MainWindow.h b/src/GSvar/MainWindow.h
index d7e9e454a..b6182833c 100644
--- a/src/GSvar/MainWindow.h
+++ b/src/GSvar/MainWindow.h
@@ -294,6 +294,11 @@ public slots:
 	void on_actionVirusDetection_triggered();
 	///Perform Burden test
 	void on_actionBurdenTest_triggered();
+	///Shows the GSvar log file
+	void on_actionOpenLogFile_triggered();
+	///Clears the log file
+	void on_actionClearLogFile_triggered();
+
 	///Load report configuration
 	void loadReportConfig();
 	///Store report configuration
diff --git a/src/GSvar/MainWindow.ui b/src/GSvar/MainWindow.ui
index 64c99b971..2e3a3b230 100644
--- a/src/GSvar/MainWindow.ui
+++ b/src/GSvar/MainWindow.ui
@@ -389,6 +389,9 @@
     <addaction name="actionSettings"/>
     <addaction name="actionEncrypt"/>
     <addaction name="separator"/>
+    <addaction name="actionOpenLogFile"/>
+    <addaction name="actionClearLogFile"/>
+    <addaction name="separator"/>
     <addaction name="actionAbout"/>
    </widget>
    <widget class="QMenu" name="menuTools">
@@ -1454,6 +1457,16 @@
     <string>Delete IGV folder</string>
    </property>
   </action>
+  <action name="actionOpenLogFile">
+   <property name="text">
+    <string>Open log file</string>
+   </property>
+  </action>
+  <action name="actionClearLogFile">
+   <property name="text">
+    <string>Clear log file</string>
+   </property>
+  </action>
  </widget>
  <layoutdefault spacing="6" margin="11"/>
  <customwidgets>
diff --git a/src/cppCORE b/src/cppCORE
index 4dc65aca2..1501467b1 160000
--- a/src/cppCORE
+++ b/src/cppCORE
@@ -1 +1 @@
-Subproject commit 4dc65aca2b425b5bdd0a6ec3ef270b63689d1511
+Subproject commit 1501467b161b08fb2678ffc9e80ff97f8562b508