private void ShowOutputButton_Click(object sender, RoutedEventArgs e)
{
ShowStdOut = true;
lock (InformationTextBox)
{
InformationTextBox.Document.Blocks.Clear();
InformationTextBox.AppendText(DockerStdOut);
}
}
private void DisplayAnyErrors(Task obj)
{
Dispatcher.Invoke(() => InformationTextBox.AppendText("Done!" + Environment.NewLine));
if (StaticTasksObservableCollection.Count > 0)
{
Dispatcher.Invoke(() => MessageBox.Show("Finished! Workflow summary is located in "
+ StaticTasksObservableCollection.First().options.AnalysisDirectory, "Spritz Workflow",
MessageBoxButton.OK, MessageBoxImage.Information));
}
IsRunning = false;
}
private void ShowTopButton_Click(object sender, RoutedEventArgs e)
{
ShowStdOut = false;
Dispatcher.Invoke(() =>
{
InformationTextBox.Document.Blocks.Clear();
Process proc = new Process();
proc.StartInfo.FileName = "Powershell.exe";
proc.StartInfo.Arguments = Everything.GenerateTopComand();
proc.StartInfo.UseShellExecute = false;
proc.StartInfo.RedirectStandardOutput = true;
proc.StartInfo.CreateNoWindow = true;
proc.Start();
StreamReader outputReader = proc.StandardOutput;
InformationTextBox.AppendText(outputReader.ReadToEnd());
proc.WaitForExit();
});
}
private void RunWorkflowButton_Click(object sender, RoutedEventArgs e)
{
try
{
if (StaticTasksObservableCollection.Count == 0)
{
MessageBox.Show("You must add a workflow before a run.", "Run Workflows", MessageBoxButton.OK, MessageBoxImage.Information);
return;
}
else if (RnaSeqFastqCollection.Any() && GetPathToFastqs().CompareTo(OutputFolderTextBox.Text) != 0) // to be edited
{
MessageBox.Show("FASTQ files do not exist in the user-defined analysis directory.", "Run Workflows", MessageBoxButton.OK, MessageBoxImage.Information);
return;
}
DynamicTasksObservableCollection = new ObservableCollection <InRunTask>();
DynamicTasksObservableCollection.Add(new InRunTask("Workflow 1", StaticTasksObservableCollection.First().options));
WorkflowTreeView.DataContext = DynamicTasksObservableCollection;
Everything = new EverythingRunnerEngine(DynamicTasksObservableCollection.Select(b => new Tuple <string, Options>(b.DisplayName, b.options)).First(), OutputFolderTextBox.Text);
InformationTextBox.Document.Blocks.Clear();
InformationTextBox.AppendText($"Command executing: Powershell.exe {Everything.GenerateCommandsDry(DockerImage)}\n\n"); // keep for debugging
InformationTextBox.AppendText($"Saving output to {Everything.PathToWorkflow}. Please monitor it there...\n\n");
IsRunning = true;
Everything.WriteConfig(StaticTasksObservableCollection.First().options);
var t = new Task(RunEverythingRunner);
t.Start();
t.ContinueWith(DisplayAnyErrors);
// update gui
RunWorkflowButton.IsEnabled = false;
ClearTasksButton.IsEnabled = true;
BtnWorkFlow.IsEnabled = false;
ResetTasksButton.IsEnabled = true;
}
catch (TaskCanceledException)
{
// Ignore error
}
}
private void OutputHandler(object source, DataReceivedEventArgs e)
{
Dispatcher.Invoke(() =>
{
if (!string.IsNullOrEmpty(e.Data))
{
string output = outputScrub.Replace(e.Data, "");
DockerStdOut += output + Environment.NewLine;
if (ShowStdOut)
{
lock (InformationTextBox)
InformationTextBox.AppendText(output + Environment.NewLine);
}
using (StreamWriter sw = File.Exists(Everything.PathToWorkflow) ? File.AppendText(Everything.PathToWorkflow) : File.CreateText(Everything.PathToWorkflow))
{
sw.WriteLine(output);
}
}
});
}
