AutoQC Loader updates

pwiz_tools/Skyline/Executables/AutoQC/AutoQC/AnnotationsFileWatcher.cs

@@ -0,0 +1,64 @@
+using System.IO;
+using SharedBatch;
+
+namespace AutoQC
+{
+
+    public class AnnotationsFileWatcher
+    {
+        private readonly Logger _logger;
+        private readonly ConfigRunner _configRunner;
+
+        private readonly FileSystemWatcher _fileWatcher;
+
+        public AnnotationsFileWatcher(Logger logger, ConfigRunner configRunner)
+        {
+            _fileWatcher = InitFileSystemWatcher();
+
+            _logger = logger;
+            _configRunner = configRunner;
+        }
+
+        private FileSystemWatcher InitFileSystemWatcher()
+        {
+            var fileWatcher = new FileSystemWatcher();
+            fileWatcher.Changed += (s, e) => FileChanged();
+            fileWatcher.Error += (s, e) => OnFileWatcherError(e);
+            return fileWatcher;
+        }
+
+        public void Init(AutoQcConfig config)
+        {
+            var mainSettings = config.MainSettings;
+
+            _fileWatcher.EnableRaisingEvents = false;
+
+            _fileWatcher.NotifyFilter = NotifyFilters.CreationTime | NotifyFilters.LastWrite;
+
+            _fileWatcher.Filter = Path.GetFileName(mainSettings.AnnotationsFilePath);
+
+            _fileWatcher.Path = Path.GetDirectoryName(mainSettings.AnnotationsFilePath);
+        }
+
+        public void StartWatching()
+        {
+            _fileWatcher.EnableRaisingEvents = true;
+        }
+
+        public void Stop()
+        {
+            _fileWatcher.EnableRaisingEvents = false;
+        }
+
+        private void FileChanged()
+        {
+            _logger.Log("Annotations file was updated.");
+            _configRunner.AnnotationsFileUpdated = true;
+        }
+
+        private void OnFileWatcherError(ErrorEventArgs e)
+        {
+            _logger.LogError(string.Format("There was an error watching the annotations file {0}.", _fileWatcher.Filter), e.GetException().ToString());
+        }
+    }
+}

pwiz_tools/Skyline/Executables/AutoQC/AutoQC/AutoQC.csproj

@@ -123,6 +123,7 @@
   <ItemGroup>
     <Compile Include="AutoQcConfig.cs" />
     <Compile Include="AutoQcConfigManager.cs" />
+    <Compile Include="AnnotationsFileWatcher.cs" />
     <Compile Include="InvalidConfigSetupForm.cs">
       <SubType>Form</SubType>
     </Compile>

pwiz_tools/Skyline/Executables/AutoQC/AutoQC/AutoQCConfigForm.cs

@@ -35,7 +35,8 @@ public partial class AutoQcConfigForm : Form
         private readonly DateTime _initialCreated;
 
         private SkylineTypeControl _skylineTypeControl;
-        private string _lastEnteredPath;
+        private string _lastEnteredPath; // last entered path to Skyline .sky file
+        private string _lastEnteredAnnotationsFilePath;
         private TabPage _lastSelectedTab;
         private SkylineSettings _currentSkylineSettings;
 
@@ -130,6 +131,10 @@ private void SetInitialMainSettings(MainSettings mainSettings)
             textAquisitionTime.Text = mainSettings.AcquisitionTime.ToString();
             comboBoxInstrumentType.SelectedItem = mainSettings.InstrumentType;
             comboBoxInstrumentType.SelectedIndex = comboBoxInstrumentType.FindStringExact(mainSettings.InstrumentType);
+            if (mainSettings.HasAnnotationsFile())
+            {
+                textAnnotationsFilePath.Text = mainSettings.AnnotationsFilePath;
+            }
         }
 
         private void SetDefaultMainSettings()
@@ -153,7 +158,8 @@ private MainSettings GetMainSettingsFromUi()
             var resultsWindow = textResultsTimeWindow.Text;
             var instrumentType = comboBoxInstrumentType.SelectedItem.ToString();
             var acquisitionTime = textAquisitionTime.Text;
-            var mainSettings = new MainSettings(skylineFilePath, folderToWatch, includeSubfolders, qcFileFilter, removeResults, resultsWindow, instrumentType, acquisitionTime);
+            var annotationsFilePath = textAnnotationsFilePath.Text;
+            var mainSettings = new MainSettings(skylineFilePath, folderToWatch, includeSubfolders, qcFileFilter, removeResults, resultsWindow, instrumentType, acquisitionTime, annotationsFilePath);
             return mainSettings;
         }
 
@@ -182,6 +188,20 @@ private void btnFolderToWatch_Click(object sender, EventArgs e)
             }
         }
 
+        private void btnAnnotationsFilePath_Click(object sender, EventArgs e)
+        {
+            var dialog = new OpenFileDialog
+            {
+                Filter = TextUtil.FileDialogFilter("CSV (Comma delimited)", TextUtil.EXT_CSV),
+                InitialDirectory = FileUtil.GetInitialDirectory(_lastEnteredAnnotationsFilePath, textSkylinePath.Text)
+            };
+            if (dialog.ShowDialog(this) == DialogResult.OK)
+            {
+                textAnnotationsFilePath.Text = dialog.FileName;
+                _lastEnteredAnnotationsFilePath = dialog.FileName;
+            }
+        }
+
         private void comboBoxFileFilter_SelectedIndexChanged(object sender, EventArgs e)
         {
             var selectedItem = comboBoxFileFilter.SelectedItem;
@@ -317,7 +337,7 @@ private void Save()
                 State.BaseState.AssertUniqueName(newConfig.Name, _action == ConfigAction.Edit);
                 newConfig.Validate(true);
             }
-            catch (ArgumentException e)
+            catch (Exception e)
             {
                 AlertDlg.ShowError(this, e.Message);
                 return;