Live fixes

ApplicationServer/AppServerPipe.cs

@@ -6,6 +6,9 @@
 
 namespace WorkflowServer
 {
+    /// <summary>
+    /// Class is used to communicate and run processing workflows on data received from the client. 
+    /// </summary>
     internal class AppServerPipe
     {
         public event EventHandler<EventArgs> PipeConnected;
@@ -23,8 +26,6 @@ internal class AppServerPipe
         private ProcessMs2ScansDelegate? Ms2Delegate { get; set; }
         // static class with processing workflows? 
         public AppServerPipe(NamedPipeServerStream pipeServer,
-            StreamWriter sw,
-            StreamReader sr,
             int ms1ScanQueueThreshold,
             int ms2ScanQueueThreshold,
             ProcessMs1ScansDelegate ms1Delegate = null,
@@ -39,83 +40,55 @@ public AppServerPipe(NamedPipeServerStream pipeServer,
             Ms2Delegate = ms2Delegate;
         }
 
+        /// <summary>
+        /// Begins the server connection; starts the async buffer reader; connects event handler methods to events. 
+        /// </summary>
         public void StartServer()
         {
             PipeConnected += (obj, sender) =>
             {
                 Console.WriteLine("Pipe client connected. Sent from event.");
             };
-            // delegate for processing needs to be used as a function. 
-            ProcessMs1ScansDelegate ms1Del = (o, scans) =>
-            {
-                // select highest m/z from the scans and send a singlescandataobject back to client
-                List<double> mzPrecursors = new();
-                foreach (var sc in scans.ListSsdo)
-                {
-                    double max = sc.YArray.Max();
-                    int posX = Array.IndexOf(sc.YArray, max);
-                    mzPrecursors.Add(sc.XArray[posX]);
-                }
-
-                foreach (var mz in mzPrecursors)
-                {
-                    SingleScanDataObject ssdoTemp = new()
-                    {
-                        ScanOrder = 2,
-                        ScanNumber = 10,
-                        PrecursorScanNumber = 3,
-                        MzPrecursor = 15,
-                        XArray = new double[] { 0, 0 },
-                        YArray = new double[] { 0, 0 }
-                    };
-                    string temp = JsonConvert.SerializeObject(ssdoTemp);
-                    byte[] buffer = Encoding.UTF8.GetBytes(temp);
-                    byte[] length = BitConverter.GetBytes(buffer.Length);
-                    byte[] finalBuffer = length.Concat(buffer).ToArray();
-                    PipeServer.Write(finalBuffer, 0, finalBuffer.Length);
-                    PipeServer.WaitForPipeDrain();
-                }
-
-            };
-
+
             PipeDataReceived += HandleDataReceived;
-            Ms1ScanQueueThresholdReached += ms1Del.Invoke;
+            Ms1ScanQueueThresholdReached += Ms1Delegate.Invoke;
             Ms2ScanQueueThresholdReached += Ms2Delegate.Invoke;
             Ms1ProcessingCompleted += (object? obj, ProcessingCompletedEventArgs sender) =>
             {
 
-
+                Console.WriteLine("Ms1 Processing Completed"); 
             };
             Ms2ProcessingCompleted += (object? obj, ProcessingCompletedEventArgs sender) =>
             {
-                byte[] buffer = Encoding.UTF8.GetBytes("15");
-                var taskResult = new ValueTask();
-                taskResult = PipeServer.WriteAsync(buffer);
-                buffer = null;
+
+                Console.WriteLine("Ms2 Processing Completed."); 
             };
 
             var connectionResult = PipeServer.BeginWaitForConnection(Connected, null);
             // wait for the connection to occur before proceeding. 
             connectionResult.AsyncWaitHandle.WaitOne();
             connectionResult.AsyncWaitHandle.Close();
-            var serializer = new JsonSerializer();
             StartReaderAsync();
-            while (PipeServer.IsConnected)
-            {
-
-            }
         }
+        /// <summary>
+        /// Used to determine which queue scan that was received from server should go into. 
+        /// </summary>
+        /// <param name="obj"></param>
+        /// <param name="eventArgs"></param>
+        /// <exception cref="ArgumentException"></exception>
         private void HandleDataReceived(object? obj, PipeEventArgs eventArgs)
         {
             // convert pipeeventargs to single scan data object
             SingleScanDataObject ssdo = eventArgs.ToSingleScanDataObject();
             if (ssdo == null) throw new ArgumentException("single scan data object is null");
 
+            // TODO: refactor and make handling more robust downstream.
             if (ssdo.ScanOrder == 1)
             {
                 ScanQueueMS1.Enqueue(ssdo);
                 if (ScanQueueMS1.Count == Ms1ScanQueueThreshold)
                 {
+                    // method raises event
                     OnMs1QueueThresholdReached(ScanQueueMS1);
                 }
             }
@@ -124,32 +97,51 @@ private void HandleDataReceived(object? obj, PipeEventArgs eventArgs)
                 ScanQueueMS2.Enqueue(ssdo);
                 if (ScanQueueMS2.Count == Ms2ScanQueueThreshold)
                 {
+                    // method raises handler
                     OnMs2QueueThresholdReached(ScanQueueMS2);
                 }
-            }
+            } // TODO: Handle scan order > 2. 
             Console.WriteLine("\n");
         }
+        /// <summary>
+        /// Triggers event that begins processing of Ms1 queue. 
+        /// </summary>
+        /// <param name="queue"></param>
         private void OnMs1QueueThresholdReached(Queue<SingleScanDataObject> queue)
         {
             Ms1ScanQueueThresholdReached?.Invoke(this,
                 new ScanQueueThresholdReachedEventArgs(queue.DequeueChunk(Ms1ScanQueueThreshold)));
         }
+        /// <summary>
+        ///  Triggers event that begins processing of Ms2 queue. 
+        /// </summary>
+        /// <param name="queue"></param>
         private void OnMs2QueueThresholdReached(Queue<SingleScanDataObject> queue)
         {
             Ms2ScanQueueThresholdReached?.Invoke(this,
                 new ScanQueueThresholdReachedEventArgs(queue.DequeueChunk(Ms2ScanQueueThreshold)));
         }
+        /// <summary>
+        /// Callback method used to wait for client pipe connection. 
+        /// </summary>
+        /// <param name="ar"></param>
         private void Connected(IAsyncResult ar)
         {
             OnConnection();
             PipeServer.EndWaitForConnection(ar);
         }
-
         private void OnConnection()
         {
             PipeConnected?.Invoke(this, EventArgs.Empty);
         }
-
+        /// <summary>
+        /// Begins asynchronous buffer reading. Converts the first four bytes into the integer size of the object contained in the rest of the buffer.
+        /// Then creates the buffer of that size and reads the data into the buffer. 
+        ///
+        /// DO NOT MODIFY OR THINK ABOUT
+        /// MODIFYING THIS METHOD UNLESS YOU 100% KNOW WHAT IT DOES AND WHAT YOU ARE CHANGING. 
+        /// </summary>
+        /// <param name="packetReceived">The Action delegate determines what is done with the byte buffer that is received.</param>
         private void StartByteReaderAsync(Action<byte[]> packetReceived)
         {
             byte[] byteDataLength = new byte[sizeof(int)];
@@ -169,11 +161,20 @@ private void StartByteReaderAsync(Action<byte[]> packetReceived)
                         });
                 });
         }
-
+        /// <summary>
+        /// Starts the reader asynchronously and triggers the PipeDataReceived event when data is received from the pipe. 
+        /// </summary>
         public void StartReaderAsync()
         {
             StartByteReaderAsync((b) =>
                 PipeDataReceived?.Invoke(this, new PipeEventArgs(b)));
         }
+
+        private void SendScanToClient(object obj, ProcessingCompletedEventArgs sender)
+        {
+            byte[] buffer = sender.Ssdo.CreateSerializedSingleScanDataObject();
+            PipeServer.WriteAsync(buffer, 0, buffer.Length); 
+            PipeServer.WaitForPipeDrain();
+        }
     }
 }

ApplicationServer/Program.cs

@@ -1,17 +1,48 @@
 using System.IO.Pipes;
-using ClientServerCommunication;
-using Data;
+using ClientServerCommLibrary;
 using InstrumentControl;
 using Newtonsoft;
 using Newtonsoft.Json;
+using WorkflowServer; 
 
 namespace ApplicationServer
 {
     public class Program
     {
         public static void Main(string[] args)
         {
+            NamedPipeServerStream pipe = new NamedPipeServerStream("test", PipeDirection.InOut,5, 
+                PipeTransmissionMode.Byte, PipeOptions.Asynchronous);
 
+            ProcessMs1ScansDelegate ms1Del = (obj, ev) =>
+            {
+                //Console.WriteLine(ev.ListSsdo.First().MaxX);
+            };
+            ProcessMs2ScansDelegate ms2Del = (obj, ev) =>
+            {
+                //Console.WriteLine(ev.ListSsdo.First().PrecursorScanNumber);
+            };
+            AppServerPipe appPipe = new(pipe, 1, 1, ms1Del, ms2Del);
+
+            bool connectedBool = false; 
+            appPipe.PipeConnected += (obj, ev) =>
+            {
+                connectedBool = true; 
+            };
+            appPipe.PipeDataReceived += (obj, ev) =>
+            {
+                var scan = ev.ToSingleScanDataObject();
+                Console.WriteLine(scan.MaxX);
+            }; 
+            appPipe.StartServer();
+            while (connectedBool)
+            {
+                //appPipe.PipeDataReceived += (obj, ev) =>
+                //{
+                //    var scan = ev.ToSingleScanDataObject();
+                //    Console.WriteLine(scan.MaxX.ToString());
+                //}; 
+            }
         }
     }
 }

ApplicationServer/Properties/launchSettings.json

@@ -1,8 +1,7 @@
 {
   "profiles": {
     "ApplicationServer": {
-      "commandName": "Project",
-      "commandLineArgs": "simple Server"
+      "commandName": "Project"
     }
   }
 }

ApplicationServer/ScanQueue/ScanQueue.cs

@@ -1,4 +1,5 @@
-using Data; 
+using ClientServerCommLibrary;
+
 
 namespace ApplicationServer
 {

ApplicationServer/ScanQueue/ThresholdReachedEventArgs.cs

@@ -1,4 +1,4 @@
-using Data; 
+using ClientServerCommLibrary;
 
 namespace ApplicationServer
 {

ApplicationServer/WorkflowServer.csproj

@@ -9,6 +9,7 @@
 
   <ItemGroup>
     <PackageReference Include="Newtonsoft.Json" Version="13.0.1" />
+    <PackageReference Include="NUnit" Version="3.13.3" />
   </ItemGroup>
 
   <ItemGroup>

Client/IScanTranslator.cs

@@ -0,0 +1,14 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using ClientServerCommLibrary;
+
+namespace Client
+{
+    public abstract class ScanTranslator
+    {
+        public abstract void Translate(SingleScanDataObject ssdo); 
+    }
+}

Client/InstrumentClient.csproj

@@ -1,5 +1,6 @@
 <?xml version="1.0" encoding="utf-8"?>
 <Project ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <Import Project="..\packages\NUnit.3.13.3\build\NUnit.props" Condition="Exists('..\packages\NUnit.3.13.3\build\NUnit.props')" />
   <Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
   <PropertyGroup>
     <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
@@ -12,6 +13,8 @@
     <FileAlignment>512</FileAlignment>
     <AutoGenerateBindingRedirects>true</AutoGenerateBindingRedirects>
     <Deterministic>true</Deterministic>
+    <NuGetPackageImportStamp>
+    </NuGetPackageImportStamp>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
     <PlatformTarget>x64</PlatformTarget>
@@ -47,6 +50,9 @@
     <Reference Include="Newtonsoft.Json, Version=13.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed, processorArchitecture=MSIL">
       <HintPath>..\packages\Newtonsoft.Json.13.0.1\lib\net45\Newtonsoft.Json.dll</HintPath>
     </Reference>
+    <Reference Include="nunit.framework, Version=3.13.3.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
+      <HintPath>..\packages\NUnit.3.13.3\lib\net45\nunit.framework.dll</HintPath>
+    </Reference>
     <Reference Include="Spectrum-1.0, Version=1.1.0.1, Culture=neutral, PublicKeyToken=c03bf447005257eb, processorArchitecture=MSIL">
       <SpecificVersion>False</SpecificVersion>
       <HintPath>..\..\..\..\..\..\Thermo\Instruments\TNG\OrbitrapFusionLumos\3.3\System\Programs\Spectrum-1.0.dll</HintPath>
@@ -73,9 +79,13 @@
     <Compile Include="Factories\ThermoTribridFactory.cs" />
     <Compile Include="InstrumentClientPipe.cs" />
     <Compile Include="InstrumentInterfaces\IInstrument.cs" />
+    <Compile Include="InstrumentInterfaces\Thermo\DataHandling\InstrumentSettingEnums.cs" />
     <Compile Include="InstrumentInterfaces\Thermo\DataHandling\MsScanExtensions.cs" />
+    <Compile Include="InstrumentInterfaces\Thermo\DataHandling\ThermoTribridSsdoMapping.cs" />
     <Compile Include="InstrumentInterfaces\Thermo\InterfaceImplementations\ThermoQE.cs" />
     <Compile Include="InstrumentInterfaces\Thermo\InterfaceImplementations\ThermoTribrid.cs" />
+    <Compile Include="InstrumentInterfaces\Thermo\ThermoScanTranslator\ThermoTribridScanTranslator.cs" />
+    <Compile Include="IScanTranslator.cs" />
     <Compile Include="MsScanReadyToSendEventArgs.cs" />
     <Compile Include="Program.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
@@ -90,11 +100,13 @@
       <Project>{0e9b5801-5167-44cc-90d3-c8caf1df8f6a}</Project>
       <Name>ClientServerCommLibrary</Name>
     </ProjectReference>
-    <ProjectReference Include="..\Data\Data.csproj">
-      <Project>{6b34249b-a513-4a4a-9ed5-cb633bcab646}</Project>
-      <Name>Data</Name>
-    </ProjectReference>
   </ItemGroup>
   <ItemGroup />
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
+  <Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
+    <PropertyGroup>
+      <ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them.  For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
+    </PropertyGroup>
+    <Error Condition="!Exists('..\packages\NUnit.3.13.3\build\NUnit.props')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\NUnit.3.13.3\build\NUnit.props'))" />
+  </Target>
 </Project>