Handling of symlinks

Author: caetera

ParseInput.cs

@@ -14,6 +14,8 @@ public class ParseInput
         /// </summary>
         private string _rawFilePath;
 
+        private string _userProvidedFilePath;
+
         private int _errors;
 
         private int _warnings;
@@ -29,12 +31,17 @@ public string RawFilePath
             set
             {
                 _rawFilePath = value;
+                _userProvidedFilePath = value;
                 if (value != null)
                 {
                     RawFileNameWithoutExtension = Path.GetFileNameWithoutExtension(value);
                 }
             }
         }
+        public string UserProvidedPath
+        {
+            get => _userProvidedFilePath;
+        }
 
         public int Errors
         {
@@ -155,5 +162,15 @@ public void NewWarn()
         {
             _warnings++;
         }
+
+        public void UpdateRealPath(string path)
+        {
+            if (path != null)
+            {
+                _userProvidedFilePath = _rawFilePath;
+                _rawFilePath = path;
+                
+            }
+        }
     }
 }

RawFileParser.cs

@@ -1,10 +1,12 @@
 using System;
 using System.IO;
 using System.Linq;
+using System.Runtime.InteropServices;
 using ThermoFisher.CommonCore.Data;
 using ThermoFisher.CommonCore.Data.Business;
 using ThermoFisher.CommonCore.Data.Interfaces;
 using ThermoRawFileParser.Writer;
+using ThermoRawFileParser.Util;
 
 namespace ThermoRawFileParser
 {
@@ -93,6 +95,26 @@ private static void ProcessFile(ParseInput parseInput)
         {
             // Create the IRawDataPlus object for accessing the RAW file
             IRawDataPlus rawFile;
+
+            //checking for symlinks
+            var fileInfo = new FileInfo(parseInput.RawFilePath);
+
+            if (fileInfo.Attributes.HasFlag(FileAttributes.ReparsePoint)) //detected path is a symlink
+            {
+                if (RuntimeInformation.IsOSPlatform(OSPlatform.Windows))
+                {
+                    var realPath = NativeMethods.GetFinalPathName(parseInput.RawFilePath);
+                    Log.DebugFormat("Detected reparse point, real path: {0}", realPath);
+                    parseInput.UpdateRealPath(realPath);
+                }
+                else //Mono should handle all non-windows platforms
+                {
+                    var realPath = Path.Combine(Path.GetDirectoryName(parseInput.RawFilePath), Mono.Unix.UnixPath.ReadLink(parseInput.RawFilePath));
+                    Log.DebugFormat("Detected reparse point, real path: {0}", realPath);
+                    parseInput.UpdateRealPath(realPath);
+                }
+            }
+            
             using (rawFile = RawFileReaderFactory.ReadFile(parseInput.RawFilePath))
             {
                 if (!rawFile.IsOpen)
@@ -155,7 +177,7 @@ private static void ProcessFile(ParseInput parseInput)
                     }
                 }
 
-                Log.Info("Finished parsing " + parseInput.RawFilePath);
+                Log.Info("Finished parsing " + parseInput.UserProvidedPath);
             }
         }
     }

ThermoRawFileParser.csproj

@@ -96,6 +96,9 @@
       <HintPath>packages\Mono.Options.6.6.0.161\lib\net40\Mono.Options.dll</HintPath>
       <Private>True</Private>
     </Reference>
+    <Reference Include="Mono.Unix, Version=7.1.0.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51, processorArchitecture=MSIL">
+      <HintPath>packages\Mono.Unix.7.1.0-final.1.21458.1\lib\net45\Mono.Unix.dll</HintPath>
+    </Reference>
     <Reference Include="mscorlib" />
     <Reference Include="Namotion.Reflection, Version=1.0.18.0, Culture=neutral, PublicKeyToken=c2f9c3bdfae56102">
       <HintPath>packages\Namotion.Reflection.1.0.18\lib\net45\Namotion.Reflection.dll</HintPath>
@@ -198,6 +201,7 @@
     <Compile Include="RawFileParser.cs" />
     <Compile Include="Util\LimitedSizeDictionary.cs" />
     <Compile Include="Util\MZArray.cs" />
+    <Compile Include="Util\NativeMethods.cs" />
     <Compile Include="Util\Peptide.cs" />
     <Compile Include="Writer\PrecursorInfo.cs" />
     <Compile Include="Writer\ScanTrailer.cs" />
@@ -248,7 +252,9 @@
     </PropertyGroup>
     <Error Condition="!Exists('packages\NUnit.3.13.1\build\NUnit.props')" Text="$([System.String]::Format('$(ErrorText)', 'packages\NUnit.3.13.1\build\NUnit.props'))" />
     <Error Condition="!Exists('packages\NUnit3TestAdapter.4.1.0\build\net35\NUnit3TestAdapter.props')" Text="$([System.String]::Format('$(ErrorText)', 'packages\NUnit3TestAdapter.4.1.0\build\net35\NUnit3TestAdapter.props'))" />
+    <Error Condition="!Exists('packages\Mono.Unix.7.1.0-final.1.21458.1\build\Mono.Unix.targets')" Text="$([System.String]::Format('$(ErrorText)', 'packages\Mono.Unix.7.1.0-final.1.21458.1\build\Mono.Unix.targets'))" />
   </Target>
+  <Import Project="packages\Mono.Unix.7.1.0-final.1.21458.1\build\Mono.Unix.targets" Condition="Exists('packages\Mono.Unix.7.1.0-final.1.21458.1\build\Mono.Unix.targets')" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.
   <Target Name="BeforeBuild">

Util/NativeMethods.cs

@@ -0,0 +1,66 @@
+using System;
+using System.ComponentModel;
+using System.IO;
+using System.Runtime.InteropServices;
+using System.Text;
+
+namespace ThermoRawFileParser.Util
+{
+    /// <summary>
+    /// Uses Windows API to resolve reparse point target
+    /// 
+    /// Kudos to user Knagis from StackOverflow
+    /// https://stackoverflow.com/questions/2302416/how-to-obtain-the-target-of-a-symbolic-link-or-reparse-point-using-net
+    /// </summary>
+    public static class NativeMethods
+    {
+        private static readonly IntPtr INVALID_HANDLE_VALUE = new IntPtr(-1);
+
+        private const uint FILE_READ_EA = 0x0008;
+        private const uint FILE_FLAG_BACKUP_SEMANTICS = 0x2000000;
+
+        [DllImport("Kernel32.dll", SetLastError = true, CharSet = CharSet.Auto)]
+        static extern uint GetFinalPathNameByHandle(IntPtr hFile, [MarshalAs(UnmanagedType.LPTStr)] StringBuilder lpszFilePath, uint cchFilePath, uint dwFlags);
+
+        [DllImport("kernel32.dll", SetLastError = true)]
+        [return: MarshalAs(UnmanagedType.Bool)]
+        static extern bool CloseHandle(IntPtr hObject);
+
+        [DllImport("kernel32.dll", CharSet = CharSet.Auto, SetLastError = true)]
+        public static extern IntPtr CreateFile(
+                [MarshalAs(UnmanagedType.LPTStr)] string filename,
+                [MarshalAs(UnmanagedType.U4)] uint access,
+                [MarshalAs(UnmanagedType.U4)] FileShare share,
+                IntPtr securityAttributes, // optional SECURITY_ATTRIBUTES struct or IntPtr.Zero
+                [MarshalAs(UnmanagedType.U4)] FileMode creationDisposition,
+                [MarshalAs(UnmanagedType.U4)] uint flagsAndAttributes,
+                IntPtr templateFile);
+
+        public static string GetFinalPathName(string path)
+        {
+            var h = CreateFile(path,
+                FILE_READ_EA,
+                FileShare.ReadWrite | FileShare.Delete,
+                IntPtr.Zero,
+                FileMode.Open,
+                FILE_FLAG_BACKUP_SEMANTICS,
+                IntPtr.Zero);
+            if (h == INVALID_HANDLE_VALUE)
+                throw new Win32Exception();
+
+            try
+            {
+                var sb = new StringBuilder(1024);
+                var res = GetFinalPathNameByHandle(h, sb, 1024, 0);
+                if (res == 0)
+                    throw new Win32Exception();
+
+                return sb.ToString();
+            }
+            finally
+            {
+                CloseHandle(h);
+            }
+        }
+    }
+}

packages.config

@@ -8,6 +8,7 @@
   <package id="log4net" version="2.0.12" targetFramework="net472" />
   <package id="MathNet.Numerics" version="4.15.0" targetFramework="net472" />
   <package id="Mono.Options" version="6.6.0.161" targetFramework="net472" />
+  <package id="Mono.Unix" version="7.1.0-final.1.21458.1" targetFramework="net472" />
   <package id="Namotion.Reflection" version="1.0.18" targetFramework="net472" />
   <package id="Newtonsoft.Json" version="13.0.1" targetFramework="net472" />
   <package id="NJsonSchema" version="10.4.0" targetFramework="net472" />