Add stdout option

Author: caetera

MainClass.cs

@@ -361,7 +361,7 @@ private static void RegularParametersParsing(string[] args)
                     h => help = h != null
                 },
                 {
-                    "version", "Prints out the library version.",
+                    "version", "Prints out the version of the executable.",
                     v => version = v != null
                 },
                 {
@@ -383,6 +383,11 @@ private static void RegularParametersParsing(string[] args)
                     "The output file. Specify this or an output directory -o. Specifying neither writes to the input directory.",
                     v => parseInput.OutputFile = v
                 },
+                {
+                    "s|stdout",
+                    "Write to standard output. Cannot be combined with file or directory output. Implies silent logging, i.e. logging level 0",
+                    v => parseInput.StdOut = v != null
+                },
                 {
                     "f=|format=",
                     "The spectra output format: 0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet. Defaults to mzML if no format is specified.",
@@ -474,8 +479,7 @@ private static void RegularParametersParsing(string[] args)
                 {
                     var helpMessage =
                         $"usage is {Assembly.GetExecutingAssembly().GetName().Name}.exe [subcommand] [options]\noptional subcommands are xic|query (use [subcommand] -h for more info]):";
-                    ShowHelp(helpMessage, null,
-                        optionSet);
+                    ShowHelp(helpMessage, null, optionSet);
                     return;
                 }
 
@@ -516,6 +520,13 @@ private static void RegularParametersParsing(string[] args)
                         "-d, --input_directory");
                 }
 
+                if (parseInput.StdOut && (parseInput.OutputFile != null || parseInput.OutputDirectory != null))
+                {
+                    throw new OptionException(
+                        "standard output cannot be combined with file or directory output",
+                        "-s, --stdout");
+                }
+
                 if (parseInput.OutputFile == null && parseInput.OutputDirectory == null)
                 {
                     if (parseInput.RawFilePath != null)
@@ -667,6 +678,11 @@ private static void RegularParametersParsing(string[] args)
                     }
                 }
 
+                if (parseInput.StdOut)
+                {
+                    parseInput.LogFormat = LogFormat.SILENT;
+                }
+
                 if (parseInput.S3Url != null && parseInput.S3AccessKeyId != null &&
                     parseInput.S3SecretAccessKey != null && parseInput.BucketName != null)
                     if (Uri.IsWellFormedUriString(parseInput.S3Url, UriKind.Absolute))

ParseInput.cs

@@ -81,6 +81,8 @@ public string RawFilePath
 
         public bool MGFPrecursor { get; set; }
 
+        public bool StdOut { get; set; }
+
         private S3Loader S3Loader { get; set; }
 
         public string S3AccessKeyId { get; set; }
@@ -112,6 +114,7 @@ public ParseInput()
             IgnoreInstrumentErrors = false;
             AllDetectors = false;
             MsLevel = allLevels;
+            StdOut = false;
         }
 
         public ParseInput(string rawFilePath, string rawDirectoryPath, string outputDirectory, OutputFormat outputFormat

RawFileParser.cs

@@ -39,37 +39,46 @@ public static void Parse(ParseInput parseInput)
                 {
                     parseInput.RawFilePath = filePath;
                     Log.Info("Started parsing " + parseInput.RawFilePath);
-                    try
-                    {
-                        ProcessFile(parseInput);
-                    }
-                    catch (UnauthorizedAccessException ex)
-                    {
-                        Log.Error(!ex.Message.IsNullOrEmpty()
-                            ? ex.Message
-                            : "Attempting to write to an unauthorized location.");
-                    }
-                    catch (Exception ex)
-                    {
-                        if (ex is RawFileParserException)
-                        {
-                            Log.Error(ex.Message);
-                        }
-                        else
-                        {
-                            Log.Error("An unexpected error occured while parsing file:" + parseInput.RawFilePath);
-                            Log.Error(ex.ToString());
-                        }
-                    }
+                    TryProcessFile(parseInput);                    
                 }
             }
             // Input raw file mode
             else
             {
                 Log.Info("Started parsing " + parseInput.RawFilePath);
 
+                TryProcessFile(parseInput);
+            }
+        }
+
+        /// <summary>
+        /// Process and extract the given RAW file and catch IO exceptions.
+        /// </summary>
+        /// <param name="parseInput">the parse input object</param>
+        private static void TryProcessFile(ParseInput parseInput)
+        {
+            try
+            {
                 ProcessFile(parseInput);
             }
+            catch (UnauthorizedAccessException ex)
+            {
+                Log.Error(!ex.Message.IsNullOrEmpty()
+                    ? ex.Message
+                    : "Attempting to write to an unauthorized location.");
+            }
+            catch (Exception ex)
+            {
+                if (ex is RawFileParserException)
+                {
+                    Log.Error(ex.Message);
+                }
+                else
+                {
+                    Log.Error("An unexpected error occured while parsing file:" + parseInput.RawFilePath);
+                    Log.Error(ex.ToString());
+                }
+            }
         }
 
         /// <summary>

Writer/SpectrumWriter.cs

@@ -55,6 +55,13 @@ protected SpectrumWriter(ParseInput parseInput)
         /// <param name="extension">The extension of the output file</param>
         protected void ConfigureWriter(string extension)
         {
+            if (ParseInput.StdOut)
+            {
+                Writer = new StreamWriter(Console.OpenStandardOutput());
+                Writer.AutoFlush = true;
+                return;
+            }
+
             if (ParseInput.OutputFile == null)
             {
                 var fullExtension = ParseInput.Gzip ? extension + ".gzip" : extension;