Support of single file output in "xic"

Author: caetera

MainClass.cs

@@ -11,6 +11,7 @@
 using System.Globalization;
 using System.Collections.Generic;
 using System.Text.RegularExpressions;
+using System.Data;
 
 namespace ThermoRawFileParser
 {
@@ -52,6 +53,8 @@ private static void XicParametersParsing(string[] args)
             XicParameters parameters = new XicParameters();
             string singleFile = null;
             string fileDirectory = null;
+            string outputFile = null;
+            string outputDirectory = null;
             string logFormatString = null;
 
             var optionSet = new OptionSet
@@ -82,10 +85,15 @@ private static void XicParametersParsing(string[] args)
                 {
                     "o=|output=",
                     "The output directory. If not specified, the output is written to the input directory",
-                    v => parameters.outputDirectory = v
+                    v => outputDirectory = v
                 },
                 {
-                    "b|base64",
+                    "b=|output_file",
+                    "The output file. Specify this or an output directory -o. Specifying neither writes to the input directory.",
+                    v => outputFile = v
+                },
+                {
+                    "6|base64",
                     "Encodes the content of the xic vectors as base 64 encoded string.",
                     v => parameters.base64 = v != null
                 },
@@ -163,7 +171,7 @@ private static void XicParametersParsing(string[] args)
                 }
 
 
-                if (parameters.outputDirectory != null && !Directory.Exists(parameters.outputDirectory))
+                if (outputDirectory != null && !Directory.Exists(outputDirectory))
                 {
                     throw new OptionException(
                         "specify a valid output location",
@@ -177,18 +185,55 @@ private static void XicParametersParsing(string[] args)
                         "-i, --input xor -d, --input_directory");
                 }
 
+                if (outputFile != null && outputDirectory != null)
+                {
+                    throw new OptionException(
+                        "cannot use an output file and an output directory simultaneously",
+                        "-b, --output_file; -o, --output");
+                }
+
                 if (singleFile != null)
                 {
                     parameters.rawFileList.Add(Path.GetFullPath(singleFile));
+                    
+                    if (outputFile != null)
+                    {
+                        parameters.outputFileList.Add(Path.GetFullPath(outputFile));
+                    }
+                    else if (outputDirectory != null)
+                    {
+                        parameters.outputFileList.Add(Path.Combine(outputDirectory ?? throw new NoNullAllowedException("Output directory cannot be null"),
+                                                        Path.GetFileNameWithoutExtension(singleFile) + ".json"));
+                    }
+                    else
+                    {
+                        parameters.outputFileList.Add(Path.Combine(Path.GetDirectoryName(Path.GetFullPath(singleFile)),
+                                                        Path.GetFileNameWithoutExtension(singleFile) + ".json"));
+                    }
                 }
                 else
                 {
+                    if (outputFile != null)
+                    {
+                        throw new OptionException("Cannot use single output file to proceess a directory, use directory output instead", "-o, --output");
+                    }
+                    else if (outputDirectory != null)
+                    {
+                        outputDirectory = Path.GetFullPath(outputDirectory);
+                    }
+                    else
+                    {
+                        outputDirectory = Path.GetFullPath(fileDirectory);
+                    }
+
                     var directoryInfo = new DirectoryInfo(Path.GetFullPath(fileDirectory));
                     var files = directoryInfo.GetFiles("*", SearchOption.TopDirectoryOnly)
                         .Where(f => f.Extension.ToLower() == ".raw").ToArray<FileInfo>();
                     foreach (var file in files)
                     {
                         parameters.rawFileList.Add(file.FullName);
+                        parameters.outputFileList.Add(Path.Combine(outputDirectory ?? throw new NoNullAllowedException("Output directory cannot be null"),
+                                                    Path.GetFileNameWithoutExtension(file.Name) + ".json"));
                     }
                 }
 

XIC/XicExecutor.cs

@@ -2,15 +2,21 @@
 using System.Data;
 using System.IO;
 using System.Text;
+using System.Reflection;
 using Newtonsoft.Json;
 using ThermoFisher.CommonCore.Data;
+using log4net;
 
 namespace ThermoRawFileParser.XIC
 {
     public static class XicExecutor
     {
+        private static readonly ILog Log =
+            LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
+
         public static void Run(XicParameters parameters)
         {
+            Log.InfoFormat("Reading and validating JSON input");
             var jsonString = File.ReadAllText(parameters.jsonFilePath, Encoding.UTF8);
             var validationErrors = JSONParser.ValidateJson(jsonString);
             if (!validationErrors.IsNullOrEmpty())
@@ -32,8 +38,13 @@ public static void Run(XicParameters parameters)
             }
 
             var xicData = JSONParser.ParseJSON(jsonString);
-            foreach (string rawFile in parameters.rawFileList)
+
+            Log.InfoFormat("Input contains {0} XICs", xicData.Content.Count);
+
+            for (int index = 0; index < parameters.rawFileList.Count; index++)
             {
+                string rawFile = (string) parameters.rawFileList[index];
+
                 var dataInstance = new XicData(xicData);
                 XicReader.ReadXic(rawFile, parameters.base64, dataInstance, ref parameters);
 
@@ -43,20 +54,7 @@ public static void Run(XicParameters parameters)
                 }
                 else
                 {
-                    // if outputDirectory has been defined, put output there.
-                    string directory;
-                    if (parameters.outputDirectory != null)
-                    {
-                        directory = parameters.outputDirectory;
-                    }
-                    // otherwise put output files into the same directory as the raw file input
-                    else
-                    {
-                        directory = Path.GetDirectoryName(rawFile);
-                    }
-
-                    var outputFileName = Path.Combine(directory ?? throw new NoNullAllowedException("Output directory cannot be null"),
-                        Path.GetFileNameWithoutExtension(rawFile) + ".json");
+                    var outputFileName = (string) parameters.outputFileList[index];
 
                     OutputXicData(dataInstance, outputFileName);
                 }

XIC/XicParameters.cs

@@ -10,9 +10,8 @@ public class XicParameters
         public bool help { get; set; }
         public ArrayList rawFileList { get; set; }
         public string jsonFilePath { get; set; }
-        public string outputDirectory { get; set; }
+        public ArrayList outputFileList { get; set; }
         public bool printJsonExample { get; set; }
-        public string outputFileName { get; set; }
         public bool base64 { get; set; }
         public bool stdout { get; set; }
         public bool Vigilant { get; set; }
@@ -25,9 +24,8 @@ public XicParameters()
             help = false;
             rawFileList = new ArrayList();
             jsonFilePath = null;
-            outputDirectory = null;
+            outputFileList = new ArrayList();
             printJsonExample = false;
-            outputFileName = null;
             base64 = false;
             stdout = false;
             Vigilant = false;
@@ -57,9 +55,8 @@ public XicParameters(XicParameters copy)
             }
 
             jsonFilePath = copy.jsonFilePath;
-            outputDirectory = copy.outputDirectory;
+            outputFileList = copy.outputFileList;
             printJsonExample = copy.printJsonExample;
-            outputFileName = copy.outputFileName;
             base64 = copy.base64;
             stdout = copy.stdout;
             LogFormat = copy.LogFormat;