Merge branch 'Metadatakeys' into unifiedStdout

Author: caetera

MainClass.cs

@@ -402,6 +402,16 @@ private static void RegularParametersParsing(string[] args)
                     "The metadata output file. By default the metadata file is written to the output directory.",
                     v => parseInput.MetadataOutputFile = v
                 },
+                {
+                    "D=|deposition_metadata",
+                    "The path to deposition metadata output file.",
+                    v => parseInput.DepositionMetadataFile = v
+                },
+                {
+                    "E=|experiment_metadata",
+                    "The path to experiment metadata output file.",
+                    v => parseInput.ExperimentMetadataFile = v
+                },
                 {
                     "g|gzip", "GZip the output file.",
                     v => parseInput.Gzip = v != null
@@ -472,13 +482,13 @@ private static void RegularParametersParsing(string[] args)
 
                 if (!extra.IsNullOrEmpty())
                 {
-                    throw new OptionException("unexpected extra arguments", null);
+                    throw new OptionException("Unexpected extra arguments", null);
                 }
 
                 if (help)
                 {
                     var helpMessage =
-                        $"usage is {Assembly.GetExecutingAssembly().GetName().Name}.exe [subcommand] [options]\noptional subcommands are xic|query (use [subcommand] -h for more info]):";
+                        $"Usage is {Assembly.GetExecutingAssembly().GetName().Name}.exe [subcommand] [options]\noptional subcommands are xic|query (use [subcommand] -h for more info]):";
                     ShowHelp(helpMessage, null, optionSet);
                     return;
                 }
@@ -579,6 +589,13 @@ private static void RegularParametersParsing(string[] args)
                     parseInput.OutputFormat = OutputFormat.MzML;
                 }
 
+                if (metadataFormatString != null &&
+                    (parseInput.DepositionMetadataFile != null || parseInput.ExperimentMetadataFile != null))
+                {
+                    throw new OptionException("Metadata format key should not be combined with explicit metadata file options",
+                        "-m, --metadata, -D, -deposition_metadata, -E, --experiment_metadata");
+                }
+
                 if (outputFormatString != null)
                 {
                     int outPutFormatInt;

ParseInput.cs

@@ -60,6 +60,10 @@ public string RawFilePath
         /// </summary>>
         public string MetadataOutputFile { get; set; }
 
+        public string DepositionMetadataFile { get; set; }
+
+        public string ExperimentMetadataFile { get; set; }
+
         /// <summary>
         /// Gzip the output file.
         /// </summary>
@@ -96,6 +100,7 @@ public string RawFilePath
         /// <summary>
         /// The raw file name.
         /// </summary>
+        //NOTE. This field does not seem to be used.
         private string rawFileName;
 
         /// <summary>

RawFileParser.cs

@@ -120,28 +120,33 @@ private static void ProcessFile(ParseInput parseInput)
 
                 if (parseInput.MetadataFormat != MetadataFormat.NONE)
                 {
-                    MetadataWriter metadataWriter;
-                    if (parseInput.MetadataOutputFile != null)
-                    {
-                        metadataWriter = new MetadataWriter(null, parseInput.MetadataOutputFile);
-                    }
-                    else
-                    {
-                        metadataWriter = new MetadataWriter(parseInput.OutputDirectory,
-                            parseInput.RawFileNameWithoutExtension);
-                    }
-
                     switch (parseInput.MetadataFormat)
                     {
                         case MetadataFormat.JSON:
-                            metadataWriter.WriteJsonMetada(rawFile, firstScanNumber, lastScanNumber);
+                            parseInput.DepositionMetadataFile = parseInput.MetadataOutputFile != null
+                                ? parseInput.MetadataOutputFile
+                                : Path.Combine(parseInput.OutputDirectory, parseInput.RawFileNameWithoutExtension) + "-metadata.json";
                             break;
                         case MetadataFormat.TXT:
-                            metadataWriter.WriteMetadata(rawFile, firstScanNumber, lastScanNumber);
+                            parseInput.ExperimentMetadataFile = parseInput.MetadataOutputFile != null
+                                ? parseInput.MetadataOutputFile
+                                : Path.Combine(parseInput.OutputDirectory, parseInput.RawFileNameWithoutExtension) + "-metadata.txt"; ;
                             break;
                     }
                 }
 
+                if (parseInput.DepositionMetadataFile != null)
+                {
+                    MetadataWriter metadataWriter = new MetadataWriter(parseInput.DepositionMetadataFile);
+                    metadataWriter.WriteJsonMetada(rawFile, firstScanNumber, lastScanNumber);
+                }
+
+                if (parseInput.ExperimentMetadataFile != null)
+                {
+                    MetadataWriter metadataWriter = new MetadataWriter(parseInput.ExperimentMetadataFile);
+                    metadataWriter.WriteMetadata(rawFile, firstScanNumber, lastScanNumber);
+                }
+
                 if (parseInput.OutputFormat != OutputFormat.NONE)
                 {
                     SpectrumWriter spectrumWriter;

Writer/MetadataWriter.cs

@@ -14,17 +14,15 @@ public class MetadataWriter
         private static readonly ILog Log =
             LogManager.GetLogger(MethodBase.GetCurrentMethod().DeclaringType);
 
-        private readonly string _outputDirectory;
         private readonly string _metadataFileName;
 
         /// <summary>
         /// Constructor.
         /// </summary>
         /// <param name="outputDirectory"></param>
         /// <param name="metadataFileName"></param>
-        public MetadataWriter(string outputDirectory, string metadataFileName)
+        public MetadataWriter(string metadataFileName)
         {
-            _outputDirectory = outputDirectory;
             _metadataFileName = metadataFileName;
         }
 
@@ -76,24 +74,7 @@ public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastSca
             };
 
             // Write the meta data to file
-            string metadataOutputPath;
-            if (_outputDirectory == null)
-            {
-                metadataOutputPath = _metadataFileName;
-            }
-            else
-            {
-                metadataOutputPath = _outputDirectory + "/" + _metadataFileName + "-metadata.txt";
-            }
-
-            File.WriteAllLines(metadataOutputPath, output.ToArray());
-
-            // Write the string array to a new file named "WriteLines.txt".
-            //using (var outputFile = new StreamWriter(metadataOutputPath))
-            //{
-            //    foreach (var line in output)
-            //        outputFile.WriteLine(line);
-            //}
+            File.WriteAllLines(_metadataFileName, output.ToArray());
         }
 
         /// <summary>
@@ -248,17 +229,7 @@ public void WriteJsonMetada(IRawDataPlus rawFile, int firstScanNumber, int lastS
             var json = JsonConvert.SerializeObject(metadata);
             json.Replace("\r\n", "\n");
 
-            string metadataOutputPath;
-            if (_outputDirectory == null)
-            {
-                metadataOutputPath = _metadataFileName;
-            }
-            else
-            {
-                metadataOutputPath = _outputDirectory + "/" + _metadataFileName + "-metadata.json";
-            }
-
-            File.WriteAllText(metadataOutputPath, json);
+            File.WriteAllText(_metadataFileName, json);
         }
 
         private static CVTerm ParseActivationType(ActivationType activation)