Fixes CLI parser

This work continues on from 38c8987

It Closes #145 and Closes #126

It adds several important features (like support for custom value parsers) and our own help text generator.

Note we are dependent on a custom build hosted by @atruskie until natemcmaster/CommandLineUtils#51 is resolved

src/Acoustics.Shared/Extensions/EnumerableExtensions.cs

@@ -7,16 +7,17 @@
 // ReSharper disable once CheckNamespace
 namespace System
 {
-    using System;
+    using Acoustics.Shared;
+    using Acoustics.Shared.Contracts;
     using Collections.Generic;
+    using JetBrains.Annotations;
     using Linq;
     using Threading.Tasks;
-    using Acoustics.Shared;
-    using Acoustics.Shared.Contracts;
 
     public static class EnumerableExtensions
     {
 
+        [ContractAnnotation("items:null => true; items:notnull => false")]
         public static bool IsNullOrEmpty<T>(this IEnumerable<T> items)
         {
             return items == null || !items.Any();
@@ -311,4 +312,4 @@ public static IEnumerable<T> Append<T>(this IEnumerable<T> items, T newItem)
             yield return newItem;
         }
     }
-}
+}

src/Acoustics.Shared/Extensions/FileInfoExtensions.cs

@@ -149,7 +149,7 @@ public static bool TryCreate(this DirectoryInfo file)
         public static FileInfo Touch(this FileInfo info)
         {
             using (File.OpenWrite(info.FullName))
-            {    
+            {
             }
 
             info.Refresh();
@@ -163,6 +163,11 @@ public static T RefreshInfo<T>(this T info)
             info.Refresh();
             return info;
         }
+
+        public static string BaseName(this FileInfo file)
+        {
+            return Path.GetFileNameWithoutExtension(file.Name);
+        }
     }
 
     public class FileInfoNameComparer : IComparer<FileInfo>, IEqualityComparer<FileInfo>

src/Acoustics.Shared/Logging/LoggedConsole.cs

@@ -100,6 +100,11 @@ public static void WriteFatalLine(string str, Exception exception)
             Log.Fatal(str, exception);
         }
 
+        public static void WriteFatalLine(string str)
+        {
+            Log.Fatal(str);
+        }
+
         public static void WriteWaitingLine<T>(Task<T> task, string message = null)
         {
             WriteLine(message ?? "Waiting...");
@@ -121,6 +126,7 @@ public static string Prompt(string prompt, bool forPassword = false, TimeSpan? t
                     {
                         return ReadHiddenLine();
                     }
+
                     var line = System.Console.ReadLine();
                     return line;
                 });

src/Acoustics.Shared/Meta.cs

@@ -11,7 +11,7 @@ namespace Acoustics.Shared
 
     public static class Meta
     {
-        public const string Description = "QUT Aacoustics Analysis Program - version ";
+        public const string Description = "QUT Ecoacoustics Analysis Programs";
 
         public const string Name = "AnalysisPrograms.exe";
 

src/Acoustics.Shared/Yaml.cs

@@ -54,9 +54,9 @@ public static void Serialize<T>(FileInfo file, T obj)
             }
         }
 
-        internal static (object, T) LoadAndDeserialize<T>(FileInfo file)
+        internal static (object, T) LoadAndDeserialize<T>(string path)
         {
-            using (var stream = file.OpenText())
+            using (var stream = File.OpenText(path))
             {
                 // allow merging in yaml back references
                 var parser = new MergingParser(new Parser(stream));

src/Acoustics.Tools/AudioUtilityRequest.cs

@@ -166,14 +166,21 @@ private bool DoValidation(bool throwExceptions)
                 return false;
             }
 
-            if (this.Channels.NotNull() && (this.Channels.Length == 0 || this.Channels.Any(c => c < 1)))
+            if (this.Channels.NotNull())
             {
-                if (throwExceptions)
+                if (this.Channels.Length == 0)
                 {
-                    throw new ChannelNotAvailableException("Channel number should be greater than 0.");
+                    this.Channels = null;
                 }
+                else if (this.Channels.Any(c => c < 1))
+                {
+                    if (throwExceptions)
+                    {
+                        throw new ChannelNotAvailableException("Channel number should be greater than 0.");
+                    }
 
-                return false;
+                    return false;
+                }
             }
 
             /*if (this.Channel.HasValue && this.MixDownToMono.HasValue && this.MixDownToMono.Value)

src/AnalysisPrograms/AED.cs

@@ -54,7 +54,7 @@ public class Aed : AbstractStrongAnalyser
         /// </summary>
         [Command(
             CommandName,
-            Description = "Acosutic event detection, for short files (~ 1min)")]
+            Description = "Acoustic event detection, for short files (~ 1min)")]
         public class Arguments : SourceConfigOutputDirArguments
         {
             public override Task<int> Execute(CommandLineApplication app)
@@ -270,7 +270,7 @@ public static void Execute(Arguments arguments)
             LoggedConsole.WriteLine(date);
 
             FileInfo recodingFile = arguments.Source;
-            var recodingBaseName = Path.GetFileNameWithoutExtension(arguments.Source.Name);
+            var recodingBaseName = recodingFile.BaseName();
             DirectoryInfo outputDir = arguments.Output.Combine(EcosoundsAedIdentifier);
             outputDir.Create();
 

src/AnalysisPrograms/AnalyseLongRecordings/AnalyseLongRecording.cs

@@ -11,6 +11,7 @@ namespace AnalysisPrograms.AnalyseLongRecordings
 {
     using System;
     using System.Collections.Generic;
+    using System.ComponentModel.DataAnnotations;
     using System.Diagnostics;
     using System.Drawing;
     using System.IO;
@@ -61,15 +62,15 @@ public static void Execute(Arguments arguments)
 
             // 1. set up the necessary files
             var sourceAudio = arguments.Source;
-            var configFile = arguments.Config;
+            var configFile = arguments.Config.ToFileInfo();
             var outputDirectory = arguments.Output;
             var tempFilesDirectory = arguments.TempDir;
 
             // if a temp dir is not given, use output dir as temp dir
             if (tempFilesDirectory == null)
             {
                 Log.Warn("No temporary directory provided, using output directory");
-                tempFilesDirectory = arguments.Output;
+                tempFilesDirectory = outputDirectory;
             }
 
             // try an automatically find the config file
@@ -137,7 +138,7 @@ public static void Execute(Arguments arguments)
             }
 
             // AT 2018-02: changed logic so default index properties loaded if not provided
-            FileInfo indicesPropertiesConfig = IndexProperties.Find(configuration, arguments.Config);
+            FileInfo indicesPropertiesConfig = IndexProperties.Find(configuration, configFile);
             if (indicesPropertiesConfig == null || !indicesPropertiesConfig.Exists)
             {
                 Log.Warn("IndexProperties config can not be found! Loading a default");
@@ -391,17 +392,12 @@ public static T FindAndCheckAnalyser<T>(string analysisIdentifier, string partia
             T analyser = analysers.FirstOrDefault(a => a.Identifier == searchName);
             if (analyser == null)
             {
-                var error = $@"###
-
-We can not determine what analysis you want to run. We tried to search for ""{searchName}""
-
-###
-";
+                var error = $"We can not determine what analysis you want to run. We tried to search for \"{searchName}\"";
                 LoggedConsole.WriteError(error);
-                var knownAnalyzers = analysers.Aggregate(string.Empty, (a, i) => a + $"\t {i.Identifier}\n");
+                var knownAnalyzers = analysers.Aggregate(string.Empty, (a, i) => a + $"  {i.Identifier}\n");
                 LoggedConsole.WriteLine("Available analysers are:\n" + knownAnalyzers);
 
-                throw new CommandLineArgumentException("Cannot find a valid IAnalyser2");
+                throw new ValidationException($"Cannot find an IAnalyser2 with the name `{searchName}`");
             }
 
             return analyser;
@@ -414,7 +410,7 @@ private static void Cleanup(Arguments args, FileInfo configFile)
         {
             if (args.WhenExitCopyConfig)
             {
-                configFile.CopyTo(Path.Combine(args.Output.FullName, args.Config.Name), true);
+                configFile.CopyTo(Path.Combine(args.Output.FullName, Path.GetFileName(args.Config)), true);
             }
 
             if (args.WhenExitCopyLog)

src/AnalysisPrograms/AnalyseLongRecordings/AnalyseLongRecordings.Arguments.cs

@@ -44,44 +44,54 @@ public Arguments()
 #endif
             }
 
-            [Option("Sets the name of the analysis to run. If not set, analysis identifer is parsed from the config file name.")]
+            [Option(Description = "Sets the name of the analysis to run. If not set, analysis identifer is parsed from the config file name.")]
             public string AnalysisIdentifier { get; set; }
 
             [Option(
-                "A TEMP directory where cut files will be stored. Use this option for efficiency (e.g. write to a RAM Disk).",
-                ShortName = "t"
-                )]
+                Description = "A TEMP directory where cut files will be stored. Use this option for efficiency (e.g. write to a RAM Disk).",
+                ShortName = "t")]
             [DirectoryExistsOrCreate(createIfNotExists: true)]
+            [LegalFilePath]
             public DirectoryInfo TempDir { get; set; }
 
-            [Option("The start offset to start analyzing from (in seconds)")]
+            [Option(
+                CommandOptionType.SingleValue,
+                Description = "The start offset to start analyzing from (in seconds)")]
             [InRange(min: 0)]
             public double? StartOffset { get; set; }
 
-            [Option("The end offset to stop analyzing (in seconds)")]
+            [Option(
+                CommandOptionType.SingleValue,
+                Description = "The end offset to stop analyzing (in seconds)")]
             [InRange(min: 0)]
             public double? EndOffset { get; set; }
 
-            [Option("Allow advancing the start of the analysis to the nearest minute. A valid datetime must be available in the file name. Seed additional notes for options.")]
+            [Option(
+                Description = "Allow advancing the start of the analysis to the nearest minute. A valid datetime must be available in the file name. Seed additional notes for options.",
+                ShortName = "")]
             public TimeAlignment AlignToMinute { get; set; } = TimeAlignment.None;
 
-            [Option("An array of channels to select. Default is all channels.")]
+            [Option(Description = "An array of channels to select. Default is all channels.")]
             public int[] Channels { get; set; } = null;
 
             [Option(
-                "Mix all selected input channels down into one mono channel. Default is to mixdown.",
-                CommandOptionType.SingleValue)]
+                CommandOptionType.SingleValue,
+                Description = "Mix all selected input channels down into one mono channel. Default is to mixdown.")]
             public bool MixDownToMono { get; set; } = true;
 
-            [Option("Whether or not run this analysis in parallel - multiple segments can be analyzed at the same time")]
+            [Option(
+                Description = "Whether or not run this analysis in parallel - multiple segments can be analyzed at the same time",
+                ShortName = "p")]
             public bool Parallel { get; set; } = false;
 
             [Option(
-                "If true, attempts to copy the executable's log file to output directory. If it can't determine an output directory, it copies to the working directory.")]
+                Description = "If true, attempts to copy the executable's log file to output directory. If it can't determine an output directory, it copies to the working directory.",
+                ShortName = "")]
             public bool WhenExitCopyLog { get; set; }
 
             [Option(
-                "If true, attempts to copy the executable's config file to output directory. If it can't determine an output directory, it copies to the working directory. If it can't find a config file, nothing is copied")]
+                Description = "If true, attempts to copy the executable's config file to output directory. If it can't determine an output directory, it copies to the working directory. If it can't find a config file, nothing is copied",
+                ShortName = "")]
             public bool WhenExitCopyConfig { get; set; }
 
             public override Task<int> Execute(CommandLineApplication app)

src/AnalysisPrograms/AnalysesAvailable.cs

@@ -19,7 +19,9 @@ namespace AnalysisPrograms
     using Recognizers.Base;
     using TowseyLibrary;
 
-    [Command("List available IAnalyzers available for use with audio2csv or eventRecognizer")]
+    [Command(
+        "AnalysesAvailable",
+        Description = "List available IAnalyzers available for use with audio2csv or eventRecognizer")]
     public class AnalysesAvailable
         : SubCommandBase
     {

src/AnalysisPrograms/AnalysisPrograms.csproj

@@ -83,7 +83,7 @@
       <HintPath>..\..\packages\MathNet.Numerics.3.20.2\lib\net40\MathNet.Numerics.dll</HintPath>
     </Reference>
     <Reference Include="McMaster.Extensions.CommandLineUtils, Version=2.2.0.0, Culture=neutral, PublicKeyToken=6f71cb76b82f055d, processorArchitecture=MSIL">
-      <HintPath>..\..\packages\McMaster.Extensions.CommandLineUtils.2.2.0-alpha.162\lib\net45\McMaster.Extensions.CommandLineUtils.dll</HintPath>
+      <HintPath>..\..\packages\McMaster.Extensions.CommandLineUtils.1.0.0-CI00005\lib\net45\McMaster.Extensions.CommandLineUtils.dll</HintPath>
     </Reference>
     <Reference Include="Microsoft.CSharp" />
     <Reference Include="Microsoft.Data.Sqlite, Version=2.0.0.0, Culture=neutral, PublicKeyToken=adb9793829ddae60, processorArchitecture=MSIL">
@@ -281,7 +281,13 @@
     <Compile Include="Production\Arguments\SourceArguments.cs" />
     <Compile Include="Production\Arguments\SourceConfigOutputDirArguments.cs" />
     <Compile Include="Production\Arguments\SubCommandBase.cs" />
+    <Compile Include="Production\CommandLineApplicationExtensions.cs" />
+    <Compile Include="Production\CustomHelpTextGenerator.cs" />
     <Compile Include="Production\FileSystemProvider.cs" />
+    <Compile Include="Production\Parsers\FileInfoParser.cs" />
+    <Compile Include="Production\Parsers\DirectoryInfoParser.cs" />
+    <Compile Include="Production\Parsers\TimeSpanParser.cs" />
+    <Compile Include="Production\Parsers\DateTimeOffsetParser.cs" />
     <Compile Include="Production\PhysicalConsoleLogger.cs" />
     <Compile Include="Production\Validation\DirectoryExistsOrCreateAttribute.cs" />
     <Compile Include="Production\Validation\ExistingFileAttribute.cs" />

src/AnalysisPrograms/Audio2InputForConvCNN.cs

@@ -81,7 +81,7 @@ private static Arguments Dev()
                 //Source = @"C:\SensorNetworks\WavFiles\ConvDNNData\ConvDNN_annotation_export_commonNameOnly_withPadding_20140829.processed.csv".ToFileInfo(),
                 Source = @"Y:\Results\2014Aug29-000000 - Mangalam Data Export\Output\ConvDNN_annotation_export_commonNameOnly_withPadding_20140829.processed.csv".ToFileInfo(),
 
-                Config = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Mangalam.Sonogram.yml".ToFileInfo(),
+                Config = @"C:\Work\GitHub\audio-analysis\AudioAnalysis\AnalysisConfigFiles\Mangalam.Sonogram.yml",
 
                 Output = (@"C:\SensorNetworks\Output\ConvDNN\" + datestamp).ToDirectoryInfo(),
             };
@@ -100,9 +100,9 @@ public static void Execute(Arguments arguments)
             }
 
             LoggedConsole.WriteLine("Generate ConvDNN images for single recording");
-            LoggedConsole.WriteLine("# Input Audio file: " + arguments.Source.Name);
-            LoggedConsole.WriteLine("# Configuration  file: " + arguments.Config.Name);
-            LoggedConsole.WriteLine("# Output directry: " + arguments.Output.Name);
+            LoggedConsole.WriteLine("# Input Audio file: " + arguments.Source);
+            LoggedConsole.WriteLine("# Configuration  file: " + arguments.Config);
+            LoggedConsole.WriteLine("# Output directry: " + arguments.Output);
 
             // Verify target event information
             if (string.IsNullOrWhiteSpace(arguments.TargetEventBounds))
@@ -128,7 +128,7 @@ public static void Execute(Arguments arguments)
             }
 
             // Grab configuration
-            var configDict = GetConfigurationForConvCnn(arguments.Config);
+            var configDict = GetConfigurationForConvCnn(arguments.Config.ToFileInfo());
 
             var result = AnalyseOneRecording(arguments.Source, configDict, localEventStart, localEventEnd, (int)minHz, (int)mazHz, arguments.Output);
             Log.InfoFormat("SpectrogramPath:" + result.SpectrogramFile);
@@ -149,21 +149,21 @@ public static void Main(Arguments arguments)
                 arguments = Dev();
             }
 
-            if (!arguments.Output.Exists)
+            var output = arguments.Output;
+            if (!output.Exists)
             {
-                arguments.Output.Create();
+                output.Create();
             }
 
             Log.InfoFormat("# PRE-PROCESS SHORT AUDIO RECORDINGS FOR Convolutional DNN");
             Log.InfoFormat("# DATE AND TIME: " + DateTime.Now);
-            Log.InfoFormat("# Input .csv file: " + arguments.Source.Name);
-            Log.InfoFormat("# Configure  file: " + arguments.Config.Name);
-            Log.InfoFormat("# Output directry: " + arguments.Output.Name);
+            Log.InfoFormat("# Input .csv file: " + arguments.Source);
+            Log.InfoFormat("# Configure  file: " + arguments.Config);
+            Log.InfoFormat("# Output directry: " + arguments.Output);
 
             // 1. set up the necessary files
             FileInfo csvFileInfo = arguments.Source;
-            FileInfo configFile = arguments.Config;
-            DirectoryInfo output = arguments.Output;
+            FileInfo configFile = arguments.Config.ToFileInfo();
 
             // 2. get the config dictionary
             var configDict = GetConfigurationForConvCnn(configFile);