public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"dir|d=",
"input directory containing NSA (and index) files to be merged",
v => _inputDir = v
},
{
"out|o=",
"output NSA file stub",
v => _outFileStub = v
}
};
var commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckDirectoryExists(_inputDir, "input directory containing NSA files", "--in")
.HasRequiredParameter(_outFileStub, "output NSA file stub", "--out")
.SkipBanner()
.ShowHelpMenu("Concatenate multiple (non-overlapping) NSA files from the same data source into one", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public async Task ConfigureServices_()
{
const int expectedReturnCode = 123456;
const string expectedTextValue = "TestText";
var testService = A.Fake <ITestService>();
A.CallTo(() => testService.ReturnCode).Returns(expectedReturnCode);
A.CallTo(() => testService.TextValue).Returns(expectedTextValue);
var consoleApp = new ConsoleAppBuilder(Array.Empty <string>())
.ConfigureServices(x => x.AddTransient(_ => testService))
.UseProgramMain <TestServiceProgramMain>()
.Build();
// Act
var result = await consoleApp.RunAsync();
// Assert
result
.Should()
.Be(expectedReturnCode);
TestServiceProgramMain.TextValue
.Should()
.Be(expectedTextValue);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"ref|r=",
"compressed reference sequence file",
v => _compressedReference = v
},
{
"in|i=",
"custom TSV file path",
v => _inputFile = v
},
{
"out|o=",
"output directory",
v => _outputDirectory = v
}
};
string commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_compressedReference, "compressed reference sequence", "--ref")
.CheckInputFilenameExists(_inputFile, "Custom variant annotation TSV", "--in")
.CheckDirectoryExists(_outputDirectory, "output", "--out")
.SkipBanner()
.ShowHelpMenu("Creates a supplementary variant annotation database from a custom input file", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"in|i=",
"OneKGenSv VCF file",
v => _inputFileName = v
},
{
"out|o=",
"output directory",
v => _outputDirectory = v
}
};
string commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_inputFileName, "OneKGenSv VCF file", "--in")
.CheckDirectoryExists(_outputDirectory, "output directory", "--out")
.SkipBanner()
.ShowHelpMenu("Convert the VCF file into BED-like format", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"tsv|t=",
"input tsv file",
v => _dosageSensitivityFile = v
},
{
"out|o=",
"output directory",
v => _outputDirectory = v
}
};
string commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.HasRequiredParameter(_outputDirectory, "output directory", "--out")
.CheckDirectoryExists(_outputDirectory, "output directory", "--out")
.CheckInputFilenameExists(_dosageSensitivityFile, "dosage sensitivity TSV file", "--tsv")
.SkipBanner()
.ShowHelpMenu("Creates a gene annotation database from dbVar data", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"ind|i=",
"input NSA index file path",
v => _inputIndexFile = v
},
{
"ver|r=",
"version file path",
v => _versionFile = v
},
{
"out|o=",
"output index file path",
v => _outputIndexFile = v
}
};
var commandLineExample = $"{command} --ind <input NSA index file path> --out <output index file path> --ver <version file path>";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_inputIndexFile, "input NSA index file path", "--ind")
.HasRequiredParameter(_outputIndexFile, "output index file path", "--out")
.CheckInputFilenameExists(_versionFile, "version file path", "--ver")
.SkipBanner()
.ShowHelpMenu("Extracts mini supplementary annotations for the given range from Nirvana Supplementary Annotations files.", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var creator = new GeneScoresMain();
var ops = new OptionSet
{
{
"in|i=",
"input gene scores {path}",
v => _inputPath = v
},
{
"out|o=",
"output directory {path}",
v => _outputDirectory = v
}
};
var commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_inputPath, "gene scores file", "--in")
.CheckDirectoryExists(_outputDirectory, "Output directory", "--out")
.SkipBanner()
.ShowHelpMenu("Reads provided OMIM data files and populates tsv file", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"uga|u=",
"universal gene archive {path}",
v => _universalGeneArchivePath = v
},
{
"ref|r=",
"input reference {filename}",
v => _inputReferencePath = v
},
{
"out|o=",
"output directory",
v => _outputDirectory = v
}
};
string commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.HasRequiredParameter(_outputDirectory, "output directory", "--out")
.CheckDirectoryExists(_outputDirectory, "output directory", "--out")
.CheckInputFilenameExists(_universalGeneArchivePath, "universal gene archive", "--uga")
.SkipBanner()
.ShowHelpMenu("Download the OMIM gene annotation data", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"in|i=",
"input BED file path",
v => _inputFile = v
},
{
"out|o=",
"output directory",
v => _outputDirectory = v
}
};
string commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_inputFile, "Mitochondrial Heteroplasmy BED file", "--in")
.CheckDirectoryExists(_outputDirectory, "output directory", "--out")
.SkipBanner()
.ShowHelpMenu("Creates a TSV file with mitochondrial heteroplasmy information", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"i|in=",
"Input XML {file}",
v => _inputXmlFile = v
},
{
"a|acc=",
"accessions",
v => _accessions = v
},
{
"o|out=",
"Output {dir}",
v => _outputDir = v
}
};
var commandLineExample = $"{command} --in <xml file> --out <output Directory> --rcv <RCV ID>";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_inputXmlFile, "input XML file", "--in")
.HasRequiredParameter(_outputDir, "output directory", "--out")
.HasRequiredParameter(_accessions, "comma separated list of accessions or folder containing mini XML files to update", "--acc")
.SkipBanner()
.ShowHelpMenu("Extracts mini supplementary annotations for the given range from Nirvana Supplementary Annotations files.", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"uga|u=",
"universal gene archive file path",
v => _universalGeneArchivePath = v
},
{
"in|i=",
"custom TSV file path",
v => _inputFile = v
},
{
"out|o=",
"output directory",
v => _outputDirectory = v
}
};
string commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_universalGeneArchivePath, "universal gene archive", "--uga")
.CheckInputFilenameExists(_inputFile, "Custom gene annotation TSV", "--in")
.CheckDirectoryExists(_outputDirectory, "output", "--out")
.SkipBanner()
.ShowHelpMenu("Creates a supplementary gene annotation database from a custom input file", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"tsv|t=",
"input tsv file",
v => _dosageMapRegionFile = v
},
{
"ref|r=",
"input reference {filename}",
v => _inputReferencePath = v
},
{
"out|o=",
"output directory",
v => _outputDirectory = v
}
};
string commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_dosageMapRegionFile, "dosage map region TSV file", "--tsv")
.CheckInputFilenameExists(_inputReferencePath, "reference sequence file", "--tsv")
.CheckDirectoryExists(_outputDirectory, "output directory", "--out")
.SkipBanner()
.ShowHelpMenu("Creates an interval annotation database from dbVar data", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"ref|r=",
"compressed reference sequence file",
v => _compressedReference = v
},
{
"in|i=",
"MITOMAP structural variants HTML file",
v => MitoMapFileNames.Add(v)
},
{
"out|o=",
"output directory",
v => _outputDirectory = v
}
};
string commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_compressedReference, "compressed reference sequence file name", "--ref")
.CheckEachFilenameExists(MitoMapFileNames, "MITOMAP structural variants HTML file", "--in")
.CheckDirectoryExists(_outputDirectory, "output directory", "--out")
.SkipBanner()
.ShowHelpMenu("Creates a supplementary database with MITOMAP structural variants annotations", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static int Main(string[] args)
{
var ops = new OptionSet
{
{
"ga=",
"genome assembly {version}",
v => _genomeAssembly = v
},
{
"out|o=",
"top-level output {directory}",
v => _outputDirectory = v
}
};
var exitCode = new ConsoleAppBuilder(args, ops)
.Parse()
.HasRequiredParameter(_genomeAssembly, "genome assembly", "--ga")
.CheckDirectoryExists(_outputDirectory, "top-level output directory", "--out")
.ShowBanner(Constants.Authors)
.ShowHelpMenu("Downloads the Nirvana data files from S3", "--ga <genome assembly> --out <output directory>")
.ShowErrors()
.Execute(ProgramExecution);
return((int)exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"src|s=",
"VCF file with dbSNP ids and data to be remapped",
v => _srcMapFile = v
},
{
"des|d=",
"VCF file (with same chromosome order as src) with destination dbSNP mapping",
v => _destMapFile = v
}
};
var commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_srcMapFile, "VCF file with dbSNP ids and data to be remapped", "--src")
.CheckInputFilenameExists(_destMapFile, "VCF file with destination dbSNP mapping", "--des")
.SkipBanner()
.ShowHelpMenu("Reads provided supplementary data files and populates tsv files", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static int Main(string[] args)
{
var ops = new OptionSet
{
{
"header|t",
"print also the header lines",
v => _printHeader = v != null
},
{
"only-header|H",
"print only the header lines",
v => _printHeaderOnly = v != null
},
{
"list|l",
"list chromosome and section names",
v => _list = v != null
},
{
"index|c",
"create index",
v => _createIndex = v != null
},
{
"in|i=",
"input",
v => _inputJson = v
},
{
"out|o=",
"compressed output file name (default:console)",
v => _outputFile = v
},
{
"query|q=",
"query range",
v => Queries.Add(v)
},
{
"section|s=",
"complete section (positions or genes) to output",
v => _section = v
}
};
var exitCode = new ConsoleAppBuilder(args, ops)
.Parse()
.CheckInputFilenameExists(_inputJson, "input Json file", "[in.json.gz]")
.DisableOutput(!_createIndex && _outputFile == null)
.ShowBanner(Constants.Authors)
.ShowHelpMenu("Indexes a Nirvana annotated JSON file", "-i in.json.gz [options]")
.ShowErrors()
.Execute(ProgramExecution);
return((int)exitCode);
}
public void ShowBanner_EnabledOutput()
{
var ops = new OptionSet {
{ "test=", "test", v => { } }
};
var banner = new ConsoleAppBuilder(null, ops).UseVersionProvider(new VersionProvider())
.Parse()
.ShowBanner("authors");
Assert.True(banner is ConsoleAppBanner);
}
public void Build_NoCommandAndProgramMainGiven_ThrowsException()
{
var builder = new ConsoleAppBuilder(Array.Empty <string>());
// Act
Action act = () => builder.Build();
// Assert
act
.Should()
.Throw <InvalidOperationException>();
}
public void VersionProvider_Set()
{
var ops = new OptionSet {
{ "test=", "test", v => { } }
};
var data = new ConsoleAppBuilder(null, ops).UseVersionProvider(new VersionProvider())
.Parse()
.Data;
Assert.True(data.VersionProvider is VersionProvider);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var ops = new OptionSet
{
{
"ref|r=",
"compressed reference sequence file",
v => _compressedReference = v
},
{
"cache|c=",
"Transcript cache prefix",
v => _transcriptCachePrefix = v
},
{
"gene|g=",
"Gene info data file from NCBI",
v => _geneInfoFile = v
},
{
"in|i=",
"input VCF file path",
v => _inputFile = v
},
{
"out|o=",
"output directory",
v => _outputDirectory = v
}
};
string commandLineExample = $"{command} [options]";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_compressedReference, "compressed reference sequence file name", "--ref")
.HasRequiredParameter(_transcriptCachePrefix, "transcript cache file", "--cache")
.CheckInputFilenameExists(CacheConstants.TranscriptPath(_transcriptCachePrefix), "transcript cache prefix", "--cache")
.HasRequiredParameter(_inputFile, "SpliceAI VCF file", "--in")
.CheckInputFilenameExists(_inputFile, "SpliceAI VCF file", "--in")
.HasRequiredParameter(_geneInfoFile, "Gene info data file from NCBI", "--gene")
.CheckInputFilenameExists(_geneInfoFile, "Gene info data file from NCBI", "--gene")
.HasRequiredParameter(_outputDirectory, "output directory", "--out")
.CheckDirectoryExists(_outputDirectory, "output directory", "--out")
.SkipBanner()
.ShowHelpMenu("Creates a supplementary database containing 1000 Genomes allele frequencies", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public static ExitCodes Run(string command, string[] commandArgs)
{
var extractor = new ExtractMiniSaMain();
var ops = new OptionSet
{
{
"ref|r=",
"compressed reference sequence file",
v => _compressedReference = v
},
{
"in|i=",
"input Nirvana Supplementary Annotations {file}",
v => _inputSuppAnnotPath = v
},
{
"name|n=",
"data source {name}",
v => _dataSourceName = v
},
{
"begin|b=",
"reference begin {position}",
(int v) => _begin = v
},
{
"end|e=",
"reference end {allele}",
(int v) => _end = v
},
{
"out|o=",
"output {directory}",
v => _miniSaDirectory = v
}
};
var commandLineExample = $"{command} --in <Supplementary Annotations path> --out <Supplementary Annotations Directory> --begin <position> --end <position> --name <dataSource>";
var exitCode = new ConsoleAppBuilder(commandArgs, ops)
.Parse()
.CheckInputFilenameExists(_inputSuppAnnotPath, "Nirvana supplementary annotations", "--in")
.CheckInputFilenameExists(_compressedReference, "Compressed reference sequence file name", "--ref")
.HasRequiredParameter <string>(_miniSaDirectory, "output directory", "--out")
.SkipBanner()
.ShowHelpMenu("Extracts mini supplementary annotations for the given range from Nirvana Supplementary Annotations files.", commandLineExample)
.ShowErrors()
.Execute(ProgramExecution);
return(exitCode);
}
public void HasRequiredDate_Exists_BadFormat()
{
string observedDate = default;
var ops = new OptionSet {
{ "date=", "date", v => observedDate = v }
};
var validator = new ConsoleAppBuilder(new[] { "--date", "garbage" }, ops)
.Parse()
.HasRequiredDate(observedDate, "date", "--date");
Assert.True(validator.Data.Errors.Count > 0);
}
public void Parse_UnsupportedOption()
{
var ops = new OptionSet {
{ "test=", "test", v => { } }
};
var data = new ConsoleAppBuilder(new[] { "--if", "-" }, ops)
.Parse()
.Data;
Assert.Single(data.Errors);
Assert.Equal(2, data.UnsupportedOps.Count);
}
public void CheckOutputFilenameSuffix_False()
{
var ops = new OptionSet {
{ "date=", "date", v => { } }
};
var validator = new ConsoleAppBuilder(new[] { "--date", "2018-03-14" }, ops)
.Parse()
.CheckOutputFilenameSuffix("test.json", ".gz", "temp");
Assert.NotEqual(ExitCodes.Success, validator.Data.ExitCode);
Assert.True(validator.Data.Errors.Count > 0);
}
public void Build_ProgramMainHasPrivateCtor_ThrowsException()
{
var builder = new ConsoleAppBuilder(Array.Empty <string>());
builder.UseProgramMain <TestProgramMainWithPrivateCtor>();
// Act
Action act = () => builder.Build();
// Assert
act
.Should()
.Throw <InvalidOperationException>();
}
public void Build_ProgramMainHasInvalidCtorArgs_ReturnsIntMinValue()
{
var builder = new ConsoleAppBuilder(Array.Empty <string>());
builder.UseProgramMain <TestProgramMainWithInvalidCtorArgs>();
// Act
Action act = () => builder.Build();
// Assert
act
.Should()
.Throw <InvalidOperationException>();
}
public async Task RunSync_DifferentRoutesToDefaultAction_ActionIsExecuted(params string[] args)
{
var consoleApp = new ConsoleAppBuilder(args)
.UseActions(x =>
x.AddController <TestMultiRouteCliController>().UseMiddleware <CliRoutingMiddleware>())
.Build();
// Act
var result = await consoleApp.RunAsync();
// Assert
result
.Should()
.Be(TestMultiRouteCliController.ExecuteReturnCode);
}
public void Build_WithStartup_StartupCreatedAndCalled()
{
var builder = new ConsoleAppBuilder(Array.Empty <string>());
builder.UseProgramMain <TestProgramMain>();
builder.UseStartup <TestStartup>();
// Act
var _ = builder.Build();
// Assert
TestStartup.ConfigureServicesIsCalled
.Should()
.BeTrue();
}
///-------------------------------------------------------------------------------------------------
/// <summary> Registers an executor for a main program. </summary>
///
/// <exception cref="InvalidOperationException"> Thrown when the program main class could not
/// be created. </exception>
///
/// <typeparam name="TProgramMain"> Type of the program main class. </typeparam>
/// <param name="consoleAppBuilder"> The consoleAppBuilder to act on. </param>
///
/// <returns> The ConsoleAppBuilder. </returns>
///-------------------------------------------------------------------------------------------------
public static ConsoleAppBuilder UseProgramMain <TProgramMain>(this ConsoleAppBuilder consoleAppBuilder)
where TProgramMain : IMain
{
return(consoleAppBuilder.UseExecutor(sp =>
{
var main = typeof(TProgramMain).CreateInstance <IMain>(sp);
if (main == null)
{
throw new InvalidOperationException();
}
return new MainExecutor(main);
}));
}
public void Parse_ShowOutput()
{
var ops = new OptionSet {
{ "test=", "test", v => { } }
};
var exitCode = new ConsoleAppBuilder(new[] { "--test", "test" }, ops)
.Parse()
.ShowBanner("authors")
.ShowHelpMenu("description", "example")
.ShowErrors()
.Execute(() => ExitCodes.Success);
Assert.Equal(ExitCodes.Success, exitCode);
}
