public void ParseCommonOptions_WithRequiredArguments_ReturnsSuccessfulResult(TemporaryDirectoryFixture tempDirectory)
{
// arrange
Option <CommonOptions> commonOptionsParser = new CommonOptionsParser();
var kmerFasta = tempDirectory.CreateFile("kmer.fa");
var bAlleleVcf = tempDirectory.GetFileLocation("ballele.vcf").Touch();
var filterBed = tempDirectory.GetFileLocation("filter.bed").Touch();
var output = tempDirectory.CreateSubdirectory("output");
var genome = tempDirectory.CreateSubdirectory("WholeGenomeFasta");
string[] stringInputArgument =
{
"-r", kmerFasta.ToString(), "-o", output.ToString(), "-g", genome.ToString(), "--b-allele-vcf", bAlleleVcf.ToString(), "--filter-bed", filterBed.ToString(), "--sample-name", "SampleName"
};
// act
ParsingResult <CommonOptions> result = commonOptionsParser.Parse(stringInputArgument);
// assert
Assert.Equal("", result.ErrorMessage);
Assert.True(result.Success);
Assert.Equal(kmerFasta, result.Result.KmerFasta);
Assert.Equal(output, result.Result.OutputDirectory);
Assert.Equal(genome, result.Result.WholeGenomeFasta);
}
public void ParseDictionaryOption_WithKeyOnlyArgument_ReturnsFailedResult(TemporaryDirectoryFixture tempDirectory)
{
// arrange
DictionaryOption dictOption = DictionaryOption.Create("dictionary", "kvp");
string key = "key1";
string[] args =
{
"--kvp", key
};
// act
var result = dictOption.Parse(args);
// assert
Assert.False(result.Success);
Assert.Contains("Error", result.ErrorMessage);
Assert.Contains("format", result.ErrorMessage);
}
public void ParseExclusiveOption_WithOnlyTwoOption_ReturnsFailedParseResult(TemporaryDirectoryFixture tempDirectory)
{
FileOption option1 = FileOption.CreateRequired("file1 option", "file1");
FileOption option2 = FileOption.CreateRequired("file2 option", "file2");
// arrange
ExclusiveFileOption multiFileOption = ExclusiveFileOption.CreateRequired(option1, option2);
var file1 = tempDirectory.CreateFile("file1");
string[] args =
{
"--file1", file1.ToString(), "--file2", file1.ToString()
};
// act
var result = multiFileOption.Parse(args);
// assert
Assert.Contains("not both", result.ErrorMessage);
Assert.False(result.Success);
}
public void ParseExclusiveOption_WithOnlyOneOption_ReturnsOneValue(TemporaryDirectoryFixture tempDirectory)
{
FileOption option1 = FileOption.CreateRequired("file1 option", "file1");
FileOption option2 = FileOption.CreateRequired("file2 option", "file2");
// arrange
ExclusiveFileOption multiFileOption = ExclusiveFileOption.CreateRequired(option1, option2);
var file1 = tempDirectory.CreateFile("file1");
string[] args =
{
"--file1", file1.ToString()
};
// act
var result = multiFileOption.Parse(args);
// assert
Assert.Equal("", result.ErrorMessage);
Assert.True(result.Success);
Assert.Equal(file1, result.Result.Result);
Assert.Equal(option1, result.Result.MatchedOption);
}
public void ParseCommonOptions_KmerFastaDoesntExist_DisplaysError(TemporaryDirectoryFixture tempDirectory)
{
// arrange
Option <CommonOptions> commonOptionsParser = new CommonOptionsParser();
var kmerFasta = tempDirectory.GetFileLocation("kmerv2.fa");
var filterBed = tempDirectory.GetFileLocation("filter.bed").Touch();
var output = tempDirectory.CreateSubdirectory("output");
var genome = tempDirectory.CreateSubdirectory("WholeGenomeFasta");
string[] stringInputArgument =
{
"-r", kmerFasta.ToString(), "-o", output.ToString(), "-g", genome.ToString(), "--filter-bed", filterBed.ToString()
};
// act
ParsingResult <CommonOptions> result = commonOptionsParser.Parse(stringInputArgument);
// assert
Assert.False(result.Success);
Assert.Contains("kmerv2.fa", result.ErrorMessage);
Assert.Contains("does not exist", result.ErrorMessage);
}
public void ParseMultiFileOption_WithMultipleFileArguments_ReturnsListOfFileLocations()
{
using (TemporaryDirectoryFixture tempDirectory = new TemporaryDirectoryFixture())
{
// arrange
MultiValueOption <IFileLocation> multiFileOption = new MultiValueOption <IFileLocation>(FileOption.CreateRequired("multiple files", "file"));
var file1 = tempDirectory.CreateFile("file1");
var file2 = tempDirectory.CreateFile("file2");
string[] args =
{
"--file", file1.ToString(), "--file", file2.ToString()
};
// act
var result = multiFileOption.Parse(args);
// assert
Assert.Equal("", result.ErrorMessage);
Assert.True(result.Success);
Assert.Equal(file1, result.Result[0]);
Assert.Equal(file2, result.Result[1]);
}
}
public void ParseDictionaryOption_WithMultipleKeyValueArguments_ReturnsDictionary(TemporaryDirectoryFixture tempDirectory)
{
// arrange
DictionaryOption dictOption = DictionaryOption.Create("dictionary", "kvp");
string key1 = "key1";
string value1 = "value1";
string key2 = "key2";
string value2 = "value2";
string[] args =
{
"--kvp", $"{key1}, {value1}", "--kvp", $"{key2}, {value2}"
};
// act
var result = dictOption.Parse(args);
// assert
Assert.Equal("", result.ErrorMessage);
Assert.True(result.Success);
Assert.Equal(value1, result.Result[key1]);
Assert.Equal(value2, result.Result[key2]);
}
public void GermlineWgsParse_WithRequiredArguments_ReturnsSuccessfulCallsetResult(string name, string description, StringWriter standardWriter,
StringWriter errorWriter, TemporaryDirectoryFixture tempDirectory)
{
// arrange
GermlineWgsModeParser germlineWgsModeParser = new GermlineWgsModeParser(name, description);
MainParser parser = GetMainParser(germlineWgsModeParser);
string[] args =
{
"-h"
};
// act
var result = parser.Parse(args, standardWriter, errorWriter);
// assert
Assert.True(result.Success);
}
public void ParseRequiredExclusiveOption_WithNeitherOptionSpecified_ReturnsFailedParseResult(TemporaryDirectoryFixture tempDirectory)
{
FileOption option1 = FileOption.CreateRequired("file1 option", "file1");
FileOption option2 = FileOption.CreateRequired("file2 option", "file2");
// arrange
ExclusiveFileOption multiFileOption = ExclusiveFileOption.CreateRequired(option1, option2);
string[] args =
{
};
// act
var result = multiFileOption.Parse(args);
// assert
Assert.Contains("must be specified", result.ErrorMessage);
Assert.False(result.Success);
}
