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 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 ParseCommonOptions_KmerFastaDoesntExist_DisplaysError(TemporaryDirectoryFixture tempDirectory)
{
// arrange
Option<CommonOptions> commonOptionsParser = new CommonOptionsParser();
var kmerFasta = tempDirectory.GetFileLocation("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.False(result.Success);
Assert.Contains("kmer.fa", result.ErrorMessage);
Assert.Contains("does not exist", result.ErrorMessage);
}
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);
}