public static void ExecuteParsingTest(string arguments, bool shouldPass, Action <PsaraOptions> assertions = null)
{
var ApplicationOptionParser = new PsaraOptionsParser();
ApplicationOptionParser.ParseArgs(arguments.Split(' '));
var Options = (ApplicationOptionParser).PsaraOptions;
if (shouldPass)
{
assertions(Options);
}
else //TODO - it would be nice to specify the actual error codes from the parsing result
{
int ErrorCode = ApplicationOptionParser.ParsingResult.ExitCode;
Assert.NotEqual(0, ApplicationOptionParser.ParsingResult.ExitCode);
Assert.NotNull(ApplicationOptionParser.ParsingResult.Exception);
}
}
public static void CreateMissingOutFolder()
{
var vcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "PsaraTestInput.vcf");
var roiPath = Path.Combine(TestPaths.LocalTestDataDirectory, "roi.txt");
var testVcfDir = Path.Combine(TestPaths.LocalScratchDirectory, "VcfDir");
var testNonexistantDir = Path.Combine(TestPaths.LocalScratchDirectory, "mockNonexistantDir");
if (Directory.Exists(testNonexistantDir))
{
Directory.Delete(testNonexistantDir);
}
//test 1: if no output directory is supplied, test the vcf directory will do.
if (!Directory.Exists(testVcfDir))
{
Directory.CreateDirectory(testVcfDir);
}
var testVcfPath = Path.Combine(testVcfDir, "PsaraTestInput.vcf");
if (!File.Exists(testVcfPath))
{
File.Copy(vcfPath, testVcfPath);
}
var arguments = new string[] { "-vcf", testVcfPath, "-roi", roiPath };
var ApplicationOptionParser = new PsaraOptionsParser();
ApplicationOptionParser.ParseArgs(arguments);
var Options = (ApplicationOptionParser).PsaraOptions;
Assert.Equal(testVcfDir, Options.OutputDirectory);
Assert.True(ApplicationOptionParser.HadSuccess);
Assert.Equal(0, ApplicationOptionParser.ParsingResult.ExitCode);
//test 2: if a non-existant output directory is supplied, check it can be created
arguments = new string[] { "-vcf", testVcfPath, "-roi", roiPath, "-outfolder", testNonexistantDir };
Assert.False(Directory.Exists(testNonexistantDir));
ApplicationOptionParser = new PsaraOptionsParser();
ApplicationOptionParser.ParseArgs(arguments);
Options = (ApplicationOptionParser).PsaraOptions;
Assert.Equal(testNonexistantDir, Options.OutputDirectory);
Assert.True(ApplicationOptionParser.HadSuccess);
Assert.Equal(0, ApplicationOptionParser.ParsingResult.ExitCode);
Assert.True(Directory.Exists(testNonexistantDir));
//test 3: if an uncreatable directory is supplied, check a parsing error is thrown
arguments = new string[] { "-vcf", testVcfPath, "-roi", roiPath, "-outfolder", "This..:&^$*%WontWOrk:!!" };
Assert.False(Directory.Exists("This..:&^$*%WontWOrk:!!"));
ApplicationOptionParser = new PsaraOptionsParser();
ApplicationOptionParser.ParseArgs(arguments);
Options = (ApplicationOptionParser).PsaraOptions;
Assert.Equal("This..:&^$*%WontWOrk:!!", Options.OutputDirectory);
Assert.True(ApplicationOptionParser.ParsingFailed);
Assert.Equal(160, ApplicationOptionParser.ParsingResult.ExitCode);
Assert.False(Directory.Exists("This..:&^$*%WontWOrk:!!"));
}
public static void CreateMissingOutFolder()
{
var vcfPath = Path.Combine(TestPaths.LocalTestDataDirectory, "PsaraTestInput.vcf");
var roiPath = Path.Combine(TestPaths.LocalTestDataDirectory, "roi.txt");
var testVcfDir = Path.Combine(TestPaths.LocalScratchDirectory, "VcfDir");
var testNonexistantDir = Path.Combine(TestPaths.LocalScratchDirectory, "mockNonexistantDir");
if (Directory.Exists(testNonexistantDir))
{
Directory.Delete(testNonexistantDir);
}
//test 1: if no output directory is supplied, test the vcf directory will do.
if (!Directory.Exists(testVcfDir))
{
Directory.CreateDirectory(testVcfDir);
}
var testVcfPath = Path.Combine(testVcfDir, "PsaraTestInput.vcf");
if (!File.Exists(testVcfPath))
{
File.Copy(vcfPath, testVcfPath);
}
var arguments = new string[] { "-vcf", testVcfPath, "-roi", roiPath };
var ApplicationOptionParser = new PsaraOptionsParser();
ApplicationOptionParser.ParseArgs(arguments);
var Options = (ApplicationOptionParser).PsaraOptions;
Assert.Equal(testVcfDir, Options.OutputDirectory);
Assert.True(ApplicationOptionParser.HadSuccess);
Assert.Equal(0, ApplicationOptionParser.ParsingResult.ExitCode);
//test 2: if a non-existant output directory is supplied, check it can be created
arguments = new string[] { "-vcf", testVcfPath, "-roi", roiPath, "-outfolder", testNonexistantDir };
Assert.False(Directory.Exists(testNonexistantDir));
ApplicationOptionParser = new PsaraOptionsParser();
ApplicationOptionParser.ParseArgs(arguments);
Options = (ApplicationOptionParser).PsaraOptions;
Assert.Equal(testNonexistantDir, Options.OutputDirectory);
Assert.True(ApplicationOptionParser.HadSuccess);
Assert.Equal(0, ApplicationOptionParser.ParsingResult.ExitCode);
Assert.True(Directory.Exists(testNonexistantDir));
//test 3: if an uncreatable directory is supplied, check a parsing error is thrown
string crazyDir = "This//..:\\&^$*%WontWOrk:!!"; //tjd, ha ha, no it can be created by UNIX...
//allow linux/unix to skip this.. otherwise they would fail for being smart..
var platform = Environment.OSVersion.Platform.ToString().ToLower();
if ((platform.Contains("unix")) || (platform.Contains("linux")))
{
Assert.True(true);
}
else
{
arguments = new string[] { "-vcf", testVcfPath, "-roi", roiPath, "-outfolder", crazyDir };
bool doesItExist = Directory.Exists(crazyDir);
Assert.False(doesItExist);
ApplicationOptionParser = new PsaraOptionsParser();
ApplicationOptionParser.ParseArgs(arguments);
Options = (ApplicationOptionParser).PsaraOptions;
Assert.Equal(crazyDir, Options.OutputDirectory);
Assert.True(ApplicationOptionParser.ParsingFailed);
Assert.Equal(160, ApplicationOptionParser.ParsingResult.ExitCode);
Assert.False(Directory.Exists(crazyDir));
}
}