public void ShowsHelpText(string template)
{
// Arrange
string msg;
string expected =
"\r\n\r\nUsage: MSPC CLI [options]\r\n\r\nOptions:" +
"\r\n -? | -h | --help Show help information" +
"\r\n -v | --version Show version information" +
"\r\n -i | --input <value> Input samples to be processed in Browser Extensible Data (BED) Format." +
"\r\n -f | --folder-input <value> Sets a path to a folder that all its containing files in BED format are considered as inputs." +
"\r\n -r | --replicate <value> Sets the replicate type of samples. Possible values are: { Bio, Biological, Tec, Technical }" +
"\r\n -w | --tauW <value> Sets weak threshold. All peaks with p-values higher than this value are considered as weak peaks." +
"\r\n -s | --tauS <value> Sets stringency threshold. All peaks with p-values lower than this value are considered as stringent peaks." +
"\r\n -g | --gamma <value> Sets combined stringency threshold. The peaks with their combined p-values satisfying this threshold will be confirmed." +
"\r\n -a | --alpha <value> Sets false discovery rate of Benjamini–Hochberg step-up procedure." +
"\r\n -c <value> Sets minimum number of overlapping peaks before combining p-values." +
"\r\n -m | --multipleIntersections <value> When multiple peaks from a sample overlap with a given peak, this argument defines which of the peaks to be considered: the one with lowest p-value, or the one with highest p-value? Possible values are: { Lowest, Highest }" +
"\r\n -d | --degreeOfParallelism <value> Set the degree of parallelism." +
"\r\n -p | --parser <value> Sets the path to the parser configuration file in JSON." +
"\r\n -o | --output <value> Sets a path where analysis results should be persisted." +
"\r\n --excludeHeader If provided, MSPC will not add a header line to its output." +
"\r\n" +
"\n\rDocumentation:\thttps://genometric.github.io/MSPC/" +
"\n\rSource Code:\thttps://github.com/Genometric/MSPC" +
"\n\rPublications:\thttps://genometric.github.io/MSPC/publications" +
"\n\r\r\n";
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run(template: template);
// Assert
Assert.Contains(expected, msg);
Assert.True(Environment.ExitCode == 0);
}
public void ReportRuntime()
{
// Arrange
string msg;
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run();
// Assert
Assert.Contains("Elapsed time: ", msg);
}
public void ErrorIfLessThanTwoSamplesAreGiven()
{
// Arrange
string msg;
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run(false, "-i rep1.bed -r bio -w 1E-2 -s 1E-8");
// Assert
Assert.Contains("at least two samples are required; 1 is given.", msg);
}
public void WarningDisplayedForInvalidC(string c, string expected)
{
// Arrange
string msg;
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run(template: $"-i sample_1 -i sample_2 -r bio -w 1E-2 -s 1E-8 -c {c}");
// Assert
Assert.Contains($"Invalid `C={c}`, it is set to `C={expected}`.", msg);
}
public void ErrorIfASpecifiedFileIsMissing()
{
// Arrange
string msg;
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run(false, "-i rep1.bed -i rep2.bed -r bio -w 1E-2 -s 1E-8");
// Assert
Assert.Contains("the following files are missing: rep1.bed; rep2.bed", msg);
}
public void DontReportSuccessfullyFinishedIfExitedAfterAnError()
{
// Arrange
List <string> messages;
// Act
using (var tmpMspc = new TmpMspc())
messages = tmpMspc.FailRun();
// Assert
Assert.DoesNotContain(messages, x => x.Contains("All processes successfully finished"));
}
public void ErrorIfARequiredArgumentIsMissing()
{
// Arrange
string msg;
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run(false, "-i rep1.bed -i rep2.bed -w 1E-2 -s 1E-8");
// Assert
Assert.Contains("the following required arguments are missing: -r|--replicate.", msg);
}
public void SuccessfulAnalysis()
{
// Arrange
string msg;
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run();
// Assert
Assert.Contains("All processes successfully finished", msg);
}
public void AssertInformingMaxPValue()
{
// Arrange
string msg;
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run();
// Assert
Assert.Contains("1.000E-003", msg);
Assert.Contains("1.000E-002", msg);
}
public void CaptureExporterExceptions()
{
// Arrange
string message;
// Act
using (var tmpMspc = new TmpMspc())
message = tmpMspc.Run(new MExporter());
// Assert
Assert.Contains("The method or operation is not implemented.", message);
Assert.DoesNotContain("All processes successfully finished", message);
}
public void HintHowToUseHelpWhenAnExceptionOccurs()
{
// Arrange
string msg;
string expected = "You may run mspc with either of [-? | -h | --help] tags for help.";
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run(template: "");
// Assert
Assert.Contains(expected, msg);
}
public void ShowVersion(string template)
{
// Arrange
string msg;
string expected = "\r\nVersion ";
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run(template: template);
// Assert
Assert.Contains(expected, msg);
}
public void ReuseExistingLogger()
{
// Arrange
List <string> messages;
// Act
using (var tmpMspc = new TmpMspc())
messages = tmpMspc.FailRun();
// Assert
Assert.Contains(messages, x => x.Contains("the following files are missing: rep1; rep2"));
Assert.Contains(messages, x => x.Contains("the following required arguments are missing: (-i|--input or -f|--folder-input)."));
}
public void AssertInformingPeaksCount()
{
// Arrange
string msg;
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run();
// Assert
Assert.Contains(" 2\t", msg);
Assert.Contains(" 3\t", msg);
}
public void RaiseExceptionWritingToIllegalPath()
{
// Arrange
string msg;
var illegalPath = "C:\\*<>*\\//";
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run(sessionPath: illegalPath);
// Assert
Assert.True(
msg.Contains("Illegal characters in path.") ||
msg.Contains("The filename, directory name, or volume label syntax is incorrect"));
}
public void WriteOutputPathExceptionToLoggerIfAvailable()
{
// Arrange
List <string> messages;
// Act
using (var tmpMspc = new TmpMspc())
messages = tmpMspc.FailRun(template2: "-i rep1 -i rep2 -o C:\\*<>*\\// -r bio -s 1e-8 -w 1e-4");
// Assert
Assert.Contains(messages, x => x.Contains("the following files are missing: rep1; rep2"));
Assert.Contains(
messages,
x => x.Contains("Illegal characters in path.") ||
x.Contains("The filename, directory name, or volume label syntax is incorrect"));
}
public void ExportPathIsReportedInConsole()
{
// Arrange
string msg;
// Act
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run();
// Assert
var rx = new Regex(".*Export Directory: (.*)\r\n.*");
var loggedOutputPath = rx.Match(msg).Groups[1].Value.Trim();
var isAValidPath = TryGetFullPath(loggedOutputPath, out _);
Assert.True(isAValidPath);
}
public void ReadDataAccordingToParserConfig()
{
// Arrange
ParserConfig cols = new ParserConfig()
{
Chr = 0,
Left = 3,
Right = 4,
Name = 1,
Strand = 2,
Summit = 6,
Value = 5,
DefaultValue = 1.23E-45,
PValueFormat = PValueFormats.minus1_Log10_pValue,
DropPeakIfInvalidValue = false,
};
var path = Environment.CurrentDirectory + Path.DirectorySeparatorChar + "MSPCTests_" + new Random().NextDouble().ToString();
using (StreamWriter w = new StreamWriter(path))
w.WriteLine(JsonConvert.SerializeObject(cols));
string rep1Path = Path.GetTempPath() + Guid.NewGuid().ToString() + ".bed";
string rep2Path = Path.GetTempPath() + Guid.NewGuid().ToString() + ".bed";
FileStream stream = File.Create(rep1Path);
using (StreamWriter writter = new StreamWriter(stream))
writter.WriteLine("chr1\tMSPC_PEAK\t.\t10\t20\t16\t15");
stream = File.Create(rep2Path);
using (StreamWriter writter = new StreamWriter(stream))
writter.WriteLine("chr1\tMSPC_PEAK\t.\t15\t25\tEEE\t20");
// Act
string msg;
using (var tmpMspc = new TmpMspc())
msg = tmpMspc.Run(createSample: false, template: string.Format("-i {0} -i {1} -p {2} -r bio -w 1e-2 -s 1e-4", rep1Path, rep2Path, path));
// Assert
Assert.Contains("1.000E-016", msg);
Assert.Contains("1.230E-045", msg);
}
public void ThrowExceptionForInvalidCultureValue()
{
// Arrange
var parserFilename =
Environment.CurrentDirectory + Path.DirectorySeparatorChar +
Guid.NewGuid().ToString() + ".json";
// Create an json file with a `culture` field containing
// invalid culture name.
using (StreamWriter w = new StreamWriter(parserFilename))
w.WriteLine("{\"Culture\":\"xyz\"}");
// Act
string msg;
using (var tmpMSPC = new TmpMspc())
msg = tmpMSPC.Run(parserFilename: parserFilename);
// Assert
Assert.Contains("Error setting value to 'Culture'", msg);
}
