/// <inheritdoc />
protected override bool ReadChunk(Stream stream, out MemoryStream chunk)
{
chunk = null;
var bytes = new byte[4];
if (stream.Read(bytes, 0, 4) == 0)
{
return(false);
}
int length = BitConverter.ToInt32(bytes, 0);
if (length <= 0 || length > BlockSize * 2)
{
UserErrorException.ThrowUserErrorException("Invalid input file format");
}
var buffer = new byte[length];
if (stream.Read(buffer, 0, length) < length)
{
UserErrorException.ThrowUserErrorException("Invalid input file format. File is too short");
}
chunk = new MemoryStream(buffer);
return(true);
}
public void UserError()
{
var exception = new UserErrorException("user error");
var observedExitCode = ExitCodeUtilities.ShowException(exception);
Assert.Equal((int)ExitCodes.UserError, observedExitCode);
}
public static void ValidateScoreValue(string value, string line)
{
if (double.TryParse(value, out _))
{
return;
}
var e = new UserErrorException(
$"{value} is not a valid score value. Scores are expected to be numbers.");
e.Data["Line"] = line;
throw e;
}
/// <summary>
/// Rethrows exception to be shown to user in some specific cases
/// </summary>
public static void ConvertFileExceptions(this Exception exception)
{
switch (exception)
{
case IOException _:
case UnauthorizedAccessException _:
case InvalidDataException _: //this is gzip case
//SecurityException _: //should not be thrown in normal run case:
UserErrorException.ThrowUserErrorException($"Error processing file: {exception.Message}");
break;
}
}
public static void Main(string[] args)
{
ExceptionManager.EnsureManagerInitialized();
args = args.Where(str => !string.IsNullOrEmpty(str)).ToArray();
if (args.Length != 3)
{
UserErrorException.ThrowUserErrorException("There should be 3 arguments");
}
bool compress = ParseMode(args[0]);
string inputPath = args[1];
string outputPath = args[2];
ZipZipProcessing.Process(inputPath, outputPath, compress);
}
public static bool RunTest(string toolchainName, Compiler compile, Exe runner, File source)
{
var destPath = tests_results.Combine(source);
var sourcePath = tests.Combine(source);
var expected = sourcePath.DropExtension().Combine(Ext(".o"));
Console.Write($"\x1b[KRunning test {source} ({toolchainName}) ");
destPath.DirName().Create();
UserErrorException exception = null;
try {
CompileToFile(compile, sourcePath, destPath);
} catch (UserErrorException e) {
exception = e;
}
if (exception != null)
{
Console.WriteLine("");
Console.WriteLine("\x1b[1;31mFail\x1b[m");
Console.WriteLine($"\x1b[1;33m{exception.Message}\x1b[m\n");
return(false);
}
else
{
var actualStr = runner.Run(destPath);
var expectedStr = expected.Read();
if (actualStr != expectedStr)
{
Console.WriteLine("\x1b[1;31mFail\x1b[m");
Console.WriteLine($"\x1b[1;33m{source}: expected {expectedStr} but got {actualStr}.\x1b[m\n");
return(false);
}
else
{
Console.Write("\x1b[1;32mOK\x1b[m\n"); // \r at the end for quiet
return(true);
}
}
}
internal void ParseHeaderLines()
{
string line;
while ((line = _reader.ReadLine()) != null)
{
if (line.StartsWith("#geneSymbol"))
{
break;
}
line = line.Trim();
(string key, string value) = line.OptimizedKeyValue();
switch (key)
{
case "#title":
JsonTag = value;
break;
case "#version":
Version = value;
break;
case "#description":
DataSourceDescription = value;
break;
default:
var e = new UserErrorException("Unexpected header tag observed");
e.Data[ExitCodeUtilities.Line] = line;
throw e;
}
}
_tags = ParserUtilities.ParseTags(line, "#geneSymbol", NumRequiredColumns);
CheckTagsAndSetJsonKeys();
Categories = ParserUtilities.ParseCategories(_reader.ReadLine(), NumRequiredColumns, _numAnnotationColumns, _annotationValidators);
Descriptions = ParserUtilities.ParseDescriptions(_reader.ReadLine(), NumRequiredColumns, _numAnnotationColumns);
ValueTypes = ParserUtilities.ParseTypes(_reader.ReadLine(), NumRequiredColumns, _numAnnotationColumns);
}
private void PrintError(UserErrorException e)
{
Console.SetForegroundColor(ConsoleColor.Red);
Console.WriteLine($"Error: {e.Message}");
Console.SetForegroundColor(ConsoleColor.Gray);
}
