public IProcess StartProcess(string fileName, string arguments,
IUserInterface userInterface,
string workingDirectory = null,
bool showOutput = true, bool showError = true,
bool killOnDispose = true)
{
FormatterParameters parameters = new FormatterParameters();
parameters.Add(fileName, Constants.CommandKey);
parameters.Add(arguments, Constants.CommandArgumentsKey);
IUserInterface formatterUserInterface = formatterPool.GetFormatter(parameters, userInterface);
ExecutionContext redirectedContext = executionContext.RedirectOutput(formatterUserInterface);
return(new ProcessFacade(fileName, arguments, workingDirectory, redirectedContext, null, showOutput, showError, killOnDispose,
environmentService.Platform, cancellationToken));
}
public IProcess StartProcessWithSetup(string fileName, string arguments,
IUserInterface userInterface, string setup,
string workingDirectory = null,
bool showOutput = true, bool showError = true,
bool killOnDispose = true)
{
string commandName = fileName;
if (setup != null)
{
commandName = $"cmd.exe";
string arguments2 = $"/c \"\"{setup}\" && \"{fileName}\" {arguments}\"";
if (environmentService.Platform == OSPlatform.Linux)
{
commandName = "/bin/sh";
arguments2 = $"-c \"'{setup}' && '{fileName}' {arguments}\"";
}
arguments = arguments2;
}
string displayName = Path.GetFileNameWithoutExtension(fileName);
FormatterParameters parameters = new FormatterParameters();
parameters.Add(commandName, Constants.CommandKey);
parameters.Add(arguments, Constants.CommandArgumentsKey);
IUserInterface formatterUserInterface = formatterPool.GetFormatter(parameters, userInterface);
ExecutionContext redirectedContext = executionContext.RedirectOutput(formatterUserInterface);
if (environmentService.Platform == OSPlatform.Linux && setup != null)
{
var fileInfo = new UnixFileInfo(setup);
fileInfo.FileAccessPermissions = fileInfo.FileAccessPermissions | FileAccessPermissions.UserExecute;
}
ProcessFacade facade = new ProcessFacade(commandName, arguments, workingDirectory, redirectedContext, displayName, showOutput, showError, killOnDispose,
environmentService.Platform, cancellationToken);
return(facade);
}
/// <summary>
/// Phylogenetic Tree Formatter General Tests
/// </summary>
/// <param name="nodeName">Xml node Name.</param>
/// <param name="formatParam">Additional parameter</param>
void PhylogeneticTreeFormatterGeneralTests(string nodeName,
FormatterParameters formatParam)
{
// Gets the expected sequence from the Xml
string filePath = string.Empty;
using (NewickParser parser = new NewickParser())
{
Tree rootTree = null;
switch (formatParam)
{
case FormatterParameters.Object:
rootTree = GetFormattedObject(false);
break;
case FormatterParameters.ObjectSingleNode:
rootTree = GetFormattedObject(true);
break;
case FormatterParameters.ParseTextReader:
filePath = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Formatter P1: File Exists in the Path '{0}'.",
filePath));
using (StreamReader reader = File.OpenText(filePath))
{
rootTree = parser.Parse(reader);
}
break;
case FormatterParameters.ParseStringBuilder:
filePath = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Formatter P1: File Exists in the Path '{0}'.",
filePath));
using (StreamReader reader = File.OpenText(filePath))
{
StringBuilder strBuilderObj =
new StringBuilder(reader.ReadToEnd());
rootTree = parser.Parse(strBuilderObj);
}
break;
default:
filePath = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Formatter P1: File Exists in the Path '{0}'.",
filePath));
rootTree = parser.Parse(filePath);
break;
}
string outputFilepath = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.OutputFilePathNode);
NewickFormatter format = new NewickFormatter();
switch (formatParam)
{
case FormatterParameters.TextWriter:
using (TextWriter writer = new StreamWriter(outputFilepath))
{
format.Format(rootTree, writer);
}
break;
case FormatterParameters.FormatString:
// Validate format String
string formatString = format.FormatString(rootTree);
string expectedFormatString = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FormatStringNode);
Assert.AreEqual(expectedFormatString, formatString);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Formatter P1: Format string '{0}' is as expected.",
formatString));
Console.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Formatter P1: Format string '{0}' is as expected.",
formatString));
break;
default:
format.Format(rootTree, outputFilepath);
break;
}
// Validate only if not a Format String
if (FormatterParameters.FormatString != formatParam)
{
// Re-parse the created file and validate the tree.
using (NewickParser newparserObj = new NewickParser())
{
Tree newrootTreeObj = null;
Assert.IsTrue(File.Exists(outputFilepath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Formatter P1: New File Exists in the Path '{0}'.",
outputFilepath));
newrootTreeObj = newparserObj.Parse(outputFilepath);
Node rootNode = newrootTreeObj.Root;
string rootBranchCount = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.RootBranchCountNode);
// Validate the root branch count
Assert.AreEqual(rootBranchCount,
rootNode.Children.Count.ToString((IFormatProvider)null));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Formatter P1: Number of Root Branches found are '{0}'.",
rootNode.Children.Count.ToString((IFormatProvider)null)));
List <string> leavesName = new List <string>();
List <double> leavesDistance = new List <double>();
// Gets all the leaves in the root node list
GetAllNodesAndEdges(rootNode, ref leavesName,
ref leavesDistance);
string[] expectedLeavesName = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.NodeNamesNode).Split(',');
string[] expectedLeavesDistance = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.EdgeDistancesNode).Split(',');
for (int i = 0; i < expectedLeavesName.Length; i++)
{
Assert.AreEqual(expectedLeavesName[i], leavesName[i]);
}
for (int i = 0; i < expectedLeavesDistance.Length; i++)
{
Assert.AreEqual(expectedLeavesDistance[i], leavesDistance[i].ToString((IFormatProvider)null));
}
ApplicationLog.WriteLine(
"Phylogenetic Tree Parser P1: The Node Names and Distance are as expected.");
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Phylogenetic Tree Parser P1: The Node Names and Distance are as expected.");
}
if (File.Exists(outputFilepath))
{
File.Delete(outputFilepath);
}
}
}
}
public bool CanFormat(FormatterParameters parameters)
{
return(parameters.TryGet(Constants.MessageFormat, out string messageFormat) &&
messageFormat == "cmake-json");
}
/// <summary>
/// Phylogenetic Tree Formatter General Tests
/// </summary>
/// <param name="nodeName">Xml node Name.</param>
/// <param name="formatParam">Additional parameter</param>
void PhylogeneticTreeFormatterGeneralTests(string nodeName,
FormatterParameters formatParam)
{
// Gets the expected sequence from the Xml
string filePath = string.Empty;
NewickParser parser = new NewickParser();
{
Tree rootTree;
switch (formatParam)
{
case FormatterParameters.Object:
rootTree = GetFormattedObject();
break;
default:
filePath = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Parser BVT: File Exists in the Path '{0}'.",
filePath));
rootTree = parser.Parse(filePath);
break;
}
string outputFilepath = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.OutputFilePathNode);
NewickFormatter format = new NewickFormatter();
switch (formatParam)
{
case FormatterParameters.Stream:
using (var writer = File.Create(outputFilepath))
{
format.Format(writer, rootTree);
}
break;
case FormatterParameters.FormatString:
// Validate format String
var formatString = format.FormatString(rootTree);
string expectedFormatString =
_utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FormatStringNode);
Assert.AreEqual(expectedFormatString, formatString);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Parser BVT: Format string '{0}' is as expected.",
formatString));
break;
default:
format.Format(rootTree, outputFilepath);
break;
}
// Validate only if not a Format String
if (FormatterParameters.FormatString != formatParam)
{
// Re-parse the created file and validate the tree.
NewickParser newparserObj = new NewickParser();
{
Tree newrootTreeObj = null;
Assert.IsTrue(File.Exists(outputFilepath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Parser BVT: New File Exists in the Path '{0}'.",
outputFilepath));
newrootTreeObj = newparserObj.Parse(outputFilepath);
Node rootNode = newrootTreeObj.Root;
string rootBranchCount = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.RootBranchCountNode);
// Validate the root branch count
Assert.AreEqual(rootBranchCount,
rootNode.Children.Count.ToString((IFormatProvider)null));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Parser BVT: Number of Root Branches found are '{0}'.",
rootNode.Children.Count.ToString((IFormatProvider)null)));
List<string> leavesName = new List<string>();
List<double> leavesDistance = new List<double>();
// Gets all the leaves in the root node list
GetAllNodesAndEdges(rootNode, ref leavesName, ref leavesDistance);
string[] expectedLeavesName = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.NodeNamesNode).Split(',');
string[] expectedLeavesDistance = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.EdgeDistancesNode).Split(',');
for (int i = 0; i < expectedLeavesName.Length; i++)
{
Assert.AreEqual(expectedLeavesName[i], leavesName[i]);
}
for (int i = 0; i < expectedLeavesDistance.Length; i++)
{
Assert.AreEqual(expectedLeavesDistance[i],
leavesDistance[i].ToString((IFormatProvider)null));
}
}
ApplicationLog.WriteLine(
"Phylogenetic Tree Parser BVT: The Node Names and Distance are as expected.");
}
if (File.Exists(outputFilepath))
File.Delete(outputFilepath);
}
}
public static async Task <CMakeConversation> Start(IProcessManager processManager,
IBinariesLocator binariesLocator,
IOutputFormatterPool formatterPool,
VirtualDirectory tempDirectory, bool isWindowsSystem,
ExecutionContext executionContext,
VirtualDirectory sourceDirectory,
VirtualDirectory binaryDirectory)
{
IProcess process = null;
NamedPipeClientStream pipeClient = null;
try
{
string pipeName = isWindowsSystem
? $"{tempDirectory.FullName}\\.cmakeserver"
: $"/tmp/cmake-server-{Guid.NewGuid().ToByteString()}";
string serverCommand = isWindowsSystem
? $"-E server --experimental --pipe=\"\\\\?\\pipe\\{pipeName}\""
: $"-E server --experimental --pipe={pipeName}";
process = processManager.StartProcess(binariesLocator.GetExecutableCommand("cmake"), serverCommand, executionContext);
pipeClient = new NamedPipeClientStream(".", pipeName,
PipeDirection.InOut, PipeOptions.Asynchronous,
TokenImpersonationLevel.Impersonation);
pipeClient.Connect(CMakeServerTimeout);
if (!pipeClient.IsConnected)
{
throw new FormattableException("Could not connect to server");
}
FormatterParameters parameters = new FormatterParameters();
parameters.Add("cmake-json", MessageFormat);
IUserInterface jsonCmakeInterface = formatterPool.GetFormatter(parameters, executionContext);
CMakeServerStream serverStream = new CMakeServerStream(pipeClient, executionContext);
CMakeHelloMessage hello = null;
do
{
foreach (string singleMessage in await serverStream.ReadMessage()
.TimeoutAfter(CMakeServerTimeout)
.ConfigureAwait(false))
{
hello = CMakeMessage.Parse <CMakeMessage>(singleMessage, jsonCmakeInterface) as CMakeHelloMessage;
}
} while (hello == null);
if (hello.SupportedProtocolVersions.All(v => v.Major != 1))
{
throw new FormattableException("CMake server does not support the protocol version 1.X. " +
$"Supported versions are {string.Join(", ", hello.SupportedProtocolVersions)}");
}
CMakeConversation conversation = new CMakeConversation(process, pipeClient, serverStream, jsonCmakeInterface);
await conversation.Handshake(sourceDirectory.FullName.Replace('\\', '/'),
binaryDirectory.FullName.Replace('\\', '/'))
.ConfigureAwait(false);
await conversation.Configure().ConfigureAwait(false);
return(conversation);
}
catch (Exception)
{
pipeClient?.Dispose();
process?.Dispose();
throw;
}
}
