/// <summary>
/// Runs an R script and blocks the current thread until the script finishes its execution.
/// </summary>
/// <param name="fileName">Path to an R script. May be a file on disk, or an embedded resource.</param>
/// <param name="arguments">Command line arguments to pass to the script.</param>
/// <param name="throwOnError">Throw on error from R?</param>
/// <returns>Standard output generated by the R script.</returns>
public string Run(string fileName, bool throwOnError = true, params string[] arguments)
{
RunAsync(fileName, arguments);
proc.WaitForExit();
string message;
if (proc.ExitCode != 0)
{
StringBuilder error = new StringBuilder("Error from R:");
error.AppendLine($"Script path: '{fileName}'");
error.AppendLine("Script contents:");
error.AppendLine(File.ReadAllText(fileName));
error.AppendLine("StdErr:");
error.AppendLine(proc.StdErr);
error.AppendLine("StdOut:");
error.AppendLine(proc.StdOut);
message = error.ToString();
if (throwOnError)
{
throw new Exception(message);
}
}
else
{
message = proc.StdOut;
}
return(message);
}
/// <summary>
/// Runs an R script and blocks the current thread until the script finishes its execution.
/// </summary>
/// <param name="fileName">Path to an R script. May be a file on disk, or an embedded resource.</param>
/// <param name="arguments">Command line arguments to pass to the script.</param>
/// <param name="throwOnError">Throw on error from R?</param>
/// <returns>Standard output generated by the R script.</returns>
public string Run(string fileName, bool throwOnError = true, params string[] arguments)
{
RunAsync(fileName, arguments);
proc.WaitForExit();
string message;
if (proc.ExitCode != 0)
{
StringBuilder error = new StringBuilder();
error.AppendLine("Error from R:");
error.AppendLine($"Script path: '{fileName}'");
error.AppendLine("StdErr:");
error.AppendLine(proc.StdErr);
error.AppendLine("StdOut:");
error.AppendLine(proc.StdOut);
error.AppendLine("Script contents:");
error.AppendLine(File.ReadAllText(fileName));
message = error.ToString();
// RSCript will exit with non-0 exit code if cancelled.
// No need to throw an exception in this case.
if (throwOnError && !cancelToken.IsCancellationRequested)
{
throw new Exception(message);
}
}
else
{
message = proc.StdOut;
}
return(message);
}
/// <summary>
/// Gets the path to an executable (uses the Unix which utility).
/// Throws if the package does not exist. Obviously this will not
/// work on Windows.
/// </summary>
private string GetPathToPackage(string package)
{
ProcessUtilities.ProcessWithRedirectedOutput findR = new ProcessUtilities.ProcessWithRedirectedOutput();
findR.Start("/usr/bin/which", package, Path.GetTempPath(), true);
findR.WaitForExit();
if (string.IsNullOrEmpty(findR.StdOut) && !string.IsNullOrEmpty(findR.StdErr))
{
// If the shell command generated anything in StdErr, we display that message.
throw new Exception("Encountered an error while searching for " + package + " installation: " + findR.StdErr);
}
return(findR.StdOut);
}
/// <summary>
/// Runs an R script and blocks the current thread until the script finishes its execution.
/// </summary>
/// <param name="fileName">Path to an R script. May be a file on disk, or an embedded resource.</param>
/// <param name="arguments">Command line arguments to pass to the script.</param>
/// <param name="throwOnError">Throw on error from R?</param>
/// <returns>Standard output generated by the R script.</returns>
public string Run(string fileName, string arguments = "", bool throwOnError = true)
{
RunAsync(fileName, arguments);
proc.WaitForExit();
if (throwOnError && proc.ExitCode != 0)
{
string message = "Error from R: " + Environment.NewLine +
proc.StdErr + Environment.NewLine +
"Script:" + Environment.NewLine +
File.ReadAllText(fileName);
throw new Exception(message);
}
return(Output);
}
public static string RunModels(string arguments)
{
string pathToModels = typeof(IModel).Assembly.Location;
ProcessUtilities.ProcessWithRedirectedOutput proc = new ProcessUtilities.ProcessWithRedirectedOutput();
proc.Start(pathToModels, arguments, Path.GetTempPath(), true);
proc.WaitForExit();
if (proc.ExitCode != 0)
{
throw new Exception(proc.StdOut);
}
return(proc.StdOut);
}
public void OnCreatedShouldFailRun()
{
string json = ReflectionUtilities.GetResourceAsString("UnitTests.Core.ApsimFile.OnCreatedError.apsimx");
string fileName = Path.Combine(Path.GetTempPath(), Guid.NewGuid().ToString() + ".apsimx");
File.WriteAllText(fileName, json);
Assembly models = typeof(IModel).Assembly;
string modelsExe = AppDomain.CurrentDomain.GetAssemblies().First(a => string.Equals(a.FullName, models.FullName, StringComparison.Ordinal)).Location;
var proc = new ProcessUtilities.ProcessWithRedirectedOutput();
proc.Start(modelsExe, fileName, Path.GetTempPath(), true);
proc.WaitForExit();
Assert.AreNotEqual(0, proc.ExitCode, "A file ran without error when an exception should have been thrown while opening the file.");
}
/// <summary>
/// Runs the R installer.
/// </summary>
/// <param name="installerPath">Path to the installer.</param>
private void InstallR(string installerPath)
{
if (installerPath == null)
{
return;
}
// Setup a working directory.
string workingDirectory = Path.Combine(Path.GetTempPath(), "RSetup");
if (!Directory.Exists(workingDirectory))
{
Directory.CreateDirectory(workingDirectory);
}
// Copy installer to working directory.
try
{
string newInstallerPath = Path.Combine(workingDirectory, Path.GetFileNameWithoutExtension(installerPath));
File.Copy(installerPath, newInstallerPath);
installerPath = newInstallerPath;
}
catch
{
}
// Check to see if installer is already running for whatever reason.
// Kill them if found.
foreach (var process in Process.GetProcessesByName(Path.GetFileNameWithoutExtension(installerPath)))
{
process.Kill();
}
// Run the installer.
var installer = new ProcessUtilities.ProcessWithRedirectedOutput();
installer.Start(installerPath, "", workingDirectory, false);
installer.WaitForExit();
}
/// <summary>
/// Runs an R script and blocks the current thread until the script finishes its execution.
/// </summary>
/// <param name="fileName">Path to an R script. May be a file on disk, or an embedded resource.</param>
/// <param name="arguments">Command line arguments to pass to the script.</param>
/// <returns>Standard output generated by the R script.</returns>
public string Run(string fileName, string arguments = "")
{
RunAsync(fileName, arguments);
proc.WaitForExit();
return(Output);
}
public void TestEditing()
{
string configFile = Path.GetTempFileName();
File.WriteAllLines(configFile, new[]
{
// Modify an array
"[Report].VariableNames = x,y,z",
// Modify a date - try a few different formats.
"[Clock].StartDate = 2000-01-01",
"[Clock].EndDate = 2000-01-10T00:00:00",
// Modify a string
"[Weather].FileName = fdsa.met",
@"[Weather2].FullFileName = .\jkl.met",
// Replace a model with a model from another file.
$"[Weather3] = {extFile}",
$"[Weather4] = {extFile};[w2]",
// Change a property of a resource model.
"[Wheat].Leaf.Photosynthesis.RUE.FixedValue = 0.4",
// Change a property of a manager script.
"[Manager].Script.Amount = 1234",
// Set an entire array.
"[Physical].BD = 1, 2, 3, 4, 5",
// Modify a single element of an array.
"[Physical].AirDry[2] = 6",
// Modify multiple elements of an array.
"[Physical].LL15[3:4] = 7",
});
string models = typeof(IModel).Assembly.Location;
string args = $"{fileName} /Edit {configFile}";
var proc = new ProcessUtilities.ProcessWithRedirectedOutput();
proc.Start(models, args, Path.GetTempPath(), true, writeToConsole: true);
proc.WaitForExit();
// Children of simulation are, in order:
// Clock, summary, zone, Weather, Weather2, w1, w2
Assert.AreEqual(null, proc.StdOut);
Assert.AreEqual(null, proc.StdErr);
Simulations file = FileFormat.ReadFromFile <Simulations>(fileName, out List <Exception> errors);
if (errors != null && errors.Count > 0)
{
throw errors[0];
}
var report = Apsim.Find(file, typeof(Models.Report)) as Models.Report;
string[] variableNames = new[] { "x", "y", "z" };
Assert.AreEqual(variableNames, report.VariableNames);
IModel sim = Apsim.Child(file, typeof(Simulation));
// Use an index-based lookup to locate child models.
// When we replace an entire model, we want to ensure
// that the replacement is inserted at the correct index.
Clock clock = sim.Children[0] as Clock;
Assert.AreEqual(new DateTime(2000, 1, 1), clock.StartDate);
Assert.AreEqual(new DateTime(2000, 1, 10), clock.EndDate);
var weather = sim.Children[3] as Models.Weather;
Assert.NotNull(weather);
Assert.AreEqual("Weather", weather.Name);
Assert.AreEqual("fdsa.met", weather.FileName);
var weather2 = sim.Children[4] as Models.Weather;
Assert.NotNull(weather2);
Assert.AreEqual("Weather2", weather2.Name);
Assert.AreEqual(@".\jkl.met", weather2.FileName);
// Weather3 and Weather4 should have been
// renamed to w1 and w2, respectively.
var weather3 = sim.Children[5] as Models.Weather;
Assert.NotNull(weather3);
Assert.AreEqual("w1", weather3.Name);
Assert.AreEqual("w1.met", weather3.FileName);
var weather4 = sim.Children[6] as Models.Weather;
Assert.NotNull(weather4);
Assert.AreEqual("w2", weather4.Name);
Assert.AreEqual("w2.met", weather4.FileName);
// The edit file operation should have changed RUE value to 0.4.
var wheat = sim.Children[2].Children[2] as Plant;
var rue = wheat.Children[6].Children[5].Children[0] as Constant;
Assert.AreEqual(0.4, rue.FixedValue);
double amount = (double)Apsim.Get(sim, "[Manager].Script.Amount");
Assert.AreEqual(1234, amount);
Physical physical = sim.Children[2].Children[4] as Physical;
Assert.AreEqual(new double[5] {
1, 2, 3, 4, 5
}, physical.BD);
Assert.AreEqual(new double[5] {
0, 6, 0, 0, 0
}, physical.AirDry);
Assert.AreEqual(new double[5] {
0, 0, 7, 7, 0
}, physical.LL15);
}
public void TestSimNameRegex()
{
string models = typeof(IModel).Assembly.Location;
IModel sim1 = Utilities.GetRunnableSim().Children[1];
sim1.Name = "sim1";
IModel sim2 = Utilities.GetRunnableSim().Children[1];
sim2.Name = "sim2";
IModel sim3 = Utilities.GetRunnableSim().Children[1];
sim3.Name = "simulation3";
IModel sim4 = Utilities.GetRunnableSim().Children[1];
sim4.Name = "Base";
Simulations sims = Simulations.Create(new[] { sim1, sim2, sim3, sim4, new DataStore() });
sims.ParentAllDescendants();
string apsimxFileName = Path.ChangeExtension(Path.GetTempFileName(), ".apsimx");
sims.Write(apsimxFileName);
// Need to quote the regex on unix systems.
string args;
if (ProcessUtilities.CurrentOS.IsWindows)
{
args = $@"{apsimxFileName} /Verbose /SimulationNameRegexPattern:sim\d";
}
else
{
args = $@"{apsimxFileName} /Verbose '/SimulationNameRegexPattern:sim\d'";
}
ProcessUtilities.ProcessWithRedirectedOutput proc = new ProcessUtilities.ProcessWithRedirectedOutput();
proc.Start(models, args, Directory.GetCurrentDirectory(), true);
proc.WaitForExit();
Assert.Null(proc.StdErr);
Assert.True(proc.StdOut.Contains("sim1"));
Assert.True(proc.StdOut.Contains("sim2"));
Assert.False(proc.StdOut.Contains("simulation3"));
Assert.False(proc.StdOut.Contains("Base"));
args = $@"{apsimxFileName} /Verbose /SimulationNameRegexPattern:sim1";
proc = new ProcessUtilities.ProcessWithRedirectedOutput();
proc.Start(models, args, Directory.GetCurrentDirectory(), true);
proc.WaitForExit();
Assert.Null(proc.StdErr);
Assert.True(proc.StdOut.Contains("sim1"));
Assert.False(proc.StdOut.Contains("sim2"));
Assert.False(proc.StdOut.Contains("simulation3"));
Assert.False(proc.StdOut.Contains("Base"));
args = $@"{apsimxFileName} /Verbose /SimulationNameRegexPattern:(simulation3)|(Base)";
proc = new ProcessUtilities.ProcessWithRedirectedOutput();
proc.Start(models, args, Directory.GetCurrentDirectory(), true);
proc.WaitForExit();
Assert.Null(proc.StdErr);
Assert.False(proc.StdOut.Contains("sim1"));
Assert.False(proc.StdOut.Contains("sim2"));
Assert.True(proc.StdOut.Contains("simulation3"));
Assert.True(proc.StdOut.Contains("Base"));
}
/// <summary>
/// Runs an R script and blocks the current thread until the script finishes its execution.
/// </summary>
/// <param name="fileName">Path to an R script.</param>
/// <returns>Standard output generated by the R script.</returns>
public string Run(string fileName)
{
RunAsync(fileName);
proc.WaitForExit();
return(Output);
}
public void TestEditing()
{
string configFile = Path.GetTempFileName();
File.WriteAllLines(configFile, new[]
{
// Modify an array
"[Report].VariableNames = x,y,z",
// Modify a date - try a few different formats.
"[Clock].StartDate = 2000-01-01",
"[Clock].EndDate = 2000-01-10T00:00:00",
// Modify a string
"[Weather].FileName = fdsa.met",
@"[Weather2].FullFileName = .\jkl.met",
// Replace a model with a model from another file.
$"[Weather3] = {extFile}",
$"[Weather4] = {extFile};[w2]",
});
string models = typeof(IModel).Assembly.Location;
string args = $"{fileName} /Edit {configFile}";
var proc = new ProcessUtilities.ProcessWithRedirectedOutput();
proc.Start(models, args, Path.GetTempPath(), true, true);
proc.WaitForExit();
// Children of simulation are, in order:
// Clock, summary, zone, Weather, Weather2, w1, w2
Assert.AreEqual(null, proc.StdOut);
Assert.AreEqual(null, proc.StdErr);
Simulations file = FileFormat.ReadFromFile <Simulations>(fileName, out List <Exception> errors);
if (errors != null && errors.Count > 0)
{
throw errors[0];
}
var report = Apsim.Find(file, typeof(Models.Report)) as Models.Report;
string[] variableNames = new[] { "x", "y", "z" };
Assert.AreEqual(variableNames, report.VariableNames);
IModel sim = Apsim.Child(file, typeof(Simulation));
// Use an index-based lookup to locate child models.
// When we replace an entire model, we want to ensure
// that the replacement is inserted at the correct index.
Clock clock = sim.Children[0] as Clock;
Assert.AreEqual(new DateTime(2000, 1, 1), clock.StartDate);
Assert.AreEqual(new DateTime(2000, 1, 10), clock.EndDate);
var weather = sim.Children[3] as Models.Weather;
Assert.NotNull(weather);
Assert.AreEqual("Weather", weather.Name);
Assert.AreEqual("fdsa.met", weather.FileName);
var weather2 = sim.Children[4] as Models.Weather;
Assert.NotNull(weather2);
Assert.AreEqual("Weather2", weather2.Name);
Assert.AreEqual(@".\jkl.met", weather2.FileName);
// Weather3 and Weather4 should have been
// renamed to w1 and w2, respectively.
var weather3 = sim.Children[5] as Models.Weather;
Assert.NotNull(weather3);
Assert.AreEqual("w1", weather3.Name);
Assert.AreEqual("w1.met", weather3.FileName);
var weather4 = sim.Children[6] as Models.Weather;
Assert.NotNull(weather4);
Assert.AreEqual("w2", weather4.Name);
Assert.AreEqual("w2.met", weather4.FileName);
}
