/// <summary>Documents the specified model.</summary>
/// <param name="modelNameToDocument">The model name to document.</param>
/// <param name="tags">The auto doc tags.</param>
/// <param name="headingLevel">The starting heading level.</param>
public void DocumentModel(string modelNameToDocument, List <AutoDocumentation.ITag> tags, int headingLevel)
{
Simulation simulation = Apsim.Find(this, typeof(Simulation)) as Simulation;
if (simulation != null)
{
// Find the model of the right name.
IModel modelToDocument = Apsim.Find(simulation, modelNameToDocument);
// If not found then find a model of the specified type.
if (modelToDocument == null)
{
modelToDocument = Apsim.Get(simulation, "[" + modelNameToDocument + "]") as IModel;
}
// If the simulation has the same name as the model we want to document, dig a bit deeper
if (modelToDocument == simulation)
{
modelToDocument = Apsim.ChildrenRecursivelyVisible(simulation).FirstOrDefault(m => m.Name.Equals(modelNameToDocument, StringComparison.OrdinalIgnoreCase));
}
// If still not found throw an error.
if (modelToDocument != null)
{
// Get the path of the model (relative to parentSimulation) to document so that
// when replacements happen below we will point to the replacement model not the
// one passed into this method.
string pathOfSimulation = Apsim.FullPath(simulation) + ".";
string pathOfModelToDocument = Apsim.FullPath(modelToDocument).Replace(pathOfSimulation, "");
// Clone the simulation
SimulationDescription simDescription = new SimulationDescription(simulation);
Simulation clonedSimulation = simDescription.ToSimulation();
// Now use the path to get the model we want to document.
modelToDocument = Apsim.Get(clonedSimulation, pathOfModelToDocument) as IModel;
if (modelToDocument == null)
{
throw new Exception("Cannot find model to document: " + modelNameToDocument);
}
// resolve all links in cloned simulation.
//Links.Resolve(clonedSimulation, true);
modelToDocument.IncludeInDocumentation = true;
foreach (IModel child in Apsim.ChildrenRecursively(modelToDocument))
{
child.IncludeInDocumentation = true;
}
Links.Resolve(modelToDocument, true, true);
// Document the model.
AutoDocumentation.DocumentModel(modelToDocument, tags, headingLevel, 0, documentAllChildren: true);
// Unresolve links.
Links.Unresolve(clonedSimulation, true);
}
}
}
/// <summary>Gets a list of simulation descriptions.</summary>
public List <SimulationDescription> GenerateSimulationDescriptions()
{
var baseSimulation = Apsim.Child(this, typeof(Simulation)) as Simulation;
// Calculate all combinations.
CalculateFactors();
// Loop through all combinations and add a simulation description to the
// list of simulations descriptions being returned to the caller.
var simulationDescriptions = new List <SimulationDescription>();
int simulationNumber = 1;
foreach (var combination in allCombinations)
{
// Create a simulation.
var simulationName = Name + "Simulation" + simulationNumber;
var simDescription = new SimulationDescription(baseSimulation, simulationName);
simDescription.Descriptors.Add(new SimulationDescription.Descriptor("SimulationName", simulationName));
// Apply each composite factor of this combination to our simulation description.
combination.ForEach(c => c.ApplyToSimulation(simDescription));
// Add simulation description to the return list of descriptions
simulationDescriptions.Add(simDescription);
simulationNumber++;
}
return(simulationDescriptions);
}
/// <summary>Gets a list of simulation descriptions.</summary>
public List <SimulationDescription> GenerateSimulationDescriptions()
{
var baseSimulation = this.FindChild <Simulation>();
// Calculate all combinations.
CalculateFactors();
// Loop through all combinations and add a simulation description to the
// list of simulations descriptions being returned to the caller.
var simulationDescriptions = new List <SimulationDescription>();
int simulationNumber = 1;
foreach (var combination in allCombinations)
{
// Create a simulation.
var simulationName = Name + "Simulation" + simulationNumber;
var simDescription = new SimulationDescription(baseSimulation, simulationName);
// Add some descriptors
int path = (simulationNumber - 1) / (Parameters.Count + 1) + 1;
simDescription.Descriptors.Add(new SimulationDescription.Descriptor("SimulationName", simulationName));
simDescription.Descriptors.Add(new SimulationDescription.Descriptor("Path", path.ToString()));
// Apply each composite factor of this combination to our simulation description.
combination.ForEach(c => c.ApplyToSimulation(simDescription));
// Add simulation description to the return list of descriptions
simulationDescriptions.Add(simDescription);
simulationNumber++;
}
Console.WriteLine($"Simulation names generated by morris:\n{string.Join("\n", simulationDescriptions.Select(s => s.Name))}");
return(simulationDescriptions);
}
public void EnsurePropertyReplacementsWork()
{
var sim = new Simulation()
{
Name = "BaseSimulation",
Children = new List <Model>()
{
new MockWeather()
{
Name = "Weather",
MaxT = 1,
StartDate = DateTime.MinValue
},
}
};
Apsim.ParentAllChildren(sim);
var simulationDescription = new SimulationDescription(sim, "CustomName");
simulationDescription.AddOverride(new PropertyReplacement("Weather.MaxT", 2));
var newSim = simulationDescription.ToSimulation();
var weather = newSim.Children[0] as MockWeather;
Assert.AreEqual(weather.MaxT, 2);
}
/// <summary>Documents the specified model.</summary>
/// <param name="modelNameToDocument">The model name to document.</param>
/// <param name="tags">The auto doc tags.</param>
/// <param name="headingLevel">The starting heading level.</param>
public void DocumentModel(string modelNameToDocument, List <AutoDocumentation.ITag> tags, int headingLevel)
{
Simulation simulation = this.FindInScope <Simulation>();
if (simulation != null)
{
// Find the model of the right name.
IModel modelToDocument = simulation.FindInScope(modelNameToDocument);
// If not found then find a model of the specified type.
if (modelToDocument == null)
{
modelToDocument = simulation.FindByPath("[" + modelNameToDocument + "]")?.Value as IModel;
}
// If the simulation has the same name as the model we want to document, dig a bit deeper
if (modelToDocument == simulation)
{
modelToDocument = simulation.FindAllDescendants().Where(m => !m.IsHidden).ToList().FirstOrDefault(m => m.Name.Equals(modelNameToDocument, StringComparison.OrdinalIgnoreCase));
}
// If still not found throw an error.
if (modelToDocument != null)
{
// Get the path of the model (relative to parentSimulation) to document so that
// when replacements happen below we will point to the replacement model not the
// one passed into this method.
string pathOfSimulation = simulation.FullPath + ".";
string pathOfModelToDocument = modelToDocument.FullPath.Replace(pathOfSimulation, "");
// Clone the simulation
SimulationDescription simDescription = new SimulationDescription(simulation);
Simulation clonedSimulation = simDescription.ToSimulation();
// Prepare the simulation for running - this perform misc cleanup tasks such
// as removing disabled models, standardising the soil, resolving links, etc.
clonedSimulation.Prepare();
FindInScope <IDataStore>().Writer.Stop();
// Now use the path to get the model we want to document.
modelToDocument = clonedSimulation.FindByPath(pathOfModelToDocument)?.Value as IModel;
if (modelToDocument == null)
{
throw new Exception("Cannot find model to document: " + modelNameToDocument);
}
// resolve all links in cloned simulation.
Links.Resolve(clonedSimulation, true);
// Document the model.
AutoDocumentation.DocumentModel(modelToDocument, tags, headingLevel, 0, documentAllChildren: true);
// Unresolve links.
Links.Unresolve(clonedSimulation, true);
}
}
}
/// <summary>
/// Perform the command
/// </summary>
public void Do(CommandHistory commandHistory)
{
Simulation clonedSimulation = null;
IEvent events = null;
try
{
List <Simulation> sims = new List <Models.Core.Simulation>();
var sim = new SimulationDescription(simulation);
sims.Add(sim.ToSimulation(explorerPresenter.ApsimXFile));
events = explorerPresenter.ApsimXFile.GetEventService(clonedSimulation);
events.ConnectEvents();
explorerPresenter.ApsimXFile.Links.Resolve(clonedSimulation);
List <ModelDoc> models = new List <ModelDoc>();
foreach (IModel model in Apsim.ChildrenRecursively(clonedSimulation))
{
ModelDoc newModelDoc = DocumentModel(model);
newModelDoc.Name = Apsim.FullPath(model);
models.Add(newModelDoc);
}
StringWriter rawXML = new StringWriter();
XmlSerializer serialiser = new XmlSerializer(typeof(List <ModelDoc>));
serialiser.Serialize(rawXML, models);
rawXML.Close();
// Load the XSL transform from the resource
Stream s = Assembly.GetExecutingAssembly().GetManifestResourceStream("ApsimNG.Resources.DebugDoc.xsl");
var transform = new XslCompiledTransform();
using (XmlReader reader = XmlReader.Create(s))
{
transform.Load(reader);
}
// Apply the transform to the reader and write it to a temporary file.
string tempFileName = Path.GetTempFileName();
File.Delete(tempFileName);
string htmlFileName = Path.ChangeExtension(tempFileName, ".html");
using (XmlReader reader = XmlReader.Create(new StringReader(rawXML.ToString())))
using (XmlWriter htmlWriter = XmlWriter.Create(htmlFileName))
{
transform.Transform(reader, htmlWriter);
}
Process.Start(htmlFileName);
}
finally
{
if (clonedSimulation != null)
{
events.DisconnectEvents();
explorerPresenter.ApsimXFile.Links.Unresolve(clonedSimulation, allLinks: true);
}
}
}
public void EnsureReplacementsNodeWorks()
{
var simulations = new Simulations()
{
Children = new List <Model>()
{
new Folder()
{
Name = "Replacements",
Children = new List <Model>()
{
new MockWeather()
{
Name = "Weather",
MaxT = 2,
StartDate = DateTime.MinValue
}
}
},
new Simulation()
{
Name = "BaseSimulation",
Children = new List <Model>()
{
new MockWeather()
{
Name = "Weather",
MaxT = 1,
StartDate = DateTime.MinValue
},
}
}
}
};
Apsim.ParentAllChildren(simulations);
var sim = simulations.Children[1] as Simulation;
var simulationDescription = new SimulationDescription(sim);
var newSim = simulationDescription.ToSimulation();
var weather = newSim.Children[0] as MockWeather;
Assert.AreEqual(weather.MaxT, 2);
// Make sure any property overrides happens after a model replacement.
simulationDescription.AddOverride(new PropertyReplacement("Weather.MaxT", 3));
newSim = simulationDescription.ToSimulation();
weather = newSim.Children[0] as MockWeather;
Assert.AreEqual(weather.MaxT, 3);
}
/// <summary>Gets a list of simulation descriptions.</summary>
public IEnumerable <SimulationDescription> GetSimulationDescriptions()
{
// Calculate all combinations.
var allCombinations = CalculateAllCombinations();
if (allCombinations != null)
{
// Find base simulation.
var baseSimulation = this.FindChild <Simulation>();
// Loop through all combinations and add a simulation description to the
// list of simulations descriptions being returned to the caller.
foreach (var combination in allCombinations)
{
// Create a simulation.
var simulationName = GetName(combination);
var simDescription = new SimulationDescription(baseSimulation, simulationName, true);
// Add an experiment descriptor.
simDescription.Descriptors.Add(new SimulationDescription.Descriptor("Experiment", Name));
// Add a simulation descriptor.
simDescription.Descriptors.Add(new SimulationDescription.Descriptor("SimulationName", simulationName));
// Don't need to add a folderName descriptor, as this will be added by the base simulation.
IEnumerable <SimulationDescription> descriptions = baseSimulation?.GenerateSimulationDescriptions();
if (descriptions == null)
{
descriptions = Enumerable.Empty <SimulationDescription>();
}
foreach (var simulationDescriptor in descriptions)
{
foreach (var descriptor in simulationDescriptor.Descriptors)
{
if (descriptor.Name != "SimulationName")
{
simDescription.Descriptors.Add(descriptor);
}
}
}
// Apply each composite factor of this combination to our simulation description.
combination.ForEach(c => c.ApplyToSimulation(simDescription));
// Add simulation description to the return list of descriptions
yield return(simDescription);
}
}
}
public SimulationDescription ToSimulationDescription()
{
var description = new SimulationDescription(null, name);
description.Descriptors.Add(new SimulationDescription.Descriptor(descriptorName1, descriptorValue1));
if (descriptorName2 != null)
{
description.Descriptors.Add(new SimulationDescription.Descriptor(descriptorName2, descriptorValue2));
}
if (descriptorName3 != null)
{
description.Descriptors.Add(new SimulationDescription.Descriptor(descriptorName3, descriptorValue3));
}
return(description);
}
/// <summary>Gets a list of simulation descriptions.</summary>
public List <SimulationDescription> GenerateSimulationDescriptions()
{
var simulationDescriptions = new List <SimulationDescription>();
// Calculate all combinations.
var allCombinations = CalculateAllCombinations();
if (allCombinations != null)
{
// Find base simulation.
var baseSimulation = Apsim.Child(this, typeof(Simulation)) as Simulation;
// Loop through all combinations and add a simulation description to the
// list of simulations descriptions being returned to the caller.
foreach (var combination in allCombinations)
{
// Create a simulation.
var simulationName = GetName(combination);
var simDescription = new SimulationDescription(baseSimulation, simulationName, true);
// Add an experiment descriptor.
simDescription.Descriptors.Add(new SimulationDescription.Descriptor("Experiment", Name));
// Add a simulation descriptor.
simDescription.Descriptors.Add(new SimulationDescription.Descriptor("SimulationName", simulationName));
// Add in simulation descriptors.
foreach (var simulationDescriptor in baseSimulation.GenerateSimulationDescriptions())
{
foreach (var descriptor in simulationDescriptor.Descriptors)
{
if (descriptor.Name != "SimulationName")
{
simDescription.Descriptors.Add(descriptor);
}
}
}
// Apply each composite factor of this combination to our simulation description.
combination.ForEach(c => c.ApplyToSimulation(simDescription));
// Add simulation description to the return list of descriptions
simulationDescriptions.Add(simDescription);
}
}
return(simulationDescriptions);
}
/// <summary>
/// Apply this CompositeFactor to the specified simulation
/// </summary>
/// <param name="simulationDescription">A description of a simulation.</param>
public void ApplyToSimulation(SimulationDescription simulationDescription)
{
ParseAllSpecifications(out List <string> allPaths, out List <object> allValues);
if (allPaths.Count > 1 && allPaths.Count != allValues.Count)
{
throw new Exception("The number of factor paths does not match the number of factor values");
}
// Add a simulation override for each path / value combination.
for (int i = 0; i != allPaths.Count; i++)
{
if (allValues[i] is IModel)
{
simulationDescription.AddOverride(new ModelReplacement(allPaths[i], allValues[i] as IModel));
}
else
{
simulationDescription.AddOverride(new PropertyReplacement(allPaths[i], allValues[i]));
}
}
if (!(Parent is Factors))
{
// Set descriptors in simulation.
string descriptorName = Name;
if (Parent != null)
{
descriptorName = Parent.Name;
}
if (Specifications != null && Specifications.Count > 0)
{
// compound factor value ie. one that has multiple specifications.
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor(descriptorName, Name));
}
else
{
if (allValues[0] is IModel)
{
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor(descriptorName, (allValues[0] as IModel).Name));
}
else
{
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor(descriptorName, allValues[0].ToString()));
}
}
}
}
/// <summary>Gets the next job to run</summary>
public List <SimulationDescription> GenerateSimulationDescriptions()
{
var simulationDescription = new SimulationDescription(this);
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor("SimulationName", Name));
foreach (var zone in Apsim.ChildrenRecursively(this, typeof(Zone)))
{
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor("Zone", zone.Name));
}
return(new List <SimulationDescription>()
{
simulationDescription
});
}
public void EnsureReplacementWithInvalidNameDoesntMatch()
{
var simulations = new Simulations()
{
Children = new List <Model>()
{
new Folder()
{
Name = "Replacements",
Children = new List <Model>()
{
new MockWeather()
{
Name = "Dummy name",
MaxT = 2,
StartDate = DateTime.MinValue
}
}
},
new Simulation()
{
Name = "BaseSimulation",
Children = new List <Model>()
{
new MockWeather()
{
Name = "Weather",
MaxT = 1,
StartDate = DateTime.MinValue
},
}
}
}
};
Apsim.ParentAllChildren(simulations);
var sim = simulations.Children[1] as Simulation;
var simulationDescription = new SimulationDescription(sim);
var newSim = simulationDescription.ToSimulation();
var weather = newSim.Children[0] as MockWeather;
// Name ('Dummy name') didn't match so property should still be 1.
Assert.AreEqual(weather.MaxT, 1);
}
/// <summary>
/// Create and return a list of series definitions for each group by field.
/// </summary>
/// <param name="varyByFieldNames">The vary by fields</param>
/// <param name="checkpointName">Checkpoint name.</param>
/// <param name="colourModifier">Checkpoint colour modifier.</param>
/// <param name="markerModifier">Checkpoint marker size modifier.</param>
/// <param name="simulationDescriptions">The simulation descriptions that are in scope.</param>
/// <param name="whereClauseForInScopeData">An SQL WHERE clause for rows that are in scope.</param>
private List <SeriesDefinition> CreateDefinitionsUsingVaryBy(List <string> varyByFieldNames,
string checkpointName,
double colourModifier,
double markerModifier,
List <SimulationDescription> simulationDescriptions,
string whereClauseForInScopeData)
{
SplitDescriptionsWithSameDescriptors(simulationDescriptions);
var definitions = new List <SeriesDefinition>();
foreach (var simulationDescription in simulationDescriptions)
{
// Determine the descriptors to pass to the new definition that will
// be created below. We only want to pass the 'vary by' descriptors.
var descriptorsForDefinition = new List <SimulationDescription.Descriptor>();
foreach (var descriptor in simulationDescription.Descriptors)
{
if (varyByFieldNames.Contains(descriptor.Name))
{
descriptorsForDefinition.Add(descriptor);
}
}
// Try and find a definition that has the same descriptors.
var foundDefinition = definitions.Find(d => SimulationDescription.Equals(d.Descriptors, descriptorsForDefinition));
// Only create a definition if there are descriptors and there isn't
// already a definition with the same descriptors.
if (descriptorsForDefinition.Count > 0 && foundDefinition == null)
{
// Create the definition.
definitions.Add(new SeriesDefinition(this,
checkpointName,
colourModifier,
markerModifier,
whereClauseForInScopeData,
Filter,
descriptorsForDefinition));
}
}
return(definitions);
}
public void EnsureModelOverrideWork()
{
var sim = new Simulation()
{
Name = "BaseSimulation",
Children = new List <Model>()
{
new MockWeather()
{
Name = "Weather",
MaxT = 1,
StartDate = DateTime.MinValue
},
}
};
Apsim.ParentAllChildren(sim);
var replacementWeather = new MockWeather()
{
Name = "Weather2",
MaxT = 2,
StartDate = DateTime.MinValue
};
var simulationDescription = new SimulationDescription(sim, "CustomName");
simulationDescription.AddOverride(new ModelReplacement("Weather", replacementWeather));
var newSim = simulationDescription.ToSimulation();
Assert.AreEqual(newSim.Name, "CustomName");
var weather = newSim.Children[0] as MockWeather;
Assert.AreEqual(weather.MaxT, 2);
// The name of the new model should be the same as the original model.
Assert.AreEqual(weather.Name, "Weather");
}
/// <summary>Gets the next job to run</summary>
public List <SimulationDescription> GenerateSimulationDescriptions()
{
var simulationDescription = new SimulationDescription(this);
// Add a folderName descriptor.
var folderNode = Apsim.Parent(this, typeof(Folder));
if (folderNode != null)
{
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor("FolderName", folderNode.Name));
}
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor("SimulationName", Name));
foreach (var zone in Apsim.ChildrenRecursively(this, typeof(Zone)))
{
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor("Zone", zone.Name));
}
return(new List <SimulationDescription>()
{
simulationDescription
});
}
/// <summary>Gets the next job to run</summary>
public List <SimulationDescription> GenerateSimulationDescriptions()
{
var simulationDescription = new SimulationDescription(this);
// Add a folderName descriptor.
var folderNode = FindAncestor <Folder>();
if (folderNode != null)
{
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor("FolderName", folderNode.Name));
}
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor("SimulationName", Name));
foreach (var zone in this.FindAllDescendants <Zone>())
{
simulationDescription.Descriptors.Add(new SimulationDescription.Descriptor("Zone", zone.Name));
}
return(new List <SimulationDescription>()
{
simulationDescription
});
}
public void EnsureSoilIsStandardised()
{
var sim = new Simulation()
{
Name = "Simulation",
Children = new List <Model>()
{
new Soil
{
Children = new List <Model>()
{
new Physical()
{
Thickness = new double[] { 100, 300, 300 },
BD = new double[] { 1.36, 1.216, 1.24 },
AirDry = new double[] { 0.135, 0.214, 0.261 },
LL15 = new double[] { 0.27, 0.267, 0.261 },
DUL = new double[] { 0.365, 0.461, 0.43 },
SAT = new double[] { 0.400, 0.481, 0.45 },
Children = new List <Model>()
{
new SoilCrop
{
Name = "Wheat",
KL = new double[] { 0.06, 0.060, 0.060 },
LL = new double[] { 0.27, 0.267, 0.261 }
}
}
},
new SoilWater(),
new Organic
{
Thickness = new double[] { 100, 300 },
Carbon = new double[] { 2, 1 }
},
new Chemical
{
Thickness = new double[] { 100, 200 },
CL = new double[] { 38, double.NaN }
},
new Sample
{
Thickness = new double[] { 500 },
SW = new double[] { 0.103 },
OC = new double[] { 1.35 },
SWUnits = Sample.SWUnitsEnum.Gravimetric
},
new Sample
{
Thickness = new double[] { 1000 },
NO3N = new double[] { 27 },
OC = new double[] { 1.35 },
SWUnits = Sample.SWUnitsEnum.Volumetric
},
new CERESSoilTemperature(),
}
}
}
};
Apsim.ParentAllChildren(sim);
var originalSoil = sim.Children[0] as Soil;
var originalWater = originalSoil.Children[0] as Physical;
originalSoil.OnCreated();
var simulationDescription = new SimulationDescription(sim);
var newSim = simulationDescription.ToSimulation();
var water = newSim.Children[0].Children[0] as Physical;
var soilOrganicMatter = newSim.Children[0].Children[2] as Organic;
var sample = newSim.Children[0].Children[4] as Sample;
// Make sure layer structures have been standardised.
Assert.AreEqual(water.Thickness, originalWater.Thickness);
Assert.AreEqual(soilOrganicMatter.Thickness, originalWater.Thickness);
Assert.AreEqual(sample.Thickness, originalWater.Thickness);
// Make sure sample units are volumetric.
Assert.AreEqual(sample.SWUnits, Sample.SWUnitsEnum.Volumetric);
}
