public void TestSerializationEvent()
{
Event x1 = CreateObject <Event>().WithName("Eve").WithDimension(DimensionLength);
x1.Formula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(1.0);
x1.ParentContainer = C0;
EventAssignment ea1 = CreateObject <EventAssignment>().WithName("Eva").WithDimension(DimensionLength);
ea1.UseAsValue = true;
ea1.Formula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(23.4);
ea1.ObjectPath = ObjectPathFactory.CreateAbsoluteObjectPath(P);
x1.AddAssignment(ea1);
ea1.ResolveChangedEntity();
IEvent x2 = SerializeAndDeserialize(x1);
x2.ParentContainer = C0;
var refResolver = new ReferencesResolver();
refResolver.ResolveReferencesIn(x2);
AssertForSpecs.AreEqualEvent(x2, x1);
}
/// <summary>
/// Copy the references for first and second Neighbor from <paramref name="sourcecNeighborhoodBuilder" /> to
/// <paramref name="targetNeighborhoodBuilder" />.
/// </summary>
/// <param name="sourcecNeighborhoodBuilder">The source neighborhood builder to copy neighbors from.</param>
/// <param name="targetNeighborhoodBuilder">The neighborhood builder to copy neighbors to.</param>
private void updateNeighborsReferences(INeighborhoodBuilder sourcecNeighborhoodBuilder, INeighborhoodBuilder targetNeighborhoodBuilder)
{
var objectPathFactory = new ObjectPathFactory(new AliasCreator());
var firstPath = objectPathFactory.CreateAbsoluteObjectPath(sourcecNeighborhoodBuilder.FirstNeighbor);
var secondPath = objectPathFactory.CreateAbsoluteObjectPath(sourcecNeighborhoodBuilder.SecondNeighbor);
foreach (var topContainer in TopContainers)
{
var firstNeighbor = firstPath.Resolve <IContainer>(topContainer);
var secondNeighbor = secondPath.Resolve <IContainer>(topContainer);
if (firstNeighbor != null)
{
targetNeighborhoodBuilder.FirstNeighbor = firstNeighbor;
}
if (secondNeighbor != null)
{
targetNeighborhoodBuilder.SecondNeighbor = secondNeighbor;
}
//both neighbors set. early exit
if (targetNeighborhoodBuilder.FirstNeighbor != null && targetNeighborhoodBuilder.SecondNeighbor != null)
{
return;
}
}
}
public void TestSerializationQuantityWithExplicitFormula()
{
Observer x1 = CreateObject <Observer>().WithName("Quentin").WithDimension(DimensionLength);
x1.ParentContainer = C1;
x1.IsFixedValue = false;
x1.Persistable = false;
x1.Formula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(23.4);
ExplicitFormula f1 = CreateObject <ExplicitFormula>().WithName("Fortunato").WithDimension(DimensionLength);
f1.AddObjectPath(ObjectPathFactory.CreateAbsoluteFormulaUsablePath(P1));
f1.AddObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P0));
f1.AddObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P2).WithAlias("Pitter"));
f1.ResolveObjectPathsFor(P);
f1.FormulaString = "Paul + Peter + Pitter";
P1.Value = 1.0;
P0.Value = 10.0;
P2.Value = 2.0;
x1.Formula = f1;
IQuantity x2 = SerializeAndDeserialize(x1);
x2.ParentContainer = C1;
x2.Formula.ResolveObjectPathsFor(x2);
AssertForSpecs.AreEqualQuantity(x2, x1);
}
/// <summary>
/// Sets all the autogenerated Molecule Start Values to the right values and updates their
/// "IsPresent" property.
/// </summary>
private void SetMoleculeStartValues(Model model)
{
foreach (var molInfo in _sbmlInformation.MoleculeInformation)
{
foreach (var msv in _moleculeStartValuesBuildingBlock)
{
if (msv.Name != molInfo.GetMoleculeBuilderName())
{
continue;
}
if (molInfo.GetContainer().Any(x => x.Name == msv.ContainerPath.LastOrDefault()))
{
msv.IsPresent = true;
msv.NegativeValuesAllowed = true;
var sbmlSpecies = molInfo.GetSpeciesIfOne();
if (sbmlSpecies == null)
{
return;
}
var sbmlUnit = GetUnit(sbmlSpecies, model);
var amountDimension = _unitDefinitionImporter.DimensionFor(sbmlUnit);
//unit is set by the Unit of SubstanceUnit
if (sbmlSpecies.isSetInitialAmount())
{
msv.StartValue = sbmlSpecies.getInitialAmount();
if (amountDimension != null)
{
msv.Dimension = amountDimension;
molInfo.SetDimension(amountDimension);
}
}
if (!sbmlSpecies.isSetInitialConcentration())
{
continue;
}
//unit is {unit of amount}/{unit of size}
var baseValue = _unitDefinitionImporter.ToMobiBaseUnit(sbmlUnit, sbmlSpecies.getInitialConcentration());
msv.StartValue = baseValue.value;
msv.Formula = _context.Create <ExplicitFormula>($"{msv.Name}_0").WithName($"{msv.Name}_0").WithDimension(amountDimension).WithFormulaString($"{baseValue.value} * {Constants.VOLUME_ALIAS}");
msv.Formula.AddObjectPath(
ObjectPathFactory.CreateFormulaUsablePathFrom(ObjectPath.PARENT_CONTAINER, Constants.Parameters.VOLUME)
.WithAlias(Constants.VOLUME_ALIAS)
.WithDimension(_moBiDimensionFactory.Dimension(Constants.Dimension.VOLUME))
);
_moleculeStartValuesBuildingBlock.AddFormula(msv.Formula);
msv.Dimension = amountDimension;
molInfo.SetDimension(amountDimension);
UseConcentrations = true;
}
else
{
msv.IsPresent = false;
msv.StartValue = 0;
}
}
}
}
protected override void Context()
{
_pathFactory = new ObjectPathFactory(new AliasCreator());
_userSettings = A.Fake <IUserSettings>();
_userSettings.CheckDimensions = true;
_buildConfiguration = A.Fake <IBuildConfiguration>();
A.CallTo(() => _buildConfiguration.BuilderFor(A <IObjectBase> ._)).ReturnsLazily(x => x.GetArgument <IObjectBase>(0));
sut = new DimensionValidator(new DimensionParser(), _pathFactory, _userSettings);
}
protected override void Context()
{
_organ = new Container().WithName("organ");
var comp = new Container().WithName("comp").WithParentContainer(_organ);
_parameter = new Parameter().WithName("P1").WithParentContainer(comp);
var objectPathFactory = new ObjectPathFactory(new AliasCreator());
sut = objectPathFactory.CreateAbsoluteFormulaUsablePath(_parameter);
}
public void TestSerializationTableFormulaWithArgument()
{
var x1 = CreateObject <TableFormulaWithXArgument>().WithName("Fortunato").WithDimension(DimensionLength);
x1.AddTableObjectPath(ObjectPathFactory.CreateAbsoluteFormulaUsablePath(P1));
x1.AddXArgumentObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P0));
var x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualTableFormulaWithArgument(x2, x1);
}
protected override void Context()
{
_topContainer = new Container().WithName("top");
_organ = new Container().WithName("organ").WithParentContainer(_topContainer);
_comp = new Container().WithName("comp").WithParentContainer(_organ);
_parameter = new DistributedParameter().WithName("P1").WithParentContainer(_comp);
new Parameter().WithName("LALA").WithParentContainer(_parameter);
_reak = A.Fake <IUsingFormula>();
A.CallTo(() => _reak.ParentContainer).Returns(_topContainer);
A.CallTo(() => _reak.RootContainer).Returns(_topContainer);
sut = new ObjectPathFactory(new AliasCreator());
}
public void TestSerializationFormulaWithObjectPathsWithoutObjectReferences()
{
ExplicitFormula x1 = CreateObject <ExplicitFormula>().WithName("Fortunato").WithDimension(DimensionLength);
x1.AddObjectPath(ObjectPathFactory.CreateAbsoluteFormulaUsablePath(P1));
x1.AddObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P0));
x1.AddObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P2).WithAlias("Pitter"));
IFormula x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualFormula(x2, x1);
}
public void TestSerialization()
{
ConstantFormula x1 = CreateObject <ConstantFormula>().WithName("Fortunato").WithDimension(DimensionLength).WithValue(5.3);
x1.AddObjectPath(ObjectPathFactory.CreateAbsoluteFormulaUsablePath(P1));
x1.AddObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P0));
x1.AddObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P2).WithAlias("Pitter"));
x1.ResolveObjectPathsFor(P);
ConstantFormula x2 = SerializeAndDeserialize(x1);
x2.ResolveObjectPathsFor(P);
AssertForSpecs.AreEqualConstantFormula(x2, x1);
}
public void TestSerialization()
{
ExplicitFormula x1 = CreateObject <ExplicitFormula>().WithName("Fortunato").WithDimension(DimensionLength);
x1.AddObjectPath(ObjectPathFactory.CreateAbsoluteFormulaUsablePath(P1));
x1.AddObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P0));
x1.AddObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P2).WithAlias("Pitter"));
x1.ResolveObjectPathsFor(P);
x1.FormulaString = "1.1 + 2.2";
ExplicitFormula x2 = SerializeAndDeserialize(x1);
x2.ResolveObjectPathsFor(P);
AssertForSpecs.AreEqualExplicitFormula(x2, x1);
}
public void TestSerializationWithDependencies()
{
ExplicitFormula x1 = CreateObject <ExplicitFormula>().WithName("Fortunato").WithDimension(DimensionLength);
x1.AddObjectPath(ObjectPathFactory.CreateAbsoluteFormulaUsablePath(P1));
x1.AddObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P0));
x1.AddObjectPath(ObjectPathFactory.CreateRelativeFormulaUsablePath(P, P2).WithAlias("Pitter"));
x1.ResolveObjectPathsFor(P);
x1.FormulaString = "Paul + Peter + Pitter";
P1.Value = 1.0;
P0.Value = 10.0;
P2.Value = 2.0;
ExplicitFormula x2 = SerializeAndDeserialize(x1);
x2.ResolveObjectPathsFor(P);
AssertForSpecs.AreEqualExplicitFormula(x2, x1);
}
protected override void Context()
{
sut = new DistributedParameter();
var pathFactory = new ObjectPathFactory(new AliasCreator());
_meanParameter = new Parameter {
Name = Constants.Distribution.MEAN
}.WithFormula(new ExplicitFormula("0"));
_stdParameter = new Parameter {
Name = Constants.Distribution.DEVIATION
}.WithFormula(new ExplicitFormula("1"));
_percentileParameter = new Parameter {
Name = Constants.Distribution.PERCENTILE
}.WithFormula(new ExplicitFormula("0.5"));
sut.Add(_meanParameter);
sut.Add(_stdParameter);
sut.Add(_percentileParameter);
sut.Formula = new NormalDistributionFormula();
sut.Formula.AddObjectPath(pathFactory.CreateRelativeFormulaUsablePath(sut, _meanParameter));
sut.Formula.AddObjectPath(pathFactory.CreateRelativeFormulaUsablePath(sut, _stdParameter));
sut.Formula.ResolveObjectPathsFor(sut);
}
protected override void Context()
{
base.Context();
var pathFactory = new ObjectPathFactory(new AliasCreator());
_distributedParameter = new DistributedParameter();
var meanParameter = new Parameter {
Name = Constants.Distribution.MEAN
}.WithFormula(new ExplicitFormula("0"));
var stdParameter = new Parameter {
Name = Constants.Distribution.DEVIATION
}.WithFormula(new ExplicitFormula("1"));
var percentileParameter = new Parameter {
Name = Constants.Distribution.PERCENTILE
}.WithFormula(new ExplicitFormula("0.7"));
_distributedParameter.Add(meanParameter);
_distributedParameter.Add(stdParameter);
_distributedParameter.Add(percentileParameter);
_distributedParameter.Formula = new NormalDistributionFormula();
_distributedParameter.Formula.AddObjectPath(pathFactory.CreateRelativeFormulaUsablePath(_distributedParameter, meanParameter));
_distributedParameter.Formula.AddObjectPath(pathFactory.CreateRelativeFormulaUsablePath(_distributedParameter, stdParameter));
}
/// <summary>
/// Gets the path to a Container by a given compartment id.
/// </summary>
protected internal IObjectPath GetPathToContainerOfCompartmentId(string compartmentId)
{
return((from container in GetMainTopContainer().Children where container.Name == compartmentId select ObjectPathFactory.CreateAbsoluteObjectPath(container)).FirstOrDefault());
}
public MolWeightDimensionConverterForFormulaUsable(IDimension sourceDimension, IDimension targetDimension) : base(sourceDimension, targetDimension)
{
_pathFactory = new ObjectPathFactory(new AliasCreator());
}
public ExcelRequestContext(string url)
: base(url)
{
m_workbook = new Workbook(this, ObjectPathFactory._CreateGlobalObjectObjectPath(this));
this._RootObject = m_workbook;
}
