protected override void Context()
{
base.Context();
_species = A.Fake <Species>();
_defaultPopulation = new SpeciesPopulation().WithName("POP");
A.CallTo(() => _species.DefaultPopulation).Returns(_defaultPopulation);
var individualSettingsDTO = new IndividualSettingsDTO();
A.CallTo(() => _individualDefaultValueRetriever.DefaultSettingFor(_defaultPopulation)).Returns(individualSettingsDTO);
var originData = new OriginData();
A.CallTo(() => _insividualSettingsMapper.MapFrom(individualSettingsDTO)).Returns(originData);
_individual = new Individual();
A.CallTo(() => _individualFactory.CreateStandardFor(originData)).Returns(_individual);
}
protected override void Context()
{
base.Context();
_originData = new OriginData {
Species = A.Fake <Species>().WithName("toto"), SpeciesPopulation = A.Fake <SpeciesPopulation>()
};
_individual = new Individual();
_invalidResults = A.Fake <ValidationResult>();
A.CallTo(() => _invalidResults.ValidationState).Returns(ValidationState.Invalid);
_organism = A.Fake <Organism>();
_neighborhoods = A.Fake <IContainer>();
_rootContainer = new RootContainer();
A.CallTo(() => _entityBaseFactory.Create <IRootContainer>()).Returns(_rootContainer);
A.CallTo(() => _entityBaseFactory.Create <Individual>()).Returns(_individual);
A.CallTo(() => _entityBaseFactory.Create <Organism>()).Returns(_organism);
A.CallTo(() => _entityBaseFactory.Create <IContainer>()).Returns(_neighborhoods);
A.CallTo(() => _entityValidator.Validate(_individual)).Returns(_invalidResults);
}
private void MainForm_Load(object sender, EventArgs e)
{
if (File.Exists(Properties.Resources.path))
{
try
{
FileStream fs = new FileStream(Properties.Resources.path, FileMode.Open);
BinaryFormatter bf = new BinaryFormatter();
oData = bf.Deserialize(fs) as OriginData;
LoadOriginDataToData();
fs.Close();
}
catch (Exception)
{
MessageBox.Show("读取数据发生了错误。\n如果您是首次使用，请删除文件Thing3.dat后重试");
}
}
}
protected override void Context()
{
base.Context();
var previousSubject = A.Fake <ISimulationSubject>();
var previousOriginData = new OriginData {
SpeciesPopulation = A.Fake <SpeciesPopulation>()
};
previousOriginData.SpeciesPopulation.IsAgeDependent = true;
A.CallTo(() => previousSubject.IsPreterm).Returns(true);
A.CallTo(() => previousSubject.OriginData).Returns(previousOriginData);
_subject.OriginData.SpeciesPopulation.IsAgeDependent = true;
A.CallTo(() => _subject.IsPreterm).Returns(false);
sut.UpdateSelectedSubject(previousSubject);
}
protected override void Context()
{
base.Context();
_originData = new OriginData
{
Age = new OriginDataParameter(5),
Species = A.Fake <Species>().WithName("toto"),
Population = A.Fake <SpeciesPopulation>(),
Weight = new OriginDataParameter()
};
_individual = new Individual();
_validationResult = new ValidationResult();
_diseaseStateImplementation = A.Fake <IDiseaseStateImplementation>();
A.CallTo(() => _diseaseStateImplementation.Validate(_originData)).Throws <OSPSuiteException>();
A.CallTo(() => _entityBaseFactory.Create <Individual>()).Returns(_individual);
A.CallTo(() => _entityValidator.Validate(_individual)).Returns(_validationResult);
A.CallTo(() => _diseaseStateImplementationRepository.CreateFor(_individual)).Returns(_diseaseStateImplementation);
}
protected override void Context()
{
_parameterQuery = A.Fake <IParameterQuery>();
_parameterFactory = A.Fake <IParameterFactory>();
_originData = new OriginData();
_param1 = A.Fake <IParameter>();
_param1.Name = "param1";
var paramDef1 = new ParameterValueMetaData
{
BuildingBlockType = PKSimBuildingBlockType.Individual
};
_param2 = A.Fake <IParameter>();
_param2.Name = "param2";
var paramDef2 = new ParameterValueMetaData
{
BuildingBlockType = PKSimBuildingBlockType.Individual
};
_param3 = A.Fake <IParameter>();
_param3.Name = "param3";
var paramDef3 = new ParameterValueMetaData
{
BuildingBlockType = PKSimBuildingBlockType.Compound
};
_valueDefinitions.Add(paramDef1);
_valueDefinitions.Add(paramDef2);
var paramRateDef1 = new ParameterRateMetaData();
paramDef3.BuildingBlockType = PKSimBuildingBlockType.Individual;
_rateDefinitions.Add(paramRateDef1);
_paramRate1 = new PKSimParameter().WithFormula(new ExplicitFormula("a formula"));
_paramRate1.Name = "RateParameter";
A.CallTo(_parameterQuery).WithReturnType <IEnumerable <ParameterValueMetaData> >().Returns(_valueDefinitions);
A.CallTo(_parameterQuery).WithReturnType <IEnumerable <ParameterDistributionMetaData> >().Returns(_distributionDefinitions);
A.CallTo(_parameterQuery).WithReturnType <IEnumerable <ParameterRateMetaData> >().Returns(_rateDefinitions);
A.CallTo(() => _parameterFactory.CreateFor(paramDef1)).Returns(_param1);
A.CallTo(() => _parameterFactory.CreateFor(paramDef2)).Returns(_param2);
A.CallTo(() => _parameterFactory.CreateFor(paramRateDef1, A <FormulaCache> ._)).Returns(_paramRate1);
sut = new ParameterContainerTask(_parameterQuery, _parameterFactory);
}
public IParameter BMIBasedOn(OriginData originData, IParameter parameterWeight, IParameter parameterHeight)
{
var standardBMI = MeanOrganismParameter(originData, CoreConstants.Parameters.BMI);
if (standardBMI == null)
{
return(null);
}
var organism = new Container().WithName(Constants.ORGANISM);
organism.Add(parameterHeight);
organism.Add(parameterWeight);
organism.Add(standardBMI);
standardBMI.Formula = _formulaFactory.BMIFormulaFor(parameterWeight, parameterHeight);
standardBMI.Formula.ResolveObjectPathsFor(standardBMI);
return(standardBMI);
}
protected override void Context()
{
base.Context();
_originData = new OriginData {
Species = new Species {
Name = "A", Icon = "B"
}, SpeciesPopulation = A.Fake <SpeciesPopulation>()
};
_individual = new Individual();
_organism = new Organism();
_neighborhoods = A.Fake <IContainer>();
_rootContainer = new RootContainer();
A.CallTo(() => _entityBaseFactory.Create <IRootContainer>()).Returns(_rootContainer);
A.CallTo(() => _entityBaseFactory.Create <Individual>()).Returns(_individual);
A.CallTo(() => _entityBaseFactory.Create <Organism>()).Returns(_organism);
A.CallTo(() => _entityBaseFactory.Create <IContainer>()).Returns(_neighborhoods);
_valueOrigin = new ValueOrigin {
Method = ValueOriginDeterminationMethods.InVitro, Source = ValueOriginSources.Database
};
_originData.UpdateValueOriginFrom(_valueOrigin);
_originData.Age = 10;
_originData.AgeUnit = _age.DisplayUnit.Name;
_organism.Add(_age);
_originData.GestationalAge = 40;
_originData.GestationalAgeUnit = _gestationalAge.DisplayUnit.Name;
_organism.Add(_gestationalAge);
_originData.Height = 170;
_originData.HeightUnit = _height.DisplayUnit.Name;
_organism.Add(_height);
_originData.Weight = 170;
_originData.WeightUnit = _weight.DisplayUnit.Name;
_organism.Add(_weight);
_originData.BMI = 170;
_originData.BMIUnit = _bmi.DisplayUnit.Name;
_organism.Add(_bmi);
}
private static bool needScaling(OriginData originData, IParameter individualParameter)
{
if (!originData.Population.IsHeightDependent)
{
return(false);
}
if (!individualParameter.IsNamed(Constants.Parameters.VOLUME))
{
return(false);
}
if (!individualParameter.ParentContainer.IsAnImplementationOf <Organ>())
{
return(false);
}
//Volume in organ
return(true);
}
public void EditModelConfiguration(ISimulationSubject selectedSubject)
{
if (selectedSubject == null)
{
return;
}
_originData = selectedSubject.OriginData;
ModelProperties modelProperties;
if (selectedModelConfiguration != null)
{
modelProperties = _modelPropertiesTask.DefaultFor(_originData, selectedModelConfiguration.ModelName);
}
else
{
modelProperties = _modelPropertiesTask.DefaultFor(_originData);
}
editModelProperties(modelProperties);
}
protected override void Context()
{
base.Context();
_discreteDistribution1 = new ParameterDistributionMetaData {
Age = 20, Mean = 5
};
_discreteDistribution2 = new ParameterDistributionMetaData {
Age = 10, Mean = 15
};
_discreteDistributions = new List <ParameterDistributionMetaData> {
_discreteDistribution1, _discreteDistribution2
};
_parameter = A.Fake <IDistributedParameter>();
var meanParameter = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("Mean");
A.CallTo(() => _parameter.MeanParameter).Returns(meanParameter);
_originData = new OriginData {
Age = 12
};
A.CallTo(() => _distrFormulaFactory.CreateDiscreteDistributionFormulaFor(_parameter, meanParameter)).Returns(new DiscreteDistributionFormula());
}
public OriginData MapFrom(IndividualSettingsDTO individualSettingsDTO)
{
var originData = new OriginData
{
Species = individualSettingsDTO.Species,
Population = individualSettingsDTO.Population,
Gender = individualSettingsDTO.Gender,
SubPopulation = subPopulationFrom(individualSettingsDTO.SubPopulation),
Age = originDataParameterFrom(individualSettingsDTO.ParameterAge),
GestationalAge = originDataParameterFrom(individualSettingsDTO.ParameterGestationalAge),
Height = originDataParameterFrom(individualSettingsDTO.ParameterHeight),
Weight = originDataParameterFrom(individualSettingsDTO.ParameterWeight),
BMI = originDataParameterFrom(individualSettingsDTO.ParameterBMI)
};
updateDiseaseState(originData, individualSettingsDTO);
originData.UpdateValueOriginFrom(individualSettingsDTO.ValueOrigin);
individualSettingsDTO.CalculationMethods.Select(cm => cm.CalculationMethod).Each(originData.AddCalculationMethod);
return(originData);
}
private void updateDiseaseState(OriginData originData, IndividualSettingsDTO individualSettingsDTO)
{
var diseaseState = individualSettingsDTO.DiseaseState;
var isHealthy = diseaseState.IsHealthy;
if (isHealthy)
{
originData.DiseaseState = null;
return;
}
originData.DiseaseState = diseaseState;
var diseaseStateParameter = individualSettingsDTO.DiseaseStateParameter;
//This is a disease state without parameters
if (diseaseStateParameter.IsNull())
{
return;
}
//disease parameters are saved in a collection and we need to save the name to differentiate them
originData.AddDiseaseStateParameter(originDataParameterFrom(diseaseStateParameter, addName: true));
}
protected override void Context()
{
_simulationPresenter = A.Fake <ICreateSimulationPresenter>();
_view = A.Fake <ISimulationSubjectConfigurationView>();
_simulationFactory = A.Fake <ISimulationFactory>();
_buildingBlockInSimulationManager = A.Fake <IBuildingBlockInSimulationManager>();
_simulation = A.Fake <Simulation>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
sut = new SimulationSubjectConfigurationPresenter(_view, _lazyLoadTask, _buildingBlockInSimulationManager);
A.CallTo(() => _view.BindTo(A <SimulationSubjectDTO> ._))
.Invokes(x => _simulationSubjectDTO = x.GetArgument <SimulationSubjectDTO>(0));
sut.InitializeWith(_simulationPresenter);
_subject = A.Fake <ISimulationSubject>();
var originData = new OriginData {
SpeciesPopulation = A.Fake <SpeciesPopulation>()
};
A.CallTo(() => _subject.OriginData).Returns(originData);
sut.Initialize();
}
protected override void Context()
{
_compartment = A.Fake <Compartment>();
A.CallTo(() => _compartment.OrganName).Returns("MyParentOrgan");
_compartment.Name = "MyComp";
var containerPath = new ObjectPath(new[] { _compartment.OrganName, _compartment.Name }).ToString();
_containerPathRetriever = A.Fake <IEntityPathResolver>();
A.CallTo(() => _containerPathRetriever.PathFor(_compartment)).Returns(containerPath);
_originData = new OriginData();
_originData.Population = new SpeciesPopulation();
var distributionDefinition = new ParameterDistributionMetaData();
var rateDefinition = new ParameterRateMetaData();
var valueDefinition = new ParameterValueMetaData();
distributionDefinition.ParameterName = "tutu";
var distributionRepository = A.Fake <IParameterDistributionRepository>();
A.CallTo(() => distributionRepository.AllFor(containerPath)).Returns(new List <ParameterDistributionMetaData> {
distributionDefinition
});
var rateRepository = A.Fake <IParameterRateRepository>();
A.CallTo(() => rateRepository.AllFor(containerPath)).Returns(new List <ParameterRateMetaData> {
rateDefinition
});
var valueRepository = A.Fake <IParameterValueRepository>();
A.CallTo(() => valueRepository.AllFor(containerPath)).Returns(new List <ParameterValueMetaData> {
valueDefinition
});
sut = new ParameterQuery(distributionRepository, valueRepository, rateRepository, _containerPathRetriever);
}
public OriginData MapFrom(IndividualSettingsDTO individualSettingsDTO)
{
var originData = new OriginData
{
Species = individualSettingsDTO.Species,
SpeciesPopulation = individualSettingsDTO.SpeciesPopulation,
Gender = individualSettingsDTO.Gender,
SubPopulation = subPopulationFrom(individualSettingsDTO.SubPopulation),
Age = individualSettingsDTO.ParameterAge.KernelValue,
AgeUnit = displayUnit(individualSettingsDTO.ParameterAge),
GestationalAge = individualSettingsDTO.ParameterGestationalAge.KernelValue,
GestationalAgeUnit = displayUnit(individualSettingsDTO.ParameterGestationalAge),
Height = individualSettingsDTO.ParameterHeight.KernelValue,
HeightUnit = displayUnit(individualSettingsDTO.ParameterHeight),
Weight = individualSettingsDTO.ParameterWeight.KernelValue,
WeightUnit = displayUnit(individualSettingsDTO.ParameterWeight),
BMI = individualSettingsDTO.ParameterBMI.KernelValue,
BMIUnit = displayUnit(individualSettingsDTO.ParameterBMI),
};
individualSettingsDTO.CalculationMethods.Select(cm => cm.CalculationMethod).Each(originData.AddCalculationMethod);
return(originData);
}
private Ontogeny forMolecule(OriginData originData, string molecule)
{
return(allFor(originData.Species.Name).FindByName(molecule) ?? new NullOntogeny());
}
public IParameter MeanHeightFor(OriginData originData)
{
return(MeanOrganismParameter(originData, CoreConstants.Parameters.MEAN_HEIGHT));
}
private double percentileFrom(IEnumerable <ParameterDistributionMetaData> allDistributionsForParameter, OriginData originData, double parameterValue)
{
var parameter = _parameterFactory.CreateFor(allDistributionsForParameter, originData);
parameter.Value = parameterValue;
return(parameter.Percentile);
}
private double postmenstrualAgeInYearsFor(OriginData originData)
{
return(postmenstrualAgeInYearsFor(originData.Age, originData.GestationalAge));
}
public double OntogenyFactorFor(Ontogeny ontogeny, string containerName, OriginData originData, RandomGenerator randomGenerator = null)
{
return(OntogenyFactorFor(ontogeny, containerName, originData.Age, originData.GestationalAge, randomGenerator));
}
private DistributedParameterValue distributedOntogenyFactorFor(Ontogeny ontogeny, string moleculeName, OriginData originData, string parameterName, string ontogenyLocation)
{
var parameterPath = new ObjectPath {
moleculeName, parameterName
};
var(mean, std, distributionType) = _ontogenyRepository.OntogenyParameterDistributionFor(ontogeny, originData, ontogenyLocation);
return(new DistributedParameterValue(parameterPath, mean, CoreConstants.DEFAULT_PERCENTILE, mean, std, distributionType));
}
public IReadOnlyList <Sample> AllPlasmaProteinOntogenyFactorForStrictBiggerThanPMA(string parameterName, OriginData originData, RandomGenerator randomGenerator = null)
{
return(AllOntogenyFactorForStrictBiggerThanPMA(forMolecule(originData, SupportedProteins[parameterName]), originData, CoreConstants.Groups.ONTOGENY_PLASMA, randomGenerator));
}
public void EditSimulation(Simulation simulation, CreationMode creationMode)
{
_originData = simulation.BuildingBlock <ISimulationSubject>().OriginData;
editModelProperties(simulation.ModelProperties);
}
public double PlasmaProteinOntogenyFactor(string protein, OriginData originData, RandomGenerator randomGenerator = null)
{
return(PlasmaProteinOntogenyFactor(protein, originData.Age, originData.GestationalAge, originData.Species.Name, randomGenerator));
}
private ParameterValue ontogenyFactorFor(Ontogeny ontogeny, string moleculeName, OriginData originData, string parameterName, string ontogenyLocation)
{
var path = new ObjectPath {
moleculeName, parameterName
};
double factor = _ontogenyRepository.OntogenyFactorFor(ontogeny, ontogenyLocation, originData);
return(new ParameterValue(path, factor, CoreConstants.DEFAULT_PERCENTILE));
}
public void AddModelParametersTo <TContainer>(TContainer parameterContainer, OriginData originData, ModelProperties modelProperties, IFormulaCache formulaCache) where TContainer : IContainer
{
addParametersTo(parameterContainer, originData, modelProperties.AllCalculationMethods().Select(cm => cm.Name), param => true, formulaCache);
}
private void addParametersTo <T>(T parameterContainer, OriginData originData, IEnumerable <string> calculationMethods) where T : IContainer
{
addParametersTo(parameterContainer, originData, calculationMethods, x => true);
}
public void AddInvididualParametersTo <TContainer>(TContainer parameterContainer, OriginData originData, string parameterName) where TContainer : IContainer
{
addParametersTo(parameterContainer, originData, originData.AllCalculationMethods().Select(cm => cm.Name),
param => param.BuildingBlockType == PKSimBuildingBlockType.Individual && string.Equals(param.ParameterName, parameterName));
}
public IReadOnlyList <Sample> AllOntogenyFactorForStrictBiggerThanPMA(Ontogeny ontogeny, OriginData originData, string containerName, RandomGenerator randomGenerator = null)
{
Start();
if (ontogeny.IsUndefined())
{
return(new List <Sample>());
}
var pma = postmenstrualAgeInYearsFor(originData);
var gaInYears = inYears(originData.GestationalAge.GetValueOrDefault(CoreConstants.NOT_PRETERM_GESTATIONAL_AGE_IN_WEEKS));
var ontogenies = AllValuesFor(ontogeny, containerName).Where(x => x.PostmenstrualAge > pma).ToList();
if (!ontogenies.Any())
{
return(new List <Sample>());
}
var factorRetriever = ontogenyFactorRetriever(randomGenerator, ontogenies);
return(ontogenies.Select(x => new Sample(x.PostmenstrualAge - gaInYears, factorRetriever(x))).ToList());
}
