protected override async Task Context()
{
await base.Context();
_project = new PKSimProject();
_newIndividual = new Individual
{
OriginData = new OriginData()
};
_newAgeRange = new ParameterRange {
ParameterName = CoreConstants.Parameters.AGE
};
_newWeightRange = new ParameterRange {
ParameterName = CoreConstants.Parameters.MEAN_WEIGHT
};
_snapshot = await sut.MapToSnapshot(_randomPopulationSettings);
_snapshot.ProportionOfFemales = _proportionOfFemale;
A.CallTo(() => _parameterRangeMapper.MapToModel(_snapshot.Age, A <ParameterRangeSnapshotContext> .That.Matches(x => x.ParameterRange == _newAgeRange))).Returns(_newAgeRange);
A.CallTo(() => _parameterRangeMapper.MapToModel(_snapshot.Weight, A <ParameterRangeSnapshotContext> .That.Matches(x => x.ParameterRange == _newWeightRange))).Returns(_newWeightRange);
A.CallTo(() => _individualMapper.MapToModel(_snapshotIndividual, _snapshotContext)).Returns(_newIndividual);
_newDiseaseStateParameterRange = new ConstrainedParameterRange {
ParameterName = _diseaseStateParameter.Name
};
_mappedSettings = new RandomPopulationSettings {
BaseIndividual = _newIndividual
};
_mappedSettings.AddParameterRange(_newDiseaseStateParameterRange);
A.CallTo(() => _populationSettingsMapper.MapFrom(_newIndividual)).Returns(_mappedSettings);
}
protected override Task Context()
{
_individualMapper = A.Fake <IndividualMapper>();
_parameterRangeMapper = A.Fake <ParameterRangeMapper>();
_genderRepository = A.Fake <IGenderRepository>();
_populationSettingsMapper = A.Fake <IIndividualToPopulationSettingsMapper>();
sut = new RandomPopulationSettingsMapper(_parameterRangeMapper, _individualMapper, _populationSettingsMapper, _genderRepository);
_ageParameterRange = new ConstrainedParameterRange {
ParameterName = CoreConstants.Parameters.AGE
};
_weightParameterRange = new ParameterRange {
ParameterName = CoreConstants.Parameters.MEAN_WEIGHT
};
A.CallTo(() => _parameterRangeMapper.MapToSnapshot(null)).Returns((Snapshots.ParameterRange)null);
_ageRangeSnapshot = new Snapshots.ParameterRange();
A.CallTo(() => _parameterRangeMapper.MapToSnapshot(_ageParameterRange)).Returns(_ageRangeSnapshot);
_weightRangeSnapshot = new Snapshots.ParameterRange();
A.CallTo(() => _parameterRangeMapper.MapToSnapshot(_weightParameterRange)).Returns(_weightRangeSnapshot);
_baseIndividual = new Individual();
_snapshotIndividual = new Snapshots.Individual();
A.CallTo(() => _individualMapper.MapToSnapshot(_baseIndividual)).Returns(_snapshotIndividual);
_randomPopulationSettings = new RandomPopulationSettings
{
NumberOfIndividuals = 10,
BaseIndividual = _baseIndividual
};
_randomPopulationSettings.AddParameterRange(_weightParameterRange);
_randomPopulationSettings.AddParameterRange(_ageParameterRange);
A.CallTo(() => _genderRepository.Female).Returns(new Gender {
Id = "Female", Name = "Female"
});
A.CallTo(() => _genderRepository.Male).Returns(new Gender {
Id = "Male", Name = "Male"
});
return(Task.FromResult(true));
}
protected override void Context()
{
base.Context();
_individual = A.Fake <Individual>();
A.CallTo(() => _individual.AvailableGenders()).Returns(new List <Gender> {
_genderRepository.Male, _genderRepository.Female
});
_populationSettings = new RandomPopulationSettings();
_batchPopSettings = new Batch.PopulationSettings();
_batchPopSettings.Population = "Population";
_batchPopSettings.MinAge = 25;
_batchPopSettings.MaxAge = 40;
_batchPopSettings.MinGestationalAge = 30;
_batchPopSettings.MinHeight = 10;
_batchPopSettings.MaxHeight = 20;
_batchPopSettings.MinWeight = double.NaN;
_batchPopSettings.MaxWeight = 40;
_batchPopSettings.MinBMI = 8;
_batchPopSettings.MaxBMI = double.NaN;
_batchPopSettings.NumberOfIndividuals = 2589;
_batchPopSettings.ProportionOfFemales = 40;
_populationSettings.AddParameterRange(new ParameterRange {
ParameterName = CoreConstants.Parameter.BMI
});
_populationSettings.AddParameterRange(new ParameterRange {
ParameterName = CoreConstants.Parameter.AGE
});
_populationSettings.AddParameterRange(new ParameterRange {
ParameterName = CoreConstants.Parameter.MEAN_HEIGHT
});
_populationSettings.AddParameterRange(new ParameterRange {
ParameterName = CoreConstants.Parameter.MEAN_WEIGHT
});
_populationSettings.AddGenderRatio(new GenderRatio {
Gender = _genderRepository.Male
});
_populationSettings.AddGenderRatio(new GenderRatio {
Gender = _genderRepository.Female
});
A.CallTo(() => _individualFactory.CreateStandardFor(A <OriginData> ._)).Returns(_individual);
A.CallTo(() => _popSettingsMapper.MapFrom(_individual)).Returns(_populationSettings);
}
protected override async Task Context()
{
await base.Context();
_newIndividual = new Individual();
_newAgeRange = new ParameterRange {
ParameterName = CoreConstants.Parameters.AGE
};
_newWeightRange = new ParameterRange {
ParameterName = CoreConstants.Parameters.MEAN_WEIGHT
};
_snapshot = await sut.MapToSnapshot(_randomPopulationSettings);
_snapshot.ProportionOfFemales = _proportionOfFemale;
A.CallTo(() => _parameterRangeMapper.MapToModel(_snapshot.Age, A <ParameterRangeSnapshotContext> .That.Matches(x => x.ParameterRange == _newAgeRange))).Returns(_newAgeRange);
A.CallTo(() => _parameterRangeMapper.MapToModel(_snapshot.Weight, A <ParameterRangeSnapshotContext> .That.Matches(x => x.ParameterRange == _newWeightRange))).Returns(_newWeightRange);
A.CallTo(() => _individualMapper.MapToModel(_snapshotIndividual, _snapshotContext)).Returns(_newIndividual);
_mappedSettings = new RandomPopulationSettings();
A.CallTo(() => _populationSettingsMapper.MapFrom(_newIndividual)).Returns(_mappedSettings);
_mappedSettings.AddParameterRange(_newAgeRange);
_mappedSettings.AddParameterRange(_newWeightRange);
_maleRatio = new GenderRatio
{
Gender = _genderRepository.Male,
Ratio = 50
};
_femaleRatio = new GenderRatio
{
Gender = _genderRepository.Female,
Ratio = 50
};
_mappedSettings.AddGenderRatio(_maleRatio);
_mappedSettings.AddGenderRatio(_femaleRatio);
_snapshot.DiseaseStateParameters = null;
}
public RandomPopulationSettings MapFrom(Individual individual)
{
//add age first
var populationSettings = new RandomPopulationSettings();
if (individual == null)
{
return(populationSettings);
}
var population = individual.OriginData.SpeciesPopulation;
populationSettings.BaseIndividual = individual;
populationSettings.NumberOfIndividuals = CoreConstants.DEFAULT_NUMBER_OF_INDIVIDUALS_IN_POPULATION;
int genderCount = individual.AvailableGenders().Count();
foreach (var gender in individual.AvailableGenders())
{
populationSettings.AddGenderRatio(new GenderRatio {
Gender = gender, Ratio = 100 / genderCount
});
}
if (population.IsAgeDependent)
{
var ageParameter = individual.Organism.Parameter(CoreConstants.Parameter.AGE);
populationSettings.AddParameterRange(constrainedParameterRangeFrom(ageParameter));
}
if (individual.IsPreterm)
{
var gestationalAgeParameter = individual.Organism.Parameter(CoreConstants.Parameter.GESTATIONAL_AGE);
populationSettings.AddParameterRange(discretedParameterRangeFrom(gestationalAgeParameter, numericListOfValues(gestationalAgeParameter)));
}
if (population.IsHeightDependent)
{
var heightParameter = individual.Organism.Parameter(CoreConstants.Parameter.MEAN_HEIGHT);
populationSettings.AddParameterRange(parameterRangeFrom(heightParameter));
}
var weightParameter = individual.Organism.Parameter(CoreConstants.Parameter.MEAN_WEIGHT);
if (population.IsAgeDependent)
{
populationSettings.AddParameterRange(parameterRangeFrom(weightParameter));
}
else
{
populationSettings.AddParameterRange(constrainedParameterRangeFrom(weightParameter));
}
if (population.IsHeightDependent)
{
var bmiParameter = individual.Organism.Parameter(CoreConstants.Parameter.BMI);
populationSettings.AddParameterRange(parameterRangeFrom(bmiParameter));
}
return(populationSettings);
}
public RandomPopulationSettings MapFrom(Individual individual)
{
var populationSettings = new RandomPopulationSettings();
if (individual == null)
{
return(populationSettings);
}
var population = individual.OriginData.Population;
populationSettings.BaseIndividual = individual;
populationSettings.NumberOfIndividuals = CoreConstants.DEFAULT_NUMBER_OF_INDIVIDUALS_IN_POPULATION;
var genderCount = individual.AvailableGenders.Count;
foreach (var gender in individual.AvailableGenders)
{
populationSettings.AddGenderRatio(new GenderRatio {
Gender = gender, Ratio = 100 / genderCount
});
}
var organism = individual.Organism;
if (individual.IsAgeDependent)
{
populationSettings.AddParameterRange(constrainedParameterRangeFrom(organism.Parameter(AGE)));
}
if (individual.IsPreterm)
{
var gestationalAgeParameter = organism.Parameter(GESTATIONAL_AGE);
populationSettings.AddParameterRange(discreteParameterRangeFrom(gestationalAgeParameter, numericListOfValues(gestationalAgeParameter)));
}
var weightParameter = organism.Parameter(MEAN_WEIGHT);
populationSettings.AddParameterRange(population.IsAgeDependent ? parameterRangeFrom(weightParameter) : constrainedParameterRangeFrom(weightParameter));
if (population.IsHeightDependent)
{
populationSettings.AddParameterRange(parameterRangeFrom(organism.Parameter(MEAN_HEIGHT)));
populationSettings.AddParameterRange(parameterRangeFrom(organism.Parameter(BMI)));
}
individual.OriginData.DiseaseStateParameters.Each(x =>
{
var parameter = individual.OriginData.DiseaseState.Parameter(x.Name);
populationSettings.AddParameterRange(constrainedParameterRangeFrom(parameter));
});
return(populationSettings);
}
public RandomPopulationSettings MapFrom(PopulationSettingsDTO populationSettingsDTO)
{
var populationSettings = new RandomPopulationSettings();
populationSettings.BaseIndividual = _cloner.Clone(populationSettingsDTO.Individual);
populationSettings.NumberOfIndividuals = populationSettingsDTO.NumberOfIndividuals.ConvertedTo <int>();
//first add one gender with ration 100 for each available gender
populationSettingsDTO.AvailableGenders().Each(g => populationSettings.AddGenderRatio(new GenderRatio {
Gender = g, Ratio = 100
}));
//in case of multiple gender, adjust the ration according to the feamales proportion
if (populationSettingsDTO.HasMultipleGenders)
{
populationSettings.GenderRatio(populationSettingsDTO.Female).Ratio = populationSettingsDTO.ProportionOfFemales;
populationSettings.GenderRatio(populationSettingsDTO.Male).Ratio = 100 - populationSettingsDTO.ProportionOfFemales;
}
populationSettingsDTO.Parameters.Each(p => populationSettings.AddParameterRange(p.ParameterRange));
return(populationSettings);
}
protected override Task Context()
{
_individualMapper = A.Fake <IndividualMapper>();
_parameterRangeMapper = A.Fake <ParameterRangeMapper>();
_genderRepository = A.Fake <IGenderRepository>();
_populationSettingsMapper = A.Fake <IIndividualToPopulationSettingsMapper>();
_logger = A.Fake <IOSPSuiteLogger>();
sut = new RandomPopulationSettingsMapper(_parameterRangeMapper, _individualMapper, _populationSettingsMapper, _genderRepository, _logger);
_ageParameterRange = new ConstrainedParameterRange {
ParameterName = CoreConstants.Parameters.AGE
};
_weightParameterRange = new ParameterRange {
ParameterName = CoreConstants.Parameters.MEAN_WEIGHT
};
A.CallTo(() => _parameterRangeMapper.MapToSnapshot(null)).Returns((Snapshots.ParameterRange)null);
_ageRangeSnapshot = new Snapshots.ParameterRange();
A.CallTo(() => _parameterRangeMapper.MapToSnapshot(_ageParameterRange)).Returns(_ageRangeSnapshot);
_weightRangeSnapshot = new Snapshots.ParameterRange();
A.CallTo(() => _parameterRangeMapper.MapToSnapshot(_weightParameterRange)).Returns(_weightRangeSnapshot);
_baseIndividual = new Individual
{
OriginData = new OriginData()
};
_diseaseStateParameter = new OriginDataParameter(10, "mg/kg", "DIS_STATE_PARAM");
_baseIndividual.OriginData.AddDiseaseStateParameter(_diseaseStateParameter);
_diseaseStateParameterRangeSnapshot = new Snapshots.ParameterRange();
_diseaseStateParameterRange = new ConstrainedParameterRange {
ParameterName = _diseaseStateParameter.Name
};
A.CallTo(() => _parameterRangeMapper.MapToSnapshot(_diseaseStateParameterRange)).Returns(_diseaseStateParameterRangeSnapshot);
_snapshotIndividual = new Snapshots.Individual();
A.CallTo(() => _individualMapper.MapToSnapshot(_baseIndividual)).Returns(_snapshotIndividual);
_randomPopulationSettings = new RandomPopulationSettings
{
NumberOfIndividuals = 10,
BaseIndividual = _baseIndividual
};
_randomPopulationSettings.AddParameterRange(_weightParameterRange);
_randomPopulationSettings.AddParameterRange(_ageParameterRange);
_randomPopulationSettings.AddParameterRange(_diseaseStateParameterRange);
A.CallTo(() => _genderRepository.Female).Returns(new Gender {
Id = "Female", Name = "Female"
});
A.CallTo(() => _genderRepository.Male).Returns(new Gender {
Id = "Male", Name = "Male"
});
_project = new PKSimProject();
_snapshotContext = new SnapshotContext(_project, ProjectVersions.Current);
return(Task.FromResult(true));
}