public void the_value_for_mean_body_weight_for_all_species_but_human_should_be_equal_to_the_weight_value()
{
var errorList = new List <string>();
foreach (var species in _speciesRepository.All().Where(x => x.Name != CoreConstants.Species.Human))
{
var individualForSpecies = _individualRetriever.DefaultIndividualFor(species);
double meanWeight = individualForSpecies.MeanWeight;
double bodyWeight = individualForSpecies.Organism.Parameter(CoreConstants.Parameter.WEIGHT).Value;
if (!ValueComparer.AreValuesEqual(meanWeight, bodyWeight, 1e-2))
{
errorList.Add(string.Format("Mean Body weight not equal to weight for '{0}': MeanWeight = {1}, BodyWeight={2}", species.Name, meanWeight, bodyWeight));
}
}
errorList.Count.ShouldBeEqualTo(0, errorList.ToString("\n"));
}
private void convertTransitTimeFor(IContainer individualToConvert)
{
if (!_defaultCache.Contains(_currentSpecies))
{
_defaultCache.Add(_defaultIndividualRetriever.DefaultIndividualFor(_currentSpecies));
}
var defaultIndividual = _defaultCache[_currentSpecies];
var defaultSITT = smallIntestineIn(defaultIndividual).Parameter(ConverterConstants.Parameter.SITT);
var defaultSITT_factor = smallIntestineIn(defaultIndividual).Parameter(ConverterConstants.Parameter.SITT_factor);
var defaultSITT_factor_slope = smallIntestineIn(defaultIndividual).Parameter(ConverterConstants.Parameter.SITT_factor_slope);
var defaultSITT_factor_intercept = smallIntestineIn(defaultIndividual).Parameter(ConverterConstants.Parameter.SITT_factor_intercept);
var defaultLITT = largeIntestineIn(defaultIndividual).Parameter(ConverterConstants.Parameter.LITT);
var defaultLITT_factor = largeIntestineIn(defaultIndividual).Parameter(ConverterConstants.Parameter.LITT_factor);
var defaultLITT_factor_slope = largeIntestineIn(defaultIndividual).Parameter(ConverterConstants.Parameter.LITT_factor_slope);
var defaultLITT_factor_intercept = largeIntestineIn(defaultIndividual).Parameter(ConverterConstants.Parameter.LITT_factor_intercept);
var defaultGET = gastricEmptyingTimeIn(defaultIndividual);
var currentGET = gastricEmptyingTimeIn(individualToConvert);
currentGET.Info.MaxValue = defaultGET.MaxValue;
var smallIntestine = smallIntestineIn(individualToConvert);
var largeIntestine = largeIntestineIn(individualToConvert);
smallIntestine.Add(_cloner.Clone(defaultSITT));
smallIntestine.Add(_cloner.Clone(defaultSITT_factor_slope));
smallIntestine.Add(_cloner.Clone(defaultSITT_factor_intercept));
largeIntestine.Add(_cloner.Clone(defaultLITT));
largeIntestine.Add(_cloner.Clone(defaultLITT_factor_slope));
largeIntestine.Add(_cloner.Clone(defaultLITT_factor_intercept));
var SITT = smallIntestine.Parameter(ConverterConstants.Parameter.SITT);
var SITT_fact_old = smallIntestine.Parameter(ConverterConstants.Parameter.SITT_factor).Value;
var P1_sin = smallIntestine.Parameter(ConverterConstants.Parameter.SITT_factor_slope).Value;
var P2_sin = smallIntestine.Parameter(ConverterConstants.Parameter.SITT_factor_intercept).Value;
var LITT = largeIntestine.Parameter(ConverterConstants.Parameter.LITT);
var LITT_fact_old = largeIntestine.Parameter(ConverterConstants.Parameter.LITT_factor).Value;
var P1_lin = largeIntestine.Parameter(ConverterConstants.Parameter.LITT_factor_slope).Value;
var P2_lin = largeIntestine.Parameter(ConverterConstants.Parameter.LITT_factor_intercept).Value;
SITT.Value = (SITT_fact_old - P2_sin) / P1_sin;
LITT.Value = (LITT_fact_old - P2_lin) / P1_lin;
//last but not least remove parameter to update formula
smallIntestine.RemoveChild(smallIntestine.Parameter(ConverterConstants.Parameter.SITT_factor));
largeIntestine.RemoveChild(largeIntestine.Parameter(ConverterConstants.Parameter.LITT_factor));
smallIntestine.Add(_cloner.Clone(defaultSITT_factor));
largeIntestine.Add(_cloner.Clone(defaultLITT_factor));
//removed unused parameters
smallIntestine.RemoveChild(smallIntestine.Parameter(ConverterConstants.Parameter.ColonArrivalTime));
largeIntestine.RemoveChild(largeIntestine.Parameter(ConverterConstants.Parameter.ExcretionTime));
_converted = true;
}
private Individual templateIndividualFor(Individual individual)
{
var species = individual.Species;
if (!_defaultCache.Contains(species))
{
_defaultCache.Add(_defaultIndividualRetriever.DefaultIndividualFor(species));
}
var defaultIndividual = _defaultCache[species];
return(defaultIndividual);
}
public ICache <Species, IParameter> VSSPhysChemFor(Compound compound)
{
var cache = new Cache <Species, IParameter>();
var protocol = _protocolFactory.Create(ProtocolMode.Simple);
_speciesRepository.All().Each(species =>
{
var defaultIndividual = _defaultIndividualRetriever.DefaultIndividualFor(species);
var simulation = _simulationFactory.CreateForVSS(protocol, defaultIndividual, compound);
cache[species] = VSSPhysChemFor(simulation, compound.Name);
});
return(cache);
}
private void addIndividualParameters(IContainer individual, Species species, string replaceRootName = null)
{
if (!_defaultCache.Contains(species))
{
_defaultCache.Add(_defaultIndividualRetriever.DefaultIndividualFor(species));
}
var defaultIndividual = _defaultCache[species];
var stomach = lumenStomachIn(individual);
var defaultStomach = lumenStomachIn(defaultIndividual);
stomach.Add(_cloner.Clone(defaultStomach.Parameter(ConverterConstants.Parameter.GET_Alpha_variability_factor)));
stomach.Add(_cloner.Clone(defaultStomach.Parameter(ConverterConstants.Parameter.GET_Beta_variability_factor)));
}
private void convertIndividualForTwoPore(Individual individual)
{
var endogenous = individual.Organism.Organ(CoreConstants.Organ.EndogenousIgG);
//already converted
if (endogenous.ContainsName(ConverterConstants.Parameter.Kass_FcRn_ligandEndo))
{
return;
}
var defaultIndividual = _defaultIndividualRetriever.DefaultIndividualFor(individual.OriginData.SpeciesPopulation);
var defaultEndogenous = defaultIndividual.Organism.Organ(CoreConstants.Organ.EndogenousIgG);
endogenous.Add(clone(defaultEndogenous, ConverterConstants.Parameter.Kass_FcRn_ligandEndo));
endogenous.Add(clone(defaultEndogenous, ConverterConstants.Parameter.Kd_FcRn_LigandEndo));
endogenous.Add(clone(defaultEndogenous, ConverterConstants.Parameter.Kd_FcRn_ligandEndo_pls_int));
var endosome = endogenous.Compartment(ConverterConstants.ContainerName.IGG_ENDOSOME);
endosome.Name = CoreConstants.Compartment.Endosome;
endogenous.Compartment(CoreConstants.Compartment.Endosome)
.Add(clone(defaultEndogenous.Compartment(CoreConstants.Compartment.Endosome), ConverterConstants.Parameter.Start_concentration_FcRn_endosome));
endogenous.Compartment(CoreConstants.Compartment.Plasma)
.Add(clone(defaultEndogenous.Compartment(CoreConstants.Compartment.Plasma), ConverterConstants.Parameter.Start_concentration_endogenous_plasma));
foreach (var container in individual.Organism.GetAllChildren <IContainer>(x => x.IsNamed(ConverterConstants.ContainerName.ENDOSOMAL_CLEARANCE)))
{
if (container.ParentContainer.IsNamed(CoreConstants.Organ.EndogenousIgG))
{
continue;
}
container.ParentContainer.RemoveChild(container);
}
var endsomeClearance = clone(defaultIndividual.Organism, ConverterConstants.ContainerName.ENDOSOMAL_CLEARANCE) as IContainer;
individual.Organism.Add(endsomeClearance);
foreach (var neighborhood in individual.Neighborhoods.GetChildren <INeighborhood>(neighborhoodIsEndosomalClearance))
{
neighborhood.SecondNeighbor = endsomeClearance;
}
}
protected override void Context()
{
_executionContext = A.Fake <IExecutionContext>();
_compoundProcess = new EnzymaticProcessWithSpecies {
InternalName = "CompoundProcess"
};
_species = new Species {
Name = "NEW_SPECIES"
};
_compoundProcess.Species = new Species {
Name = "OLD_SPECIES"
};
sut = new SetSpeciesInCompoundProcessCommand(_compoundProcess, _species);
_defaultIndividualRetriever = A.Fake <IDefaultIndividualRetriever>();
A.CallTo(() => _executionContext.Resolve <IDefaultIndividualRetriever>()).Returns(_defaultIndividualRetriever);
_parameterMappingRepository = A.Fake <ICompoundProcessParameterMappingRepository>();
A.CallTo(() => _executionContext.Resolve <ICompoundProcessParameterMappingRepository>()).Returns(_parameterMappingRepository);
_individualParameter = DomainHelperForSpecs.ConstantParameterWithValue(value: 25).WithName("Matching");
_individualParameter.ValueOrigin.Method = ValueOriginDeterminationMethods.Assumption;
_individualParameter.ValueOrigin.Source = ValueOriginSources.ParameterIdentification;
_organism = new Organism {
_individualParameter
};
_individual = new Individual {
Root = new RootContainer {
_organism
}
};
A.CallTo(() => _defaultIndividualRetriever.DefaultIndividualFor(_species)).Returns(_individual);
_matchingIndividualParameter = DomainHelperForSpecs.ConstantParameterWithValue(isDefault: true).WithName("Matching");
_nonMatchingIndividualParameter = DomainHelperForSpecs.ConstantParameterWithValue(isDefault: true).WithName("NonMatching");
_compoundProcess.Add(_matchingIndividualParameter);
_compoundProcess.Add(_nonMatchingIndividualParameter);
_objectPath = new ObjectPath(_organism.Name, _individualParameter.Name);
A.CallTo(() => _parameterMappingRepository.HasMappedParameterFor(_compoundProcess.InternalName, _matchingIndividualParameter.Name)).Returns(true);
A.CallTo(() => _parameterMappingRepository.MappedParameterPathFor(_compoundProcess.InternalName, _matchingIndividualParameter.Name)).Returns(_objectPath);
}
