protected override void Context()
{
sut = new ExpressionContainersRetriever();
var objectPathFactory = new ObjectPathFactoryForSpecs();
var entityPathResolver = new EntityPathResolverForSpecs();
_liver.Add(_intLiver);
_liver.Add(_cellLiver);
_liver.Add(_plsLiver);
_liver.Add(_bcLiver);
_liver.Add(_endoLiver);
_kidney.Add(_intKidney);
_kidney.Add(_cellKidney);
_kidney.Add(_plsKidney);
_kidney.Add(_bcKidney);
_kidney.Add(_endoKidney);
_lumen.Add(_duodenum);
_organism.Add(_liver);
_organism.Add(_kidney);
_organism.Add(_lumen);
_protein = new IndividualEnzyme();
_protein.Add(new MoleculeExpressionContainer {
OrganPath = objectPathFactory.CreateObjectPathFrom(CoreConstants.Compartment.BloodCells)
}.WithName(CoreConstants.Compartment.BloodCells));
_protein.Add(new MoleculeExpressionContainer {
OrganPath = objectPathFactory.CreateObjectPathFrom(CoreConstants.Compartment.Plasma)
}.WithName(CoreConstants.Compartment.Plasma));
_protein.Add(new MoleculeExpressionContainer {
OrganPath = objectPathFactory.CreateObjectPathFrom(CoreConstants.Compartment.VascularEndothelium)
}.WithName(CoreConstants.Compartment.VascularEndothelium));
_protein.Add(new MoleculeExpressionContainer {
OrganPath = entityPathResolver.ObjectPathFor(_liver)
}.WithName(CoreConstants.Organ.Liver));
_protein.Add(new MoleculeExpressionContainer {
OrganPath = entityPathResolver.ObjectPathFor(_kidney)
}.WithName(CoreConstants.Organ.Kidney));
_protein.Add(new MoleculeExpressionContainer {
OrganPath = entityPathResolver.ObjectPathFor(_lumen), GroupName = CoreConstants.Groups.GI_LUMEN, ContainerName = _duodenum.Name
}.WithName(CoreConstants.ContainerName.LumenSegmentNameFor("Duodenum")));
}
public static Individual CreateIndividual()
{
var originData = new OriginData();
originData.SubPopulation = new SubPopulation();
originData.Species = new Species().WithName("Species");
originData.Gender = new Gender().WithName("Gender");
originData.SpeciesPopulation = new SpeciesPopulation().WithName("Population");
var pvv = new ParameterValueVersion().WithName("PVVName");
var category = new ParameterValueVersionCategory().WithName("CategoryName");
category.Add(pvv);
originData.SubPopulation.AddParameterValueVersion(pvv);
var organism = new Organism().WithName("Organism").WithId("OrganismId");
var organLiver = new Organ().WithName(CoreConstants.Organ.Liver).WithId("LiverId");
organLiver.OrganType = OrganType.Liver;
var periportal = new Compartment().WithName(CoreConstants.Compartment.Periportal).WithId("PeriportalId");
periportal.Add(new Container().WithName(CoreConstants.Compartment.Intracellular).WithId("PeriportalIntracellular"));
var pericentral = new Compartment().WithName(CoreConstants.Compartment.Pericentral).WithId("PericentralId");
pericentral.Add(new Container().WithName(CoreConstants.Compartment.Intracellular).WithId("PericentralIntracellular"));
organLiver.Add(periportal);
organLiver.Add(pericentral);
var organKidney = new Organ().WithName(CoreConstants.Organ.Kidney).WithId("KidneyId");
organKidney.OrganType = OrganType.Kidney;
organKidney.Add(new Compartment {
Visible = true
}.WithName(CoreConstants.Compartment.Plasma).WithId("KidneyPlasma"));
var lumen = new Organ().WithName("GiTract").WithId("GiTract");
lumen.OrganType = OrganType.Lumen;
var duodenum = new Compartment().WithName("Duodenum").WithId("Duodenum");
var caecum = new Compartment().WithName("Caecum").WithId("Caecum");
var dimension = Constants.Dimension.NO_DIMENSION;
var parameterLiver = new PKSimParameter().WithName("PLiver").WithId("PLiverId").WithFormula(new ExplicitFormula("1").WithId("1")).WithDimension(dimension);
parameterLiver.Info = new ParameterValueMetaData {
DefaultValue = 1
};
var parameterKidney = new PKSimParameter().WithName("PKidney").WithId("PKidneyId").WithFormula(new ExplicitFormula("2").WithId("2")).WithDimension(dimension);
parameterKidney.Info = new ParameterValueMetaData {
DefaultValue = 2
};
var parameterOrganism = new PKSimParameter().WithName(ParameterInOrganism).WithId("POrganismId").WithFormula(new ExplicitFormula("3").WithId("3")).WithDimension(dimension);
parameterOrganism.Info = new ParameterValueMetaData {
DefaultValue = 3
};
organLiver.Add(parameterLiver);
organKidney.Add(parameterKidney);
organism.Add(organLiver);
organism.Add(organKidney);
organism.Add(lumen);
organism.Add(parameterOrganism);
lumen.Add(duodenum);
lumen.Add(caecum);
var individual = new Individual {
OriginData = originData
}.WithName("Individual").WithId("IndividualId");
individual.Add(organism);
return(individual);
}
public static Individual CreateIndividual(string speciesName = "Species")
{
var originData = new OriginData
{
SubPopulation = new SubPopulation(),
Species = new Species {
DisplayName = speciesName, Id = speciesName
}.WithName(speciesName),
Gender = new Gender().WithName("Gender"),
Population = new SpeciesPopulation().WithName("Population"),
};
var pvv = new ParameterValueVersion().WithName("PVVName");
var category = new ParameterValueVersionCategory().WithName("CategoryName");
category.Add(pvv);
originData.SubPopulation.AddParameterValueVersion(pvv);
var organism = new Organism().WithName(Constants.ORGANISM).WithId("OrganismId");
var organLiver = new Organ().WithName(CoreConstants.Organ.LIVER).WithId("LiverId");
organLiver.OrganType = OrganType.TissueOrgansNotInGiTract;
var periportal = new Compartment().WithName(CoreConstants.Compartment.PERIPORTAL).WithId("PeriportalId");
periportal.Add(new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithId("PeriportalIntracellular"));
var pericentral = new Compartment().WithName(CoreConstants.Compartment.PERICENTRAL).WithId("PericentralId");
pericentral.Add(new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithId("PericentralIntracellular"));
organLiver.Add(periportal);
organLiver.Add(pericentral);
var organKidney = new Organ().WithName(CoreConstants.Organ.KIDNEY).WithId("KidneyId");
organKidney.OrganType = OrganType.TissueOrgansNotInGiTract;
organKidney.Add(new Compartment {
Visible = true
}.WithName(CoreConstants.Compartment.PLASMA).WithId("KidneyPlasma"));
var lumen = new Organ().WithName("GiTract").WithId("GiTract");
lumen.OrganType = OrganType.Lumen;
var duodenum = new Compartment().WithName("Duodenum").WithId("Duodenum");
var caecum = new Compartment().WithName("Caecum").WithId("Caecum");
var dimension = Constants.Dimension.NO_DIMENSION;
var parameterLiver = new PKSimParameter().WithName("PLiver").WithId("PLiverId").WithFormula(new ExplicitFormula("1").WithId("1")).WithDimension(dimension);
parameterLiver.Info = new ParameterValueMetaData {
DefaultValue = 1
};
var parameterKidney = new PKSimParameter().WithName("PKidney").WithId("PKidneyId").WithFormula(new ExplicitFormula("2").WithId("2")).WithDimension(dimension);
parameterKidney.Info = new ParameterValueMetaData {
DefaultValue = 2
};
var parameterOrganism = new PKSimParameter().WithName(ParameterInOrganism).WithId("POrganismId").WithFormula(new ExplicitFormula("3").WithId("3")).WithDimension(dimension);
parameterOrganism.Info = new ParameterValueMetaData {
DefaultValue = 3
};
organLiver.Add(parameterLiver);
organKidney.Add(parameterKidney);
organism.Add(organLiver);
organism.Add(organKidney);
organism.Add(lumen);
organism.Add(parameterOrganism);
lumen.Add(duodenum);
lumen.Add(caecum);
var individual = new Individual {
OriginData = originData
}.WithName("Individual").WithId("IndividualId");
individual.Add(organism);
return(individual);
}