protected override void Context()
{
base.Context();
_simulation = A.Fake <Simulation>();
_mixedInhibition = new InhibitionProcess {
InteractionType = InteractionType.MixedInhibition
}.WithName("MixedInhibition");
_competitiveInhibition = new InhibitionProcess {
InteractionType = InteractionType.CompetitiveInhibition
}.WithName("CompetitiveInhibition");
_compound1 = new Compound().WithName("Compound1");
_compound2 = new Compound().WithName("Compound2");
_compound2.AddProcess(_mixedInhibition);
_compound2.AddProcess(_competitiveInhibition);
_interactionProperties = new InteractionProperties();
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound1, _compound2 });
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _mixedInhibition.Name, CompoundName = _compound2.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _competitiveInhibition.Name, CompoundName = _compound2.Name
});
}
protected override void Context()
{
_simulation = A.Fake <Simulation>();
_mixedInhibition1 = new InhibitionProcess {
InteractionType = InteractionType.MixedInhibition
}.WithName("MixedInhibition1");
_mixedInhibition2 = new InhibitionProcess {
InteractionType = InteractionType.MixedInhibition
}.WithName("MixedInhibition2");
_compound1 = new Compound().WithName("Compound1");
_compound2 = new Compound().WithName("Compound2");
_compound2.AddProcess(_mixedInhibition1);
_compound2.AddProcess(_mixedInhibition2);
_interactionProperties = new InteractionProperties();
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound1, _compound2 });
sut = new MixedInhibitionKineticUpdaterSpecification(new ObjectPathFactoryForSpecs(), A.Fake <IDimensionRepository>(), new InteractionTask());
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _mixedInhibition1.Name, CompoundName = _compound2.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _mixedInhibition2.Name, CompoundName = _compound2.Name
});
}
protected override void Context()
{
_project = new PKSimProject();
_projectRetriever = A.Fake <IProjectRetriever>();
A.CallTo(() => _projectRetriever.CurrentProject).Returns(_project);
_compound1 = A.Fake <Compound>();
_compound1.IsLoaded = false;
_compound2 = new Compound {
IsLoaded = true
};
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "A", Name = "P1"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "C", Name = "P2"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "B", Name = "P3"
});
_individual1 = A.Fake <Individual>();
_individual1.IsLoaded = false;
_individual2 = new Individual {
IsLoaded = true
};
_individual2.AddMolecule(new IndividualEnzyme().WithName("B"));
_individual2.AddMolecule(new IndividualEnzyme().WithName("D"));
_project.AddBuildingBlock(_compound1);
_project.AddBuildingBlock(_compound2);
_project.AddBuildingBlock(_individual1);
_project.AddBuildingBlock(_individual2);
sut = new UsedMoleculeRepository(_projectRetriever);
}
protected override void Context()
{
_project = new PKSimProject();
_projectRetriever = A.Fake <IPKSimProjectRetriever>();
_transporterContainerTemplateRepository = A.Fake <ITransporterContainerTemplateRepository>();
A.CallTo(() => _projectRetriever.Current).Returns(_project);
_compound1 = A.Fake <Compound>();
_compound1.IsLoaded = false;
_compound2 = new Compound {
IsLoaded = true
};
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "ProjA", Name = "P1"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "ProjC", Name = "P2"
});
_compound2.AddProcess(new EnzymaticProcess {
MoleculeName = "ProjB", Name = "P3"
});
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>();
_expressionProfile = A.Fake <ExpressionProfile>();
_expressionProfile.IsLoaded = true;
A.CallTo(() => _expressionProfile.MoleculeName).Returns("ProjE");
_project.AddBuildingBlock(_compound1);
_project.AddBuildingBlock(_compound2);
_project.AddBuildingBlock(_expressionProfile);
sut = new UsedMoleculeRepository(_projectRetriever, _ontogenyRepository, _moleculeParameterRepository, _transporterContainerTemplateRepository);
var molParam1 = new MoleculeParameter {
MoleculeName = "DbB"
};
var molParam2 = new MoleculeParameter {
MoleculeName = "DbA"
};
A.CallTo(() => _moleculeParameterRepository.All()).Returns(new[] { molParam1, molParam2 });
A.CallTo(() => _transporterContainerTemplateRepository.AllTransporterNames).Returns(new[] { "ATRANS1", "TRANS2" });
A.CallTo(() => _ontogenyRepository.AllFor(CoreConstants.Species.HUMAN)).Returns(new[] { new DatabaseOntogeny {
Name = "OntoC"
} });
}
public override void GlobalContext()
{
base.GlobalContext();
_otherCompound = DomainFactoryForSpecs.CreateStandardCompound().WithName("OtherCompound");
_otherProtocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol().WithName("OtherProtocol");
_otherCompound.AddProcess(_cloneManager.Clone(_metabolizationProcess));
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, new[] { _compound, _otherCompound }, new[] { _protocol, _otherProtocol, })
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesFor(_compound.Name)
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _compound.Name, ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
_simulation.CompoundPropertiesFor(_otherCompound.Name)
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _otherCompound.Name, ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
_cloneManager = IoC.Resolve <ICloneManager>();
_enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
_transporterFactory = IoC.Resolve <IIndividualTransporterFactory>();
_modelPropertiesTask = IoC.Resolve <IModelPropertiesTask>();
_modelConfigurationRepository = IoC.Resolve <IModelConfigurationRepository>();
_compound = DomainFactoryForSpecs.CreateStandardCompound();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_enzyme = _enzymeFactory.CreateFor(_individual).DowncastTo <IndividualEnzyme>().WithName("CYP");
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Plasma).Value = _relExpNormPls;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.BloodCells).Value = _relExpNormBloodCells;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.VascularEndothelium).Value = _relExpVascEndo;
_individual.AddMolecule(_enzyme);
_hct = _individual.Organism.Parameter(CoreConstants.Parameters.HCT).Value;
_metabolizationProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>());
_metabolizationProcess.Name = "My Partial Process";
_metabolizationProcess.Parameter(ConverterConstants.Parameter.CLspec).Value = 15;
_compound.AddProcess(_metabolizationProcess);
_simulationRunOptions = new SimulationRunOptions {
RaiseEvents = false
};
}
public override void GlobalContext()
{
base.GlobalContext();
_buildConfigurationTask = IoC.Resolve <IBuildConfigurationTask>();
_entityPathResolver = IoC.Resolve <IEntityPathResolver>();
var enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
var compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
var cloneManager = IoC.Resolve <ICloneManager>();
_compound = DomainFactoryForSpecs.CreateStandardCompound();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_enzyme = enzymeFactory.AddMoleculeTo(_individual, "CYP").DowncastTo <IndividualEnzyme>();
_metabolizationProcess = cloneManager.Clone(compoundProcessRepository
.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>());
_metabolizationProcess.Name = "My Partial Process";
_metabolizationProcess.Parameter(ConverterConstants.Parameters.CLspec).Value = 15;
_compound.AddProcess(_metabolizationProcess);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.MetabolizationSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
ProcessName = _metabolizationProcess.Name, MoleculeName = _enzyme.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
protected override void Context()
{
_interactionProcessRetriever = A.Fake <IInteractionProcessRetriever>();
_view = A.Fake <ISimulationCompoundInteractionSelectionView>();
sut = new SimulationCompoundInteractionSelectionPresenter(_view, _interactionProcessRetriever);
_interactionProperties = new InteractionProperties();
_allSimulationInteractionProcesses = new List <SimulationPartialProcess>();
_simulation = A.Fake <Simulation>();
var individual = new Individual().WithName("Enzyme");
_molecule1 = new IndividualEnzyme().WithName("CYP3A4");
_undefinedLiver = new IndividualEnzyme().WithName(CoreConstants.Molecule.UndefinedLiver);
individual.AddMolecule(_molecule1);
individual.AddMolecule(_undefinedLiver);
_interactionProcess1 = new InhibitionProcess().WithName("INTERACTION1");
_interactionProcess2 = new InhibitionProcess().WithName("INTERACTION2");
_interactionProcess3 = new InhibitionProcess().WithName("INTERACTION3");
var comp1 = new Compound();
comp1.AddProcess(_interactionProcess1);
var comp2 = new Compound();
comp2.AddProcess(_interactionProcess2);
comp2.AddProcess(_interactionProcess3);
_allSimulationInteractionProcesses.Add(new SimulationPartialProcess {
CompoundProcess = _interactionProcess1, IndividualMolecule = _molecule1
});
_allSimulationInteractionProcesses.Add(new SimulationPartialProcess {
CompoundProcess = _interactionProcess2, IndividualMolecule = _molecule1
});
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Individual).Returns(individual);
A.CallTo(() => _simulation.Compounds).Returns(new[] { comp1, comp2 });
A.CallTo(_interactionProcessRetriever).WithReturnType <IReadOnlyList <SimulationPartialProcess> >()
.Invokes(x => _useDefaultMap = x.GetArgument <bool>(2))
.Returns(_allSimulationInteractionProcesses);
A.CallTo(() => _view.BindTo(A <IEnumerable <SimulationInteractionProcessSelectionDTO> > ._))
.Invokes(x => _allSimulationInteractionProcessSelectionDTO = x.GetArgument <IEnumerable <SimulationInteractionProcessSelectionDTO> >(0));
}
private SystemicProcess addLiverPlasmaClearanceTo(Compound compound)
{
var liverClearance = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.LIVER_CLEARANCE).DowncastTo <SystemicProcess>());
liverClearance.Name = "My Liver Process";
liverClearance.Parameter(ConverterConstants.Parameter.PlasmaClearance).Value = 10;
compound.AddProcess(liverClearance);
return(liverClearance);
}
protected EnzymaticProcess AddEnzymaticProcess(Compound compound, IndividualEnzyme enzyme)
{
var compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
var cloneManager = IoC.Resolve <ICloneManager>();
var enzymaticProcess = cloneManager.Clone(compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <EnzymaticProcess>());
enzymaticProcess.Name = "My Partial Process " + enzyme.Name;
enzymaticProcess.MoleculeName = enzyme.Name;
enzymaticProcess.Parameter(ConverterConstants.Parameters.CLspec).Value = 10;
compound.AddProcess(enzymaticProcess);
return(enzymaticProcess);
}
protected override void Context()
{
_simulation = A.Fake <Simulation>();
_irreversibleInhibition1 = new InhibitionProcess {
InteractionType = InteractionType.IrreversibleInhibition
}.WithName("IrreversibleInhibition1");
_irreversibleInhibition2 = new InhibitionProcess {
InteractionType = InteractionType.IrreversibleInhibition
}.WithName("IrreversibleInhibition2");
_uncompetitiveInhibition = new InhibitionProcess {
InteractionType = InteractionType.UncompetitiveInhibition
}.WithName("UncompetitiveInhibition");
_compound1 = new Compound().WithName("Compound1");
_compound1.AddProcess(_irreversibleInhibition1);
_compound1.AddProcess(_uncompetitiveInhibition);
_compound2 = new Compound().WithName("Compound2");
_compound2.AddProcess(_irreversibleInhibition2);
_interactionProperties = new InteractionProperties();
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound1, _compound2 });
_objectPathFactory = new ObjectPathFactoryForSpecs();
_dimensionRepository = A.Fake <IDimensionRepository>();
_interactionTask = new InteractionTask();
sut = new IrreversibleInhibitionKineticUpdaterSpecification(_objectPathFactory, _dimensionRepository, _interactionTask);
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _irreversibleInhibition1.Name, CompoundName = _compound1.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _irreversibleInhibition2.Name, CompoundName = _compound2.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _uncompetitiveInhibition.Name, CompoundName = _compound2.Name
});
}
protected override void Context()
{
base.Context();
_moleculeMappable = new IndividualEnzyme().WithName("MoleculeMapped");
_moleculeAlreadySelected = new IndividualEnzyme().WithName("MoleculeAlreadySelected");
_moleculeNotMapped = new IndividualEnzyme().WithName("MoleculeNotMapped");
_inhibitionProcess1 = new InhibitionProcess().WithName("InhibitionProcess1");
_inhibitionProcess2 = new InhibitionProcess().WithName("InhibitionProcess2");
_inductionProcess1 = new InductionProcess().WithName("InductionProcess1");
_inhibitionProcess3 = new InhibitionProcess().WithName("InhibitionProcess3");
_individual.AddMolecule(_moleculeNotMapped);
_individual.AddMolecule(_moleculeMappable);
_individual.AddMolecule(_moleculeAlreadySelected);
_compound.AddProcess(_inhibitionProcess1);
_compound2 = new Compound().WithName("Comp2");
_compound2.AddProcess(_inhibitionProcess2);
_inhibitionProcess2.MoleculeName = _moleculeMappable.Name;
_compound2.AddProcess(_inhibitionProcess3);
_inhibitionProcess3.MoleculeName = _moleculeMappable.Name;
_compound2.AddProcess(_inductionProcess1);
_inductionProcess1.MoleculeName = _moleculeMappable.Name;
var interactionProperties = new InteractionProperties();
interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeAlreadySelected.Name, ProcessName = _inhibitionProcess1.Name, CompoundName = _compound.Name
});
A.CallTo(() => _simulation.InteractionProperties).Returns(interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound, _compound2 });
}
protected override void Context()
{
base.Context();
_metabolite = new Compound().WithName("METABOLITE");
_subMetabolite = new Compound().WithName("SUB_METABOLITE");
_compound.AddProcess(new EnzymaticProcess {
MetaboliteName = _metabolite.Name
});
_metabolite.AddProcess(new EnzymaticProcess {
MetaboliteName = _subMetabolite.Name
});
A.CallTo(() => _buildingBlockRepository.All <Compound>()).Returns(new[] { _compound, _metabolite, _subMetabolite });
A.CallTo(() => _buildingBlockTask.LoadFromTemplate <Compound>(PKSimBuildingBlockType.Compound)).Returns(new[] { _compound, _metabolite, _subMetabolite });
}
protected override void Context()
{
base.Context();
_metabolite = new Compound().WithName("METABOLITE");
_subMetabolite = new Compound().WithName("SUB_METABOLITE");
_compound.AddProcess(new EnzymaticProcess {
MetaboliteName = _metabolite.Name
});
_metabolite.AddProcess(new EnzymaticProcess {
MetaboliteName = _subMetabolite.Name
});
_subMetabolite.AddProcess(new EnzymaticProcess {
MetaboliteName = _compound.Name
});
A.CallTo(() => _buildingBlockRepository.All <Compound>()).Returns(new[] { _compound, _metabolite, _subMetabolite });
A.CallTo(_dialogCreator).WithReturnType <ViewResult>().Returns(ViewResult.Yes);
}
protected override void Context()
{
base.Context();
_compound1 = new Compound().WithName(_drugName);
_compound1.AddProcess(_uncompetitiveInhibition1);
_compound2 = new Compound().WithName("Compound2");
_compound2.AddProcess(_uncompetitiveInhibition2);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound1, _compound2 });
_interactionProperties.ClearInteractions();
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _uncompetitiveInhibition1.Name, CompoundName = _compound1.Name
});
_interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeName, ProcessName = _uncompetitiveInhibition2.Name, CompoundName = _compound2.Name
});
}
protected override void Context()
{
base.Context();
_formulaCache = new FormulaCache();
_protein = new MoleculeBuilder().WithName("CYP3A4");
_interactionProcess = new InductionProcess().WithName("Induction");
_interactionProcess.InternalName = "AA";
_compound = new Compound().WithName("Inhibitor");
_compound.AddProcess(_interactionProcess);
_template = new PKSimReaction();
A.CallTo(() => _simulationActiveProcessRepository.ProcessFor <PKSimReaction>(_interactionProcess.InternalName)).Returns(_template);
var reaction = new PKSimReaction {
Formula = new ExplicitFormula().WithName("ABC")
};
reaction.Formula.AddObjectPath(new FormulaUsablePath(CoreConstants.KeyWords.Protein, "P1").WithAlias("P1"));
reaction.Formula.AddObjectPath(new FormulaUsablePath(CoreConstants.KeyWords.Reaction, "R1").WithAlias("R1"));
reaction.Formula.AddObjectPath(new FormulaUsablePath(CoreConstants.KeyWords.Molecule, "M11").WithAlias("M1"));
A.CallTo(() => _cloneManager.Clone <IReactionBuilder>(_template)).Returns(reaction);
}