protected override void Context()
{
base.Context();
var existingProcess = new TFirstProcess {
MoleculeName = "CYP", DataSource = "Lab", Id = "1"
};
_newProcess = new TFirstProcess {
MoleculeName = "CYP", DataSource = "Lab2", Id = "2"
};
_compoundProcessNode1 = new CompoundProcessNode(existingProcess);
_compoundProcessNode2 = new CompoundProcessNode(_newProcess);
_moleculeNode1 = new PartialProcessMoleculeNode("CYP", new TFirstProcess());
_moleculeNode1.AddChild(_compoundProcessNode1);
var moleculeNode2 = new PartialProcessMoleculeNode("CYP", new TSeconProcess());
moleculeNode2.AddChild(_compoundProcessNode2);
A.CallTo(() => _partialProcessNodeMapper.MapFrom(existingProcess)).Returns(_moleculeNode1);
A.CallTo(() => _partialProcessNodeMapper.MapFrom(_newProcess)).Returns(moleculeNode2);
A.CallTo(() => _view.TreeView.NodeById(_moleculeNode1.Id)).Returns(_moleculeNode1);
sut.Handle(new AddCompoundProcessEvent {
Entity = existingProcess
});
}
public override void GlobalContext()
{
base.GlobalContext();
_transporter = _transporterFactory.CreateFor(_individual, "TRANS", TransportType.Efflux).DowncastTo <IndividualTransporter>();
var transportContainer = _individual.AllMoleculeContainersFor <TransporterExpressionContainer>(_transporter)
.First(x => x.LogicalContainer.IsNamed(CoreConstants.Organ.BRAIN));
transportContainer.TransportDirection = TransportDirectionId.InfluxBrainPlasmaToInterstitial;
_individual.AddMolecule(_transporter);
_transportProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.ACTIVE_TRANSPORT_SPECIFIC_MM)
.DowncastTo <PartialProcess>());
_transportProcess.Name = "My Transport Process";
_compound.AddProcess(_transportProcess);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection
{
CompoundName = _compound.Name, ProcessName = _transportProcess.Name, MoleculeName = _transporter.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public RootNodeType MapFrom(PartialProcess partialProcess)
{
var type = partialProcess.GetType();
if (type.IsAnImplementationOf <EnzymaticProcess>())
{
return(PKSimRootNodeTypes.CompoundMetabolizingEnzymes);
}
if (type.IsAnImplementationOf <SpecificBindingPartialProcess>())
{
return(PKSimRootNodeTypes.CompoundProteinBindingPartners);
}
if (type.IsAnImplementationOf <InhibitionProcess>())
{
return(PKSimRootNodeTypes.InhibitionProcess);
}
if (type.IsAnImplementationOf <InductionProcess>())
{
return(PKSimRootNodeTypes.InductionProcess);
}
if (type.IsAnImplementationOf <TransportPartialProcess>())
{
return(PKSimRootNodeTypes.CompoundTransportProteins);
}
throw new ArgumentException(partialProcess.ToString());
}
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);
}
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();
_transporterContainerTemplateRepository = IoC.Resolve <ITransporterContainerTemplateRepository>();
var allTransporters = _transporterContainerTemplateRepository.TransportersFor(_individual.Species.Name, CoreConstants.Organ.Brain);
var influxBBB = allTransporters.Where(x => x.MembraneLocation == MembraneLocation.BloodBrainBarrier)
.FirstOrDefault(x => x.TransportType == TransportType.Influx);
_transporter = _transporterFactory.CreateFor(_individual).DowncastTo <IndividualTransporter>().WithName("TRANS");
var transportContainer = _transporter.ExpressionContainer(CoreConstants.Organ.Brain).DowncastTo <TransporterExpressionContainer>();
transportContainer.UpdatePropertiesFrom(influxBBB);
_individual.AddMolecule(_transporter);
_transportProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.ACTIVE_TRANSPORT_SPECIFIC_MM)
.DowncastTo <PartialProcess>());
_transportProcess.Name = "My Transport Process";
_compound.AddProcess(_transportProcess);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _compound.Name, ProcessName = _transportProcess.Name, MoleculeName = _transporter.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public ITreeNode MapFrom(PartialProcess partialProcess)
{
//protein id should be created using the process type as well since the same protein might be used for e.g transporter and metabolism
var moleculeNode = _treeNodeFactory.CreateFor(partialProcess, partialProcess.MoleculeName);
moleculeNode.AddChild(_treeNodeFactory.CreateFor(partialProcess).WithIcon(ApplicationIcons.IconByName(partialProcess.Icon)));
return(moleculeNode);
}
private void report(PartialProcess partialProcess, MarkdownTracker tracker)
{
tracker.AddValue(PKSimConstants.UI.Molecule, partialProcess.MoleculeName);
switch (partialProcess)
{
case EnzymaticProcess enzymaticProcess when !string.IsNullOrEmpty(enzymaticProcess.MetaboliteName):
tracker.AddValue(PKSimConstants.UI.Metabolite, enzymaticProcess.MetaboliteName);
break;
}
}
public PartialProcessDTO MapFrom(PartialProcess partialProcess, Compound compound)
{
return(new PartialProcessDTO(partialProcess)
{
MoleculeName = partialProcess.MoleculeName,
DataSource = partialProcess.DataSource,
Compound = compound,
Species = partialProcess.Species
});
}
private void updatePartialProcessProperties(PartialProcess partialProcess, SnapshotCompoundProcess snapshot)
{
if (partialProcess == null)
{
return;
}
partialProcess.MoleculeName = snapshot.Molecule;
if (partialProcess is EnzymaticProcess enzymaticProcess)
{
enzymaticProcess.MetaboliteName = snapshot.Metabolite;
}
}
private void addPartialProcessToView(PartialProcess partialProcess, RootNodeType parentNodeType)
{
var partialProcessesNode = _view.NodeByType(parentNodeType);
var moleculeNode = _partialProcessNodeMapper.MapFrom(partialProcess);
var existingMoleculeNode = _view.NodeById(moleculeNode.Id);
//a node for the molecule was already added, promote the children
if (existingMoleculeNode != null)
{
moleculeNode.Children.Each(existingMoleculeNode.AddChild);
}
else
{
partialProcessesNode.AddChild(moleculeNode);
}
//this refreshed whole process node
_view.AddNode(partialProcessesNode);
}
protected override void Context()
{
_compound = BatchToolFactoryForSpecs.Compound();
_compound.Name = "sim";
_compound.IsSmallMolecule = true;
_partialProcess = new PartialProcess();
_partialProcess.MoleculeName = "CYP";
_partialProcess.InternalName = "Metabolization_firstOrder";
_partialProcess.DataSource = "Lab";
_partialProcess.ParameterValues.Add("P1", 5);
_partialProcess.ParameterValues.Add("CLSpec", 3);
_systemicProcess = new SystemicProcess();
_systemicProcess.InternalName = "PlasmaClearance";
_systemicProcess.DataSource = "Lab";
_systemicProcess.ParameterValues.Add("P4", 5);
_systemicProcess.ParameterValues.Add("CL", 3);
_compound.PartialProcesses.Add(_partialProcess);
_compound.SystemicProcesses.Add(_systemicProcess);
_settings = new JsonSerializerSettings {
NullValueHandling = NullValueHandling.Ignore
};
}
public void CompoundProcessSelectionChanged(SimulationInteractionProcessSelectionDTO dto, PartialProcess interactionProcess)
{
if (processAlreadySelected(interactionProcess))
{
refreshView();
throw new CannotSelectThePartialProcessMoreThanOnceException(interactionProcess);
}
dto.SimulationPartialProcess.CompoundProcess = interactionProcess;
updateWaring();
}
public void CompoundProcessChanged(TPartialProcessDTO simulationPartialProcessDTO, PartialProcess partialProcess)
{
if (partialProcessAlreadySelected(partialProcess))
{
throw new CannotSelectThePartialProcessMoreThanOnceException(partialProcess);
}
simulationPartialProcessDTO.SimulationPartialProcess.CompoundProcess = partialProcess;
}
public CannotSelectThePartialProcessMoreThanOnceException(PartialProcess partialProcess) : base(PKSimConstants.Error.CannotSelectTheSamePartialProcessMoreThanOnce(partialProcess.ToString()))
{
}
public ITreeNode CreateFor(PartialProcess partialProcess, string proteinName) => new PartialProcessMoleculeNode(proteinName, partialProcess);
public ITreeNode CreateFor(PartialProcess partialProcess) => new CompoundProcessNode(partialProcess);
public PartialProcessMoleculeNode(string proteinName, PartialProcess process)
: base(proteinName, CoreConstants.CompositeNameFor(process.GetProcessClass(), proteinName))
{
PartialProcessType = process.GetType();
}
private bool partialProcessAlreadySelected(PartialProcess partialProcess)
{
return(isSelected(partialProcess) && _allPartialProcessesDTO.Any(x => Equals(x.CompoundProcess, partialProcess)));
}
private bool isSelected(PartialProcess partialProcess)
{
return(!Equals(partialProcess, _notSelectedPartialProcess));
}
private void addPartialProcessToView(PartialProcess partialProcess)
{
addPartialProcessToView(partialProcess, _partialProcessToRootNodeTypeMapper.MapFrom(partialProcess));
}
private bool isSelected(PartialProcess interactionProcess)
{
return(!Equals(interactionProcess, _noInteractionProcessSelection));
}
public ITreeNode CreateFor(PartialProcess partialProcess)
{
return(new CompoundProcessNode(partialProcess));
}
public PartialProcessRetriever()
{
NotSelectedPartialProcess = null;
}
private static SimulationPartialProcess newSimulationPartialProcess <TIndividualMolecule>(TIndividualMolecule individualMolecule, PartialProcess partialProcess, IPartialProcessMapping partialProcessMapping = null)
where TIndividualMolecule : IndividualMolecule
{
return(new SimulationPartialProcess {
CompoundProcess = partialProcess, IndividualMolecule = individualMolecule, PartialProcessMapping = partialProcessMapping
});
}
public void UpdateProperties(PartialProcess partialProcess, PartialProcessDTO partialProcessDTO)
{
partialProcess.Name = partialProcessDTO.Name;
partialProcess.DataSource = partialProcessDTO.DataSource;
partialProcess.MoleculeName = partialProcessDTO.MoleculeName;
}
private bool processAlreadySelected(PartialProcess interactionProcess)
{
return(isSelected(interactionProcess) &&
_allInteractionProcessesDTO.Any(x => Equals(x.CompoundProcess, interactionProcess)));
}
