public IPKSimBuildingBlock CreateCloneFor(IPKSimBuildingBlock buildingBlockToClone)
{
//This should never fail
var expressionProfile = buildingBlockToClone.DowncastTo <ExpressionProfile>();
var(molecule, _) = expressionProfile;
_dto = _expressionProfileDTOMapper.MapFrom(expressionProfile);
_view.Caption = Captions.CloneObjectBase(PKSimConstants.ObjectTypes.ExpressionProfile, buildingBlockToClone.Name);
_view.BindTo(_dto);
_view.Display();
if (_view.Canceled)
{
return(null);
}
//create a new expression profile using the same molecule name as the original so that we can update the values. Then we rename
var newExpressionProfile = _expressionProfileFactory.Create(molecule.MoleculeType, _dto.Species.Name, molecule.Name);
newExpressionProfile.Category = _dto.Category;
//synchronize values
_expressionProfileUpdater.SynchronizeExpressionProfileWithExpressionProfile(expressionProfile, newExpressionProfile);
//rename using the new name
_expressionProfileUpdater.UpdateMoleculeName(newExpressionProfile, _dto.MoleculeName);
return(newExpressionProfile);
}
public IPKSimCommand Create <TMolecule>() where TMolecule : IndividualMolecule
{
//Just for edit
ExpressionProfile = _expressionProfileFactory.Create <TMolecule>();
_dto = _expressionProfileDTOMapper.MapFrom(ExpressionProfile);
_view.Caption = PKSimConstants.UI.CreateExpressionProfile;
_view.BindTo(_dto);
_view.Display();
if (_view.Canceled)
{
return(new PKSimEmptyCommand());
}
//we create a new one with all new features
ExpressionProfile = _expressionProfileFactory.Create <TMolecule>(_dto.Species, _dto.MoleculeName);
ExpressionProfile.Category = _dto.Category;
_moleculeParameterTask.SetDefaultFor(ExpressionProfile);
//Action
return(new PKSimMacroCommand());
}
protected override void Context()
{
_view = A.Fake <ICreateExpressionProfileView>();
_expressionProfileFactory = A.Fake <IExpressionProfileFactory>();
_expressionProfileDTOMapper = A.Fake <IExpressionProfileToExpressionProfileDTOMapper>();
_moleculeParameterTask = A.Fake <IMoleculeParameterTask>();
_dialogCreator = A.Fake <IDialogCreator>();
sut = new CreateExpressionProfilePresenter(_view, _expressionProfileFactory, _expressionProfileDTOMapper, _moleculeParameterTask, _dialogCreator);
_expressionProfile = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>();
_updatedExpressionProfile = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>();
_expressionProfileDTO = new ExpressionProfileDTO
{
Species = new Species(),
MoleculeName = "TOTO"
};
A.CallTo(() => _expressionProfileFactory.Create <IndividualEnzyme>()).Returns(_expressionProfile);
A.CallTo(() => _expressionProfileDTOMapper.MapFrom(_expressionProfile)).Returns(_expressionProfileDTO);
A.CallTo(() => _expressionProfileFactory.Create <IndividualEnzyme>(_expressionProfileDTO.Species, _expressionProfileDTO.MoleculeName))
.Returns(_updatedExpressionProfile);
}
public override async Task <ModelExpressionProfile> MapToModel(SnapshotExpressionProfile snapshot, SnapshotContext snapshotContext)
{
var expressionProfile = _expressionProfileFactory.Create(snapshot.Type, snapshot.Species, snapshot.Molecule);
expressionProfile.Description = snapshot.Description;
expressionProfile.Category = snapshot.Category;
var(molecule, individual) = expressionProfile;
//Update molecule properties first
updateMoleculePropertiesToMolecule(molecule, snapshot, individual, snapshotContext);
//Then override all parameters that were set
await _parameterMapper.MapLocalizedParameters(snapshot.Parameters, individual, snapshotContext, !snapshotContext.IsV9FormatOrEarlier);
var snapshotWithSubjectContext = new SnapshotContextWithSubject(individual, snapshotContext);
var ontogeny = await _ontogenyMapper.MapToModel(snapshot.Ontogeny, snapshotWithSubjectContext);
_ontogenyTask.SetOntogenyForMolecule(molecule, ontogeny, individual);
var context = new ExpressionContainerMapperContext(snapshotContext)
{
Molecule = molecule,
ExpressionParameters = individual.AllExpressionParametersFor(molecule),
MoleculeExpressionContainers = individual.AllMoleculeContainersFor(molecule),
};
await _expressionContainerMapper.MapToModels(snapshot.Expression, context);
//We need to normalize relative expressions when loading from old format
if (snapshotContext.IsV9FormatOrEarlier)
{
//Make sure we load the default parameters from db just in case we were dealing with a standard molecule
_moleculeParameterTask.SetDefaultMoleculeParameters(molecule);
//Global parameters were saved directly under the snapshot parameter
await updateGlobalMoleculeParameters(snapshot, molecule, snapshotContext);
NormalizeRelativeExpressionCommand.NormalizeExpressions(individual, molecule);
}
return(expressionProfile);
}
private void addExpressionProfilesUsedBySimulationSubjectToProject(ISimulationSubject simulationSubject)
{
var project = _projectRetriever.Current;
foreach (var molecule in simulationSubject.AllMolecules())
{
var defaultExpressionProfileName = CoreConstants.ContainerName.ExpressionProfileName(molecule.Name, simulationSubject.Species, simulationSubject.Name);
var expressionProfileName = _containerTask.CreateUniqueName(project.All <ExpressionProfile>(), defaultExpressionProfileName, canUseBaseName: true);
var expressionProfile = _expressionProfileFactory.Create(molecule.GetType(), simulationSubject.Species, molecule.Name);
//Use a unique name in project
expressionProfile.Name = expressionProfileName;
_expressionProfileUpdater.SynchronizeExpressionProfileWithSimulationSubject(expressionProfile, simulationSubject);
//Some parameters are probably marked as FixedValue event thought they have not changed (Formula=>constant) due to change in
//definition of Fraction expressed basolateral going from a constant to a formula. We reset is fixed value and default state
expressionProfile.Individual.AllMoleculeParametersFor(expressionProfile.Molecule)
.Where(x => !x.Visible)
.Where(x => x.IsFixedValue)
.Each(x => x.IsFixedValue = false);
expressionProfile.Individual.AllMoleculeParametersFor(expressionProfile.Molecule)
.Where(x => !x.Editable)
.Where(x => !x.IsDefault)
.Each(x => x.IsDefault = true);
//only add at the end once the expression profile has been updated
simulationSubject.AddExpressionProfile(expressionProfile);
project.AddBuildingBlock(expressionProfile);
_registrationTask.Register(expressionProfile);
_eventPublisher.PublishEvent(new BuildingBlockAddedEvent(expressionProfile, _projectRetriever.Current));
}
_converted = true;
}
