protected override void Context()
{
_view = A.Fake <IMoleculesView>();
A.CallTo(() => _view.TreeView).Returns(A.Fake <IUxTreeView>());
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <Individual> >();
_treeNodeFactory = A.Fake <ITreeNodeFactory>();
_contextMenyFactory = A.Fake <ITreeNodeContextMenuFactory>();
_dialogCreator = A.Fake <IDialogCreator>();
_entityTask = A.Fake <IEntityTask>();
_commandRegister = A.Fake <ICommandCollector>();
_expressionsPresenterMapper = A.Fake <IRootNodeToIndividualExpressionsPresenterMapper <Individual> >();
_noitemInSelectionPresenter = A.Fake <INoItemInSelectionPresenter>();
_enzymeList = new List <IndividualEnzyme>();
_moleculeList = new List <IndividualMolecule>();
_otherProteinList = new List <IndividualOtherProtein>();
_transporterList = new List <IndividualTransporter>();
_individual = A.Fake <Individual>();
_enzymeFolderNode = new RootNode(PKSimRootNodeTypes.IndividualMetabolizingEnzymes);
_otherProteinsFolderNode = new RootNode(PKSimRootNodeTypes.IndividualProteinBindingPartners);
_transporterFolderNode = new RootNode(PKSimRootNodeTypes.IndividualTransportProteins);
A.CallTo(() => _individual.AllMolecules <IndividualEnzyme>()).Returns(_enzymeList);
A.CallTo(() => _individual.AllMolecules <IndividualOtherProtein>()).Returns(_otherProteinList);
A.CallTo(() => _individual.AllMolecules <IndividualTransporter>()).Returns(_transporterList);
A.CallTo(() => _individual.AllMolecules()).Returns(_moleculeList);
A.CallTo(() => _treeNodeFactory.CreateFor(PKSimRootNodeTypes.IndividualMetabolizingEnzymes)).Returns(_enzymeFolderNode);
A.CallTo(() => _treeNodeFactory.CreateFor(PKSimRootNodeTypes.IndividualProteinBindingPartners)).Returns(_otherProteinsFolderNode);
A.CallTo(() => _treeNodeFactory.CreateFor(PKSimRootNodeTypes.IndividualTransportProteins)).Returns(_transporterFolderNode);
A.CallTo(() => _view.TreeView.NodeById(PKSimRootNodeTypes.IndividualMetabolizingEnzymes.Id)).Returns(_enzymeFolderNode);
A.CallTo(() => _view.TreeView.NodeById(PKSimRootNodeTypes.IndividualProteinBindingPartners.Id)).Returns(_otherProteinsFolderNode);
A.CallTo(() => _view.TreeView.NodeById(PKSimRootNodeTypes.IndividualTransportProteins.Id)).Returns(_transporterFolderNode);
sut = new IndividualMoleculesPresenter(_view, _moleculeExpressionTask, _treeNodeFactory, _contextMenyFactory, _dialogCreator, _entityTask, _expressionsPresenterMapper, _noitemInSelectionPresenter);
sut.InitializeWith(_commandRegister);
}
public void Visit(Individual individual)
{
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
performCommonConversion(individual);
Visit(individual.OriginData);
foreach (var transporter in individual.AllMolecules <IndividualTransporter>().SelectMany(x => x.AllExpressionsContainers()))
{
var oldProcessNames = transporter.ProcessNames.ToList();
transporter.ClearProcessNames();
foreach (var processName in oldProcessNames)
{
transporter.AddProcessName(processName.Replace("_MM", ""));
}
}
//change container type for molecules
foreach (var molecule in individual.AllMolecules())
{
molecule.ContainerType = ContainerType.Molecule;
updateOntogeny(molecule);
}
//special parameters that need conversion by hand
convertIndividualParameters(individual.Organism);
convertIndividualForTwoPore(individual);
var human = _defaultIndividualRetriever.DefaultHuman();
individual.Organism.Add(clone(human.Organism, CoreConstants.Parameters.ONTOGENY_FACTOR_ALBUMIN));
individual.Organism.Add(clone(human.Organism, CoreConstants.Parameters.ONTOGENY_FACTOR_AGP));
individual.Organism.Add(clone(human.Organism, CoreConstants.Parameters.PLASMA_PROTEIN_SCALE_FACTOR));
if (!individual.IsHuman)
{
individual.OriginData.AddCalculationMethod(_calculationMethodRepository.FindByName("MucosaVolume_Animals"));
}
else
{
individual.OriginData.AddCalculationMethod(_calculationMethodRepository.FindByName("MucosaVolume_Human"));
individual.OriginData.GestationalAge = CoreConstants.NOT_PRETERM_GESTATIONAL_AGE_IN_WEEKS;
individual.OriginData.GestationalAgeUnit = CoreConstants.Units.Weeks;
var gestationalAge = human.Organism.Parameter(Constants.Parameters.GESTATIONAL_AGE);
if (!individual.Organism.ContainsName(Constants.Parameters.GESTATIONAL_AGE))
{
individual.Organism.Add(_cloner.Clone(gestationalAge));
}
}
}
public void should_have_set_the_ontogeny_factor_as_visible()
{
foreach (var plasmaOntogenyFactoryName in CoreConstants.Parameter.AllPlasmaProteinOntogenyFactors)
{
_individual.Organism.Parameter(plasmaOntogenyFactoryName).Visible.ShouldBeTrue();
}
foreach (var molecule in _individual.AllMolecules())
{
molecule.OntogenyFactorParameter.Visible.ShouldBeTrue();
molecule.OntogenyFactorGIParameter.Visible.ShouldBeTrue();
}
}
public void should_have_removed_the_ontogeny_factor_from_all_container_in_the_individual()
{
foreach (var molecule in _individual.AllMolecules())
{
molecule.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR).ShouldNotBeNull();
if (molecule.Name != CoreConstants.Molecule.UndefinedLiver)
{
molecule.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR_GI).ShouldNotBeNull();
}
foreach (var container in molecule.AllExpressionsContainers())
{
container.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR).ShouldBeNull();
}
}
}
public void should_have_converted_the_protein_expression_container_in_molecule_expression_container()
{
_individual.AllMolecules().Count().ShouldBeEqualTo(1);
_population.AllMolecules().Count().ShouldBeEqualTo(1);
_indSimulation.Individual.AllMolecules().Count().ShouldBeEqualTo(1);
_popSimulation.Population.AllMolecules().Count().ShouldBeEqualTo(1);
}
private void assertTransporterHaveTheRightTransportName(Individual individual)
{
foreach (var transporter in individual.AllMolecules <IndividualTransporter>())
{
transporter.AllInducedProcesses().Each(p => p.Contains("_MM").ShouldBeFalse());
}
}
public void should_have_changed_the_container_type_of_all_individual_molecule()
{
foreach (var molecule in _individual.AllMolecules())
{
molecule.ContainerType.ShouldBeEqualTo(ContainerType.Molecule);
}
}
public void should_have_replaced_the_reference_to_liver_with_pericentral_and_periportal_in_the_database_query()
{
var enzyme = _individual.AllMolecules().First();
enzyme.QueryConfiguration.Contains(CoreConstants.Compartment.Pericentral).ShouldBeTrue();
enzyme.QueryConfiguration.Contains(CoreConstants.Compartment.Periportal).ShouldBeTrue();
}
private void validateIndividual(Individual individual)
{
var molecule = individual.AllMolecules().First();
molecule.Ontogeny.ShouldNotBeNull();
molecule.OntogenyFactorParameter.ShouldNotBeNull();
molecule.OntogenyFactorGIParameter.ShouldNotBeNull();
}
public void Update(Individual sourceIndividual, Individual targetIndividual)
{
foreach (var molecule in sourceIndividual.AllMolecules())
{
var newMolecule = _cloner.Clone(molecule);
targetIndividual.AddMolecule(newMolecule);
//we have to reset the new ontogeny for the molecule
_ontogenyTask.SetOntogenyForMolecule(newMolecule, newMolecule.Ontogeny, targetIndividual);
}
}
private void verifyIndividual(Individual individual)
{
individual.AllMolecules <IndividualProtein>().Each(m =>
{
m.Localization.ShouldNotBeEqualTo(Localization.None);
//Should have created parameters in most compartments. About 30+
var allExpressionParameters = individual.AllExpressionParametersFor(m);
allExpressionParameters.Count.ShouldBeGreaterThan(30);
});
}
public void Update(Individual sourceIndividual, Individual targetIndividual)
{
foreach (var molecule in sourceIndividual.AllMolecules())
{
var newMolecule = _cloner.Clone(molecule);
targetIndividual.AddMolecule(newMolecule);
//Make sure parameters that user defined parameters are reset to default to ensure proper scaling
resetMoleculeParametersToDefault(newMolecule);
//we have to reset the ontogeny for the molecule based on the target individual properties
_ontogenyTask.SetOntogenyForMolecule(newMolecule, newMolecule.Ontogeny, targetIndividual);
}
}
private void updateLiverExpressions(Individual individual)
{
individual.AllMolecules().Each(updateLiverMoleculeExpression);
}
private void addIndividualMolecules(IEnumerable <CompoundProperties> compoundPropertiesList)
{
//first of all: add undefined proteins that are created internaly and are necessary to use the systemic processes
compoundPropertiesList.Select(x => x.Processes).Each(addUndefinedProteinForSystemicProcessesToIndividual);
_individual.AllMolecules().Each(addMolecule);
}
public void should_have_set_the_dimension_of_relative_expression_in_individual_molecules_to_dimensionsless()
{
_individual.AllMolecules().SelectMany(x => x.AllExpressionsContainers())
.Select(x => x.RelativeExpressionParameter)
.Each(p => p.Dimension.ShouldBeEqualTo(Constants.Dimension.NO_DIMENSION));
}