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()
{
_executionContext = A.Fake <IExecutionContext>();
_project = new PKSimProject();
A.CallTo(() => _executionContext.CurrentProject).Returns(_project);
_compound = new Compound().WithId("Tralala").WithName("Tralala");
_project.AddBuildingBlock(_compound);
_proc = new EnzymaticProcess().WithName("ActProc1");
var serializedStream = new byte[1];
A.CallTo(() => _executionContext.Serialize(_proc)).Returns(serializedStream);
A.CallTo(() => _executionContext.Deserialize <PKSim.Core.Model.CompoundProcess>(serializedStream)).Returns(_proc);
A.CallTo(() => _executionContext.Get <Compound>(_compound.Id)).Returns(_compound);
A.CallTo(() => _executionContext.Get <PKSim.Core.Model.CompoundProcess>(_proc.Id)).Returns(_proc);
sut = new AddProcessToCompoundCommand(_proc, _compound, _executionContext);
}
public override void GlobalContext()
{
base.GlobalContext();
_sim1 = new IndividualSimulation
{
Id = "Sim1",
Name = "Sim1",
IsLoaded = true,
Model = new Model {
Root = new Container()
}
};
_sim1.Model.Root.Add(new Container {
new Parameter().WithName("P")
}.WithName("Liver"));
var objectBaseRepository = IoC.Resolve <IWithIdRepository>();
var workspace = IoC.Resolve <IWorkspace>();
_project = IoC.Resolve <IPKSimProject>();
workspace.Project = _project;
objectBaseRepository.Register(_sim1);
_project.AddBuildingBlock(_sim1);
_sensitivityAnalysis = new SensitivityAnalysis
{
Name = "SA",
Simulation = _sim1
};
_sensitivityParameter1 = DomainHelperForSpecs.SensitivityParameter(range: 0.5d, steps: 5);
_parameterSelection1 = new ParameterSelection(_sim1, new QuantitySelection("Liver|P", QuantityType.Parameter));
_sensitivityParameter1.ParameterSelection = _parameterSelection1;
_sensitivityAnalysis.AddSensitivityParameter(_sensitivityParameter1);
_deserializedSensitivityAnalysis = SerializeAndDeserialize(_sensitivityAnalysis);
}
public void should_add_the_new_simulation_to_the_project()
{
A.CallTo(() => _project.AddBuildingBlock(_newSimulation)).MustHaveHappened();
}
public override void GlobalContext()
{
base.GlobalContext();
_observedData = DomainHelperForSpecs.ObservedData();
_sim1 = new IndividualSimulation
{
Id = "Sim1",
Name = "Sim1",
IsLoaded = true,
Model = new Model {
Root = new Container()
}
};
_sim1.Model.Root.Add(new Container {
new Parameter().WithName("P")
}.WithName("Liver"));
_sim2 = new IndividualSimulation
{
Id = "Sim2",
Name = "Sim2",
IsLoaded = true,
Model = new Model {
Root = new Container()
}
};
_sim2.Model.Root.Add(new Container {
new Parameter().WithName("P")
}.WithName("Liver"));
_objectBaseRepository = IoC.Resolve <IWithIdRepository>();
var workspace = IoC.Resolve <IWorkspace>();
_project = IoC.Resolve <IPKSimProject>();
workspace.Project = _project;
_objectBaseRepository.Register(_sim1);
_objectBaseRepository.Register(_sim2);
_project.AddObservedData(_observedData);
_project.AddBuildingBlock(_sim1);
_project.AddBuildingBlock(_sim2);
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.AddSimulation(_sim1);
_parameterIdentification.AddSimulation(_sim2);
_outputMapping = new OutputMapping
{
WeightedObservedData = new WeightedObservedData(_observedData),
OutputSelection = new SimulationQuantitySelection(_sim1, new QuantitySelection("A|B", QuantityType.Metabolite)),
Weight = 5,
Scaling = Scalings.Log
};
_outputMapping.WeightedObservedData.Weights[1] = 10;
_parameterIdentification.AddOutputMapping(_outputMapping);
_identificationParameter = DomainHelperForSpecs.IdentificationParameter(min: 1, max: 10, startValue: 5);
_parameterSelection1 = new ParameterSelection(_sim1, new QuantitySelection("Liver|P", QuantityType.Parameter));
_parameterSelection2 = new ParameterSelection(_sim2, new QuantitySelection("Liver|P", QuantityType.Parameter));
_identificationParameter.AddLinkedParameter(_parameterSelection1);
_identificationParameter.AddLinkedParameter(_parameterSelection2);
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
_identificationParameter.Scaling = Scalings.Linear;
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("AA");
_parameterIdentification.AlgorithmProperties.Add(new ExtendedProperty <double> {
Name = "Toto", Value = 5
});
_runResult = new ParameterIdentificationRunResult();
_parameterIdentification.AddResult(_runResult);
_parameterIdentification.AddAnalysis(new ParameterIdentificationPredictedVsObservedChart());
_parameterIdentification.AddAnalysis(new ParameterIdentificationTimeProfileChart());
_parameterIdentification.AddAnalysis(new ParameterIdentificationResidualHistogram());
_parameterIdentification.AddAnalysis(new ParameterIdentificationResidualVsTimeChart());
GlobalBecause();
}
protected override void Context()
{
_view = A.Fake <IBuildingBlockExplorerView>();
A.CallTo(() => _view.TreeView).Returns(A.Fake <IUxTreeView>());
_regionResolver = A.Fake <IRegionResolver>();
_region = A.Fake <IRegion>();
A.CallTo(() => _regionResolver.RegionWithName(RegionNames.BuildingBlockExplorer)).Returns(_region);
_project = new PKSimProject();
var compound = A.Fake <Compound>().WithName("compound");
_individual = A.Fake <Individual>().WithName("individual");
A.CallTo(() => _individual.BuildingBlockType).Returns(PKSimBuildingBlockType.Individual);
A.CallTo(() => _individual.Species).Returns(new Species());
_project.AddBuildingBlock(_individual);
_project.AddBuildingBlock(compound);
_observedDataInExplorerPresenter = A.Fake <IObservedDataInExplorerPresenter>();
_buildingBlockIconRetriever = A.Fake <IBuildingBlockIconRetriever>();
_treeNodeFactory = A.Fake <ITreeNodeFactory>();
_contextMenuFactory = A.Fake <ITreeNodeContextMenuFactory>();
_buildingBlockTask = A.Fake <IBuildingBlockTask>();
_toolTipCreator = A.Fake <IToolTipPartCreator>();
_projectRetriever = A.Fake <IProjectRetriever>();
_classificationPresenter = A.Fake <IClassificationPresenter>();
_multipleTreeNodeContextMenuFactory = A.Fake <IMultipleTreeNodeContextMenuFactory>();
sut = new BuildingBlockExplorerPresenter(_view, _treeNodeFactory, _contextMenuFactory, _multipleTreeNodeContextMenuFactory, _buildingBlockIconRetriever, _regionResolver,
_buildingBlockTask, _toolTipCreator, _projectRetriever, _classificationPresenter, _observedDataInExplorerPresenter);
_compoundFolderNode = new RootNode(PKSimRootNodeTypes.CompoundFolder);
_individualFolderNode = new RootNode(PKSimRootNodeTypes.IndividualFolder);
_formulationFolderNode = new RootNode(PKSimRootNodeTypes.FormulationFolder);
_protocolFolderNode = new RootNode(PKSimRootNodeTypes.ProtocolFolder);
_populationFolderNode = new RootNode(PKSimRootNodeTypes.PopulationFolder);
_eventRootNode = new RootNode(PKSimRootNodeTypes.EventFolder);
_simulationNode = new SimulationNode(new ClassifiableSimulation {
Subject = new IndividualSimulation {
Id = "1"
}
});
_compoundNode = new ObjectWithIdAndNameNode <Compound>(compound);
_individualNode = new ObjectWithIdAndNameNode <Individual>(_individual);
_observationRootNode = new RootNode(RootNodeTypes.ObservedDataFolder);
A.CallTo(() => _treeNodeFactory.CreateFor(PKSimRootNodeTypes.CompoundFolder)).Returns(_compoundFolderNode);
A.CallTo(() => _treeNodeFactory.CreateFor(PKSimRootNodeTypes.IndividualFolder)).Returns(_individualFolderNode);
A.CallTo(() => _treeNodeFactory.CreateFor(PKSimRootNodeTypes.ProtocolFolder)).Returns(_protocolFolderNode);
A.CallTo(() => _treeNodeFactory.CreateFor(PKSimRootNodeTypes.FormulationFolder)).Returns(_formulationFolderNode);
A.CallTo(() => _treeNodeFactory.CreateFor(PKSimRootNodeTypes.PopulationFolder)).Returns(_populationFolderNode);
A.CallTo(() => _treeNodeFactory.CreateFor(RootNodeTypes.ObservedDataFolder)).Returns(_observationRootNode);
A.CallTo(() => _treeNodeFactory.CreateFor(PKSimRootNodeTypes.EventFolder)).Returns(_eventRootNode);
A.CallTo(() => _treeNodeFactory.CreateFor(_individual)).Returns(_individualNode);
A.CallTo(() => _treeNodeFactory.CreateFor(compound)).Returns(_compoundNode);
A.CallTo(() => _view.TreeView.NodeById(PKSimRootNodeTypes.CompoundFolder.Id)).Returns(_compoundFolderNode);
A.CallTo(() => _view.TreeView.NodeById(PKSimRootNodeTypes.IndividualFolder.Id)).Returns(_individualFolderNode);
A.CallTo(() => _view.TreeView.NodeById(PKSimRootNodeTypes.ProtocolFolder.Id)).Returns(_protocolFolderNode);
A.CallTo(() => _view.TreeView.NodeById(PKSimRootNodeTypes.FormulationFolder.Id)).Returns(_formulationFolderNode);
A.CallTo(() => _view.TreeView.NodeById(PKSimRootNodeTypes.PopulationFolder.Id)).Returns(_populationFolderNode);
A.CallTo(() => _view.TreeView.NodeById(RootNodeTypes.ObservedDataFolder.Id)).Returns(_observationRootNode);
A.CallTo(() => _view.TreeView.NodeById(PKSimRootNodeTypes.EventFolder.Id)).Returns(_eventRootNode);
A.CallTo(() => _view.AddNode(A <ITreeNode> ._)).ReturnsLazily(s => s.Arguments[0].DowncastTo <ITreeNode>());
}