protected override void Context()
{
base.Context();
var displayUnitRetriever = IoC.Resolve <IDisplayUnitRetriever>();
var f1 = new ExplicitFormula("CL*conc").WithName("formula");
var r1 = new ReactionBuilder().WithName("Reaction").WithFormula(f1);
r1.AddEduct(new ReactionPartnerBuilder("Drug", 1));
r1.AddEduct(new ReactionPartnerBuilder("Metab", 1));
r1.AddModifier("Cyp");
var concentrationDimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
var p1Formula = new ConstantFormula(2).WithDimension(concentrationDimension);
var p11 = new Parameter().WithName("P1").WithFormula(p1Formula).WithParentContainer(r1);
var f2 = new ExplicitFormula("CL*conc").WithName("formula");
var r2 = new ReactionBuilder().WithName("Reaction").WithFormula(f2);
r2.AddEduct(new ReactionPartnerBuilder("Drug", 1));
r2.AddEduct(new ReactionPartnerBuilder("Metab", 1));
r2.AddModifier("Cyp");
var p12Forumla = new ConstantFormula(3).WithDimension(concentrationDimension);
var p12 = new Parameter().WithName("P1").WithFormula(p12Forumla).WithParentContainer(r2);
_object1 = r1;
_object2 = r2;
_preferredUnit = concentrationDimension.Units.ElementAt(0);
A.CallTo(() => displayUnitRetriever.PreferredUnitFor(p1Formula, null)).Returns(_preferredUnit);
A.CallTo(() => displayUnitRetriever.PreferredUnitFor(p12Forumla, null)).Returns(_preferredUnit);
}
protected override void Context()
{
base.Context();
var reactionBuilder = new ReactionBuilder().WithName("R1");
_parameter = new Parameter().WithName("P1").WithMode(ParameterBuildMode.Local).WithParentContainer(reactionBuilder);
}
protected override void Context()
{
_simulation = new ModelCoreSimulation();
var root = new Container();
root.Add(new EventGroup());
_simulation.Model = new Model();
_simulation.Model.Root = root;
_simulation.BuildConfiguration = new BuildConfiguration();
var reactionBuildingBlock = new ReactionBuildingBlock();
var reactionAtoB = new ReactionBuilder();
var reactionBtoA = new ReactionBuilder();
var partnerA = new ReactionPartnerBuilder("A", 0);
var partnerB = new ReactionPartnerBuilder("B", 0);
//Making both reactions dependent on each other
reactionAtoB.AddProduct(partnerA);
reactionBtoA.AddProduct(partnerB);
reactionAtoB.AddEduct(partnerB);
reactionBtoA.AddEduct(partnerA);
reactionBuildingBlock.Add(reactionAtoB);
reactionBuildingBlock.Add(reactionBtoA);
_simulation.BuildConfiguration.Reactions = reactionBuildingBlock;
}
protected override void Context()
{
base.Context();
_project = new MoBiProject();
var molecule = new MoleculeBuilder().WithName(_moleculeName);
var moleculeParameter = new Parameter().WithName(_moleculeParameterName);
molecule.Add(moleculeParameter);
var molecules = new MoleculeBuildingBlock()
{
molecule
};
_project.AddBuildingBlock(molecules);
var parameter = new Parameter().WithName(_parameterName);
var root = new Container().WithName("Root");
root.Add(parameter);
var spatialStructure = new MoBiSpatialStructure().WithTopContainer(root);
_project.AddBuildingBlock(spatialStructure);
var reactionBuilder = new ReactionBuilder().WithName(_reactionName);
var reactions = new MoBiReactionBuildingBlock()
{
reactionBuilder
};
_project.AddBuildingBlock(reactions);
A.CallTo(() => _context.CurrentProject).Returns(_project);
}
protected override void Context()
{
base.Context();
_reactionBuilder = new ReactionBuilder {
Dimension = DomainHelperForSpecs.ConcentrationPerTimeDimension
};
A.CallTo(() => _reactionDimensionRetriever.SelectedDimensionMode).Returns(ReactionDimensionMode.AmountBased);
}
protected override void Context()
{
base.Context();
_reactionParameter = new Parameter().WithName("RP");
var reactionBuilder = new ReactionBuilder();
reactionBuilder.Add(_reactionParameter);
}
protected ReactionBuilder createReaction()
{
var reaction = new ReactionBuilder();
reaction.AddEduct(new ReactionPartnerBuilder("educt", 1.0));
reaction.AddProduct(new ReactionPartnerBuilder("product", 1.0));
reaction.AddModifier("modifier");
return(reaction);
}
protected override void Context()
{
_reactionBuildingBlock = new MoBiReactionBuildingBlock();
_moBiReactionDiagramManager = A.Fake <IMoBiReactionDiagramManager>();
_reactionBuildingBlock.DiagramManager = _moBiReactionDiagramManager;
_reaction = new ReactionBuilder().WithName("R");
_reaction.AddModifier("old");
sut = new ChangeModifierCommand("new", "old", _reaction, _reactionBuildingBlock);
}
protected IReactionBuilder CreateReactionForCompoundAndMetabolite(string[] products, params string[] educts)
{
var reaction = new ReactionBuilder();
educts.Each(educt => reaction.AddEduct(new ReactionPartnerBuilder(educt, 1)));
products.Each(product => reaction.AddProduct(new ReactionPartnerBuilder(product, 1)));
return(reaction);
}
protected override void Context()
{
base.Context();
createReaction();
_sourceReaction = createReaction();
_targetReaction = new ReactionBuilder();
_sourceBuildingBlock.Add(_sourceReaction);
_targetBuildingBlock.Add(_targetReaction);
}
protected override void Context()
{
base.Context();
_sourceBuilder = new ReactionBuilder {
Name = "builder"
};
A.CallTo(() => _sourceBuildingBlock.DiagramModel.FindByName(_sourceBuilder.Name)).Returns(null);
}
protected override void Context()
{
base.Context();
_formulaCache = new FormulaCache();
_protein = A.Fake <IMoleculeBuilder>().WithName("CYP3A4");
var reaction = new ReactionBuilder {
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"));
_template = A.Fake <IReactionBuilder>().WithName(CoreConstants.Reaction.TURNOVER);
A.CallTo(() => _cloneManager.Clone(_template)).Returns(reaction);
}
private IEnumerable <IReactionBuilder> getReactions()
{
var r1 = new ReactionBuilder();
r1.AddEduct(new ReactionPartnerBuilder("C", 2.0));
r1.AddProduct(new ReactionPartnerBuilder("D1", 1.0));
r1.Name = "name";
r1.WithKinetic(new ExplicitFormula("k1*C"));
r1.Description = "description";
yield return(r1);
yield return(A.Fake <IReactionBuilder>());
}
protected override void Context()
{
_quantity = _parameter;
base.Context();
var reaction = new ReactionBuilder();
reaction.AddParameter(_parameter);
var reactionBuildingBlock = new ReactionBuildingBlock {
reaction
};
_buildingBlockInfo.UntypedBuildingBlock = reactionBuildingBlock;
}
protected override void Context()
{
_oldMoleculeName = "A";
_newMoleculeName = "B";
_reaction = new ReactionBuilder().WithId("R");
_reactionPartner = new ReactionPartnerBuilder(_oldMoleculeName, 3);
_buildingBlock = A.Fake <IMoBiReactionBuildingBlock>().WithId("BB");
_context = A.Fake <IMoBiContext>();
A.CallTo(() => _context.Get <IReactionBuilder>(_reaction.Id)).Returns(_reaction);
A.CallTo(() => _context.Get <IMoBiReactionBuildingBlock>(_buildingBlock.Id)).Returns(_buildingBlock);
AddPartnerToReaction();
_diagramManager = A.Fake <IMoBiReactionDiagramManager>();
A.CallTo(() => _buildingBlock.DiagramManager).Returns(_diagramManager);
sut = new EditReactionPartnerMoleculeNameCommand(_newMoleculeName, _reaction, _reactionPartner, _buildingBlock);
}
protected override void Context()
{
base.Context();
createReaction();
_sourceReaction = createReaction();
_targetReaction = createReaction();
_sourceBuildingBlock.Add(_sourceReaction);
_targetBuildingBlock = A.Fake <IMoBiReactionBuildingBlock>();
A.CallTo(_targetBuildingBlock).WithReturnType <IEnumerable <IReactionBuilder> >().Returns(new[] { _targetReaction });
var moleculeNodes = createMoleculeNodes();
A.CallTo(() => _targetBuildingBlock.AllMolecules).Returns(moleculeNodes.Select(x => x.Name));
}
protected override void Context()
{
base.Context();
_reaction1 = new ReactionBuilder().WithName("Reaction");
_parameter = new Parameter().WithName("ReferencFrom").WithParentContainer(_reaction1);
_otherParameter = new Parameter().WithName("ToReference").WithParentContainer(_reaction1);
_reaction2 = new ReactionBuilder().WithName("Reaction2");
_reaction3 = new ReactionBuilder().WithName("A Reaction");
_otherParameter2 = new Parameter().WithName("ToReference").WithParentContainer(_reaction2);
_reactionBuilidingBlock = new ReactionBuildingBlock();
_reactionBuilidingBlock.Add(_reaction1);
_reactionBuilidingBlock.Add(_reaction2);
_reactionBuilidingBlock.Add(_reaction3);
}
protected override void Context()
{
base.Context();
_reactionBuildingBlock = new ReactionBuildingBlock();
_firstNode = A.Fake <IBaseNode>();
A.CallTo(() => _firstNode.Id).Returns("Id1");
A.CallTo(() => _firstNode.Name).Returns("Name");
_secondBuilder = new ReactionBuilder {
Name = "Name", Id = "Id2"
};
_simulation.Reactions = _reactionBuildingBlock;
_reactionBuildingBlock.Add(_secondBuilder);
_diagramModel = A.Fake <IDiagramModel>();
A.CallTo(() => _simulation.ReactionDiagramModel).Returns(_diagramModel);
A.CallTo(() => _diagramModel.FindByName(_secondBuilder.Name)).Returns(_firstNode);
}
protected override void Context()
{
base.Context();
_targetBuildingBlock.Add(new ReactionBuilder {
Name = "reactionName"
});
_sourceBuilder = new ReactionBuilder {
Name = "reactionName"
};
_sourceBuildingBlock.Add(_sourceBuilder);
_sourceNode = A.Fake <IBaseNode>();
_targetNode = A.Fake <IBaseNode>();
A.CallTo(() => _sourceBuildingBlock.DiagramModel.FindByName("reactionName")).Returns(_sourceNode);
A.CallTo(() => _targetBuildingBlock.DiagramModel.FindByName("reactionName")).Returns(_targetNode);
}
protected override void Context()
{
base.Context();
_project = new MoBiProject();
var molecule = new MoleculeBuilder().WithName(_moleculeName);
var moleculeParameter = new Parameter().WithName(_moleculeParameterName);
molecule.Add(moleculeParameter);
var molecules = new MoleculeBuildingBlock()
{
molecule
};
_project.AddBuildingBlock(molecules);
var parameter = new Parameter().WithName(_parameterName);
var root = new Container().WithName(_topContainerName);
root.Add(parameter);
var spatialStructure = new MoBiSpatialStructure().WithTopContainer(root);
spatialStructure.GlobalMoleculeDependentProperties = new Container().WithName(Constants.MOLECULE_PROPERTIES);
spatialStructure.NeighborhoodsContainer = new Container().WithName(Constants.NEIGHBORHOODS);
_project.AddBuildingBlock(spatialStructure);
var reactionBuilder = new ReactionBuilder().WithName(_reactionName);
var reactions = new MoBiReactionBuildingBlock()
{
reactionBuilder
};
_project.AddBuildingBlock(reactions);
_project.AddSimulation(new MoBiSimulation().WithName(_simulationName));
var eventGroupBuilder = new EventGroupBuilder().WithName(_eventGroupName);
var eventGroupBuildingBlock = new EventGroupBuildingBlock();
eventGroupBuildingBlock.Add(eventGroupBuilder);
_project.AddBuildingBlock(eventGroupBuildingBlock);
A.CallTo(() => _context.CurrentProject).Returns(_project);
}
protected override void Context()
{
base.Context();
var f1 = new ExplicitFormula("CL*conc").WithName("formula");
var r1 = new ReactionBuilder().WithName("Reaction").WithFormula(f1);
r1.AddEduct(new ReactionPartnerBuilder("Drug", 1));
r1.AddEduct(new ReactionPartnerBuilder("Metab", 1));
r1.AddModifier("Cyp");
var p11 = new Parameter().WithName("P1").WithFormula(new ConstantFormula(2)).WithParentContainer(r1);
var f2 = new ExplicitFormula("CL*conc").WithName("formula");
var r2 = new ReactionBuilder().WithName("Reaction").WithFormula(f2);
r2.AddEduct(new ReactionPartnerBuilder("Drug", 1));
r2.AddEduct(new ReactionPartnerBuilder("Metab2", 1));
r2.AddModifier("Cyp");
var p12 = new Parameter().WithName("P1").WithFormula(new ConstantFormula(2)).WithParentContainer(r2);
_object1 = r1;
_object2 = r2;
}
protected override void Context()
{
base.Context();
_reactionBuildingBlock = new MoBiReactionBuildingBlock
{
DiagramModel = new DiagramModel(),
DiagramManager = new MoBiReactionDiagramManager()
};
_moBiReactionDiagramManager = _reactionBuildingBlock.DiagramManager.DowncastTo <IReactionDiagramManager <IMoBiReactionBuildingBlock> >();
_moBiReactionDiagramManager.InitializeWith(_reactionBuildingBlock, A.Fake <IDiagramOptions>());
_molecule = new MoleculeBuilder().WithId("moleculeId").WithName("moleculeName");
_reaction = new ReactionBuilder().WithId("reactionId");
_reaction.AddEduct(new ReactionPartnerBuilder(_molecule.Name, 1.0));
_reactionBuildingBlock.Add(_reaction);
_moBiReactionDiagramManager.AddObjectBase(_reaction);
_moBiReactionDiagramManager.AddMolecule(_reaction, "moleculeName");
_moleculeNode = _moBiReactionDiagramManager.GetMoleculeNodes("moleculeName").FirstOrDefault();
_reactionNode = _moBiReactionDiagramManager.PkModel.DiagramModel.GetAllChildren <ReactionNode>().FirstOrDefault();
_interactionTask = A.Fake <IInteractionTasksForChildren <IMoBiReactionBuildingBlock, IReactionBuilder> >();
_activeSubjectRetriever = A.Fake <IActiveSubjectRetriever>();
var reactionLink = new ReactionLink();
reactionLink.Initialize(ReactionLinkType.Educt, _reactionNode, _moleculeNode);
sut.Edit(_reactionBuildingBlock);
var removeReactionCommand = new RemoveCommandFor <IMoBiReactionBuildingBlock, IReactionBuilder>(_interactionTask, _moBiContext, _activeSubjectRetriever);
A.CallTo(() => _moBiContext.Get <IReactionBuilder>(_reaction.Id)).Returns(_reaction);
A.CallTo(() => _moBiContext.Resolve <RemoveCommandFor <IMoBiReactionBuildingBlock, IReactionBuilder> >()).Returns(removeReactionCommand);
A.CallTo(() => _activeSubjectRetriever.Active <IBuildingBlock>()).Returns(_reactionBuildingBlock);
A.CallTo(() => _interactionTask.Remove(_reaction, _reactionBuildingBlock, _reactionBuildingBlock, A <bool> ._)).Invokes(x => _reactionBuildingBlock.Remove(_reaction));
}
protected override void Context()
{
_reactionBuilder = new ReactionBuilder();
sut = new ReactionBuilderToObjectBaseSummaryDTOMapper(new StoichiometricStringCreator(new ReactionPartnerToReactionPartnerBuilderMapper()), new ObjectTypeResolver());
}
protected override void Context()
{
sut = new ReactionBuilder();
}
private MoBiCommand moveDiagramNodes(MoBiReactionBuildingBlock source, MoBiReactionBuildingBlock target)
{
IReactionBuilder sourceBuilder = new ReactionBuilder().WithName("sourceBuilder");
return(sut.MoveDiagramNodes(source, target, sourceBuilder, sourceBuilder.Name) as MoBiCommand);
}
public override void Register()
{
Register(ReactionBuilder.For <IHomeStore>(SomeAction)
.Observe(x => x.Value));
}
