public override void Execute(IExecutionContext context)
{
ObjectType = context.TypeFor(_molecule);
var containerName = string.IsNullOrEmpty(_simulationSubject.Name) ? CoreConstants.ContainerName.NameTemplate : _simulationSubject.Name;
Description = PKSimConstants.Command.AddEntityToContainer(ObjectType, _molecule.Name, context.TypeFor(_simulationSubject), containerName);
//First add the protein expression to the individual so that undo will be available
Add(AddMoleculeToSimulationSubjectCommand(_molecule, _simulationSubject, context));
//Then update the new expression values
foreach (var expressionResult in _queryExpressionResults.ExpressionResults)
{
Add(new SetRelativeExpressionCommand(_molecule.GetRelativeExpressionParameterFor(expressionResult.ContainerName), expressionResult.RelativeExpression));
}
Add(new NormalizeRelativeExpressionCommand(_molecule, context));
//update properties from first command
this.UpdatePropertiesFrom(All().FirstOrDefault());
base.Execute(context);
//clear references
_molecule = null;
_queryExpressionResults = null;
_simulationSubject = null;
}
protected AddMoleculeExpressionsFromQueryToSimulationSubjectCommand(IndividualMolecule molecule, QueryExpressionResults queryExpressionResults, TSimulationSubject simulationSubject)
{
_molecule = molecule;
_queryExpressionResults = queryExpressionResults;
_simulationSubject = simulationSubject;
CommandType = PKSimConstants.Command.CommandTypeAdd;
ExtendedDescription = queryExpressionResults.Description;
}
protected override void Context()
{
base.Context();
_expressionProfile = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>();
_querySettings = A.Fake <QueryExpressionSettings>();
_queryResults = A.Fake <QueryExpressionResults>();
A.CallTo(() => _querySettingsMapper.MapFrom(_expressionProfile.Molecule, _expressionProfile.Individual, "NAME")).Returns(_querySettings);
A.CallTo(() => _proteinExpressionPresenter.Start()).Returns(true);
A.CallTo(() => _proteinExpressionPresenter.GetQueryResults()).Returns(_queryResults);
}
public EditIndividualMoleculeExpressionInSimulationSubjectFromQueryCommand(IndividualMolecule molecule, QueryExpressionResults queryExpressionResults, ISimulationSubject simulationSubject)
{
_molecule = molecule;
_queryExpressionResults = queryExpressionResults;
_simulationSubject = simulationSubject;
CommandType = PKSimConstants.Command.CommandTypeEdit;
var containerName = string.IsNullOrEmpty(simulationSubject.Name) ? CoreConstants.ContainerName.NameTemplate : simulationSubject.Name;
Description = PKSimConstants.Command.AddEntityToContainer(ObjectType, molecule.Name, PKSimConstants.ObjectTypes.Individual, containerName);
ExtendedDescription = queryExpressionResults.Description;
}
protected override void Context()
{
base.Context();
_clonedProtein = A.Fake <IndividualMolecule>();
A.CallTo(() => _clonedProtein.AllExpressionsContainers()).Returns(_molecule.AllExpressionsContainers());
_individual.AddMolecule(_molecule);
_querySettings = A.Fake <QueryExpressionSettings>();
_queryResults = A.Fake <QueryExpressionResults>();
A.CallTo(() => _executionContext.Clone(_molecule)).Returns(_clonedProtein);
A.CallTo(() => _querySettingsMapper.MapFrom(_molecule)).Returns(_querySettings);
A.CallTo(() => _proteinExpressionPresenter.Start()).Returns(true);
A.CallTo(() => _proteinExpressionPresenter.GetQueryResults()).Returns(_queryResults);
}
protected override void Context()
{
_context = A.Fake <IExecutionContext>();
var expressionProfile = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>();
(_molecule, _) = expressionProfile;
_protein = _molecule.DowncastTo <IndividualProtein>();
_result = new QueryExpressionResults(_expressionResults);
_simulationSubject = A.Fake <ISimulationSubject>();
sut = new EditIndividualMoleculeExpressionInSimulationSubjectFromQueryCommand(_molecule, _result, _simulationSubject);
A.CallTo(() => _simulationSubject.AllExpressionParametersFor(_molecule)).Returns(_allExpressionParameters);
}
protected override void Context()
{
base.Context();
_querySettings = A.Fake <QueryExpressionSettings>();
_queryResults = new QueryExpressionResults(new List <ExpressionResult>());
_queryResults.ProteinName = _moleculeName;
A.CallTo(() => _querySettingsMapper.MapFrom(_molecule)).Returns(_querySettings);
A.CallTo(() => _proteinExpressionDbPathManager.HasDatabaseFor(_individual.Species)).Returns(true);
A.CallTo(() => _proteinExpressionPresenter.Start()).Returns(true);
A.CallTo(() => _proteinExpressionPresenter.GetQueryResults()).Returns(_queryResults);
_queryResults.QueryConfiguration = _queryConfiguration;
A.CallTo(() => _containerTask.CreateUniqueName(_individual, _queryResults.ProteinName, true)).Returns(_renamedName);
A.CallTo(() => _executionContext.BuildingBlockContaining(_molecule)).Returns(_individual);
}
protected override void Context()
{
base.Context();
sut.IsEditMode = true;
_expressionProfileDTO.MoleculeName = "MOLECULE";
_result = new QueryExpressionResults(new ExpressionResult[] { })
{
ProteinName = "NEW_NAME"
};
A.CallTo(() => _expressionProfileProteinDatabaseTask.CanQueryProteinExpressionsFor(_expressionProfile)).Returns(true);
A.CallTo(() => _expressionProfileProteinDatabaseTask.QueryDatabase(_expressionProfile, _expressionProfileDTO.MoleculeName))
.Returns(_result);
}
protected override void Context()
{
base.Context();
sut.IsEditMode = false;
_command = A.Fake <IPKSimCommand>();
_result = new QueryExpressionResults(new ExpressionResult[] { })
{
ProteinName = "NEW_NAME"
};
sut.Edit(_expressionProfile);
_expressionProfileDTO.MoleculeName = "MOLECULE";
A.CallTo(() => _expressionProfileProteinDatabaseTask.CanQueryProteinExpressionsFor(_expressionProfile)).Returns(true);
A.CallTo(() => _expressionProfileProteinDatabaseTask.QueryDatabase(_expressionProfile, _expressionProfileDTO.MoleculeName))
.Returns(_result);
A.CallTo(() => _expressionProfileUpdater.UpdateExpressionFromQuery(_expressionProfile, _result)).Returns(_command);
}
public override void Execute(IExecutionContext context)
{
ObjectType = context.TypeFor(_molecule);
var containerName = string.IsNullOrEmpty(_simulationSubject.Name) ? CoreConstants.ContainerName.NameTemplate : _simulationSubject.Name;
Description = PKSimConstants.Command.AddEntityToContainer(ObjectType, _molecule.Name, context.TypeFor(_simulationSubject), containerName);
var allExpressionParameters = _simulationSubject.AllExpressionParametersFor(_molecule);
//Then update only the expression values that have changed
foreach (var expressionResult in _queryExpressionResults.ExpressionResults)
{
var expressionParameter = allExpressionParameters[expressionResult.ContainerName];
if (expressionParameter.Value == expressionResult.RelativeExpression)
{
continue;
}
Add(new SetExpressionProfileValueCommand(expressionParameter, expressionResult.RelativeExpression, updateSimulationSubjects: false));
}
Add(new NormalizeRelativeExpressionCommand(_molecule, _simulationSubject, context));
//update properties from first command
this.UpdatePropertiesFrom(All().FirstOrDefault());
//Execute the command first to update all relative expressions
base.Execute(context);
//special treatment for protein where we have to update localization after the fact
if (_molecule is IndividualProtein protein)
{
updateLocalizationForProtein(protein, context);
}
// update depending object
var updateTask = context.Resolve <IExpressionProfileUpdater>();
updateTask.SynchronizeAllSimulationSubjectsWithExpressionProfile(_simulationSubject);
//clear references
_molecule = null;
_queryExpressionResults = null;
_simulationSubject = null;
}
public QueryExpressionResults GetQueryResults()
{
var expResults = new List <ExpressionResult>();
string selectedUnit = PresenterAt(ExpressionItems.Transfer).GetSelectedUnit();
SelectTransferData(selectedUnit, selectedUnit);
DataTable transferData = PresenterAt(ExpressionItems.Transfer).GetData();
foreach (DataRow row in transferData.Rows)
{
string containerName = row[ColumnNamesOfTransferTable.Container.ToString()].ToString();
double expRelValue;
if (row[ColumnNamesOfTransferTable.RelativeExpressionNew.ToString()] == DBNull.Value)
{
expRelValue = 0;
}
else
{
expRelValue = (double)row[ColumnNamesOfTransferTable.RelativeExpressionNew.ToString()];
}
var expResult = new ExpressionResult {
ContainerName = containerName, RelativeExpression = expRelValue
};
expResults.Add(expResult);
}
_queryExpressionResults = new QueryExpressionResults(expResults)
{
ProteinName = _proteinName,
SelectedUnit = selectedUnit,
QueryConfiguration = getQueryConfiguration(),
Description = getQueryDescription()
};
return(_queryExpressionResults);
}
public EditIndividualMoleculeExpressionInIndividualFromQueryCommand(IndividualMolecule originalMolecule, IndividualMolecule editedMolecule, QueryExpressionResults queryExpressionResults,
Individual individual) : base(originalMolecule, editedMolecule, queryExpressionResults, individual)
{
}
public ICommand EditMolecule(IndividualMolecule moleculeToEdit, IndividualMolecule editedMolecule, QueryExpressionResults queryResults, Population population)
{
return(new EditIndividualMoleculeExpressionInPopulationFromQueryCommand(moleculeToEdit, editedMolecule, queryResults, population).Run(_executionContext));
}
public EditIndividualMoleculeExpressionInPopulationFromQueryCommand(IndividualMolecule originalMolecule, IndividualMolecule editedMolecule, QueryExpressionResults queryExpressionResults,
Population population) : base(originalMolecule, editedMolecule, queryExpressionResults, population)
{
}
public AddMoleculeExpressionsFromQueryToPopulationCommand(IndividualMolecule molecule, QueryExpressionResults queryExpressionResults, Population population)
: base(molecule, queryExpressionResults, population)
{
}
public ICommand AddMoleculeTo(IndividualMolecule molecule, Population population, QueryExpressionResults queryExpressionResults)
{
var baseCommand = new AddMoleculeExpressionsFromQueryToPopulationCommand(molecule, queryExpressionResults, population);
return(addMoleculeToPopulation(molecule, population, baseCommand));
}
public ICommand UpdateExpressionFromQuery(ExpressionProfile expressionProfile, QueryExpressionResults queryResults)
{
var(molecule, individual) = expressionProfile;
molecule.QueryConfiguration = queryResults.QueryConfiguration;
return(new EditIndividualMoleculeExpressionInSimulationSubjectFromQueryCommand(molecule, queryResults, individual)
.Run(_executionContext));
}
private ICommand addMoleculeTo <TMolecule>(TMolecule molecule, TSimulationSubject simulationSubject, QueryExpressionResults queryExpressionResults) where TMolecule : IndividualMolecule
{
var command = _simulationSubjectExpressionTask.AddMoleculeTo(molecule, simulationSubject, queryExpressionResults);
setDefaultFor(molecule, simulationSubject, queryExpressionResults.ProteinName);
return(command);
}
private ICommand editMolecule <TMolecule>(TMolecule moleculeToEdit, TMolecule editedMolecule, QueryExpressionResults queryResults, TSimulationSubject simulationSubject)
where TMolecule : IndividualMolecule
{
return(_simulationSubjectExpressionTask.EditMolecule(moleculeToEdit, editedMolecule, queryResults, simulationSubject));
}
protected override void Because()
{
_result = sut.QueryDatabase(_expressionProfile, "NAME");
}
public AddMoleculeExpressionsFromQueryToIndividualCommand(IndividualMolecule molecule, QueryExpressionResults queryExpressionResults, Individual individual) :
base(molecule, queryExpressionResults, individual)
{
}
public ICommand AddMoleculeTo(IndividualMolecule molecule, Individual individual, QueryExpressionResults queryExpressionResults)
{
return(new AddMoleculeExpressionsFromQueryToIndividualCommand(molecule, queryExpressionResults, individual).Run(_executionContext));
}
