public ICommand UpdateMoleculeName(ExpressionProfile expressionProfile, string newMoleculeName)
{
var command = new PKSimMacroCommand();
var oldMoleculeName = expressionProfile.MoleculeName;
//we are not renaming anything
if (string.Equals(newMoleculeName, oldMoleculeName))
{
return(command);
}
var(_, individual) = expressionProfile;
var mainCommand = renameMoleculeReferences(individual, oldMoleculeName, newMoleculeName);
command.Add(mainCommand);
command.UpdatePropertiesFrom(mainCommand);
allSimulationSubjectsUsing(expressionProfile).Each(x =>
{
_lazyLoadTask.Load(x);
command.Add(renameMoleculeReferences(x, oldMoleculeName, newMoleculeName));
});
return(command);
}
private ICommand setParameterValue(IParameter sourceParameter, IParameter targetParameter, bool forceUpdate)
{
//Always update the default value of the target parameter
targetParameter.DefaultValue = sourceParameter.DefaultValue;
if (!forceUpdate && areValuesEqual(targetParameter, sourceParameter))
{
//same value but not same display unit, simply update the display unit
if (sourceParameter.DisplayUnit == targetParameter.DisplayUnit)
{
return(null);
}
return(_parameterTask.SetParameterDisplayUnit(targetParameter, sourceParameter.DisplayUnit));
}
var setValueCommand = _parameterTask.SetParameterValue(targetParameter, sourceParameter.Value);
//Only value differs
if (sourceParameter.DisplayUnit == targetParameter.DisplayUnit)
{
return(setValueCommand);
}
//in that case, we create a macro command that updates value and unit
var setDisplayUnitCommand = _parameterTask.SetParameterDisplayUnit(targetParameter, sourceParameter.DisplayUnit);
var macroCommand = new PKSimMacroCommand {
CommandType = setValueCommand.CommandType, ObjectType = setValueCommand.ObjectType, Description = PKSimConstants.Command.SetParameterValueAndDisplayUnitDescription
};
macroCommand.Add(setValueCommand);
macroCommand.Add(setDisplayUnitCommand);
return(macroCommand);
}
private IOSPSuiteCommand withUpdatedDefaultStateAndValue(IOSPSuiteCommand executedCommand, IParameter parameter, bool shouldChangeVersion = true, bool shouldUpdateDefaultStateAndValueOriginForDefaultParameter = true)
{
if (!shouldUpdateDefaultStateAndValueOriginForDefaultParameter)
{
return(executedCommand);
}
if (!parameter.IsDefault)
{
return(executedCommand);
}
if (executedCommand.IsEmpty())
{
return(executedCommand);
}
var macroCommand = new PKSimMacroCommand().WithHistoryEntriesFrom(executedCommand);
macroCommand.Add(executedCommand);
macroCommand.Add(new SetParameterDefaultStateCommand(parameter, isDefault: false)
{
ShouldChangeVersion = shouldChangeVersion
}.Run(_executionContext).AsHidden());
var setValueOriginCommand = setParameterValueOrigin(parameter, ValueOrigin.Unknown, shouldChangeVersion).AsHidden();
macroCommand.Add(setValueOriginCommand);
return(macroCommand);
}
private IPKSimMacroCommand updateParameters(PathCache <IParameter> allParameters, ParameterVariationSet parameterVariationSet)
{
var macroCommand = new PKSimMacroCommand();
foreach (var parameterValue in parameterVariationSet.ParameterValues)
{
var parameterPath = parameterValue.ParameterPath;
var parameter = allParameters[parameterPath];
if (parameter == null)
{
//try with adding the name of the simulation at first
parameterPath = $"{Simulation.Name}{ObjectPath.PATH_DELIMITER}{parameterPath}";
parameter = allParameters[parameterPath];
if (parameter == null)
{
_logger.AddWarning($"Parameter with path '{parameterValue.ParameterPath}' not found!");
continue;
}
}
_logger.AddDebug($"Parameter '{parameterValue.ParameterPath}' value set from '{parameter.Value} to '{parameterValue.Value}'.");
macroCommand.Add(new SetParameterValueCommand(parameter, parameterValue.Value));
}
return(macroCommand.Run(_executionContext));
}
public ICommand UpdateParametersFromSimulationInBuildingBlock(Simulation simulation, IPKSimBuildingBlock templateBuildingBlock)
{
//Update the building block in the simulation based on the same template
var usedBuildingBlock = simulation.UsedBuildingBlockByTemplateId(templateBuildingBlock.Id);
//Template was not used in the simulation...return
if (usedBuildingBlock == null)
{
return(null);
}
var buildingBlockType = _executionContext.TypeFor(templateBuildingBlock);
var templateParameters = parametersToUpdateFrom(templateBuildingBlock);
var usedBuildingBlockParameters = parametersToUpdateFrom(usedBuildingBlock.BuildingBlock);
var updateCommands = new PKSimMacroCommand
{
ObjectType = buildingBlockType,
BuildingBlockType = buildingBlockType,
BuildingBlockName = templateBuildingBlock.Name,
CommandType = PKSimConstants.Command.CommandTypeUpdate,
Description = PKSimConstants.Command.UpdateTemplateBuildingBlockCommandDescription(buildingBlockType, templateBuildingBlock.Name, simulation.Name)
};
_executionContext.UpdateBuildingBlockPropertiesInCommand(updateCommands, templateBuildingBlock);
//First Update the parameters in the template building block (the parameter in the used building block are synchronized with the one used in the simulation)
var updateTemplateParametersCommand = updateParameterValues(usedBuildingBlockParameters, templateParameters);
updateTemplateParametersCommand.Description = PKSimConstants.Command.UpdateTemplateParameterCommandDescription(templateBuildingBlock.Name, buildingBlockType, simulation.Name);
_executionContext.UpdateBuildingBlockPropertiesInCommand(updateTemplateParametersCommand, templateBuildingBlock);
updateCommands.Add(updateTemplateParametersCommand);
//Last, see if we have some special cases to handle
var synchronizeCommand = synchronizeBuildingBlocks(templateBuildingBlock, updateTemplateParametersCommand);
updateCommands.Add(synchronizeCommand);
//now make sure that the used building block is updated with the template building block info
updateCommands.Add(new UpdateUsedBuildingBlockInfoCommand(simulation, usedBuildingBlock, templateBuildingBlock, _executionContext).Run(_executionContext));
_executionContext.PublishEvent(new BuildingBlockUpdatedEvent(templateBuildingBlock));
return(updateCommands);
}
protected override void Context()
{
_macroCommand = new PKSimMacroCommand();
_macroCommand.Description = "my name is " + CoreConstants.ContainerName.NameTemplate;
_macroCommand.ExtendedDescription = "my extended is " + CoreConstants.ContainerName.NameTemplate;
_subCommand = A.Fake <IPKSimCommand>();
_subCommand.Description = null;
_subCommand.ExtendedDescription = "extended is " + CoreConstants.ContainerName.NameTemplate;
_macroCommand.Add(_subCommand);
}
private ICommand withUpdatedValueOrigin(ICommand command, IParameter sourceParameter, IParameter targetParameter)
{
if (Equals(sourceParameter.ValueOrigin, targetParameter.ValueOrigin))
{
return(command);
}
var updateValueOriginCommand = _parameterTask.SetParameterValueOrigin(targetParameter, sourceParameter.ValueOrigin);
if (command == null)
{
return(updateValueOriginCommand);
}
var macroCommand = new PKSimMacroCommand {
CommandType = command.CommandType, ObjectType = command.ObjectType, Description = command.Description
};
macroCommand.Add(command);
macroCommand.Add(updateValueOriginCommand);
return(macroCommand);
}
public ICommand UpdateParametersFromBuildingBlockInSimulation(IPKSimBuildingBlock templateBuildingBlock, Simulation simulation)
{
//Update the building block in the simulation based on the same template
var usedBuildingBlock = simulation.UsedBuildingBlockByTemplateId(templateBuildingBlock.Id);
//Template was not used in the simulation...return
if (usedBuildingBlock == null)
{
return(null);
}
string buildingBlockType = _executionContext.TypeFor(templateBuildingBlock);
var templateParameters = parametersToUpdateFrom(templateBuildingBlock);
var usedBuildingBlockParameters = parametersToUpdateFrom(usedBuildingBlock.BuildingBlock);
var updateCommands = new PKSimMacroCommand();
//First Update the parameters in the used building block (internal command, should be visible = false)
var updateUsedBuildingBlockParameterCommand = updateParameterValues(templateParameters, usedBuildingBlockParameters);
updateUsedBuildingBlockParameterCommand.Visible = false;
updateUsedBuildingBlockParameterCommand.Description = PKSimConstants.Command.UpdateUsedBuildingBlockParameterCommandDescription(templateBuildingBlock.Name, buildingBlockType, simulation.Name);
updateCommands.Add(updateUsedBuildingBlockParameterCommand);
//then update the values in the simulation from the used building block
foreach (var command in updateParameterValues(usedBuildingBlockParameters, simulation, usedBuildingBlock.BuildingBlockType))
{
updateCommands.Add(command);
}
//now make sure that the used building block is updated with the template building block info
updateCommands.Add(new UpdateUsedBuildingBlockInfoCommand(simulation, usedBuildingBlock, templateBuildingBlock, _executionContext).Run(_executionContext));
updateCommands.ObjectType = PKSimConstants.ObjectTypes.Simulation;
updateCommands.CommandType = PKSimConstants.Command.CommandTypeUpdate;
updateCommands.Description = PKSimConstants.Command.UpdateBuildingBlockCommandDescription(buildingBlockType, templateBuildingBlock.Name, simulation.Name);
_executionContext.UpdateBuildinBlockPropertiesInCommand(updateCommands, simulation);
return(updateCommands);
}
public ICommand UpdateParametersFromSimulationInBuildingBlock(Simulation simulation, IPKSimBuildingBlock templateBuildingBlock)
{
//Update the building block in the simulation based on the same template
var usedBuildingBlock = simulation.UsedBuildingBlockByTemplateId(templateBuildingBlock.Id);
//Template was not used in the simulation...return
if (usedBuildingBlock == null)
{
return(null);
}
var buildingBlockType = _executionContext.TypeFor(templateBuildingBlock);
var templateParameters = _containerTask.CacheAllChildren <IParameter>(templateBuildingBlock);
var usedBuildingBlockParameters = _containerTask.CacheAllChildren <IParameter>(usedBuildingBlock.BuildingBlock);
var updateCommands = new PKSimMacroCommand();
//First Update the parameters in the template building block (the parameter in the used building block are synchronized with the one used in the simulation)
var updateTemplateParametersCommand = updateParameterValues(usedBuildingBlockParameters, templateParameters);
updateTemplateParametersCommand.Description = PKSimConstants.Command.UpdateTemplateParameterCommandDescription(templateBuildingBlock.Name, buildingBlockType, simulation.Name);
_executionContext.UpdateBuildinBlockPropertiesInCommand(updateTemplateParametersCommand, templateBuildingBlock);
updateCommands.Add(updateTemplateParametersCommand);
//now make sure that the used building block is updated with the template building block info
updateCommands.Add(new UpdateUsedBuildingBlockInfoCommand(simulation, usedBuildingBlock, templateBuildingBlock, _executionContext).Run(_executionContext));
updateCommands.ObjectType = buildingBlockType;
updateCommands.BuildingBlockType = buildingBlockType;
updateCommands.BuildingBlockName = templateBuildingBlock.Name;
updateCommands.CommandType = PKSimConstants.Command.CommandTypeUpdate;
updateCommands.Description = PKSimConstants.Command.UpdateTemplateBuildingBlockCommandDescription(buildingBlockType, templateBuildingBlock.Name, simulation.Name);
_executionContext.UpdateBuildinBlockPropertiesInCommand(updateCommands, templateBuildingBlock);
_executionContext.PublishEvent(new BuildingBlockUpdatedEvent(templateBuildingBlock));
return(updateCommands);
}
private ICommand setParameterValue(IParameter sourceParameter, IParameter targetParameter, bool forceUpdate)
{
//If the parameter we are updating from is a default parameter, the target parameter should either remain as is (default or not default)
bool shouldUpdateDefaultState = !sourceParameter.IsDefault;
//Always update the default value of the target parameter
targetParameter.DefaultValue = sourceParameter.DefaultValue;
if (!forceUpdate && areValuesEqual(targetParameter, sourceParameter))
{
//same value but not same display unit, simply update the display unit
if (areDisplayUnitsEqual(targetParameter, sourceParameter))
{
return(null);
}
return(_parameterTask.SetParameterDisplayUnit(targetParameter, sourceParameter.DisplayUnit, shouldUpdateDefaultState));
}
var setValueCommand = _parameterTask.SetParameterValue(targetParameter, sourceParameter.Value, shouldUpdateDefaultState);
//Only value differs
if (areDisplayUnitsEqual(targetParameter, sourceParameter))
{
return(setValueCommand);
}
//in that case, we create a macro command that updates value and unit
var setDisplayUnitCommand = _parameterTask.SetParameterDisplayUnit(targetParameter, sourceParameter.DisplayUnit, shouldUpdateDefaultState);
var macroCommand = new PKSimMacroCommand {
CommandType = setValueCommand.CommandType, ObjectType = setValueCommand.ObjectType, Description = PKSimConstants.Command.SetParameterValueAndDisplayUnitDescription
};
macroCommand.Add(setValueCommand);
macroCommand.Add(setDisplayUnitCommand);
return(macroCommand);
}
private IPKSimCommand createProcessFor <TCompoundProcess, TCreateProcessPresenter>(Compound compound, IEnumerable <TCompoundProcess> templates, string defaultMoleculeName)
where TCompoundProcess : CompoundProcess
where TCreateProcessPresenter : ICreateProcessPresenter
{
using (var editPresenter = _applicationController.Start <TCreateProcessPresenter>())
{
var partialPresenter = editPresenter as ICreatePartialProcessPresenter;
if (partialPresenter != null)
{
partialPresenter.DefaultMoleculeName = defaultMoleculeName;
}
var editCommands = editPresenter.CreateProcess(compound, templates);
//Canceled by user
if (editCommands.IsEmpty())
{
return(editCommands);
}
var process = editPresenter.Process;
//create + add command are added as one action into the history
var overallCommand = new PKSimMacroCommand {
CommandType = PKSimConstants.Command.CommandTypeAdd
};
_executionContext.UpdateBuildingBlockPropertiesInCommand(overallCommand, compound);
//First add process to compound so that it will be available for later rollbacks
var addProcessToCompound = new AddProcessToCompoundCommand(process, compound, _executionContext).Run(_executionContext);
overallCommand.Add(addProcessToCompound);
overallCommand.Description = addProcessToCompound.Description;
overallCommand.ObjectType = addProcessToCompound.ObjectType;
_executionContext.UpdateBuildingBlockPropertiesInCommand(editCommands, compound);
var macroCommand = editCommands as IPKSimMacroCommand;
if (macroCommand != null)
{
macroCommand.ReplaceNameTemplateWithName(compound.Name);
macroCommand.ReplaceTypeTemplateWithType(_executionContext.TypeFor(compound));
macroCommand.All().Each(overallCommand.Add);
}
return(overallCommand);
}
}
public IOSPSuiteCommand UpdateValues(PathCache <IParameter> sourceParameters, PathCache <IParameter> targetParameters, bool updateParameterOriginId = true)
{
var updateCommands = new PKSimMacroCommand {
CommandType = PKSimConstants.Command.CommandTypeEdit, ObjectType = PKSimConstants.ObjectTypes.Parameter
};
//should update non distributed parameter first and then distributed parameter
foreach (var sourceParameter in sourceParameters.KeyValues.OrderBy(x => x.Value.IsDistributed()))
{
var targetParameter = targetParameters[sourceParameter.Key];
if (targetParameter == null)
{
continue;
}
updateCommands.Add(UpdateValue(sourceParameter.Value, targetParameter, updateParameterOriginId));
}
return(updateCommands);
}
public bool Delete <TBuildingBlock>(IReadOnlyList <TBuildingBlock> buildingBlocksToDelete) where TBuildingBlock : class, IPKSimBuildingBlock
{
if (!buildingBlocksToDelete.Any())
{
return(true);
}
var buildingBlockType = _entityTask.TypeFor(buildingBlocksToDelete.First());
foreach (var buildingBlockToDelete in buildingBlocksToDelete)
{
var simulationsUsingBuildingBlockToDelete = _buildingBlockInSimulationManager.SimulationsUsing(buildingBlockToDelete).ToList();
if (simulationsUsingBuildingBlockToDelete.Any())
{
throw new CannotDeleteBuildingBlockException(buildingBlockToDelete.Name, buildingBlockType, simulationsUsingBuildingBlockToDelete);
}
}
var viewResult = _dialogCreator.MessageBoxYesNo(PKSimConstants.UI.ReallyDeleteObjectOfType(buildingBlockType, buildingBlocksToDelete.AllNames().ToArray()));
if (viewResult == ViewResult.No)
{
return(false);
}
buildingBlocksToDelete.OfType <Simulation>().Each(simulation => _simulationReferenceUpdater.RemoveSimulationFromParameterIdentificationsAndSensitivityAnalyses(simulation));
var macoCommand = new PKSimMacroCommand
{
CommandType = PKSimConstants.Command.CommandTypeDelete,
ObjectType = buildingBlockType,
BuildingBlockType = buildingBlockType,
Description = PKSimConstants.Command.ObjectsDeletedFromProject(buildingBlockType),
};
buildingBlocksToDelete.Each(x => macoCommand.Add(DeleteCommand(x)));
AddCommandToHistory(macoCommand.Run(_executionContext));
buildingBlocksToDelete.Each(RemovePresenterSettings);
return(true);
}
public ICommand UpdateValuesByName(IEnumerable <IParameter> sourceParameters, IEnumerable <IParameter> targetParameters)
{
var updateCommands = new PKSimMacroCommand {
CommandType = PKSimConstants.Command.CommandTypeEdit, ObjectType = PKSimConstants.ObjectTypes.Parameter
};
var targetParameterCache = new Cache <string, IParameter>(p => p.Name, key => null);
targetParameterCache.AddRange(targetParameters);
foreach (var sourceParameter in sourceParameters)
{
var targetParameter = targetParameterCache[sourceParameter.Name];
if (targetParameter == null)
{
continue;
}
updateCommands.Add(UpdateValue(sourceParameter, targetParameter));
}
return(updateCommands);
}
public void ScaleIndividual(Individual individualToScale)
{
_buildingBlockTask.Load(individualToScale);
using (var presenter = _applicationController.Start <IScaleIndividualPresenter>())
{
var scaleCommand = presenter.ScaleIndividual(individualToScale);
//User cancel action. return
if (scaleCommand.IsEmpty())
{
return;
}
var scaledIndividual = presenter.Individual;
var overallCommand = new PKSimMacroCommand
{
CommandType = PKSimConstants.Command.CommandTypeScale,
ObjectType = PKSimConstants.ObjectTypes.Individual,
Description = PKSimConstants.Command.ScaleIndividualDescription(individualToScale.Name, scaledIndividual.Name),
BuildingBlockName = scaledIndividual.Name,
BuildingBlockType = PKSimConstants.ObjectTypes.Individual
};
//indvidual was not scaled but cloned. Create a new individual
var addToProjectCommand = new AddBuildingBlockToProjectCommand(scaledIndividual, _executionContext).Run(_executionContext);
overallCommand.Add(addToProjectCommand);
//these needs to be done afterwards in order to be able to undo the scaling action
var macroCommand = scaleCommand as IPKSimMacroCommand;
if (macroCommand != null)
{
macroCommand.All().Each(overallCommand.Add);
}
overallCommand.ReplaceNameTemplateWithName(scaledIndividual.Name);
overallCommand.ReplaceTypeTemplateWithType(PKSimConstants.ObjectTypes.Individual);
_buildingBlockTask.AddCommandToHistory(overallCommand);
}
}
public IPKSimCommand SetTargetOrgan(ISchemaItem schemaItem, string targetOrgan, string targetCompartment)
{
var organCommand = new SetSchemaItemTargetOrganCommand(schemaItem, targetOrgan, _executionContext);
if (schemaItem.TargetCompartment == targetCompartment)
{
return(organCommand.Run(_executionContext));
}
var macroCommand = new PKSimMacroCommand {
CommandType = organCommand.CommandType, Description = organCommand.Description, ObjectType = organCommand.ObjectType
};
organCommand.Visible = false;
var compartmentCommand = new SetSchemaItemTargetCompartmentCommand(schemaItem, targetCompartment, _executionContext)
{
Visible = false
};
macroCommand.Add(organCommand, compartmentCommand);
return(macroCommand.Run(_executionContext));
}
public void ScaleIndividual(Individual individualToScale)
{
_buildingBlockTask.Load(individualToScale);
using (var presenter = _applicationController.Start <IScaleIndividualPresenter>())
{
var scaleCommand = presenter.ScaleIndividual(individualToScale);
//User cancel action. return
if (scaleCommand.IsEmpty())
{
return;
}
var scaledIndividual = presenter.Individual;
var overallCommand = new PKSimMacroCommand
{
CommandType = PKSimConstants.Command.CommandTypeScale,
ObjectType = PKSimConstants.ObjectTypes.Individual,
Description = PKSimConstants.Command.ScaleIndividualDescription(individualToScale.Name, scaledIndividual.Name),
BuildingBlockName = scaledIndividual.Name,
BuildingBlockType = PKSimConstants.ObjectTypes.Individual
};
//Do not add to history as the add action should be part of the overall command
var addToProjectCommand = _buildingBlockTask.AddToProject(scaledIndividual, addToHistory: false);
overallCommand.Add(addToProjectCommand);
//these needs to be done afterwards in order to be able to undo the scaling action
var macroCommand = scaleCommand as IPKSimMacroCommand;
macroCommand?.All().Each(overallCommand.Add);
overallCommand.ReplaceNameTemplateWithName(scaledIndividual.Name);
overallCommand.ReplaceTypeTemplateWithType(PKSimConstants.ObjectTypes.Individual);
_buildingBlockTask.AddCommandToHistory(overallCommand);
}
}
private ICommand synchronizeBuildingBlocks(IPKSimBuildingBlock templateBuildingBlock, IPKSimMacroCommand updateTemplateParametersCommand)
{
var simulationSubject = templateBuildingBlock as ISimulationSubject;
//For now, deal with update from Individual or Population into Expression Profile
if (simulationSubject == null)
{
return(new PKSimEmptyCommand());
}
var allExpressionProfileParameterValueCommand = updateTemplateParametersCommand.All()
.OfType <SetExpressionProfileValueCommand>()
.ToList();
if (!allExpressionProfileParameterValueCommand.Any())
{
return(new PKSimEmptyCommand());
}
var expressionProfilesToUpdate = new HashSet <ExpressionProfile>();
var macroCommand = new PKSimMacroCommand();
//We have some commands related to expression profile. We need to update the expression profile
foreach (var parameterCommand in allExpressionProfileParameterValueCommand)
{
var simulationSubjectParameter = _executionContext.Get <IParameter>(parameterCommand.ParameterId);
if (simulationSubjectParameter == null)
{
continue;
}
//This should be the id of the parameter in the expression profile
var expressionProfileParameterId = simulationSubjectParameter.Origin.ParameterId;
var expressionProfileParameter = _executionContext.Get <IParameter>(expressionProfileParameterId);
if (expressionProfileParameter == null)
{
continue;
}
var expressionProfile = _executionContext.BuildingBlockContaining(expressionProfileParameter) as ExpressionProfile;
if (expressionProfile == null)
{
continue;
}
expressionProfilesToUpdate.Add(expressionProfile);
//We do not update the simulation subject. It will be done at the end of the loop
var command = new SetExpressionProfileValueCommand(expressionProfileParameter, simulationSubjectParameter.Value, updateSimulationSubjects: false);
macroCommand.Add(command);
}
macroCommand.Run(_executionContext);
_executionContext.UpdateBuildingBlockPropertiesInCommand(macroCommand, templateBuildingBlock);
//Now that our expression profile are updated, we need to trigger the synchronization in all building blocks
expressionProfilesToUpdate.Each(x => _expressionProfileUpdater.SynchronizeAllSimulationSubjectsWithExpressionProfile(x));
return(macroCommand);
}