public IReadOnlyList <IBuildingBlockSnapshot> BuildingBlocksByType(PKSimBuildingBlockType buildingBlockType)
{
switch (buildingBlockType)
{
case PKSimBuildingBlockType.ExpressionProfile:
return(ExpressionProfiles);
case PKSimBuildingBlockType.Compound:
return(Compounds);
case PKSimBuildingBlockType.Formulation:
return(Formulations);
case PKSimBuildingBlockType.Protocol:
return(Protocols);
case PKSimBuildingBlockType.Individual:
return(Individuals);
case PKSimBuildingBlockType.Population:
return(Populations);
case PKSimBuildingBlockType.Event:
return(Events);
case PKSimBuildingBlockType.Simulation:
return(Simulations);
case PKSimBuildingBlockType.ObserverSet:
return(ObserverSets);
default:
return(null);
}
}
public IReadOnlyList <TBuildingBlock> LoadFromSnapshot <TBuildingBlock>(PKSimBuildingBlockType buildingBlockType) where TBuildingBlock : class, IPKSimBuildingBlock
{
using (var presenter = _applicationController.Start <ILoadFromSnapshotPresenter <TBuildingBlock> >())
{
var buildingBlocks = presenter.LoadModelFromSnapshot();
return(addBuildingBlocksToProject(buildingBlocks).ToList());
}
}
public async Task <T> LoadModelFromProjectFileAsync <T>(string fileName, PKSimBuildingBlockType buildingBlockType, string buildingBlockName)
{
var projectSnapshot = await LoadSnapshotFromFileAsync <Project>(fileName);
var snapshot = projectSnapshot.BuildingBlockByTypeAndName(buildingBlockType, buildingBlockName);
return(await loadModelFromSnapshot <T>(snapshot));
}
private IParameter create(PKSimBuildingBlockType buildingBlockType)
{
var parameter = A.Fake <IParameter>();
parameter.CanBeVaried = false;
parameter.CanBeVariedInPopulation = false;
A.CallTo(() => parameter.BuildingBlockType).Returns(buildingBlockType);
return(parameter);
}
private TemplateType typeFrom(PKSimBuildingBlockType buildingBlockType)
{
if (buildingBlockType == PKSimBuildingBlockType.SimulationSubject)
{
return(TemplateType.Individual | TemplateType.Population);
}
return(EnumHelper.ParseValue <TemplateType>(buildingBlockType.ToString()));
}
public IReadOnlyList <TBuildingBlock> LoadFromTemplate <TBuildingBlock>(PKSimBuildingBlockType buildingBlockType) where TBuildingBlock : class, IPKSimBuildingBlock
{
using (var presenter = _applicationController.Start <ITemplatePresenter>())
{
var buildingBlocks = presenter.LoadFromTemplate <TBuildingBlock>(typeFrom(buildingBlockType));
return(addBuildingBlocksToProject(buildingBlocks).ToList());
}
}
private static bool canFilterUnchangedParameters(PKSimBuildingBlockType buildingBlockType)
{
//Exclude Protocol for now because of the 1to n relationship between building block parameters and simulation parameters
return(buildingBlockType.IsOneOf(
PKSimBuildingBlockType.Compound,
PKSimBuildingBlockType.Formulation,
PKSimBuildingBlockType.Individual,
PKSimBuildingBlockType.Event,
PKSimBuildingBlockType.Population));
}
public ParameterInfo()
{
//Min value and Max value should be initialized to null to avoid serialization issues
CanBeVaried = true;
MinValue = null;
MinIsAllowed = false;
MaxValue = null;
MaxIsAllowed = false;
Visible = true;
GroupName = Constants.Groups.UNDEFINED;
Sequence = 1;
ReferenceId = 0;
BuildingBlockType = PKSimBuildingBlockType.Simulation;
}
protected override IReadOnlyList <Compound> LoadFromTemplate(PKSimBuildingBlockType buildingBlockType)
{
var loadedCompounds = base.LoadFromTemplate(buildingBlockType);
if (loadedCompounds.Count <= 1)
{
return(loadedCompounds);
}
//one compound and one or more metabolites
warnUserIfMetabolitesDoNotMatch(loadedCompounds);
return(loadedCompounds);
}
private string getContainerPathToRename(PKSimBuildingBlockType buildingBlockType)
{
switch (buildingBlockType)
{
case PKSimBuildingBlockType.Formulation:
case PKSimBuildingBlockType.Protocol:
return(Constants.APPLICATIONS);
case PKSimBuildingBlockType.Event:
return(Constants.EVENTS);
default:
throw new ArgumentOutOfRangeException("buildingBlockType");
}
}
public IReadOnlyList <TBuildingBlock> LoadFromTemplate <TBuildingBlock>(PKSimBuildingBlockType buildingBlockType) where TBuildingBlock : class, IPKSimBuildingBlock
{
var loadedBuildingBlocks = new List <TBuildingBlock>();
using (var presenter = _applicationController.Start <ITemplatePresenter>())
{
var buildingBlocks = presenter.LoadFromTemplate <TBuildingBlock>(typeFrom(buildingBlockType));
buildingBlocks.Each(bb =>
{
var command = AddToProject(bb, editBuildingBlock: false);
if (!command.IsEmpty())
{
loadedBuildingBlocks.Add(bb);
}
});
return(loadedBuildingBlocks);
}
}
public IParameter CreateFor(string parameterName, double defaultValue, PKSimBuildingBlockType buildingBlockType)
{
return(CreateFor(parameterName, defaultValue, Constants.Dimension.DIMENSIONLESS, buildingBlockType));
}
public IParameter CreateFor(string parameterName, PKSimBuildingBlockType buildingBlockType)
{
return(CreateFor(parameterName, double.NaN, buildingBlockType));
}
public UsedBuildingBlock(string templateId, PKSimBuildingBlockType buildingBlockType)
{
TemplateId = templateId;
BuildingBlockType = buildingBlockType;
}
public static bool IsOneOf(this PKSimBuildingBlockType buildingBlockType, params PKSimBuildingBlockType[] typesToCompare)
{
return(typesToCompare.Any(b => buildingBlockType.Is(b)));
}
public void UpdateUsedBuildingBlockInSimulationFromTemplate(Simulation simulation, IPKSimBuildingBlock templateBuildingBlock, PKSimBuildingBlockType buildingBlockType)
{
if (!templateBuildingBlockCanBeUpdatedAsSingle(buildingBlockType))
{
throw new ArgumentException($"Should not call this function with a building block of type '{buildingBlockType}'");
}
var previousUsedBuildingBlock = simulation.UsedBuildingBlockInSimulation(buildingBlockType);
var newUsedBuildingBlock = _buildingBlockMapper.MapFrom(templateBuildingBlock, previousUsedBuildingBlock);
simulation.RemoveUsedBuildingBlock(previousUsedBuildingBlock);
simulation.AddUsedBuildingBlock(newUsedBuildingBlock);
}
protected PKSimBuildingBlock(PKSimBuildingBlockType buildingBlockType) : this()
{
_buildingBlockType = buildingBlockType;
Icon = buildingBlockType.ToString();
}
/// <summary>
/// Update parameter values from the used building block into the simulationm
/// </summary>
/// <param name="usedBuildingBlockParameters">All used building blocks parameters</param>
/// <param name="simulation">simulation for which parameters should be updated</param>
/// <param name="buildingBlockType">Type of parameters to update</param>
private IEnumerable <ICommand> updateParameterValues(IEnumerable <IParameter> usedBuildingBlockParameters, Simulation simulation, PKSimBuildingBlockType buildingBlockType)
{
var simulationParameterCache = new Cache <string, List <IParameter> >(onMissingKey: x => new List <IParameter>());
foreach (var parameter in simulation.ParametersOfType(buildingBlockType))
{
var originParameterId = parameter.Origin.ParameterId;
if (!simulationParameterCache.Contains(originParameterId))
{
simulationParameterCache[originParameterId] = new List <IParameter>();
}
simulationParameterCache[originParameterId].Add(parameter);
}
return(from parameter in usedBuildingBlockParameters.OrderBy(x => x.IsDistributed())
let simParams = simulationParameterCache[parameter.Id]
from simParam in simParams
select _parameterSetUpdater.UpdateValue(parameter, simParam));
}
private void addUsedBuildingBlock(Simulation simulation, ITreeNode simulationNode, PKSimBuildingBlockType buildingBlockType)
{
foreach (var usedBuildingBlock in simulation.UsedBuildingBlocksInSimulation(buildingBlockType))
{
_treeNodeFactory.CreateFor(simulation, usedBuildingBlock)
.WithIcon(_buildingBlockIconRetriever.IconFor(usedBuildingBlock))
.WithText(usedBuildingBlock.Name)
.Under(simulationNode);
}
}
private bool templateBuildingBlockCanBeUpdatedAsSingle(PKSimBuildingBlockType buildingBlockType)
{
return(buildingBlockType.IsOneOf(PKSimBuildingBlockType.Individual, PKSimBuildingBlockType.Population));
}
public static bool IsOfType(this IParameter parameter, PKSimBuildingBlockType buildingBlockType)
{
return(parameter.BuildingBlockType.Is(buildingBlockType));
}
/// <summary>
/// return all parameters defined with the given building block type
/// </summary>
public virtual IEnumerable <IParameter> ParametersOfType(PKSimBuildingBlockType buildingBlockType)
{
//Do not need neighborhood parameters, since neighborhood is defined a a child of root
return(All <IParameter>().Where(p => p.IsOfType(buildingBlockType)));
}
/// <summary>
/// Returns the building block used in the simulation with the given building block type
/// </summary>
public virtual UsedBuildingBlock UsedBuildingBlockInSimulation(PKSimBuildingBlockType buildingBlockType)
{
return(UsedBuildingBlocksInSimulation(buildingBlockType).SingleOrDefault());
}
public void UpdateMultipleUsedBuildingBlockInSimulationFromTemplate(Simulation simulation, IEnumerable <IPKSimBuildingBlock> templateBuildingBlocks, PKSimBuildingBlockType buildingBlockType)
{
var allTemplates = templateBuildingBlocks.ToList();
if (!allTemplates.Any())
{
simulation.RemoveAllBuildingBlockOfType(buildingBlockType);
}
if (!templateBuildingBlockCanBeUpdatedAsMultiple(buildingBlockType))
{
throw new ArgumentException($"Should not call this function with a building block of type '{buildingBlockType}'");
}
//templateBuildingBlocks contains all the building block that have been selected
//remove the one that are not used anymore . Used to list to remove while looping
foreach (var usedBuildingBlock in simulation.UsedBuildingBlocksInSimulation(buildingBlockType).ToList())
{
//template is used, continue
if (allTemplates.ExistsById(usedBuildingBlock.TemplateId))
{
continue;
}
//user defined building block reused?
if (allTemplates.ExistsById(usedBuildingBlock.Id))
{
continue;
}
simulation.RemoveUsedBuildingBlock(usedBuildingBlock);
}
allTemplates.Each(bb => addUsedBuildingBlockToSimulation(simulation, bb));
}
public IParameter CreateFor(string parameterName, double defaultValue, string dimensionName, PKSimBuildingBlockType buildingBlockType)
{
var parameterValueDefinition = new ParameterValueMetaData
{
ParameterName = parameterName,
DefaultValue = defaultValue,
Dimension = dimensionName,
BuildingBlockType = buildingBlockType,
};
return(CreateFor(parameterValueDefinition));
}
public IBuildingBlockSnapshot BuildingBlockByTypeAndName(PKSimBuildingBlockType buildingBlockType, string name) => BuildingBlocksByType(buildingBlockType)?.FindByName(name);
public virtual string BuildingBlockName(PKSimBuildingBlockType buildingBlockType)
{
var usedBuildingBlock = UsedBuildingBlockInSimulation(buildingBlockType);
return(usedBuildingBlock == null ? string.Empty : usedBuildingBlock.Name);
}
private bool templateBuildingBlockCanBeUpdatedAsMultiple(PKSimBuildingBlockType buildingBlockType)
{
return(!templateBuildingBlockCanBeUpdatedAsSingle(buildingBlockType));
}
/// <summary>
/// Remove the building blocks as used in the simulation by type
/// </summary>
public virtual void RemoveAllBuildingBlockOfType(PKSimBuildingBlockType buildingBlockType)
{
var allBuildingBlocksOfType = _usedBuildingBlocks.Where(x => x.BuildingBlockType.Is(buildingBlockType)).ToList();
allBuildingBlocksOfType.Each(RemoveUsedBuildingBlock);
}
/// <summary>
/// Returns all the buildng block with the given type used in the simulation
/// </summary>
public virtual IEnumerable <UsedBuildingBlock> UsedBuildingBlocksInSimulation(PKSimBuildingBlockType buildingBlockType)
{
return(from usedBuildingBlock in UsedBuildingBlocks
where usedBuildingBlock.BuildingBlockType.Is(buildingBlockType)
select usedBuildingBlock);
}