public static ICache <string, T> ToCache <T>(this IEnumerable <T> elements, Func <T, string> getKey) where T : class
{
var cache = new Cache <string, T>(getKey, x => null);
cache.AddRange(elements);
return(cache);
}
private DataRepository synchronize(DataRepository oldResultsToUpdate, DataRepository newResults)
{
var newResultsCache = new Cache <QuantityInfo, DataColumn>(col => col.QuantityInfo);
newResultsCache.AddRange(newResults);
//remove column that do not exist in the new results
removeDeletedColumns(oldResultsToUpdate, newResultsCache);
//first update base grid columns
var baseGridColumns = oldResultsToUpdate.Where(col => col.IsBaseGrid());
baseGridColumns.Each(baseGrid => updateColumnValues(baseGrid, newResultsCache));
//then update non base grid columnds
var columns = oldResultsToUpdate.AllButBaseGrid();
columns.Each(col => updateColumnValues(col, newResultsCache));
//finally for all new columns, create a copy with the accurate base grid reference
var oldResultsCache = new Cache <QuantityInfo, DataColumn>(col => col.QuantityInfo);
oldResultsCache.AddRange(oldResultsToUpdate);
var newColumns = newResults.Where(col => !oldResultsCache.Contains(col.QuantityInfo));
newColumns.Each(col => oldResultsToUpdate.Add(cloneColumn(oldResultsCache, col)));
return(oldResultsToUpdate);
}
private ICache <int, FlatSpeciesContainer> speciesSubContainers(string species, int parentContainerId)
{
var result = new Cache <int, FlatSpeciesContainer>(flatContainer => flatContainer.Id);
result.AddRange(_speciesContainerRepo.AllSubContainer(species, parentContainerId));
return(result);
}
private void adjustParameterVisibility()
{
if (!Formulation.IsParticleDissolution)
{
return;
}
var cache = new Cache <string, IParameter>(p => p.Name);
cache.AddRange(_formulationDTO.Parameters);
cache.Each(p => p.Visible = true);
var particleDisperseSystem = cache[CoreConstants.Parameter.PARTICLE_DISPERSE_SYSTEM];
var particleDistribution = cache[CoreConstants.Parameter.PARTICLE_SIZE_DISTRIBUTION];
var parameterToHide = new List <string>();
if (particleDisperseSystem.Value == CoreConstants.Parameter.MONODISPERSE)
{
parameterToHide.AddRange(CoreConstants.Parameter.HiddenParameterForMonodisperse);
}
else if (particleDistribution.Value == CoreConstants.Parameter.PARTICLE_SIZE_DISTRIBUTION_NORMAL)
{
parameterToHide.AddRange(CoreConstants.Parameter.HiddenParameterForPolydisperseNormal);
}
else
{
parameterToHide.AddRange(CoreConstants.Parameter.HiddenParameterForPolydisperseLogNormal);
}
parameterToHide.Each(p => cache[p].Visible = false);
}
private ICache <int, FlatPopulationContainer> populationSubContainers(SpeciesPopulation population, FlatContainer parentContainer)
{
var result = new Cache <int, FlatPopulationContainer>(x => x.Id);
result.AddRange(_populationContainerRepo.AllSubContainerFor(population.Name, parentContainer.Id));
return(result);
}
private ICache <string, INeighborhood> createNeighborhoodCache(IModel model)
{
var cloneNeighborhoods = new Cache <string, INeighborhood>(nh => nh.Name);
cloneNeighborhoods.AddRange(model.Neighborhoods.GetChildren <INeighborhood>());
return(cloneNeighborhoods);
}
private Cache <string, UsedBuildingBlock> ofType(IEnumerable <UsedBuildingBlock> usedBuildingBlocks, PKSimBuildingBlockType buildingBlockType)
{
var cache = new Cache <string, UsedBuildingBlock>(x => x.Name, x => null);
cache.AddRange(usedBuildingBlocks.Where(x => x.BuildingBlockType.Is(buildingBlockType)));
return(cache);
}
public ResidualsResult Calculate(IReadOnlyList <SimulationRunResults> simulationsResults, IReadOnlyList <OutputMapping> allOutputMappings)
{
if (simulationsResults.Any(x => !x.Success))
{
return(residualResultWithErrorFrom(simulationsResults));
}
var simulationColumnsCache = new Cache <string, DataColumn>(x => x.PathAsString, x => null);
simulationsResults.Select(x => x.Results).Each(repo => simulationColumnsCache.AddRange(repo.AllButBaseGrid()));
var residualResult = new ResidualsResult();
foreach (var outputMapping in allOutputMappings)
{
var simulationColumn = simulationColumnsCache[outputMapping.FullOutputPath];
if (simulationColumn == null)
{
residualResult.ExceptionOccured = true;
residualResult.ExceptionMessage = Error.CannotFindSimulationResultsForOutput(outputMapping.FullOutputPath);
return(residualResult);
}
var outputResiduals = calculateOutputResiduals(simulationColumn, outputMapping);
residualResult.AddOutputResiduals(outputMapping.FullOutputPath, outputMapping.WeightedObservedData, outputResiduals);
}
return(residualResult);
}
private DataTable createDataToExport(Simulation simulation)
{
//Id Time Output1 Output2 ... OutputN
var dataTable = new DataTable();
if (!simulation.HasResults)
{
return(dataTable);
}
var simulationResults = simulation.Results;
var allQuantities = _quantityRetriever.QuantitiesFrom(simulation);
dataTable.AddColumn <int>(CoreConstants.SimulationResults.IndividualId);
dataTable.AddColumn <string>(CoreConstants.NameWithUnitFor(CoreConstants.SimulationResults.Time, _timeDimension.BaseUnit));
var allQuantityPaths = simulationResults.AllQuantityPaths();
foreach (var quantityPath in allQuantityPaths)
{
var quantity = allQuantities[quantityPath];
if (quantity == null)
{
continue;
}
dataTable.AddColumn <string>(CoreConstants.NameWithUnitFor(quantityPath, quantity.Dimension.BaseUnit));
}
dataTable.BeginLoadData();
int numberOfValues = simulationResults.Time.Length;
foreach (var individualResults in simulationResults.OrderBy(x => x.IndividualId))
{
var allQuantitiesCache = new Cache <string, QuantityValues>(x => x.QuantityPath);
allQuantitiesCache.AddRange(individualResults);
for (int i = 0; i < numberOfValues; i++)
{
var row = dataTable.NewRow();
row[CoreConstants.SimulationResults.IndividualId] = individualResults.IndividualId;
row[CoreConstants.NameWithUnitFor(CoreConstants.SimulationResults.Time, _timeDimension.BaseUnit)] = simulationResults.Time[i].ConvertedTo <string>();
foreach (var quantityPath in allQuantityPaths)
{
var quantity = allQuantities[quantityPath];
if (quantity == null)
{
continue;
}
row[CoreConstants.NameWithUnitFor(quantityPath, quantity.Dimension.BaseUnit)] = allQuantitiesCache[quantityPath][i].ConvertedTo <string>();
}
dataTable.Rows.Add(row);
}
}
dataTable.EndLoadData();
return(dataTable);
}
public static ICache <string, T> ToCache <T>(this IEnumerable <T> startValues) where T : class, IStartValue
{
var cache = new Cache <string, T>(x => x.Path.ToString(), x => null);
cache.AddRange(startValues);
return(cache);
}
public void LoadFromSession(ISession session)
{
Clear();
var allCommandMetaData = session.CreateCriteria <CommandMetaData>().List <CommandMetaData>();
_allCommandMetaData.AddRange(allCommandMetaData);
cacheParentChildrenRelationship();
}
private void cacheUsedBuildingBlockAndParametersFromSimulation(Simulation simulation)
{
simulation.UsedBuildingBlocks.Each(x =>
{
_usedBuildingBlockCache.Add(x);
_buildingBlockParameterCache.AddRange(x.BuildingBlock.GetAllChildren <IParameter>());
});
}
public void CreatePaneOrder()
{
//without ToList sortedPanes is empty after Clear
var sortedPanes = _allPanes.OrderBy(x => x, this).ToList();
_allPanes.Clear();
_allPanes.AddRange(sortedPanes);
}
public CreateIndividualResults CreateIndividual(IndividualCharacteristics individualCharacteristics)
{
var originData = originDataFrom(individualCharacteristics);
var moleculeOntogenies = individualCharacteristics.MoleculeOntogenies;
var individual = _individualFactory.CreateAndOptimizeFor(originData, individualCharacteristics.Seed);
var individualProperties = _individualValuesMapper.MapFrom(individual);
var allIndividualParameters = individualProperties.ParameterValues;
var ontogenyParameters = _ontogenyFactorsRetriever.FactorsFor(originData, moleculeOntogenies).Select(x => new ParameterValueWithUnit(x));
var allDistributedParameterCache = _containerTask.CacheAllChildren <IDistributedParameter>(individual);
var allIndividualParametersCache = _containerTask.CacheAllChildren <IParameter>(individual);
var distributedParameters = new Cache <string, ParameterValueWithUnit>(x => x.ParameterPath);
var derivedParameters = new List <ParameterValueWithUnit>();
//Add Age and Height parameter that is not distributed at the moment
if (originData.Population.IsAgeDependent)
{
distributedParameters.Add(parameterValueFrom(individual.Organism.Parameter(CoreConstants.Parameters.AGE)));
distributedParameters.Add(parameterValueFrom(individual.Organism.Parameter(Constants.Parameters.GESTATIONAL_AGE)));
}
if (originData.Population.IsHeightDependent)
{
distributedParameters.Add(parameterValueFrom(individual.Organism.Parameter(CoreConstants.Parameters.HEIGHT)));
}
distributedParameters.Add(parameterValueFrom(individual.Organism.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR_AGP)));
distributedParameters.Add(parameterValueFrom(individual.Organism.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR_ALBUMIN)));
foreach (var individualParameter in allIndividualParameters)
{
var parameter = allIndividualParametersCache[individualParameter.ParameterPath];
if (parameter == null)
{
continue;
}
var parameterValue = new ParameterValueWithUnit(individualParameter, parameter?.BaseUnitName());
if (allDistributedParameterCache.Contains(individualParameter.ParameterPath))
{
distributedParameters.Add(parameterValue);
}
//Do not add parameters that were added specifically
else if (!distributedParameters.Contains(individualParameter.ParameterPath))
{
derivedParameters.Add(parameterValue);
}
}
//add Ontogeny parameters
distributedParameters.AddRange(ontogenyParameters);
return(new CreateIndividualResults(distributedParameters.ToArray(), derivedParameters.ToArray(), individual.Seed));
}
private void finalizeTranports(IModel cloneModel, IEnumerable <ITransport> tmp, IEnumerable <ITransport> sourceTransports)
{
var cloneTransports = new Cache <string, ITransport>(x => x.Name);
cloneTransports.AddRange(tmp);
foreach (var transport in sourceTransports)
{
var cloneTransport = cloneTransports[transport.Name];
resolveAmounts(cloneModel, transport, cloneTransport);
}
}
public void VehicleFamilyCache_Populate()
{
Cache.AddRange(AdditionalFamilies);
Cache.Populate();
var cacheObjects = Cache.GetCachedObjects().ToArray();
// Since Populate() clears the cache if it isn't empty, there should be only one item even though we
// added the additional families. Then, Populate() gathers all families in the family storage location.
// Since the Angara family is the only one saved there, it should be the only family in the cache.
Assert.IsTrue(cacheObjects.Length == 1);
Assert.IsTrue(cacheObjects.Contains(Family, Comparer));
}
public void LauncherCollectionCache_Populate()
{
Cache.AddRange(AdditionalCollections);
Cache.Populate();
var cacheObjects = Cache.GetCachedObjects().ToArray();
// Since Populate() clears the cache if it isn't empty, there should be only one item even though we
// added the additional collections. Then, Populate() gathers all collections in the storage location.
// Since the A5 collection is the only one saved there, it should be the only collection in the cache.
Assert.IsTrue(cacheObjects.Length == 1);
Assert.IsTrue(cacheObjects.Contains(Collection, Comparer));
}
public void VehicleFamilyCache_Refresh()
{
Cache.AddRange(AdditionalFamilies);
Cache.Refresh();
var cacheObjects = Cache.GetCachedObjects().ToArray();
var falcon = cacheObjects.SingleOrDefault(e => e.Name == "Falcon");
// We added the additional launchers and then refreshed the cache. Since the only family saved in
// the storage location is the Angara family, then it should be the only one in the cached objects.
Assert.IsTrue(cacheObjects.Contains(Family, Comparer));
Assert.IsTrue(!cacheObjects.Contains(falcon));
}
private void finalizeEventContainer(IContainer sourceEventGroup, IContainer cloneEventGroup, IModel cloneModel)
{
var sourceContainer = sourceEventGroup.GetChildren <IContainer>();
var cloneContainer = new Cache <string, IContainer>(x => x.Name);
cloneContainer.AddRange(cloneEventGroup.GetChildren <IContainer>());
foreach (var source in sourceContainer)
{
var clone = cloneContainer[source.Name];
finalizeEventContainer(source, clone, cloneModel);
}
finalizeTransportsInMoleculeParentContainer(cloneModel, sourceEventGroup, cloneEventGroup);
}
protected override void DoStart()
{
_allDiseaseSates.AddRange(_flatDiseaseStateRepository.All().MapAllUsing(_diseaseStateMapper));
foreach (var query in _flatPopulationDiseaseStateRepository.All().GroupBy(x => x.Population))
{
var population = _populationRepository.FindByName(query.Key);
var diseaseStates = new List<DiseaseState>();
diseaseStates.AddRange(query.Select(x => _allDiseaseSates[x.DiseaseState]));
_allDiseaseStatePerPopulation[population] = diseaseStates;
}
_healthyState = _allDiseaseSates.FindByName(CoreConstants.DiseaseStates.HEALTHY);
}
public void LauncherCollectionCache_Refresh()
{
Cache.AddRange(AdditionalCollections);
Cache.Refresh();
var cacheObjects = Cache.GetCachedObjects().ToArray();
var falcon = cacheObjects.SingleOrDefault(e => e.Name == "Falcon");
// We added the additional collections and then refreshed the cache. Since the only collection saved in
// the storage location is the A5 collection, then it should be the only one in the cached objects.
Assert.IsTrue(cacheObjects.Contains(Collection, Comparer));
Assert.IsTrue(!cacheObjects.Contains(falcon));
}
private IEnumerable <DataColumn> selectedCurves(DataRepository dataRepository)
{
var selectedQuantities = new Cache <string, QuantitySelection>(x => x.Path);
selectedQuantities.AddRange(_quantitySelectionPresenter.SelectedQuantities());
foreach (var dataColumn in dataRepository.Where(c => c.QuantityInfo != null))
{
var path = dataColumn.QuantityInfo.PathAsString;
if (selectedQuantities.Contains(path))
{
yield return(dataColumn);
}
}
}
private void addNodesForParametersUnder(ITreeNode node, IEnumerable <IParameter> allParameters)
{
var cache = new Cache <PathElements, IParameter>(_pathElementsMapper.MapFrom);
cache.AddRange(allParameters);
if (parameterHaveSameDisplayNamesAsOneParentGroup(cache.Keys, node))
{
createNodeHierarchyWithoutParameterNameUnder(node, cache);
}
else
{
createNodeHierarchyWithParameterNameUnder(node, cache);
}
}
public void LauncherCache_AddRange()
{
Cache.Clear();
Cache.AddRange(AdditionalLaunchers);
var cacheObjects = Cache.GetCachedObjects().ToArray();
var falcon9 = cacheObjects.SingleOrDefault(e => e.Name == "Falcon 9");
var deltaII = cacheObjects.SingleOrDefault(e => e.Name == "Delta II");
var atlasV = cacheObjects.SingleOrDefault(e => e.Name == "Atlas V");
// We cleared the cache and then added the additional launchers, so it should only contain those three launchers.
Assert.IsTrue(cacheObjects.Contains(falcon9));
Assert.IsTrue(cacheObjects.Contains(deltaII));
Assert.IsTrue(cacheObjects.Contains(atlasV));
Assert.IsTrue(cacheObjects.Length == 3);
}
public void LauncherCollectionCache_AddRange()
{
Cache.Clear();
Cache.AddRange(AdditionalCollections);
var cacheObjects = Cache.GetCachedObjects().ToArray();
var falcon = cacheObjects.SingleOrDefault(e => e.Name == "Falcon");
var delta = cacheObjects.SingleOrDefault(e => e.Name == "Delta");
var atlas = cacheObjects.SingleOrDefault(e => e.Name == "Atlas");
// We cleared the cache and then added the additional collections, so it should only contain those three collections.
Assert.IsTrue(cacheObjects.Contains(falcon));
Assert.IsTrue(cacheObjects.Contains(delta));
Assert.IsTrue(cacheObjects.Contains(atlas));
Assert.IsTrue(cacheObjects.Length == 3);
}
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 Save(IHistoryManager historyManager, ISession session)
{
//only save history that were not saved yet
var savedHistory = new Cache <string, HistoryItemMetaData>(x => x.Id, x => null);
savedHistory.AddRange(allHistoryItemMetaData(session));
int sequence = 0;
foreach (var historyItem in historyManager.History)
{
var savedHistoryItem = savedHistory[historyItem.Id];
if (savedHistoryItem == null)
{
saveNewHistoryItem(historyItem, sequence, session);
}
else if (commentHasChanged(savedHistoryItem, historyItem))
{
updateComment(savedHistoryItem, historyItem, session);
}
sequence++;
}
}
public DataRepository CreateRepository(IModelCoreSimulation simulation, SimModelNET.ISimulation simModelSimulation, string repositoryName = null)
{
var repository = new DataRepository().WithName(repositoryName ?? _dataNamingService.GetNewRepositoryName());
var allPersitableQuantities = new Cache <string, IQuantity>(q => _objectPathFactory.CreateAbsoluteObjectPath(q).ToString(), x => null);
allPersitableQuantities.AddRange(simulation.Model.Root.GetAllChildren <IQuantity>(x => x.Persistable));
var time = createTimeGrid(simModelSimulation.SimulationTimes);
foreach (var quantityValue in simModelSimulation.AllValues)
{
var quantity = allPersitableQuantities[quantityValue.Path];
if (quantity == null)
{
continue;
}
repository.Add(createColumn(time, quantity, quantityValue, quantityValue.Path.ToPathArray(), simulation));
}
return(repository);
}
private DataTable createResultDataToExport(Simulation simulation)
{
//Id Time Output1 Output2 ... OutputN
var dataTable = new DataTable(simulation.Name);
if (!simulation.HasResults)
{
return(dataTable);
}
var simulationResults = simulation.Results;
var allQuantities = _quantityRetriever.QuantitiesFrom(simulation);
var timeColumnName = Constants.NameWithUnitFor(CoreConstants.SimulationResults.TIME, _timeDimension.BaseUnit);
var quantityPathCache = new Cache <string, string>();
dataTable.AddColumn <int>(CoreConstants.SimulationResults.INDIVIDUAL_ID);
dataTable.AddColumn <string>(timeColumnName);
var allQuantityPaths = simulationResults.AllQuantityPaths();
foreach (var quantityPath in allQuantityPaths)
{
var quantity = allQuantities[quantityPath];
if (quantity == null)
{
continue;
}
//export results in base unit so that they can be computed automatically from matlab scripts
quantityPathCache[quantityPath] = Constants.NameWithUnitFor(quantityPath, quantity.Dimension.BaseUnit);
dataTable.AddColumn <string>(quantityPathCache[quantityPath]);
}
dataTable.BeginLoadData();
int numberOfValues = simulationResults.Time.Length;
foreach (var individualResults in simulationResults.OrderBy(x => x.IndividualId))
{
var allQuantitiesCache = new Cache <string, QuantityValues>(x => x.QuantityPath);
allQuantitiesCache.AddRange(individualResults);
for (int i = 0; i < numberOfValues; i++)
{
var row = dataTable.NewRow();
row[CoreConstants.SimulationResults.INDIVIDUAL_ID] = individualResults.IndividualId;
row[timeColumnName] = simulationResults.Time[i].ConvertedTo <string>();
foreach (var quantityPath in allQuantityPaths)
{
var quantity = allQuantities[quantityPath];
if (quantity == null)
{
continue;
}
row[quantityPathCache[quantityPath]] = allQuantitiesCache[quantityPath][i].ConvertedTo <string>();
}
dataTable.Rows.Add(row);
}
}
dataTable.EndLoadData();
return(dataTable);
}
protected override void Because()
{
var allMenuWithShortCuts = sut.All().Where(x => x.Shortcut != Keys.None);
_allEntriesWithShortCuts.AddRange(allMenuWithShortCuts);
}
