protected override void FillUpReport(RandomPopulationSettings populationSettings, ReportPart reportPart)
{
var baseOnIndividualPart = new ReportPart().WithTitle(PKSimConstants.UI.BasedOnIndividual);
baseOnIndividualPart.AddToContent(populationSettings.BaseIndividual.Name);
var numberOfIndividualPart = new ReportPart().WithTitle(PKSimConstants.UI.NumberOfIndividuals);
numberOfIndividualPart.AddToContent(populationSettings.NumberOfIndividuals.ToString(CultureInfo.InvariantCulture));
var genderRatioPart = new ReportPart().WithTitle(PKSimConstants.UI.GenderRatio);
foreach (var genderRatio in populationSettings.GenderRatios)
{
genderRatioPart.AddToContent(_reportGenerator.ReportFor(genderRatio).Content);
}
var parameterRangePart = new ReportPart().WithTitle(PKSimConstants.UI.PopulationParameterRanges);
foreach (var parameterRange in populationSettings.ParameterRanges)
{
parameterRangePart.AddToContent(_reportGenerator.ReportFor(parameterRange).Content);
}
reportPart.AddPart(baseOnIndividualPart);
reportPart.AddPart(numberOfIndividualPart);
reportPart.AddPart(genderRatioPart);
reportPart.AddPart(parameterRangePart);
}
public ReportPart BuildDifferenceBetween(Simulation sourceSimulation, Simulation targetSimulation)
{
//compare building blocks
var reportPart = new ReportPart();
var sourceReport = BuildFor(sourceSimulation).ToStringReport().Split('\n').ToList();
var targetReport = BuildFor(targetSimulation).ToStringReport().Split('\n').ToList();
var tempSourceReport = new List <string>(sourceReport);
foreach (var line in tempSourceReport)
{
if (!targetReport.Contains(line))
{
continue;
}
targetReport.Remove(line);
sourceReport.Remove(line);
}
var beforePart = new ReportPart().WithTitle("Before");
beforePart.AddToContent(sourceReport.ToString("\n"));
var afterPart = new ReportPart().WithTitle("After");
afterPart.AddToContent(targetReport.ToString("\n"));
reportPart.AddPart(beforePart);
reportPart.AddPart(afterPart);
return(reportPart);
}
protected override void FillUpReport(Simulation simulation, ReportPart reportPart)
{
var title = string.Format("{0} '{1}'", PKSimConstants.ObjectTypes.Simulation, simulation.Name);
reportPart.AddPart(_reportGenerator.ReportFor(simulation.UsedBuildingBlocks).WithTitle(title));
reportPart.AddPart(_reportGenerator.ReportFor(simulation.Creation).WithTitle(PKSimConstants.UI.Origin));
reportPart.AddPart(_reportGenerator.ReportFor(simulation.Properties));
}
public void Visit(Simulation simulation)
{
var report = new ReportPart();
report.AddPart(_reportGenerator.ReportFor(simulation.UsedBuildingBlocks));
report.AddPart(_reportGenerator.ReportFor(simulation.Creation));
_report = report.ToStringReport();
}
protected override void FillUpReport(SimulationProperties simulationProperties, ReportPart reportPart)
{
var part = new ReportPart {
Title = PKSimConstants.UI.AllowAging
};
part.AddToContent(simulationProperties.AllowAging ? PKSimConstants.UI.Yes : PKSimConstants.UI.No);
reportPart.AddPart(part);
reportPart.AddPart(_reportGenerator.ReportFor(simulationProperties.ModelProperties));
reportPart.AddPart(_reportGenerator.ReportFor(simulationProperties.EventProperties));
}
protected override void FillUpReport(OriginData originData, ReportPart reportPart)
{
var populationProperties = new TablePart(keyName: PKSimConstants.UI.PopulationProperties, valueName: PKSimConstants.UI.Value)
{
Title = PKSimConstants.UI.PopulationProperties
};
populationProperties.AddIs(PKSimConstants.UI.Species, originData.Species.DisplayName);
populationProperties.AddIs(PKSimConstants.UI.Population, originData.SpeciesPopulation.DisplayName);
populationProperties.AddIs(PKSimConstants.UI.Gender, originData.Gender.DisplayName);
var individualProperties = new TablePart(PKSimConstants.UI.IndividualParameters, PKSimConstants.UI.Value, PKSimConstants.UI.Unit)
{
Title = PKSimConstants.UI.IndividualParameters
};
individualProperties.Types[PKSimConstants.UI.Value] = typeof(double);
if (originData.SpeciesPopulation.IsAgeDependent)
{
if (originData.Age.HasValue)
{
individualProperties.AddIs(PKSimConstants.UI.Age, displayValueFor(originData.Age.Value, _dimensionRepository.AgeInYears, originData.AgeUnit), originData.AgeUnit);
}
if (originData.SpeciesPopulation.IsPreterm && originData.GestationalAge.HasValue)
{
individualProperties.AddIs(PKSimConstants.UI.GestationalAge, displayValueFor(originData.GestationalAge.Value, _dimensionRepository.AgeInWeeks, originData.GestationalAgeUnit), originData.GestationalAgeUnit);
}
}
individualProperties.AddIs(PKSimConstants.UI.Weight, displayValueFor(originData.Weight, _dimensionRepository.Mass, originData.WeightUnit), originData.WeightUnit);
if (originData.SpeciesPopulation.IsHeightDependent)
{
if (originData.Height.HasValue)
{
individualProperties.AddIs(PKSimConstants.UI.Height, displayValueFor(originData.Height.Value, _dimensionRepository.Length, originData.HeightUnit), originData.HeightUnit);
}
if (originData.BMI.HasValue)
{
individualProperties.AddIs(PKSimConstants.UI.BMI, displayValueFor(originData.BMI.Value, _dimensionRepository.BMI, originData.BMIUnit), originData.BMIUnit);
}
}
reportPart.AddPart(populationProperties);
reportPart.AddPart(individualProperties);
reportPart.AddPart(_reportGenerator.ReportFor(originData.SubPopulation));
reportPart.AddPart(_reportGenerator.ReportFor(originData.AllCalculationMethods()));
}
protected override void FillUpReport(IEnumerable <CalculationMethod> calculationMethods, ReportPart reportPart)
{
var calcMethodPart = new TablePart(keyName: PKSimConstants.UI.Category, valueName: PKSimConstants.UI.CalculationMethods)
{
Title = PKSimConstants.UI.CalculationMethods
};
foreach (var calculationMethod in calculationMethods)
{
var currentCalculationMethod = calculationMethod;
var category = _calculationMethodCategoryRepository.FindBy(currentCalculationMethod.Category);
var allCalculationMethods = category.AllItems().ToList();
if (allCalculationMethods.Count == 1)
{
continue;
}
//more than one cm in this category. Check that this is not only due to different models
allCalculationMethods.Remove(calculationMethod);
var allModelsUsedInCategory = allCalculationMethods.SelectMany(x => x.AllModels).Distinct();
var allSpeciesUsedInCategory = allCalculationMethods.SelectMany(x => x.AllSpecies).Distinct();
//at least another category available in the model and species
if (allModelsUsedInCategory.Any(x => currentCalculationMethod.AllModels.Contains(x)) &&
allSpeciesUsedInCategory.Any(x => currentCalculationMethod.AllSpecies.Contains(x)))
{
calcMethodPart.AddIs(_representationInfoRepository.DisplayNameFor(category),
_representationInfoRepository.DisplayNameFor(calculationMethod));
}
}
reportPart.AddPart(calcMethodPart);
}
protected override void FillUpReport(Simulation simulation, ReportPart reportPart)
{
var title = $"{PKSimConstants.ObjectTypes.Simulation} '{simulation.Name}'";
reportPart.AddPart(_reportGenerator.ReportFor(simulation.UsedBuildingBlocks).WithTitle(title));
reportPart.AddPart(_reportGenerator.ReportFor(simulation.Creation).WithTitle(PKSimConstants.UI.Origin));
reportPart.AddPart(_reportGenerator.ReportFor(simulation.Properties));
//Add special node with calculation methods per compound. Because the compound might be lazy loaded,
//it is potentially not available in the compound properties
simulation.UsedBuildingBlocksInSimulation(PKSimBuildingBlockType.Compound).ToList().Each((x, index) =>
{
var compoundPropertiesWithName = new CompoundPropertiesCalculationMethods(x.Name, simulation.CompoundPropertiesList[index]);
reportPart.AddPart(_reportGenerator.ReportFor(compoundPropertiesWithName));
});
}
protected override void FillUpReport(DataRepository dataRepository, ReportPart reportPart)
{
reportPart.Title = PKSimConstants.ObjectTypes.ObservedData;
reportPart.AddToContent(dataRepository.Name);
reportPart.AddPart(_reportGenerator.ReportFor(dataRepository.ExtendedProperties));
foreach (var column in dataRepository.AllButBaseGrid())
{
if (column.DataInfo == null)
{
continue;
}
reportPart.AddPart(_reportGenerator.ReportFor(column));
}
}
protected override void FillUpReport(Schema schema, ReportPart reportPart)
{
reportPart.Title = schema.Name;
reportPart.AddToContent(_reportGenerator.ReportFor(schema.StartTime));
reportPart.AddToContent(_reportGenerator.ReportFor(schema.TimeBetweenRepetitions));
reportPart.AddToContent(_reportGenerator.ReportFor(schema.NumberOfRepetitions));
schema.SchemaItems.Each(x => reportPart.AddPart(_reportGenerator.ReportFor(x)));
}
protected override void FillUpReport(DataColumn column, ReportPart reportPart)
{
if (column.DataInfo == null)
{
return;
}
reportPart.AddPart(_reportGenerator.ReportFor(column.DataInfo.ExtendedProperties).WithTitle(column.Name));
}
protected override void FillUpReport(CompoundProperties compoundProperties, ReportPart reportPart)
{
var processes = compoundProperties.Processes;
var compoundConfig = new TablePart(PKSimConstants.UI.Parameter, PKSimConstants.UI.AlternativeInCompound)
{
Title = PKSimConstants.UI.SimulationCompoundsConfiguration
};
foreach (var alternativeSelection in compoundProperties.CompoundGroupSelections)
{
var parameterName = _representationInfoRepository.DisplayNameFor(RepresentationObjectType.GROUP, alternativeSelection.GroupName);
compoundConfig.AddIs(parameterName, alternativeSelection.AlternativeName);
}
reportPart.AddPart(compoundConfig);
reportPart.AddPart(_reportGenerator.ReportFor(processes.MetabolizationSelection).WithTitle(PKSimConstants.UI.SimulationMetabolism));
reportPart.AddPart(_reportGenerator.ReportFor(processes.TransportAndExcretionSelection).WithTitle(PKSimConstants.UI.SimulationTransportAndExcretion));
reportPart.AddPart(_reportGenerator.ReportFor(processes.SpecificBindingSelection).WithTitle(PKSimConstants.UI.SimulationSpecificBinding));
}
protected override void FillUpReport(Formulation formulation, ReportPart reportPart)
{
reportPart.Title = _infoRepository.DisplayNameFor(RepresentationObjectType.CONTAINER, formulation.FormulationType);
string parameterTableCaption = PKSimConstants.UI.ParametersDefinedIn(formulation.Name);
if (formulation.IsDissolved)
{
reportPart.AddToContent(PKSimConstants.UI.NoParameter);
return;
}
TablePart tablePart;
if (!formulation.IsParticleDissolution)
{
var parameterList = new ParameterList(parameterTableCaption, formulation.AllVisibleParameters());
tablePart = parameterList.ToTable(_infoRepository);
}
else
{
var particleDisperseSystem = formulation.Parameter(Constants.Parameters.PARTICLE_DISPERSE_SYSTEM);
var particleDistribution = formulation.Parameter(Constants.Parameters.PARTICLE_SIZE_DISTRIBUTION);
var displayParticleDistribution = _infoRepository.DisplayNameFor(particleDistribution);
tablePart = new TablePart(PKSimConstants.UI.Parameter)
{
Caption = parameterTableCaption
};
if (particleDisperseSystem.Value == CoreConstants.Parameters.MONODISPERSE)
{
tablePart.AddIs(_infoRepository.DisplayNameFor(particleDisperseSystem), PKSimConstants.UI.Monodisperse);
tablePart.AddIs(formulation.Parameter(CoreConstants.Parameters.PARTICLE_RADIUS_MEAN), _infoRepository);
}
else
{
tablePart.AddIs(_infoRepository.DisplayNameFor(particleDisperseSystem), PKSimConstants.UI.Polydisperse);
if (particleDistribution.Value == CoreConstants.Parameters.PARTICLE_SIZE_DISTRIBUTION_NORMAL)
{
tablePart.AddIs(displayParticleDistribution, PKSimConstants.UI.Normal);
tablePart.AddIs(formulation.Parameter(CoreConstants.Parameters.PARTICLE_RADIUS_MEAN), _infoRepository);
tablePart.AddIs(formulation.Parameter(CoreConstants.Parameters.PARTICLE_RADIUS_STD_DEVIATION), _infoRepository);
}
else
{
tablePart.AddIs(displayParticleDistribution, PKSimConstants.UI.LogNormal);
tablePart.AddIs(formulation.Parameter(CoreConstants.Parameters.PARTICLE_LOG_DISTRIBUTION_MEAN), _infoRepository);
tablePart.AddIs(formulation.Parameter(CoreConstants.Parameters.PARTICLE_LOG_VARIATION_COEFF), _infoRepository);
}
}
}
tablePart.Title = reportPart.Title;
reportPart.AddPart(tablePart);
}
protected override void FillUpReport(CompoundPropertiesCalculationMethods compoundPropertiesCalculationMethods, ReportPart reportPart)
{
var(compoundName, compoundProperties) = compoundPropertiesCalculationMethods;
//Because the compound might be lazy loaded, it is potentially not available in the compound properties
var compoundNameToUse = compoundProperties.Compound?.Name ?? compoundName;
var calculationMethodReport = _reportGenerator.ReportFor(compoundProperties.AllCalculationMethods()).WithTitle(compoundNameToUse);
reportPart.AddPart(calculationMethodReport);
}
protected override void FillUpReport(ImportPopulationSettings populationSettings, ReportPart reportPart)
{
var baseOnIndividualPart = new ReportPart().WithTitle(PKSimConstants.UI.BasedOnIndividual);
baseOnIndividualPart.AddToContent(populationSettings.BaseIndividual.Name);
var numberOfIndividuals = populationSettings.AllFiles.Sum(x => x.NumberOfIndividuals);
var numberOfIndividualPart = new ReportPart().WithTitle(PKSimConstants.UI.NumberOfIndividuals);
numberOfIndividualPart.AddToContent(numberOfIndividuals.ToString(CultureInfo.InvariantCulture));
var part = new ReportPart().WithTitle(PKSimConstants.UI.CreatedUsingFiles);
foreach (var populationFiles in populationSettings.AllFiles)
{
part.AddToContent(FileHelper.ShortenPathName(populationFiles.FilePath, 50));
}
reportPart.AddPart(baseOnIndividualPart);
reportPart.AddPart(numberOfIndividualPart);
reportPart.AddPart(part);
}
protected override void FillUpReport(Compound compound, ReportPart reportPart)
{
reportPart.AddPart(_reportGenerator.ReportFor(compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY)));
reportPart.AddToContent(_reportGenerator.ReportFor(compound.Parameter(Constants.Parameters.MOL_WEIGHT)));
reportPart.AddToContent(_reportGenerator.ReportFor(compound.Parameter(CoreConstants.Parameters.EFFECTIVE_MOLECULAR_WEIGHT)));
reportPart.AddToContent(_reportGenerator.ReportFor(compound.Parameter(CoreConstants.Parameters.IS_SMALL_MOLECULE)));
if (compound.IsNeutral)
{
reportPart.AddToContent(PKSimConstants.UI.CompoundTypeNeutral);
}
else
{
addCompoundTypePart(reportPart, compound, CoreConstants.Parameters.PARAMETER_PKA1, CoreConstants.Parameters.COMPOUND_TYPE1);
addCompoundTypePart(reportPart, compound, CoreConstants.Parameters.PARAMETER_PKA2, CoreConstants.Parameters.COMPOUND_TYPE2);
addCompoundTypePart(reportPart, compound, CoreConstants.Parameters.PARAMETER_PKA3, CoreConstants.Parameters.COMPOUND_TYPE3);
}
var fractionUnboundReport = _reportGenerator.ReportFor(compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_FRACTION_UNBOUND));
fractionUnboundReport.AddToContent(_reportGenerator.ReportFor(compound.Parameter(CoreConstants.Parameters.PLASMA_PROTEIN_BINDING_PARTNER)));
reportPart.AddPart(fractionUnboundReport);
}
protected override void FillUpReport(IPopulationAnalysisField populationAnalysisField, ReportPart reportPart)
{
reportPart.Title = _objectTypeResolver.TypeFor(populationAnalysisField);
reportPart.AddToContent(populationAnalysisField.Name);
var groupingField = populationAnalysisField as PopulationAnalysisGroupingField;
if (groupingField == null)
{
return;
}
reportPart.AddPart(_reportGenerator.ReportFor(groupingField.GroupingDefinition));
}
protected override void FillUpReport(PopulationSimulationComparison simulationComparison, ReportPart reportPart)
{
base.FillUpReport(simulationComparison, reportPart);
var part = new ReportPart {
Title = PKSimConstants.UI.ReferenceSimulation
};
if (simulationComparison.HasReference)
{
part.AddToContent(simulationComparison.ReferenceSimulation.Name);
}
else
{
part.AddToContent(PKSimConstants.UI.None);
}
reportPart.AddPart(part);
}
protected override void FillUpReport(AdvancedProtocol advancedProtocol, ReportPart reportPart)
{
reportPart.Title = PKSimConstants.UI.AdvancedProtocolMode;
advancedProtocol.AllSchemas.Each(s => reportPart.AddPart(_reportGenerator.ReportFor(s)));
}
protected override void FillUpReport(ModelProperties modelProperties, ReportPart reportPart)
{
reportPart.Title = PKSimConstants.UI.SimulationModelConfiguration;
reportPart.AddToContent(_representationInfoRepository.DisplayNameFor(RepresentationObjectType.MODEL, modelProperties.ModelConfiguration.ModelName));
reportPart.AddPart(_reportGenerator.ReportFor(modelProperties.AllCalculationMethods()));
}
protected override void FillUpReport(OriginData originData, ReportPart reportPart)
{
var populationProperties = new TablePart(keyName: PKSimConstants.UI.PopulationProperties, valueName: PKSimConstants.UI.Value)
{
Title = PKSimConstants.UI.PopulationProperties
};
populationProperties.AddIs(PKSimConstants.UI.Species, originData.Species.DisplayName);
populationProperties.AddIs(PKSimConstants.UI.Population, originData.Population.DisplayName);
populationProperties.AddIs(PKSimConstants.UI.Gender, originData.Gender.DisplayName);
var individualProperties = new TablePart(PKSimConstants.UI.IndividualParameters, PKSimConstants.UI.Value, PKSimConstants.UI.Unit)
{
Title = PKSimConstants.UI.IndividualParameters,
Types =
{
[PKSimConstants.UI.Value] = typeof(double)
}
};
if (originData.Population.IsAgeDependent)
{
if (originData.Age != null)
{
individualProperties.AddIs(PKSimConstants.UI.Age, displayValueFor(originData.Age), originData.Age.Unit);
}
if (originData.Population.IsPreterm && originData.GestationalAge != null)
{
individualProperties.AddIs(PKSimConstants.UI.GestationalAge, displayValueFor(originData.GestationalAge), originData.GestationalAge.Unit);
}
}
individualProperties.AddIs(PKSimConstants.UI.Weight, displayValueFor(originData.Weight), originData.Weight.Unit);
if (originData.Population.IsHeightDependent)
{
if (originData.Height != null)
{
individualProperties.AddIs(PKSimConstants.UI.Height, displayValueFor(originData.Height), originData.Height.Unit);
}
if (originData.BMI != null)
{
individualProperties.AddIs(PKSimConstants.UI.BMI, displayValueFor(originData.BMI), originData.BMI.Unit);
}
}
reportPart.AddPart(populationProperties);
reportPart.AddPart(individualProperties);
var diseaseState = originData.DiseaseState;
if (diseaseState != null)
{
var diseaseStateProperties = new TablePart(PKSimConstants.UI.DiseaseState, PKSimConstants.UI.Value, PKSimConstants.UI.Unit)
{
Title = diseaseState.DisplayName
};
originData.DiseaseStateParameters.Each(x =>
{
var parameter = diseaseState.Parameter(x.Name);
var displayName = _representationInfoRepository.DisplayNameFor(parameter);
diseaseStateProperties.AddIs(displayName, displayValueFor(x), x.Unit);
});
reportPart.AddPart(diseaseStateProperties);
}
reportPart.AddPart(_reportGenerator.ReportFor(originData.SubPopulation));
reportPart.AddPart(_reportGenerator.ReportFor(originData.AllCalculationMethods()));
}