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 void should_have_created_the_expected_number_of_rows_in_the_datatable()
{
_dataTable.Rows.Count.ShouldBeEqualTo(6);
_dataTable.AllValuesInColumn <float>(_xAxis.Caption).ShouldOnlyContain(1, 2, 3, 1, 2, 3);
var values = _dataTable.AllValuesInColumn <object>(CoreConstants.CompositeNameFor(PKSimConstants.UI.LowerValue, _yAxis.Caption));
values[0].ShouldBeEqualTo(DBNull.Value);
values[1].ShouldBeEqualTo(20);
values[2].ShouldBeEqualTo(10);
values[3].ShouldBeEqualTo(20);
values[4].ShouldBeEqualTo(30);
values[5].ShouldBeEqualTo(DBNull.Value);
values = _dataTable.AllValuesInColumn <object>(_yAxis.Caption);
values[0].ShouldBeEqualTo(10);
values[1].ShouldBeEqualTo(DBNull.Value);
values[2].ShouldBeEqualTo(10);
values[3].ShouldBeEqualTo(20);
values[4].ShouldBeEqualTo(30);
values[5].ShouldBeEqualTo(40);
values = _dataTable.AllValuesInColumn <object>(CoreConstants.CompositeNameFor(PKSimConstants.UI.UpperValue, _yAxis.Caption));
values[0].ShouldBeEqualTo(DBNull.Value);
values[1].ShouldBeEqualTo(30);
values[2].ShouldBeEqualTo(10);
values[3].ShouldBeEqualTo(20);
values[4].ShouldBeEqualTo(30);
values[5].ShouldBeEqualTo(DBNull.Value);
}
protected override void Context()
{
base.Context();
_entity = new Observer().WithName(CoreConstants.CompositeNameFor(CoreConstants.Observer.FRACTION_OF_DOSE, _drugName, CoreConstants.Organ.Liver, CoreConstants.Compartment.Intracellular))
.WithParentContainer(_drugContainerInLiverCell)
.WithDimension(_fractionDimension);
}
private void updateInteractionFactor(IContainer processParameterContainer, string moleculeName, IEnumerable <IInteractionKineticUpdaterSpecification> allUpdatingKinetics, IFormulaCache formulaCache, string parameterName, Func <IParameter, string> createFormulaAction)
{
var interactionFactor = processParameterContainer.Parameter(parameterName);
if (!allUpdatingKinetics.Any() || interactionFactor == null)
{
return;
}
var formulaName = CoreConstants.CompositeNameFor(processParameterContainer.Name, moleculeName, parameterName);
var formula = formulaCache.FindByName(formulaName) as ExplicitFormula;
if (formula != null)
{
interactionFactor.Formula = formula;
return;
}
formula = _objectBaseFactory.Create <ExplicitFormula>()
.WithName(formulaName)
.WithDimension(interactionFactor.Dimension);
interactionFactor.Formula = formula;
formula.FormulaString = createFormulaAction(interactionFactor);
formulaCache.Add(formula);
}
private IReactionBuilder createReactionFromProcess(IMoleculeBuilder moleculeBuilder, CompoundProcess process,
IReadOnlyCollection <string> forbiddenNames)
{
var reactionName = CoreConstants.CompositeNameFor(moleculeBuilder.Name, process.Name);
return(createReactionFromProcess(process, reactionName, forbiddenNames));
}
private void addLiverZoneCompartmentObserver(IObserverBuilder observerBuilder, string compartment, IObserverBuildingBlock observerBuildingBlock, Compound compound)
{
var observerName = CoreConstants.CompositeNameFor(observerBuilder.Name, CoreConstants.Organ.Liver, compartment);
if (observerBuildingBlock.ExistsByName(observerName))
{
return;
}
var observer = _objectBaseFactory.Create <IContainerObserverBuilder>()
.WithName(observerName)
.WithDimension(_dimensionRepository.Fraction);
observer.ForAll = false;
observerBuilder.MoleculeNames().Each(observer.AddMoleculeName);
observer.ContainerCriteria = Create.Criteria(x => x.With(CoreConstants.Organ.Liver)
.And.With(compartment)
.And.Not(CoreConstants.Compartment.Pericentral)
.And.Not(CoreConstants.Compartment.Periportal));
var formula = _objectBaseFactory.Create <ExplicitFormula>()
.WithName(observerName)
.WithFormulaString("(M_periportal + M_pericentral)/" + TOTAL_DRUG_MASS_ALIAS)
.WithDimension(_dimensionRepository.Fraction);
formula.AddObjectPath(createZoneAmoutPath(compartment, CoreConstants.Compartment.Periportal, "M_periportal"));
formula.AddObjectPath(createZoneAmoutPath(compartment, CoreConstants.Compartment.Pericentral, "M_pericentral"));
formula.AddObjectPath(createTotalDrugMassObjectPath(compound.Name));
observer.Formula = formula;
observerBuildingBlock.Add(observer);
observerBuildingBlock.AddFormula(formula);
}
private void updateOutputFolderFrom(string outputFolder)
{
OutputFolder = outputFolder;
if (string.IsNullOrEmpty(LogFileFullPath))
{
LogFileFullPath = CoreConstants.DefaultBatchLogFullPath(OutputFolder);
}
}
private IReactionBuilder createReactionFromProcess(CompoundProcess process, string reactionName, IReadOnlyCollection <string> forbiddenNames)
{
//retrieve process for the simulation and create a clone
var reaction = createReactionFromProcess(process, _simulationActiveProcessRepository.ProcessFor <PKSimReaction>(process.InternalName), reactionName, forbiddenNames);
//make sure formula name is unique as it can be shared among processes
reaction.Formula.Name = CoreConstants.CompositeNameFor(reaction.Name, reaction.Formula.Name);
return(reaction);
}
public void should_have_created_the_expected_number_of_columns_in_the_datatable()
{
_dataTable.Columns.Count.ShouldBeEqualTo(6);
_dataTable.Columns[_xAxis.Caption].ShouldNotBeNull();
_dataTable.Columns[CoreConstants.CompositeNameFor(PKSimConstants.UI.LowerValue, _yAxis.Caption)].ShouldNotBeNull();
_dataTable.Columns[_yAxis.Caption].ShouldNotBeNull();
_dataTable.Columns[CoreConstants.CompositeNameFor(PKSimConstants.UI.UpperValue, _yAxis.Caption)].ShouldNotBeNull();
}
public void should_have_created_a_reaction_using_the_metabolite_as_product_in_liver_pericentral_intracellular()
{
var reactionInLiver = _simulation.Model.Root.EntityAt <IReaction>(Constants.ORGANISM, CoreConstants.Organ.LIVER,
CoreConstants.Compartment.PERICENTRAL, CoreConstants.Compartment.INTRACELLULAR,
CoreConstants.CompositeNameFor(_compound.Name, _parentMetabolizationCYP3A4.Name));
reactionInLiver.ShouldNotBeNull();
reactionInLiver.Products.Find(x => x.Partner.Name == _metabolite.Name).ShouldNotBeNull();
}
public void should_have_created_the_expected_number_of_columns_in_the_pivoted_datatable()
{
_pivotedDataTable.Columns.Count.ShouldBeEqualTo(5);
_pivotedDataTable.Columns.Contains(_xAxis.Caption).ShouldBeTrue();
_pivotedDataTable.Columns[_xAxis.Caption].DataType.ShouldBeEqualTo(typeof(float));
_pivotedDataTable.Columns.Contains(string.Format("Male.Liver({0})", CoreConstants.CompositeNameFor(PKSimConstants.UI.LowerValue, _yAxis.Caption))).ShouldBeTrue();
_pivotedDataTable.Columns.Contains(string.Format("Male.Liver({0})", _yAxis.Caption)).ShouldBeTrue();
_pivotedDataTable.Columns.Contains(string.Format("Male.Liver({0})", CoreConstants.CompositeNameFor(PKSimConstants.UI.UpperValue, _yAxis.Caption))).ShouldBeTrue();
_pivotedDataTable.Columns.Contains(string.Format("Female.Kidney({0})", _yAxis.Caption)).ShouldBeTrue();
}
public void should_have_created_the_expected_number_of_rows_in_the_datatable()
{
_dataTable.Rows.Count.ShouldBeEqualTo(3);
_dataTable.AllValuesInColumn <float>(_xAxis.Caption).ShouldOnlyContain(1, 2, 3);
_dataTable.AllValuesInColumn <float>(CoreConstants.CompositeNameFor(PKSimConstants.UI.Minimum, _xAxis.Caption)).ShouldOnlyContain(0, 1.8f, 2f);
_dataTable.AllValuesInColumn <float>(CoreConstants.CompositeNameFor(PKSimConstants.UI.LowerPercentile, _yAxis.Caption)).ShouldOnlyContain(10, 20, 30);
_dataTable.AllValuesInColumn <float>(_yAxis.Caption).ShouldOnlyContain(20, 30, 40);
_dataTable.AllValuesInColumn <float>(CoreConstants.CompositeNameFor(PKSimConstants.UI.UpperPercentile, _yAxis.Caption)).ShouldOnlyContain(30, 40, 50);
_dataTable.AllValuesInColumn <float>(CoreConstants.CompositeNameFor(PKSimConstants.UI.Maximum, _xAxis.Caption)).ShouldOnlyContain(1.5f, 2.5f, 4f);
}
public virtual void SelectOutputFolder()
{
var outputFolder = _dialogCreator.AskForFolder("Select output folder where results will be exported", CoreConstants.DirectoryKey.BATCH);
if (string.IsNullOrEmpty(outputFolder))
{
return;
}
_dto.OutputFolder = outputFolder;
_logFileFullPath = CoreConstants.DefaultBatchLogFullPath(outputFolder);
}
public void should_create_a_fraction_of_dose_observer_for_the_unspecified_metabolite_in_the_liver_as_sum_of_the_fraction_in_liver_periportal_and_liver_pericentral()
{
var enzymaticProcessSelection = ProcessSelectionFor(_parentMetabolizationCYP2D6);
var observerName = CoreConstants.Observer.ObserverNameFrom(CoreConstants.Observer.FRACTION_OF_DOSE, _compound.Name);
var liverCellCYP2D6 = _simulation.Model.Root.EntityAt <Container>(Constants.ORGANISM, CoreConstants.Organ.LIVER, CoreConstants.Compartment.INTRACELLULAR, enzymaticProcessSelection.ProductName());
var observerLiverCell = liverCellCYP2D6.Children.FindByName(CoreConstants.CompositeNameFor(observerName, CoreConstants.Organ.LIVER, CoreConstants.Compartment.INTRACELLULAR)).DowncastTo <IObserver>();
observerLiverCell.ShouldNotBeNull();
observerLiverCell.Formula.DowncastTo <ExplicitFormula>().FormulaString.ShouldBeEqualTo("(M_periportal + M_pericentral)/TotalDrugMass");
}
public void the_created_process_should_have_two_parameters_enzyme_concentration_and_cl_spec_per_enzyme_hidden_set_to_one()
{
var processName = CoreConstants.CompositeNameFor(_compound.Name, _liverClearance.Name);
var processContainer = _simulation.Model.Root.EntityAt <Container>(processName);
processContainer.Parameter(CoreConstantsForSpecs.Parameter.ENZYME_CONCENTRATION).Value.ShouldBeEqualTo(1);
processContainer.Parameter(CoreConstantsForSpecs.Parameter.ENZYME_CONCENTRATION).Visible.ShouldBeFalse();
processContainer.Parameter(CoreConstantsForSpecs.Parameter.CL_SPEC_PER_ENZYME).Value.ShouldBeEqualTo(processContainer.Parameter(CoreConstants.Parameters.SPECIFIC_CLEARANCE).Value);
processContainer.Parameter(CoreConstantsForSpecs.Parameter.CL_SPEC_PER_ENZYME).Visible.ShouldBeFalse();
}
private static string createDataGroupingNameFor(bool hasOnlyOneDoseUnit, Compound compound, SchemaItemDTO schemaItemDTO)
{
var baseName = schemaItemDTO.DisplayName;
if (!string.IsNullOrEmpty(compound.Name))
{
baseName = CoreConstants.CompositeNameFor(baseName, compound.Name);
}
return(hasOnlyOneDoseUnit ? baseName : Constants.NameWithUnitFor(baseName, schemaItemDTO.DoseParameter.DisplayUnit));
}
private string compoundProcessName(IParameter parameter)
{
var process = parameter.ParentContainer;
var processName = process.Name;
if (process.ContainerType == ContainerType.Reaction || process.ParentContainer == null)
{
return(processName);
}
return(CoreConstants.CompositeNameFor(process.ParentContainer.Name, processName));
}
public void should_have_created_the_expected_number_of_columns_in_the_datatable()
{
_dataTable.Columns.Count.ShouldBeEqualTo(9);
_dataTable.Columns[_xAxis.Caption].ShouldNotBeNull();
_dataTable.Columns[CoreConstants.CompositeNameFor(PKSimConstants.UI.Minimum, _xAxis.Caption)].ShouldNotBeNull();
_dataTable.Columns[CoreConstants.CompositeNameFor(PKSimConstants.UI.Maximum, _xAxis.Caption)].ShouldNotBeNull();
_dataTable.Columns[PKSimConstants.UI.NumberOfIndividuals].ShouldNotBeNull();
_dataTable.Columns[_yAxis.Caption].ShouldNotBeNull();
_dataTable.Columns[CoreConstants.CompositeNameFor(PKSimConstants.UI.LowerPercentile, _yAxis.Caption)].ShouldNotBeNull();
_dataTable.Columns[CoreConstants.CompositeNameFor(PKSimConstants.UI.UpperPercentile, _yAxis.Caption)].ShouldNotBeNull();
}
private async Task exportPopulationSimulationToCsvAsync(PopulationSimulation populationSimulation, string outputFolder, string projectName)
{
var populationFile = CoreConstants.DefaultPopulationExportNameFor(populationSimulation.Name);
var populationFileFullPath = csvPathUnder(outputFolder, populationFile, projectName);
_populationExportTask.ExportToCSV(populationSimulation, populationFileFullPath);
await exportSimulationResultsToCsv(populationSimulation, outputFolder, projectName);
var populationPKAnalysesFile = CoreConstants.DefaultPKAnalysesExportNameFor(populationSimulation.Name);
var populationPKAnalysesFullPath = csvPathUnder(outputFolder, populationPKAnalysesFile, projectName);
await _simulationExportTask.ExportPKAnalysesToCSVAsync(populationSimulation, populationPKAnalysesFullPath);
}
public IReactionBuilder TurnoverReactionFrom(IReactionBuilder templateReaction, IMoleculeBuilder protein, IReadOnlyCollection <string> forbiddenNames, IFormulaCache formulaCache)
{
var reaction = createReactionFromProcess(templateReaction, forbiddenNames);
reaction.Name = reactionNameFor(reaction.Name, protein.Name);
reaction.Formula.Name = CoreConstants.CompositeNameFor(reaction.Name, reaction.Formula.Name);
replaceKeywordsInProcess(reaction, new[] { CoreConstants.KeyWords.Protein, CoreConstants.KeyWords.Reaction }, new[] { protein.Name, reaction.Name });
reaction.AddProduct(new ReactionPartnerBuilder(protein.Name, 1));
formulaCache.Add(reaction.Formula);
return(reaction);
}
private IReactionBuilder interactionReactionFrom(InteractionProcess interactionProcess, IMoleculeBuilder protein, IReadOnlyCollection <string> forbiddenNames, IFormulaCache formulaCache)
{
var compound = interactionProcess.ParentCompound;
var reactionName = CoreConstants.CompositeNameFor(compound.Name, interactionProcess.Name);
var reaction = createReactionFromProcess(interactionProcess, reactionName, forbiddenNames);
//replace keywords
replaceKeywordsInProcess(reaction, new[] { CoreConstants.KeyWords.Molecule, CoreConstants.KeyWords.Protein, CoreConstants.KeyWords.Reaction },
new[] { compound.Name, protein.Name, interactionProcess.Name });
formulaCache.Add(reaction.Formula);
return(reaction);
}
protected override void AddSpecificChartColumns(DataTable dataTable, CurveData <RangeXValue, RangeYValue> curveData, bool exportForPivot)
{
_xValueColumn = curveData.XAxis.Caption;
_yValueColumn = curveData.YAxis.Caption;
_yLowerPercentileColumn = CoreConstants.CompositeNameFor(PKSimConstants.UI.LowerPercentile, _yValueColumn);
_yUpperPercentileColumn = CoreConstants.CompositeNameFor(PKSimConstants.UI.UpperPercentile, _yValueColumn);
_xMinimumColumn = CoreConstants.CompositeNameFor(PKSimConstants.UI.Minimum, _xValueColumn);
_xMaximumColumn = CoreConstants.CompositeNameFor(PKSimConstants.UI.Maximum, _xValueColumn);
_xNumberOfIndividualsColumn = PKSimConstants.UI.NumberOfIndividuals;
dataTable.AddColumn <float>(_xMinimumColumn);
dataTable.AddColumn <float>(_xValueColumn);
dataTable.AddColumn <float>(_xMaximumColumn);
dataTable.AddColumn <float>(_xNumberOfIndividualsColumn);
dataTable.AddColumn <float>(_yLowerPercentileColumn);
dataTable.AddColumn <float>(_yValueColumn);
dataTable.AddColumn <float>(_yUpperPercentileColumn);
}
private void addDynamicParameterGroupNodeTo(ITreeNode node, string subGroupName, IEnumerable <IParameter> allParameters, Func <IParameter, string> keySelector, Func <string, bool> keyAvailableFunc)
{
var group = node.TagAsObject.DowncastTo <IGroup>();
var allGroupParameters = _parameterGroupTask.ParametersInTopGroup(group.Name, allParameters);
foreach (var parametersForNewGroup in allGroupParameters.GroupBy(keySelector).OrderBy(x => x.Key))
{
if (!keyAvailableFunc(parametersForNewGroup.Key))
{
continue;
}
var compositeKey = CoreConstants.CompositeNameFor(subGroupName, parametersForNewGroup.Key);
var parameterContainer = parametersForNewGroup.First().ParentContainer;
var dynamicNode = _treeNodeFactory.CreateDynamicGroup(compositeKey, parametersForNewGroup.Key, parametersForNewGroup);
dynamicNode.Icon = ApplicationIcons.IconByNameOrDefault(parameterContainer.Icon, node.Icon);
node.AddChild(dynamicNode);
}
}
protected override void TypedDeserialize(SystemicProcessSelection systemicProcessSelection, XElement element, SerializationContext context)
{
base.TypedDeserialize(systemicProcessSelection, element, context);
//in 5.0.1, name of process did not contain data source.
if (systemicProcessSelection.ProcessType == null || string.IsNullOrEmpty(systemicProcessSelection.ProcessName))
{
return;
}
var systemicProcessName = systemicProcessSelection.ProcessType.DisplayName;
if (systemicProcessSelection.ProcessName.Contains(systemicProcessName))
{
return;
}
//we need to adjust the process name
systemicProcessSelection.ProcessName = CoreConstants.CompositeNameFor(systemicProcessName, systemicProcessSelection.ProcessName);
}
protected override void AddSpecificChartColumns(DataTable dataTable, CurveData <TimeProfileXValue, TimeProfileYValue> curveData, bool exportForPivot)
{
_xValueColumn = curveData.XAxis.Caption;
_yValueColumn = curveData.YAxis.Caption;
_yLowerValueColumn = CoreConstants.CompositeNameFor(PKSimConstants.UI.LowerValue, _yValueColumn);
_yUpperValueColumn = CoreConstants.CompositeNameFor(PKSimConstants.UI.UpperValue, _yValueColumn);
//Export xValueColumn as string to enable correct pivot on x values
if (exportForPivot)
{
dataTable.AddColumn <string>(_xValueColumn);
}
else
{
dataTable.AddColumn <float>(_xValueColumn);
}
dataTable.AddColumn <float>(_yLowerValueColumn);
dataTable.AddColumn <float>(_yValueColumn);
dataTable.AddColumn <float>(_yUpperValueColumn);
}
public void should_return_a_reaction_having_the_expected_name()
{
_reaction.Name.ShouldBeEqualTo(CoreConstants.CompositeNameFor(_compound.Name, _interactionProcess.Name));
}
public void should_have_set_the_name_of_the_kinetic_to_the_name_of_the_incoming_process_combine_with_the_name_of_the_formula()
{
_reaction.Formula.Name.ShouldBeEqualTo(CoreConstants.CompositeNameFor(_reaction.Name, "KINETIC"));
}
public void should_have_set_the_name_of_the_reaction_to_the_name_of_the_incoming_process_combine_with_the_name_of_the_drug()
{
_reaction.Name.ShouldBeEqualTo(CoreConstants.CompositeNameFor(_drug.Name, _process.Name));
}
protected override async Task Context()
{
await base.Context();
_simulation = A.Fake <Simulation>().WithName("Sim");
A.CallTo(() => _simulation.HasResults).Returns(true);
_fileFullPath = "file full path";
A.CallTo(() => _dialogCreator.AskForFileToSave(PKSimConstants.UI.ExportSimulationResultsToCSV, Constants.Filter.CSV_FILE_FILTER, Constants.DirectoryKey.REPORT, CoreConstants.DefaultResultsExportNameFor(_simulation.Name), null))
.Returns(_fileFullPath);
}
protected override async Task Context()
{
await base.Context();
_simulation = A.Fake <IndividualSimulation>();
A.CallTo(() => _simulation.HasResults).Returns(true);
A.CallTo(() => _simulation.Name).Returns("toto");
A.CallTo(() => _simulation.DataRepository).Returns(new DataRepository());
_excelFile = "tralala";
A.CallTo(() => _dialogCreator.AskForFileToSave(PKSimConstants.UI.ExportSimulationResultsToExcel, Constants.Filter.EXCEL_SAVE_FILE_FILTER, Constants.DirectoryKey.REPORT, CoreConstants.DefaultResultsExportNameFor(_simulation.Name), null)).Returns(_excelFile);
}