protected override void Context()
{
base.Context();
_formulaCache = new FormulaCache();
_compoundFactory = IoC.Resolve <ICompoundFactory>();
_parameterAlternativeFactory = IoC.Resolve <IParameterAlternativeFactory>();
_compound = _compoundFactory.Create().WithName("Comp");
_compound.Parameter(Constants.Parameters.MOL_WEIGHT).Value = 250;
//Two simple parameters without alternatives
//one parameter defined as a constant for which an alternative was also specififed
var lipoGroup = _compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY);
_alternativeLipo1 = _parameterAlternativeFactory.CreateAlternativeFor(lipoGroup).WithName("ALT_LIPO1").WithId("ALT_LIPO1");
_alternativeLipo1.Parameter(CoreConstants.Parameters.LIPOPHILICITY).Value = 2;
_alternativeLipo2 = _parameterAlternativeFactory.CreateAlternativeFor(lipoGroup).WithName("ALT_LIPO2").WithId("ALT_LIPO2");
_alternativeLipo2.Parameter(CoreConstants.Parameters.LIPOPHILICITY).Value = 5;
lipoGroup.AddAlternative(_alternativeLipo1);
lipoGroup.AddAlternative(_alternativeLipo2);
//one parameter defined as a formula with a default calculated alternative
var permAlternativeGroup = _compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_PERMEABILITY);
//value cannot be changed by user
_alternativePerm1 = _parameterAlternativeFactory.CreateDefaultAlternativeFor(permAlternativeGroup).WithName("ALT_PERM1").WithId("ALT_PERM1");
_alternativePerm2 = _parameterAlternativeFactory.CreateAlternativeFor(permAlternativeGroup).WithName("ALT_PERM2").WithId("ALT_PERM2");
_alternativePerm2.Parameter(CoreConstants.Parameters.PERMEABILITY).Value = 10;
permAlternativeGroup.AddAlternative(_alternativePerm1);
permAlternativeGroup.AddAlternative(_alternativePerm2);
}
public Converter740To80(
ICompoundFactory compoundFactory,
ICloner cloner)
{
_templateCompound = new Lazy <Compound>(compoundFactory.Create);
_cloner = cloner;
}
public ObservedDataToCompoundMappingPresenter(IObservedDataToCompoundMappingView view, ICompoundFactory compoundFactory) : base(view)
{
_compoundFactory = compoundFactory;
_undefinedCompound = _compoundFactory.Create().WithName(PKSimConstants.UI.Undefined);
_allAvailableCompounds = new List <PKSim.Core.Model.Compound> {
_undefinedCompound
};
view.CancelVisible = false;
}
public CreateCompoundPresenter(ICreateCompoundView view, ISubPresenterItemManager <ICompoundItemPresenter> subPresenterItemManager, IDialogCreator dialogCreator,
ICompoundFactory compoundFactory, IObjectBaseDTOFactory objectBaseDTOFactory, IBuildingBlockPropertiesMapper propertiesMapper)
: base(view, subPresenterItemManager, CompoundItems.All, dialogCreator)
{
_compoundFactory = compoundFactory;
_objectBaseDTOFactory = objectBaseDTOFactory;
_propertiesMapper = propertiesMapper;
AllowQuickFinish = true;
}
public CompoundMapper(
ParameterMapper parameterMapper,
AlternativeMapper alternativeMapper,
CalculationMethodCacheMapper calculationMethodCacheMapper,
CompoundProcessMapper processMapper,
ICompoundFactory compoundFactory) : base(parameterMapper)
{
_alternativeMapper = alternativeMapper;
_calculationMethodCacheMapper = calculationMethodCacheMapper;
_processMapper = processMapper;
_compoundFactory = compoundFactory;
}
protected override void Context()
{
_parameterAlternativeFactory = A.Fake <IParameterAlternativeFactory>();
_applicationController = A.Fake <IApplicationController>();
_executionContext = A.Fake <IExecutionContext>();
_entityTask = A.Fake <IEntityTask>();
_formulaFactory = A.Fake <IFormulaFactory>();
_parameterTask = A.Fake <IParameterTask>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_compoundFactory = new CompoundFactoryForSpecs();
sut = new CompoundAlternativeTask(_parameterAlternativeFactory, _applicationController,
_executionContext, _compoundFactory, _entityTask, _formulaFactory, _parameterTask, _buildingBlockRepository);
}
public CompoundAlternativeTask(IParameterAlternativeFactory parameterAlternativeFactory, IApplicationController applicationController,
IExecutionContext executionContext, ICompoundFactory compoundFactory, IEntityTask entityTask,
IFormulaFactory formulaFactory, IParameterTask parameterTask, IBuildingBlockRepository buildingBlockRepository)
{
_parameterAlternativeFactory = parameterAlternativeFactory;
_applicationController = applicationController;
_executionContext = executionContext;
_compoundFactory = compoundFactory;
_entityTask = entityTask;
_formulaFactory = formulaFactory;
_parameterTask = parameterTask;
_buildingBlockRepository = buildingBlockRepository;
}
public CompoundMapper(ICompoundFactory compoundFactory, ICompoundProcessRepository compoundProcessRepository,
IBatchLogger batchLogger, ICloner cloner,
ICompoundCalculationMethodCategoryRepository calculationMethodCategoryRepository,
ICalculationMethodRepository calculationMethodRepository, ICompoundProcessTask compoundProcessTask, ISpeciesRepository speciesRepository)
{
_compoundFactory = compoundFactory;
_compoundProcessRepository = compoundProcessRepository;
_batchLogger = batchLogger;
_cloner = cloner;
_calculationMethodCategoryRepository = calculationMethodCategoryRepository;
_calculationMethodRepository = calculationMethodRepository;
_compoundProcessTask = compoundProcessTask;
_speciesRepository = speciesRepository;
}
protected override void Context()
{
_parameterAlternativeFactory = A.Fake <IParameterAlternativeFactory>();
_executionContext = A.Fake <IExecutionContext>();
_formulaFactory = A.Fake <IFormulaFactory>();
_parameterTask = A.Fake <IParameterTask>();
_buildingBlockRepository = A.Fake <IBuildingBlockRepository>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_dataImporter = A.Fake <IDataImporter>();
_compoundFactory = new CompoundFactoryForSpecs();
sut = new CompoundAlternativeTask(_parameterAlternativeFactory,
_executionContext, _compoundFactory, _formulaFactory, _parameterTask,
_buildingBlockRepository, _dimensionRepository, _dataImporter);
}
public CompoundAlternativeTask(
IParameterAlternativeFactory parameterAlternativeFactory,
IExecutionContext executionContext,
ICompoundFactory compoundFactory,
IFormulaFactory formulaFactory,
IParameterTask parameterTask,
IBuildingBlockRepository buildingBlockRepository,
IDimensionRepository dimensionRepository,
IDataImporter dataImporter)
{
_parameterAlternativeFactory = parameterAlternativeFactory;
_executionContext = executionContext;
_compoundFactory = compoundFactory;
_formulaFactory = formulaFactory;
_parameterTask = parameterTask;
_buildingBlockRepository = buildingBlockRepository;
_dimensionRepository = dimensionRepository;
_dataImporter = dataImporter;
}
protected override Task Context()
{
_alternativeMapper = A.Fake <AlternativeMapper>();
_parameterMapper = A.Fake <ParameterMapper>();
_calculationMethodCacheMapper = A.Fake <CalculationMethodCacheMapper>();
_processMapper = A.Fake <CompoundProcessMapper>();
_compoundFactory = A.Fake <ICompoundFactory>();
sut = new CompoundMapper(_parameterMapper, _alternativeMapper, _calculationMethodCacheMapper, _processMapper, _compoundFactory);
_compound = new Model.Compound
{
Name = "Compound",
Description = "Description"
};
addPkAParameters(_compound, 0, 8, CompoundType.Base);
addPkAParameters(_compound, 1, 4, CompoundType.Acid);
addPkAParameters(_compound, 2, 7, CompoundType.Neutral);
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_FRACTION_UNBOUND));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_SOLUBILITY));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_INTESTINAL_PERMEABILITY));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_PERMEABILITY));
_compound.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.IS_SMALL_MOLECULE));
_compound.Add(DomainHelperForSpecs.ConstantParameterWithValue((int)PlasmaProteinBindingPartner.Glycoprotein).WithName(CoreConstants.Parameters.PLASMA_PROTEIN_BINDING_PARTNER));
_partialProcess = new EnzymaticProcess().WithName("EnzymaticProcess");
_systemicProcess = new SystemicProcess().WithName("SystemicProcess");
_compound.AddProcess(_partialProcess);
_compound.AddProcess(_systemicProcess);
_calculationMethodCacheSnapshot = new CalculationMethodCache();
A.CallTo(() => _calculationMethodCacheMapper.MapToSnapshot(_compound.CalculationMethodCache)).Returns(_calculationMethodCacheSnapshot);
_snapshotProcess1 = new CompoundProcess();
_snapshotProcess2 = new CompoundProcess();
A.CallTo(() => _processMapper.MapToSnapshot(_partialProcess)).Returns(_snapshotProcess1);
A.CallTo(() => _processMapper.MapToSnapshot(_systemicProcess)).Returns(_snapshotProcess2);
return(_completed);
}
public Converter721To730(
ICompoundFactory compoundFactory,
ICloner cloner,
ICreationMetaDataFactory creationMetaDataFactory,
IContainerTask containerTask,
IFormulationRepository formulationRepository,
IEventGroupRepository eventGroupRepository,
Converter710To730 coreConverter,
ICompoundProcessRepository compoundProcessRepository,
ISchemaItemRepository schemaItemRepository
)
{
_compoundFactory = compoundFactory;
_cloner = cloner;
_creationMetaDataFactory = creationMetaDataFactory;
_containerTask = containerTask;
_formulationRepository = formulationRepository;
_eventGroupRepository = eventGroupRepository;
_coreConverter = coreConverter;
_compoundProcessRepository = compoundProcessRepository;
_schemaItemRepository = schemaItemRepository;
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_alternativeMapper = A.Fake <AlternativeMapper>();
_calculationMethodCacheMapper = A.Fake <CalculationMethodCacheMapper>();
_processMapper = A.Fake <CompoundProcessMapper>();
_compoundFactory = A.Fake <ICompoundFactory>();
_valueOriginMapper = A.Fake <ValueOriginMapper>();
sut = new CompoundMapper(_parameterMapper, _alternativeMapper, _calculationMethodCacheMapper, _processMapper, _valueOriginMapper, _compoundFactory);
_compound = new Model.Compound
{
Name = "Compound",
Description = "Description"
};
_pkaValueOrigin = new ValueOrigin {
Method = ValueOriginDeterminationMethods.InVitro, Description = "PKA"
};
_snapshotValueOrigin = new Snapshots.ValueOrigin {
Method = ValueOriginDeterminationMethodId.InVivo, Description = "PKA"
};
addPkAParameters(_compound, 0, 8, CompoundType.Base);
addPkAParameters(_compound, 1, 4, CompoundType.Acid);
addPkAParameters(_compound, 2, 7, CompoundType.Neutral);
_compoundIntestinalPermeabilityAlternativeGroup = createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_INTESTINAL_PERMEABILITY);
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_FRACTION_UNBOUND));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_SOLUBILITY));
_compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_PERMEABILITY));
_compound.AddParameterAlternativeGroup(_compoundIntestinalPermeabilityAlternativeGroup);
_compoundIntestinalPermeabilityAlternativeGroup.DefaultAlternative.IsDefault = true;
//Calculated alternative will not be the default alternative for intestinal perm
_calculatedAlternative = new ParameterAlternative {
Name = PKSimConstants.UI.CalculatedAlernative, IsDefault = false
};
_compoundIntestinalPermeabilityAlternativeGroup.AddAlternative(_calculatedAlternative);
//Mapping of a calculated alternative returns null
A.CallTo(() => _alternativeMapper.MapToSnapshot(_calculatedAlternative)).Returns(Task.FromResult <Alternative>(null));
_compound.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.IS_SMALL_MOLECULE));
_compound.Add(DomainHelperForSpecs.ConstantParameterWithValue((int)PlasmaProteinBindingPartner.Glycoprotein).WithName(CoreConstants.Parameters.PLASMA_PROTEIN_BINDING_PARTNER));
_partialProcess = new EnzymaticProcess().WithName("EnzymaticProcess");
_systemicProcess = new SystemicProcess().WithName("SystemicProcess");
_compound.AddProcess(_partialProcess);
_compound.AddProcess(_systemicProcess);
_calculationMethodCacheSnapshot = new CalculationMethodCache();
A.CallTo(() => _calculationMethodCacheMapper.MapToSnapshot(_compound.CalculationMethodCache)).Returns(_calculationMethodCacheSnapshot);
_snapshotProcess1 = new CompoundProcess();
_snapshotProcess2 = new CompoundProcess();
A.CallTo(() => _processMapper.MapToSnapshot(_partialProcess)).Returns(_snapshotProcess1);
A.CallTo(() => _processMapper.MapToSnapshot(_systemicProcess)).Returns(_snapshotProcess2);
_molweightParameter = DomainHelperForSpecs.ConstantParameterWithValue(400).WithName(Constants.Parameters.MOL_WEIGHT);
_molweightParameter.ValueOrigin.Method = ValueOriginDeterminationMethods.InVivo;
//Do not update F value origin to ensure that it's being synchronized when mapping from snapshot
_halogenFParameter = DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(Constants.Parameters.F);
_compound.Add(_molweightParameter);
_compound.Add(_halogenFParameter);
return(_completed);
}
public CompoundBuilder(ICompoundFactory <TInA, TInB, TResult> factory) => _factory = factory;
public CompoundConverter(ICompoundFactory compoundFactory, ICloner cloner)
{
_compoundFactory = compoundFactory;
_cloner = cloner;
}
