protected override void Context()
{
base.Context();
_process = A.Fake <SystemicProcess>();
_renameCommand = A.Fake <IPKSimCommand>();
A.CallTo(() => _compoundProcessTask.RenameDataSource(_process)).Returns(_renameCommand);
}
protected override void Context()
{
base.Context();
var proc1 = A.Fake <EnzymaticProcess>().WithName("proc1");
var proc2 = A.Fake <EnzymaticProcess>().WithName("proc2");
_node1 = A.Fake <ITreeNode>();
A.CallTo(() => _node1.Id).Returns("1");
_node2 = A.Fake <ITreeNode>();
A.CallTo(() => _node2.Id).Returns("2");
_compound.Add(proc1);
_compound.Add(proc2);
_systemicProcess = new SystemicProcess {
SystemicProcessType = SystemicProcessTypes.Hepatic
};
_compound.AddProcess(_systemicProcess);
A.CallTo(() => _partialProcessNodeMapper.MapFrom(proc1)).Returns(_node1);
A.CallTo(() => _partialProcessNodeMapper.MapFrom(proc2)).Returns(_node2);
//nodes not added yet to the tree
A.CallTo(() => _view.TreeView.NodeById(_node1.Id)).Returns(null);
A.CallTo(() => _view.TreeView.NodeById(_node2.Id)).Returns(null);
_hepaticClearanceNode = _treeNodeFactory.CreateFor(SystemicProcessNodeType.HepaticClearance);
A.CallTo(() => _view.TreeView.NodeById(_hepaticClearanceNode.Id)).Returns(_hepaticClearanceNode);
}
public void UpdateProperties(SystemicProcess systemicProcess, SystemicProcessDTO systemicProcessDTO)
{
systemicProcess.Name = systemicProcessDTO.Name;
systemicProcess.DataSource = systemicProcessDTO.DataSource;
systemicProcess.Species = systemicProcessDTO.Species;
systemicProcess.Description = systemicProcessDTO.Description;
}
protected override Task Context()
{
sut = new ProcessMappingMapper();
_compound = new Compound
{
Name = "COMP",
};
_enzymaticProcess = new EnzymaticProcess().WithName("MetaProcess");
_enzymaticProcessSelection = new EnzymaticProcessSelection
{
CompoundName = _compound.Name,
MetaboliteName = "META",
MoleculeName = "CYP",
ProcessName = _enzymaticProcess.Name
};
_specificBindingProcess = new SpecificBindingPartialProcess().WithName("BindingProcess");
_specificBindingPartialProcessSelection = new ProcessSelection
{
CompoundName = _compound.Name,
MoleculeName = "BINDER",
ProcessName = _specificBindingProcess.Name
};
_transportSystemicProcess = new SystemicProcess
{
Name = "SystemicTransport",
SystemicProcessType = SystemicProcessTypes.GFR
};
_transportSystemicProcessSelection = new SystemicProcessSelection
{
CompoundName = _compound.Name,
ProcessName = _transportSystemicProcess.Name,
ProcessType = _transportSystemicProcess.SystemicProcessType
};
_interactionProcess = new InductionProcess().WithName("InteractionProcess");
_interactionSelection = new InteractionSelection
{
CompoundName = _compound.Name,
ProcessName = _interactionProcess.Name,
MoleculeName = "INHIBITOR"
};
_compound.AddProcess(_enzymaticProcess);
_compound.AddProcess(_transportSystemicProcess);
_compound.AddProcess(_interactionProcess);
_compound.AddProcess(_specificBindingProcess);
return(_completed);
}
private void updateLipophilicityReferences(SystemicProcess systemicProcess, string parameterName)
{
var parameter = systemicProcess.Parameter(parameterName);
if (parameter == null)
{
return;
}
foreach (var objectPath in parameter.Formula.ObjectPaths)
{
objectPath.Replace(ConverterConstants.Parameter.Lipophilicity, CoreConstants.Parameter.LIPOPHILICITY_EXPERIMENT);
}
}
public SystemicProcessDTO MapFrom(SystemicProcess systemicProcess, Compound compound)
{
var systemicProcessDTO = new SystemicProcessDTO(systemicProcess)
{
ContainerType = _objectTypeResolver.TypeFor(compound),
Compound = compound,
SystemicProcessType = systemicProcess.SystemicProcessType.DisplayName,
DataSource = systemicProcess.DataSource,
Species = systemicProcess.Species,
Description = systemicProcess.Description
};
systemicProcessDTO.AddUsedNames(compound.AllProcesses <CompoundProcess>().Select(x => x.Name));
return(systemicProcessDTO);
}
public override void GlobalContext()
{
base.GlobalContext();
_kidneyProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstants.Process.KIDNEY_CLEARANCE).DowncastTo <SystemicProcess>());
_kidneyProcess.Name = "My Kidney Process";
_kidneyProcess.Parameter(ConverterConstants.Parameter.PlasmaClearance).Value = 10;
_compound.AddProcess(_kidneyProcess);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol).DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddSystemicProcessSelection(new SystemicProcessSelection {
ProcessName = _kidneyProcess.Name, ProcessType = _kidneyProcess.SystemicProcessType
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_processGFR = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.GLOMERULAR_FILTRATION).DowncastTo <SystemicProcess>());
_processGFR.Name = "My GFR Process";
_processGFR.Parameter(CoreConstants.Parameters.GFR_FRACTION).Value = 0.8;
_compound.AddProcess(_processGFR);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol).DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddSystemicProcessSelection(new SystemicProcessSelection {
ProcessName = _processGFR.Name, ProcessType = _processGFR.SystemicProcessType
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_process = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(ProcessName).DowncastTo <SystemicProcess>());
_process.Name = "My Liver Process";
_process.Parameter(ConverterConstants.Parameter.CLspec).Value = 1;
_compound.AddProcess(_process);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol).DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesFor(_compound.Name)
.Processes
.MetabolizationSelection
.AddSystemicProcessSelection(new SystemicProcessSelection {
ProcessName = _process.Name, ProcessType = _process.SystemicProcessType
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
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);
}
protected override void Context()
{
base.Context();
_compound = new Compound();
var fuGroup = new ParameterAlternativeGroup().WithName(CoreConstants.Groups.COMPOUND_FRACTION_UNBOUND);
_fuAlternative = new ParameterAlternative().WithName("MyFu");
_fuAlternative.Add(DomainHelperForSpecs.ConstantParameterWithValue(0.2).WithName(CoreConstants.Parameter.FractionUnbound));
_fuAlternative.IsDefault = true;
fuGroup.AddAlternative(_fuAlternative);
_compound.AddParameterAlternativeGroup(fuGroup);
_template = new SystemicProcess();
_p1 = DomainHelperForSpecs.ConstantParameterWithValue(0.5).WithName(CoreConstants.Parameter.FRATION_UNBOUND_EXPERIMENT);
_p2 = DomainHelperForSpecs.ConstantParameterWithValue(0.9).WithName("toto");
_template.Add(_p1);
_template.Add(_p2);
_clone = new SystemicProcess();
_clone.Add(DomainHelperForSpecs.ConstantParameterWithValue(0.5).WithName(CoreConstants.Parameter.FRATION_UNBOUND_EXPERIMENT));
A.CallTo(() => _executionContext.Clone(_template)).Returns(_clone);
}
protected override void Context()
{
_compound = BatchToolFactoryForSpecs.Compound();
_compound.Name = "sim";
_compound.IsSmallMolecule = true;
_partialProcess = new PartialProcess();
_partialProcess.MoleculeName = "CYP";
_partialProcess.InternalName = "Metabolization_firstOrder";
_partialProcess.DataSource = "Lab";
_partialProcess.ParameterValues.Add("P1", 5);
_partialProcess.ParameterValues.Add("CLSpec", 3);
_systemicProcess = new SystemicProcess();
_systemicProcess.InternalName = "PlasmaClearance";
_systemicProcess.DataSource = "Lab";
_systemicProcess.ParameterValues.Add("P4", 5);
_systemicProcess.ParameterValues.Add("CL", 3);
_compound.PartialProcesses.Add(_partialProcess);
_compound.SystemicProcesses.Add(_systemicProcess);
_settings = new JsonSerializerSettings {
NullValueHandling = NullValueHandling.Ignore
};
}
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 ITreeNode CreateFor(SystemicProcess systemicProcess) => new CompoundProcessNode(systemicProcess);
private void addSystemicProcessToView(SystemicProcess systemicProcess)
{
var node = addSystemicProcessToTree(systemicProcess, _view.NodeByType(_systemicProcessToRootNodeTypeMapper.MapFrom(systemicProcess.SystemicProcessType)));
_view.AddNode(node);
}
private ITreeNode addSystemicProcessToTree(SystemicProcess systemicProcess, ITreeNode systemicProcessContainerNode)
{
return(_treeNodeFactory.CreateFor(systemicProcess).Under(systemicProcessContainerNode));
}
protected override Task Context()
{
_calculationMethodCacheMapper = A.Fake <CalculationMethodCacheMapper>();
_processMappingMapper = A.Fake <ProcessMappingMapper>();
_logger = A.Fake <ILogger>();
_project = new PKSimProject();
_calculationMethodSnapshot = new CalculationMethodCache();
sut = new CompoundPropertiesMapper(_calculationMethodCacheMapper, _processMappingMapper, _logger);
_compoundGroupSelectionOneAlternative = new CompoundGroupSelection
{
AlternativeName = "ALT1",
GroupName = "ALTERNATIVE_GROUP_1"
};
_compoundGroupSelectionTwoAlternatives = new CompoundGroupSelection
{
AlternativeName = "ALT2",
GroupName = "ALTERNATIVE_GROUP_2"
};
_compound = new Compound
{
Name = "COMP",
};
_protocol = new SimpleProtocol
{
Name = "PROTOCOL"
};
_parameterAlternativeGroupWithOneAlternative = new ParameterAlternativeGroup {
Name = _compoundGroupSelectionOneAlternative.GroupName
};
_parameterAlternativeGroupWithTwoAlternatives = new ParameterAlternativeGroup {
Name = _compoundGroupSelectionTwoAlternatives.GroupName
};
_parameterAlternativeGroupWithTwoAlternatives.AddAlternative(new ParameterAlternative {
Name = "ALT1"
});
_parameterAlternativeGroupWithTwoAlternatives.AddAlternative(new ParameterAlternative {
Name = "ALT2"
});
_compound.AddParameterAlternativeGroup(_parameterAlternativeGroupWithOneAlternative);
_compound.AddParameterAlternativeGroup(_parameterAlternativeGroupWithTwoAlternatives);
_compoundProperties = new Model.CompoundProperties();
_compoundProperties.AddCompoundGroupSelection(_compoundGroupSelectionOneAlternative);
_compoundProperties.AddCompoundGroupSelection(_compoundGroupSelectionTwoAlternatives);
_compoundProperties.Compound = _compound;
_enzymaticProcess = new EnzymaticProcess {
Name = "EnzymaticProcess"
};
_anotherEnzymaticProcess = new EnzymaticProcess {
Name = "AnotherEnzymaticProcess", MoleculeName = "CYP3A4"
};
_specificBindingProcess = new SpecificBindingPartialProcess {
Name = "SpecificBinding"
};
_gfrTransportProcess = new SystemicProcess {
Name = "Transport", SystemicProcessType = SystemicProcessTypes.GFR
};
_hepaticEnzymaticProcess = new SystemicProcess {
Name = "Plasma Clearance", SystemicProcessType = SystemicProcessTypes.Hepatic
};
_compound.AddProcess(_enzymaticProcess);
_compound.AddProcess(_specificBindingProcess);
_compound.AddProcess(_gfrTransportProcess);
_compound.AddProcess(_hepaticEnzymaticProcess);
_enzymaticPartialProcessSelection = new EnzymaticProcessSelection {
ProcessName = _enzymaticProcess.Name
};
_noEnzymaticSystemicProcessSelection = new SystemicProcessSelection {
ProcessType = SystemicProcessTypes.Hepatic
};
_specificBindingPartialProcessSelection = new ProcessSelection {
ProcessName = _specificBindingProcess.Name
};
_transportSystemicProcessSelection = new SystemicProcessSelection {
ProcessName = _gfrTransportProcess.Name, ProcessType = _gfrTransportProcess.SystemicProcessType,
};
_noEnzymaticPartialProcessSelection = new EnzymaticProcessSelection {
MoleculeName = _anotherEnzymaticProcess.MoleculeName
};
_compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(_enzymaticPartialProcessSelection);
_compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(_noEnzymaticPartialProcessSelection);
_compoundProperties.Processes.MetabolizationSelection.AddSystemicProcessSelection(_noEnzymaticSystemicProcessSelection);
_compoundProperties.Processes.SpecificBindingSelection.AddPartialProcessSelection(_specificBindingPartialProcessSelection);
_compoundProperties.Processes.TransportAndExcretionSelection.AddSystemicProcessSelection(_transportSystemicProcessSelection);
_snapshotProcess1 = new CompoundProcessSelection {
Name = _enzymaticPartialProcessSelection.ProcessName
};
_snapshotProcess2 = new CompoundProcessSelection {
Name = _specificBindingPartialProcessSelection.ProcessName
};
_snapshotProcess3 = new CompoundProcessSelection {
Name = _transportSystemicProcessSelection.ProcessName
};
_snapshotProcess4 = new CompoundProcessSelection {
SystemicProcessType = _noEnzymaticSystemicProcessSelection.ProcessType.SystemicProcessTypeId.ToString()
};
_snapshotProcess5 = new CompoundProcessSelection {
MoleculeName = _noEnzymaticPartialProcessSelection.MoleculeName
};
_formulation = new Formulation
{
Id = "123456"
};
_compoundProperties.ProtocolProperties.Protocol = _protocol;
_compoundProperties.ProtocolProperties.AddFormulationMapping(new FormulationMapping
{
FormulationKey = "F1",
TemplateFormulationId = _formulation.Id
});
_project.AddBuildingBlock(_formulation);
A.CallTo(() => _calculationMethodCacheMapper.MapToSnapshot(_compoundProperties.CalculationMethodCache)).Returns(_calculationMethodSnapshot);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_enzymaticPartialProcessSelection)).Returns(_snapshotProcess1);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_specificBindingPartialProcessSelection)).Returns(_snapshotProcess2);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_transportSystemicProcessSelection)).Returns(_snapshotProcess3);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noEnzymaticSystemicProcessSelection)).Returns(_snapshotProcess4);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noEnzymaticPartialProcessSelection)).Returns(_snapshotProcess5);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess1, _enzymaticProcess)).Returns(_enzymaticPartialProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess2, _specificBindingProcess)).Returns(_specificBindingPartialProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess3, _gfrTransportProcess)).Returns(_transportSystemicProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess4, A <NotSelectedSystemicProcess> ._)).Returns(_noEnzymaticSystemicProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess5, A <EnzymaticProcess> ._)).Returns(_noEnzymaticPartialProcessSelection);
return(_completed);
}
public ITreeNode CreateFor(SystemicProcess systemicProcess)
{
return(new CompoundProcessNode(systemicProcess));
}
