public Formulation AddFormulationForDefinition(int definitionId, Formulation formulation)
{
formulation.DefinitionId = definitionId;
Formulation fm = entities.Formulations.Add(formulation);
SaveChanges();
return fm;
}
public void Visit(Formulation formulation)
{
if (!formulation.FormulationType.IsOneOf(CoreConstants.Formulation.Weibull, CoreConstants.Formulation.Lint80, CoreConstants.Formulation.Table))
{
return;
}
var templateFormulation = _formulationRepository.FormulationBy(formulation.FormulationType);
var useAsSuspension = _cloner.Clone(templateFormulation.Parameter(CoreConstants.Parameters.USE_AS_SUSPENSION));
useAsSuspension.Value = 0;
formulation.Add(useAsSuspension);
_converted = true;
}
protected override void Context()
{
base.Context();
_tableParameter = new PKSimParameter();
_formulation = new Formulation {
FormulationType = CoreConstants.Formulation.Table
};
_formulation.Add(_tableParameter);
_formulationDTO = A.Fake <FormulationDTO>();
_formulationDTO.Parameters = new[] { _tableParameter };
_formulationDTO.Type = new FormulationTypeDTO {
Id = "oral"
};
A.CallTo(() => _formulationDTOMapper.MapFrom(_formulation)).Returns(_formulationDTO);
A.CallTo(() => _tableFormulationPresenter.EditedFormula).Returns(new TableFormula());
}
protected override async Task Context()
{
await base.Context();
_snapshotType = typeof(Snapshots.Formulation);
_snapshot1 = new Snapshots.Formulation();
_snapshot2 = new Snapshots.Formulation();
_formulation1 = new Formulation();
_formulation2 = new Formulation();
A.CallTo(() => _snapshotMapper.SnapshotTypeFor <Formulation>()).Returns(_snapshotType);
A.CallTo(_dialogCreator).WithReturnType <string>().Returns(_fileName);
A.CallTo(() => _jsonSerializer.DeserializeAsArray(_fileName, _snapshotType)).Returns(new[] { _snapshot1, _snapshot2 });
A.CallTo(() => _snapshotMapper.MapToModel(_snapshot1)).Returns(_formulation1);
A.CallTo(() => _snapshotMapper.MapToModel(_snapshot2)).Returns(_formulation2);
}
protected override void Context()
{
base.Context();
_formulation = A.Fake <Formulation>();
_formulation.Id = "simFormulation";
_simulation = new IndividualSimulation();
var usedBuildingBlock = new UsedBuildingBlock("templateId", PKSimBuildingBlockType.Formulation);
_simulation.AddUsedBuildingBlock(usedBuildingBlock);
usedBuildingBlock.BuildingBlock = _formulation;
_formulationMappingDTO = new FormulationMappingDTO {
ApplicationType = ApplicationTypes.Oral, Selection = new FormulationSelectionDTO {
BuildingBlock = _formulation
}, FormulationKey = "tata"
};
}
public override void OnInspectorGUI()
{
var other = Array.Find(formulations, x => x != formulation && Formulation.CheckMaterialsDuplicate(formulation, x));
if (other)
{
EditorGUILayout.HelpBox($"配方材料重复！配置路径：\n{AssetDatabase.GetAssetPath(other)}", MessageType.Error);
}
for (int i = 0; i < formulation.Materials.Count; i++)
{
bool bre = false;
var left = formulation.Materials[i];
if (!left.IsValid)
{
EditorGUILayout.HelpBox("该配方未补充完整", MessageType.Warning);
break;
}
for (int j = 0; j < formulation.Materials.Count; j++)
{
var right = formulation.Materials[j];
if (i != j && left.MakingType == right.MakingType)
{
if (left.MakingType == MakingType.SingleItem && left.Item == right.Item || left.MakingType == MakingType.SameType && left.MaterialType == right.MaterialType)
{
EditorGUILayout.HelpBox($"第[{i + 1}]和第[{j + 1}]个材料重复！", MessageType.Error);
bre = true;
}
}
if (bre)
{
break;
}
}
if (bre)
{
break;
}
}
serializedObject.UpdateIfRequiredOrScript();
EditorGUI.BeginChangeCheck();
EditorGUILayout.PropertyField(remark, new GUIContent("备注"));
listDrawer.DoLayoutDraw();
if (EditorGUI.EndChangeCheck())
{
serializedObject.ApplyModifiedProperties();
}
}
protected float[][][] _binParticlesFractionPerSegment; //no of particles fraction[particles bin][lumen segment][time]
public override void GlobalContext()
{
base.GlobalContext();
_compound.Name = "C1";
_protocol = DomainFactoryForSpecs.CreateStandardOralProtocol();
_formulation = DomainFactoryForSpecs.CreateParticlesFormulation(NumberOfBins);
//user defined actions in the building blocks
SetupBuildingBlocks();
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(
_individual, _compound, _protocol, allowAging: false, formulation: _formulation) as IndividualSimulation;
//setup compound processes
SetupProcesses();
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
//user defined actions in simulations, different for every test scenario
SetupSimulation();
if (DisableIntestinalAbsorptionAndLuminalFlow)
{
//disable intestinal absorption and luminal flow to feces for easier mass balance checks
MoleculeProperties(CoreConstants.Parameters.INTESTINAL_PERMEABILITY).Value = 0;
IntestinalTransitRateFor(CoreConstants.Compartment.Rectum).Value = 0;
}
//store initial drug mass
_appliedDrugMass = Application.Container(CoreConstants.ContainerName.ProtocolSchemaItem)
.Parameter(CoreConstantsForSpecs.Parameter.DRUG_MASS).Value.ToFloat();
//Get paths for output quantities of interest
(var lumenPaths, var binSolidDrugPaths, var binInsolubleDrugPaths,
var binSolidDrugPerSegmentPaths, var binParticlesFractionPerSegmentPaths) = outputPaths(NumberOfBins);
//add quantities of interest to the simulation outputs
addOutputs(lumenPaths, binSolidDrugPaths, binInsolubleDrugPaths, binSolidDrugPerSegmentPaths, binParticlesFractionPerSegmentPaths);
RunSimulation(_simulation).Wait();
//fill simulation output times and values required for all further tests
fillSimulationOutputs(lumenPaths, binSolidDrugPaths, binInsolubleDrugPaths, binSolidDrugPerSegmentPaths, binParticlesFractionPerSegmentPaths);
}
public void EditFormulation(Formulation formulation)
{
Formulation = formulation;
_formulationDTO = _formulationDTOMapper.MapFrom(formulation);
adjustParameterVisibility();
if (Formulation.IsTable)
{
_view.AddParameterView(_tableFormulationPresenter.BaseView);
_tableFormulationPresenter.Edit(formulation);
}
else
{
_formulationParametersPresenter.Edit(_formulationDTO.Parameters);
_view.AddParameterView(_formulationParametersPresenter.View);
}
updatePlot();
_view.BindTo(_formulationDTO);
}
protected override void Context()
{
base.Context();
var formulation = new Formulation().WithName("F");
_simulation = new IndividualSimulation {
Properties = new SimulationProperties()
};
var formulationUsedInSimulation = new Formulation().WithName("F");
var compoundProperties = new CompoundProperties();
compoundProperties.ProtocolProperties.AddFormulationMapping(new FormulationMapping {
Formulation = formulation
});
compoundProperties.ProtocolProperties.AddFormulationMapping(new FormulationMapping {
Formulation = formulationUsedInSimulation
});
_simulation.Properties.AddCompoundProperties(compoundProperties);
}
protected override double ValueFor(Formulation formulation, double time)
{
if (time <= _lagTime)
{
return(0);
}
if (time - _lagTime <= _dissTime80)
{
return(0.8 * (time - _lagTime) / _dissTime80);
}
if (time - _lagTime < 3.0 / 2 * _dissTime80)
{
return(1 - 0.8 * Math.Pow((time - _lagTime - 3.0 / 2 * _dissTime80) / _dissTime80, 2));
}
return(1);
}
protected override void Context()
{
base.Context();
_templateFormulation = A.Fake <Formulation>();
_formulation1 = A.Fake <Formulation>().WithName("f1");
_formulation1.Id = "1";
_formulation2 = A.Fake <Formulation>().WithName("f2");
_formulation2.Id = "2";
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock(_formulation1.Id, PKSimBuildingBlockType.Formulation)
{
BuildingBlock = _formulation1
});
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock(_formulation2.Id, PKSimBuildingBlockType.Formulation)
{
BuildingBlock = _formulation2
});
A.CallTo(() => _buildingBlockRepository.ById <Formulation>("template")).Returns(_templateFormulation);
A.CallTo(() => _buildingBlockRepository.ById <Formulation>("does not exist")).Returns(null);
}
protected override void Context()
{
_individual = new Individual().WithName("Individual");
_compound = new Compound().WithName("Compound");
_formulation = new Formulation().WithName("Formulation");
_protocol = new Protocol().WithName("Protocol");
_population = new Population().WithName("Population");
_event = new Event().WithName("Event");
sut = new SnapshotProject
{
Compounds = new[] { _compound },
Formulations = new[] { _formulation },
Protocols = new[] { _protocol },
Individuals = new[] { _individual },
Populations = new[] { _population },
Events = new[] { _event }
};
}
public Formulation Get(string formulationType)
{
string sql = "SELECT * FROM Formulations WHERE FormulationType=@formulationType";
this.command = new SqlCommand(sql, this.db.Conn);
this.command.Parameters.AddWithValue("@formulationType", formulationType);
this.db.Conn.Open();
SqlDataReader reader = this.command.ExecuteReader();
Formulation f = new Formulation();
if (reader.Read())
{
f.Id = Convert.ToInt32(reader["Id"]);
f.FormulationType = reader["FormulationType"].ToString();
}
this.db.Conn.Close();
return(f);
}
/// <summary>Creates the formulation.</summary>
/// <param name="formulation">The formulation.</param>
/// <returns>A JSON encoded success indicator</returns>
public JsonResult Create(Formulation formulation)
{
try
{
var farmContext = new PicolEntities();
farmContext.Formulations.Add(formulation);
farmContext.SaveChanges();
return(new JsonNetResult {
Data = new { Error = false, Formulation = formulation }, MaxJsonLength = int.MaxValue, JsonRequestBehavior = JsonRequestBehavior.AllowGet
});
}
catch (Exception e)
{
// Signal the error to be logged by elmah
ErrorSignal.FromCurrentContext().Raise(e);
return(new JsonNetResult {
Data = new { Error = true, ErrorMessage = "Failed save formulation." }, MaxJsonLength = int.MaxValue, JsonRequestBehavior = JsonRequestBehavior.AllowGet
});
}
}
protected override void Context()
{
_view = A.Fake <ISimulationCompoundProtocolFormulationView>();
_formulationTask = A.Fake <IFormulationTask>();
_formulationMappingMapper = A.Fake <IFormulationMappingDTOToFormulationMappingMapper>();
_formulationFromMappingRetriever = A.Fake <IFormulationFromMappingRetriever>();
_formulation1 = new Formulation();
_formulation2 = new Formulation();
_protocol = A.Fake <Protocol>();
_compound = A.Fake <Compound>();
_simulation = A.Fake <Simulation>();
_protocolProperties = A.Fake <ProtocolProperties>();
var compoundProperties = new CompoundProperties();
A.CallTo(() => _simulation.CompoundPropertiesFor(_compound)).Returns(compoundProperties);
compoundProperties.ProtocolProperties = _protocolProperties;
_protocolProperties.Protocol = _protocol;
A.CallTo(() => _formulationTask.All()).Returns(new[] { _formulation1, _formulation2 });
_buildingBlockSelectionDisplayer = A.Fake <IBuildingBlockSelectionDisplayer>();
sut = new SimulationCompoundProtocolFormulationPresenter(_view, _formulationTask, _formulationMappingMapper, _formulationFromMappingRetriever, _buildingBlockSelectionDisplayer);
}
protected override void Context()
{
base.Context();
_formulation = new Formulation();
_simulation = new IndividualSimulation {
Properties = new SimulationProperties()
};
_formulationUsedInSimulation = new Formulation();
_usedBuildingBlockFormulation = new UsedBuildingBlock("template", PKSimBuildingBlockType.Formulation)
{
BuildingBlock = _formulationUsedInSimulation
};
var compoundProperties = new CompoundProperties();
var formulationMapping = new FormulationMapping {
Formulation = _formulation
};
compoundProperties.ProtocolProperties.AddFormulationMapping(formulationMapping);
_simulation.Properties.AddCompoundProperties(compoundProperties);
A.CallTo(() => _buildingBlockMapper.MapFrom(_formulation, null)).Returns(_usedBuildingBlockFormulation);
}
/// <summary>Updates the formulation.</summary>
/// <param name="formulation">The formulation.</param>
/// <returns>A JSON encoded success indicator</returns>
public JsonResult Update(Formulation formulation)
{
try
{
var farmContext = new PicolEntities();
farmContext.Formulations.Attach(formulation);
farmContext.Entry(formulation).State = System.Data.Entity.EntityState.Modified;
farmContext.SaveChanges();
return(new JsonNetResult {
Data = new { Error = false }, MaxJsonLength = int.MaxValue, JsonRequestBehavior = JsonRequestBehavior.AllowGet
});
}
catch (Exception e)
{
// Signal the error to be logged by elmah
ErrorSignal.FromCurrentContext().Raise(e);
return(new JsonNetResult {
Data = new { Error = true, ErrorMessage = "Failed to update formulation." }, MaxJsonLength = int.MaxValue, JsonRequestBehavior = JsonRequestBehavior.AllowGet
});
}
}
public List <Formulation> GetAll()
{
string sql = "SELECT * FROM Formulations";
this.command = new SqlCommand(sql, this.db.Conn);
this.db.Conn.Open();
SqlDataReader reader = this.command.ExecuteReader();
List <Formulation> flist = new List <Formulation>();
while (reader.Read())
{
Formulation f = new Formulation();
f.Id = Convert.ToInt32(reader["Id"]);
f.FormulationType = reader["FormulationType"].ToString();
flist.Add(f);
}
this.db.Close();
return(flist);
}
public ProcessResult AddFormulation(int definitionId,
int studentId,
string specificdifference)
{
var definition = GetDefinition(definitionId);
if (definition == null)
{
return(ProcessResults.DefinitionNotExisting);
}
var formulation = new Formulation
{
AddedDate = DateTime.Now,
DefinitionId = definitionId,
StudentId = studentId,
SpecificDifference = specificdifference,
};
entities.Formulations.Add(formulation);
SaveChanges();
return(ProcessResults.FormulationSuccessfullyAdded);
}
protected override void Context()
{
base.Context();
_formulationTypeDTO = new FormulationTypeDTO {
Id = "trala"
};
_formulation = A.Fake <Formulation>();
_formulationDTO = new FormulationDTO {
Type = _formulationTypeDTO
};
A.CallTo(() => _formulationDTOMapper.MapFrom(_formulation)).Returns(_formulationDTO);
sut.EditFormulation(_formulation);
sut.FormulationTypeChanged += e =>
{
_eventRaised = true;
_valueRaised = e;
};
var templateFormulation = A.Fake <Formulation>();
A.CallTo(() => _cloner.Clone(templateFormulation)).Returns(_formulation);
A.CallTo(() => _formulationRepository.FormulationBy(_formulationTypeDTO.Id)).Returns(templateFormulation);
}
private IEventGroupBuilder createFormulationAsEventGroupBuilderFrom(Formulation formulation)
{
var formulationBuilder = _objectBaseFactory.Create <IEventGroupBuilder>();
formulationBuilder.UpdatePropertiesFrom(formulation, _cloneManagerForBuildingBlock);
foreach (var parameter in formulation.AllParameters())
{
var builderParameter = _cloneManagerForBuildingBlock.Clone(parameter);
//reset the origin in any case since it might have been set by clone
builderParameter.Origin.ParameterId = string.Empty;
formulationBuilder.Add(builderParameter);
}
_parameterIdUpdater.UpdateBuildingBlockId(formulationBuilder, formulation);
_parameterIdUpdater.UpdateParameterIds(formulation, formulationBuilder);
if (formulation.FormulationType.Equals(CoreConstants.Formulation.Particles))
{
setParticleRadiusDistributionParametersToLockedAndInvisible(formulationBuilder);
}
return(formulationBuilder);
}
public override bool IsSatisfiedBy(Formulation formulation)
{
return(formulation.FormulationType == CoreConstants.Formulation.Dissolved);
}
protected override void CacheParameterValueFor(Formulation formulation)
{
/*nothng to do */
}
protected override void CacheParameterValueFor(Formulation formulation)
{
_lagTime = formulation.Parameter(CoreConstants.Parameters.LAG_TIME).Value;
_dissTime80 = formulation.Parameter(CoreConstants.Parameters.DISS_TIME80).Value;
}
protected override void CacheParameterValueFor(Formulation formulation)
{
_tHalf = formulation.Parameter(CoreConstants.Parameters.HALF_LIFE).Value;
}
public override bool IsSatisfiedBy(Formulation formulation)
{
return(formulation.FormulationType == CoreConstants.Formulation.FirstOrder);
}
protected override double ValueFor(Formulation formulation, double time)
{
return(1);
}
public override bool IsSatisfiedBy(Formulation formulation)
{
return(formulation.FormulationType == CoreConstants.Formulation.FIRST_ORDER);
}
public void Visit(Formulation objToVisit)
{
openPresenter(objToVisit);
}
protected override double ValueFor(Formulation formulation, double time)
{
return(1 - Math.Exp(-Math.Log(2) * time / _tHalf));
}
public void Visit(Formulation formulation)
{
performCommonConversion(formulation);
}
