protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_formulationRepository = A.Fake <IFormulationRepository>();
_cloner = A.Fake <ICloner>();
sut = new FormulationMapper(_parameterMapper, _formulationRepository, _cloner);
_parameter1 = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: false)
.WithName("Param1");
_parameter2 = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: true)
.WithName("Param2");
_hiddenParameter = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: false)
.WithName("Param3");
_hiddenParameter.Visible = false;
_formulation = new Formulation
{
Name = "Form",
FormulationType = "Weibul",
Description = "Amazing formulation"
};
_formulation.Add(_parameter1);
_formulation.Add(_parameter2);
_formulation.Add(_hiddenParameter);
A.CallTo(() => _parameterMapper.MapToSnapshot(_parameter1)).Returns(new Parameter().WithName(_parameter1.Name));
A.CallTo(() => _parameterMapper.MapToSnapshot(_parameter2)).Returns(new Parameter().WithName(_parameter2.Name));
A.CallTo(() => _parameterMapper.MapToSnapshot(_hiddenParameter)).Returns(new Parameter().WithName(_hiddenParameter.Name));
return(Task.FromResult(true));
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_schemaItemMapper = A.Fake <SchemaItemMapper>();
_schemaFactory = A.Fake <ISchemaFactory>();
sut = new SchemaMapper(_parameterMapper, _schemaItemMapper, _schemaFactory);
_schemaItem = new SchemaItem().WithName("Item1");
_schema = new Schema
{
Description = "Hello",
Name = "Tralala"
};
_schema.AddSchemaItem(_schemaItem);
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(3).WithName("Param1");
//Schema item parameters that have a value IsDefault true should still be saved to snapshot
_parameter1 = DomainHelperForSpecs.ConstantParameterWithValue(1, isDefault: true).WithName(Constants.Parameters.START_TIME);
_parameter2 = DomainHelperForSpecs.ConstantParameterWithValue(2, isDefault: true).WithName(CoreConstants.Parameters.NUMBER_OF_REPETITIONS);
_parameter3 = DomainHelperForSpecs.ConstantParameterWithValue(3, isDefault: true).WithName(CoreConstants.Parameters.TIME_BETWEEN_REPETITIONS);
_schema.Add(_parameter);
_schema.Add(_parameter1);
_schema.Add(_parameter2);
_schema.Add(_parameter3);
A.CallTo(() => _parameterMapper.MapToSnapshot(_parameter)).Returns(new Snapshots.Parameter().WithName(_parameter.Name));
A.CallTo(() => _parameterMapper.MapToSnapshot(_parameter1)).Returns(new Snapshots.Parameter().WithName(_parameter1.Name));
A.CallTo(() => _parameterMapper.MapToSnapshot(_parameter2)).Returns(new Snapshots.Parameter().WithName(_parameter2.Name));
A.CallTo(() => _parameterMapper.MapToSnapshot(_parameter3)).Returns(new Snapshots.Parameter().WithName(_parameter3.Name));
A.CallTo(() => _schemaItemMapper.MapToSnapshot(_schemaItem)).Returns(new Snapshots.SchemaItem().WithName(_schemaItem.Name));
return(Task.FromResult(true));
}
protected override void Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_eventFactory = A.Fake <IEventFactory>();
sut = new EventMapper(_parameterMapper, _eventFactory);
_parameter1 = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: false)
.WithName("Param1");
_parameter2 = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: true)
.WithName("Param2");
_hiddenParameter = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: false)
.WithName("Param3");
_hiddenParameter.Visible = false;
_event = new PKSimEvent
{
Name = "Event",
TemplateName = "TemplateEventName",
Description = "Amazing event"
};
_event.Add(_parameter1);
_event.Add(_parameter2);
_event.Add(_hiddenParameter);
A.CallTo(() => _parameterMapper.MapToSnapshot(_parameter1)).Returns(new Parameter().WithName(_parameter1.Name));
A.CallTo(() => _parameterMapper.MapToSnapshot(_parameter2)).Returns(new Parameter().WithName(_parameter2.Name));
A.CallTo(() => _parameterMapper.MapToSnapshot(_hiddenParameter)).Returns(new Parameter().WithName(_hiddenParameter.Name));
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_advancedParameterFactory = A.Fake <IAdvancedParameterFactory>();
_logger = A.Fake <ILogger>();
_advancedParameter = new AdvancedParameter
{
DistributedParameter = DomainHelperForSpecs.NormalDistributedParameter(10, 5),
ParameterPath = "ParameterPath",
Name = "ParameterName"
};
_originalSeed = _advancedParameter.Seed;
sut = new AdvancedParameterMapper(_parameterMapper, _advancedParameterFactory, _entityPathResolver, _logger);
_meanSnapshot = new Parameter
{
Name = _advancedParameter.DistributedParameter.MeanParameter.Name,
};
_deviationSnapshot = new Parameter
{
Name = _advancedParameter.DistributedParameter.DeviationParameter.Name,
};
A.CallTo(() => _parameterMapper.MapToSnapshot(_advancedParameter.DistributedParameter.MeanParameter)).Returns(_meanSnapshot);
A.CallTo(() => _parameterMapper.MapToSnapshot(_advancedParameter.DistributedParameter.DeviationParameter)).Returns(_deviationSnapshot);
return(Task.FromResult(true));
}
/// <summary>
/// <para>Executes a stored procedure on the specified database.</para>
/// </summary>
/// <param name="database">
/// <para>The <see cref="Database"/> on which the sproc should be executed.</para>
/// </param>
/// <param name="procedureName">
/// <para>The name of the sproc to execute.</para>
/// </param>
/// <param name="parameterMapper">
/// <para>A delegate that will populate the parameters in the sproc call.
/// Specify <see langword="null"/> if the sproc does not require parameters.</para>
/// </param>
/// <param name="outputMapper">
/// <para>A delegate that will read the value of the parameters returned
/// by the sproc call. Specify <see langword="null"/> if no output parameters
/// have been provided by the <paramref name="parameterMapper"/> delegate.</para>
/// </param>
/// <returns>
/// <para>The value returned by as part of the result set.</para>
/// </returns>
/// <exception cref="ArgumentNullException">
/// <para>The argument <paramref name="database"/> is <see langword="null"/>.</para>
/// <para>-or-</para>
/// <para>The argument <paramref name="procedureName"/> is <see langword="null"/>.</para>
/// </exception>
/// <exception cref="SafeProcedureException">
/// <para>An unexpected exception has been encountered during the sproc call.</para>
/// </exception>
public static object ExecuteScalar(Database database, string procedureName, ParameterMapper parameterMapper, OutputParameterMapper outputMapper)
{
if (database == null)
{
throw new ArgumentNullException("database");
}
if (procedureName == null)
{
throw new ArgumentNullException("procedureName");
}
object result;
try
{
using (SqlConnection connection = database.GetOpenConnection())
{
result = ExecuteScalar(database, connection, procedureName, parameterMapper, outputMapper);
}
}
catch (SafeProcedureException)
{
throw;
}
catch (Exception e)
{
throw new SafeProcedureException(database, procedureName, e);
}
return(result);
}
/// <summary>
/// Executes and returns an open IRecordSet, which encapsulates an OPEN DATAREADER. DISPOSE IN FINALLY CLAUSE.
/// </summary>
/// <param name="database"></param>
/// <param name="procedureName"></param>
/// <param name="parameterMapper"></param>
/// <returns></returns>
/// <param name="objectInstance"></param>
public static IRecordSet Execute <T>(Database database, string procedureName,
ParameterMapper <T> parameterMapper, T objectInstance)
{
MySqlConnection connection = database.GetConnection();
MySqlCommand command = CommandFactory.CreateParameterMappedCommand <T>(
connection, database.InstanceName, procedureName, parameterMapper, objectInstance);
if (log.IsDebugEnabled)
{
log.MethodDebugFormat(LOG_PREFIX, "Database: {0}, Procedure: {1}, Parameters: {2}", database.InstanceName, procedureName, DebugUtil.GetParameterString(command));
}
try
{
command.Connection.Open();
IRecordSet record = new DataRecord(command.ExecuteReader(CommandBehavior.CloseConnection));
return(record);
}
catch (Exception exc)
{
command.Connection.Close();
throw new Dongbo.Data.Exceptions.DatabaseExecutionException(database, procedureName, command, exc);
}
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_schemaItemMapper = A.Fake <SchemaItemMapper>();
_schemaFactory = A.Fake <ISchemaFactory>();
sut = new SchemaMapper(_parameterMapper, _schemaItemMapper, _schemaFactory);
_schemaItem = new SchemaItem().WithName("Item1");
_schema = new Schema
{
Description = "Hello",
Name = "Tralala"
};
_schema.AddSchemaItem(_schemaItem);
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(3).WithName("Param1");
_schema.Add(_parameter);
A.CallTo(() => _parameterMapper.MapToSnapshot(_parameter)).Returns(new Snapshots.Parameter().WithName(_parameter.Name));
A.CallTo(() => _schemaItemMapper.MapToSnapshot(_schemaItem)).Returns(new Snapshots.SchemaItem().WithName(_schemaItem.Name));
return(Task.FromResult(true));
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_outputIntervalFactory = A.Fake <IOutputIntervalFactory>();
sut = new OutputIntervalMapper(_parameterMapper, _outputIntervalFactory);
_outputInterval = new OutputInterval
{
Name = "Interval"
};
_endTimeParameter = DomainHelperForSpecs.ConstantParameterWithValue(1, isDefault: true).WithName(Constants.Parameters.END_TIME);
_resolutionParameter = DomainHelperForSpecs.ConstantParameterWithValue(1, isDefault: true).WithName(Constants.Parameters.RESOLUTION);
_anotherParameter = DomainHelperForSpecs.ConstantParameterWithValue(1, isDefault: false).WithName("Another");
_outputInterval.Add(_endTimeParameter);
_outputInterval.Add(_anotherParameter);
_outputInterval.Add(_resolutionParameter);
_endTimeSnapshotParameter = new Parameter().WithName(_endTimeParameter.Name);
_anotherSnapshotParameter = new Parameter().WithName(_anotherParameter.Name);
_resolutionSnapshotParameter = new Parameter().WithName(_resolutionParameter.Name);
A.CallTo(() => _parameterMapper.MapToSnapshot(_endTimeParameter)).Returns(_endTimeSnapshotParameter);
A.CallTo(() => _parameterMapper.MapToSnapshot(_anotherParameter)).Returns(_anotherSnapshotParameter);
A.CallTo(() => _parameterMapper.MapToSnapshot(_resolutionParameter)).Returns(_resolutionSnapshotParameter);
return(_completed);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_eventMappingFactory = A.Fake <IEventMappingFactory>();
sut = new EventMappingMapper(_parameterMapper, _eventMappingFactory);
_event = new PKSimEvent()
.WithName("E1")
.WithId("EventId");
_eventMapping = new EventMapping
{
TemplateEventId = _event.Id,
StartTime = DomainHelperForSpecs.ConstantParameterWithValue(1)
};
_snapshotEventStartTime1 = new Parameter {
Name = "P1"
};
_project = new PKSimProject();
_project.AddBuildingBlock(_event);
A.CallTo(() => _parameterMapper.MapToSnapshot(_eventMapping.StartTime)).Returns(_snapshotEventStartTime1);
return(_completed);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_moleculeMapper = A.Fake <MoleculeMapper>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_individualFactory = A.Fake <IIndividualFactory>();
_originDataMapper = A.Fake <OriginDataMapper>();
sut = new IndividualMapper(_parameterMapper, _moleculeMapper, _originDataMapper, _individualFactory);
_individual = DomainHelperForSpecs.CreateIndividual();
_individual.Name = "Ind";
_individual.Description = "Model Description";
_parameterLiver = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.Liver, "PLiver");
_parameterKidney = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.Kidney, "PKidney");
_parameterLiver.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.Value = 40;
_parameterKidney.ValueDiffersFromDefault().ShouldBeTrue();
_enzyme = new IndividualEnzyme
{
Name = "Enz",
};
_individual.AddMolecule(_enzyme);
_transporter = new IndividualTransporter
{
Name = "Trans",
};
_individual.AddMolecule(_transporter);
_enzymeSnapshot = new Molecule {
Type = QuantityType.Enzyme
};
_transporterSnapshot = new Molecule {
Type = QuantityType.Transporter
};
A.CallTo(() => _moleculeMapper.MapToSnapshot(_enzyme)).Returns(_enzymeSnapshot);
A.CallTo(() => _moleculeMapper.MapToSnapshot(_transporter)).Returns(_transporterSnapshot);
_originDataSnapshot = new OriginData();
A.CallTo(() => _originDataMapper.MapToSnapshot(_individual.OriginData)).Returns(_originDataSnapshot);
_localizedParameterKidney = new LocalizedParameter {
Path = "Organism|Kidney|PKidney"
};
A.CallTo(() => _parameterMapper.LocalizedParametersFrom(A <IEnumerable <IParameter> > .That.Contains(_parameterKidney))).Returns(new[] { _localizedParameterKidney });
return(_completed);
}
protected InputSourceStatementProcessor()
{
sinMapper = new ParameterMapper <SinusoidalBehavior>();
expMapper = new ParameterMapper <ExponentialBehavior>();
pulseMapper = new ParameterMapper <PulseBehavior>();
amMapper = new ParameterMapper <AmBehavior>();
sffmMapper = new ParameterMapper <SffmBehavior>();
dcMapper = new ParameterMapper <ConstantBehavior>();
InitMappers();
MinArgs = 3;
}
public void MapsProperties()
{
var mapper = new ParameterMapper <DiodeParams>();
mapper.Target = DiodeParams.Default;
mapper.Map(p => p.SaturationCurrent, "IS");
mapper.Map(p => p.SaturationCurrent, 0);
mapper.Set("IS", 1);
Assert.Equal(1, mapper.Target.SaturationCurrent);
mapper.Set(0, 45);
Assert.Equal(45, mapper.Target.SaturationCurrent);
}
/// <summary>
/// <para>Executes a SQL stored procedure on a provided connection.</para>
/// </summary>
/// <param name="database">
/// <para>The <see cref="Database"/> to which the specified connection
/// object belongs. This object is for informational purposes only,
/// and will not be used to create new connections.</para>
/// </param>
/// <param name="connection">
/// <para>The <see cref="SqlConnection"/> on which to execute sproc.
/// If this connection is not yet open, it will be opened and closed.
/// If this connection is already open, it will NOT be closed. In this case,
/// the caller is responsible for its disposal.</para>
/// </param>
/// <param name="procedureName">
/// <para>The name of the sproc to execute.</para>
/// </param>
/// <param name="parameterMapper">
/// <para>A delegate that will populate the parameters in the sproc call.
/// Specify <see langword="null"/> if the sproc does not require parameters.</para>
/// </param>
/// <param name="outputMapper">
/// <para>A delegate that will read the value of the parameters returned
/// by the sproc call. Specify <see langword="null"/> if no output parameters
/// have been provided by the <paramref name="parameterMapper"/> delegate.</para>
/// </param>
/// <returns>
/// <para>An <see cref="Int32"/> value indicating the number of rows
/// affected by this sproc call.</para>
/// </returns>
/// <exception cref="ArgumentNullException">
/// <para>The argument <paramref name="database"/> is <see langword="null"/>.</para>
/// <para>-or-</para>
/// <para>The argument <paramref name="connection"/> is <see langword="null"/>.</para>
/// <para>-or-</para>
/// <para>The argument <paramref name="procedureName"/> is <see langword="null"/>.</para>
/// </exception>
/// <exception cref="SafeProcedureException">
/// <para>An unexpected exception has been encountered during the sproc call.</para>
/// </exception>
public static int ExecuteNonQuery(Database database, SqlConnection connection, string procedureName,
ParameterMapper parameterMapper, OutputParameterMapper outputMapper)
{
if (database == null)
{
throw new ArgumentNullException("database");
}
if (connection == null)
{
throw new ArgumentNullException("connection");
}
if (procedureName == null)
{
throw new ArgumentNullException("procedureName");
}
int result = 0;
try
{
SqlCommand command = CommandFactory.CreateParameterMappedCommand(connection, procedureName, parameterMapper);
bool doClose = false;
if (connection.State != ConnectionState.Open)
{
doClose = true;
connection.Open();
}
result = command.ExecuteNonQuery();
if (doClose)
{
connection.Close();
}
if (outputMapper != null)
{
ParameterSet outputParams = new ParameterSet(command.Parameters);
outputMapper(outputParams);
}
}
catch (Exception e)
{
throw new SafeProcedureException(database, procedureName, e);
}
return(result);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_expressionProfileMapper = A.Fake <ExpressionProfileMapper>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_individualFactory = A.Fake <IIndividualFactory>();
_originDataMapper = A.Fake <OriginDataMapper>();
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <ModelIndividual> >();
sut = new IndividualMapper(_parameterMapper, _expressionProfileMapper, _originDataMapper, _individualFactory, _moleculeExpressionTask);
_individual = DomainHelperForSpecs.CreateIndividual();
_individual.Name = "Ind";
_individual.Description = "Model Description";
var kidney = _individual.EntityAt <IContainer>(Constants.ORGANISM, CoreConstants.Organ.KIDNEY);
_parameterLiver = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.LIVER, "PLiver");
_parameterKidney = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.KIDNEY, "PKidney");
_parameterKidneyRelExp = DomainHelperForSpecs.ConstantParameterWithValue().WithName(CoreConstants.Parameters.REL_EXP);
_parameterKidneyRelExp.DefaultValue = 10;
kidney.Add(_parameterKidneyRelExp);
_parameterLiver.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.Value = 40;
_parameterKidney.ValueDiffersFromDefault().ShouldBeTrue();
_parameterKidneyRelExp.Value = 50;
_parameterKidneyRelExp.ValueDiffersFromDefault().ShouldBeTrue();
_expressionProfile1 = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>(moleculeName: "Enz");
_expressionProfile2 = DomainHelperForSpecs.CreateExpressionProfile <IndividualTransporter>(moleculeName: "Trans");
_individual.AddExpressionProfile(_expressionProfile1);
_individual.AddExpressionProfile(_expressionProfile2);
_originDataSnapshot = new OriginData();
A.CallTo(() => _originDataMapper.MapToSnapshot(_individual.OriginData)).Returns(_originDataSnapshot);
_localizedParameterKidney = new LocalizedParameter {
Path = "Organism|Kidney|PKidney"
};
A.CallTo(() => _parameterMapper.LocalizedParametersFrom(A <IEnumerable <IParameter> > ._))
.Invokes(x => _mappedParameters = x.GetArgument <IEnumerable <IParameter> >(0).ToList())
.Returns(new[] { _localizedParameterKidney });
return(_completed);
}
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);
}
/// <summary>
/// Executes and returns an open IRecordSet, which encapsulates an OPEN DATAREADER. DISPOSE IN FINALLY CLAUSE.
/// </summary>
/// <param name="database"></param>
/// <param name="procedureName"></param>
/// <param name="parameterMapper"></param>
/// <returns></returns>
public static IRecordSet Execute(Database database, string procedureName, ParameterMapper parameterMapper)
{
SqlConnection connection = database.GetConnection();
SqlCommand command = CommandFactory.CreateParameterMappedCommand(connection, procedureName, parameterMapper);
try
{
command.Connection.Open();
IRecordSet record = new DataRecord(command.ExecuteReader(CommandBehavior.CloseConnection));
return(record);
}
catch (Exception exc)
{
command.Connection.Close();
throw new Core.Data.Exceptions.DatabaseExecutionException(database, procedureName, command, exc);
}
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_schemaMapper = A.Fake <SchemaMapper>();
_protocolFactory = A.Fake <IProtocolFactory>();
_dimensionRepository = A.Fake <IDimensionRepository>();
sut = new ProtocolMapper(_parameterMapper, _protocolFactory, _schemaMapper, _dimensionRepository);
_simpleProtocol = new SimpleProtocol
{
ApplicationType = ApplicationTypes.Intravenous,
DosingInterval = DosingIntervals.DI_6_6_12,
Name = "Simple Protocol",
Description = "Simple Protocol description",
};
_simpleProtocol.Add(DomainHelperForSpecs.ConstantParameterWithValue(3).WithName(Constants.Parameters.START_TIME));
_simpleProtocol.Add(DomainHelperForSpecs.ConstantParameterWithValue(4).WithName(CoreConstants.Parameters.INPUT_DOSE));
_simpleProtocol.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(Constants.Parameters.END_TIME));
A.CallTo(() => _parameterMapper.MapToSnapshot(_simpleProtocol.StartTime)).Returns(new Parameter().WithName(_simpleProtocol.StartTime.Name));
A.CallTo(() => _parameterMapper.MapToSnapshot(_simpleProtocol.Dose)).Returns(new Parameter().WithName(_simpleProtocol.Dose.Name));
A.CallTo(() => _parameterMapper.MapToSnapshot(_simpleProtocol.EndTimeParameter)).Returns(new Parameter().WithName(_simpleProtocol.EndTimeParameter.Name));
_advancedProtocol = new AdvancedProtocol
{
Name = "Advanced Protocol",
Description = "Advanced Protocol description",
TimeUnit = DomainHelperForSpecs.TimeDimensionForSpecs().DefaultUnit,
};
_schema = new Schema().WithName("Schema1");
_advancedProtocol.AddSchema(_schema);
_advancedProtocolParameter = DomainHelperForSpecs.ConstantParameterWithValue(3).WithName("AdvancedProtocolParameter");
_advancedProtocol.Add(_advancedProtocolParameter);
A.CallTo(() => _parameterMapper.MapToSnapshot(_advancedProtocolParameter)).Returns(new Parameter().WithName(_advancedProtocolParameter.Name));
_snapshotSchema = new Snapshots.Schema().WithName(_schema.Name);
A.CallTo(() => _schemaMapper.MapToSnapshot(_schema)).Returns(_snapshotSchema);
A.CallTo(() => _dimensionRepository.Time).Returns(DomainHelperForSpecs.TimeDimensionForSpecs());
return(Task.FromResult(true));
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_identificationParameterFactory = A.Fake <IIdentificationParameterFactory>();
_logger = A.Fake <IOSPSuiteLogger>();
_identificationParameterTask = A.Fake <IIdentificationParameterTask>();
sut = new IdentificationParameterMapper(_parameterMapper, _identificationParameterFactory, _identificationParameterTask, _logger);
_identificationParameter = new IdentificationParameter
{
IsFixed = true,
UseAsFactor = true,
Scaling = Scalings.Linear
};
_startValueParameter = DomainHelperForSpecs.ConstantParameterWithValue().WithName(Constants.Parameters.START_VALUE);
_identificationParameter.Add(_startValueParameter);
_identificationParameter.Name = "PARAM";
_parameter1 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P1");
_parameter2 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P2");
_simulation = A.Fake <Simulation>().WithName("S");
_simulation.Model.Root = new Container {
_parameter1, _parameter2
};
_identificationParameter.Scaling = Scalings.Linear;
_parameterSelection1 = new ParameterSelection(_simulation, _parameter1.Name);
_parameterSelection2 = new ParameterSelection(_simulation, _parameter2.Name);
_identificationParameter.AddLinkedParameter(_parameterSelection1);
_identificationParameter.AddLinkedParameter(_parameterSelection2);
_snapshotStartValueParameter = new Parameter();
A.CallTo(() => _parameterMapper.MapToSnapshot(_startValueParameter)).Returns(_snapshotStartValueParameter);
_project = new PKSimProject();
_project.AddBuildingBlock(_simulation);
_snapshotContext = new SnapshotContext(_project, ProjectVersions.Current);
_parameterIdentification = new ParameterIdentification();
_parameterIdentificationContext = new ParameterIdentificationContext(_parameterIdentification, _snapshotContext);
return(_completed);
}
/// <summary>
/// Call pseudo async NonQuery execution
/// </summary>
/// <param name="database"></param>
/// <param name="procedureName"></param>
/// <param name="parameterMapper"></param>
/// <param name="resultMapper"></param>
/// <returns></returns>
public static int ExecuteNonQuery(Database database, string procedureName, ParameterMapper parameterMapper)
{
SqlConnection connection = database.GetAsyncConnection();
SqlCommand command = CommandFactory.CreateParameterMappedCommand(connection, procedureName, parameterMapper);
bool isCompleted = false;
int result = 0;
try
{
connection.Open();
command.BeginExecuteNonQuery(
//Begin delegate
delegate(IAsyncResult ar)
{
SqlCommand locCommand = ar.AsyncState as SqlCommand;
try
{
result = locCommand.EndExecuteNonQuery(ar);
}
finally
{
CloseAsyncConnection(locCommand);
isCompleted = true;
}
}
//End delegate
, command);
}
catch //If an exception is thrown during the connection
{
CloseAsyncConnection(command);
throw;
}
while (!isCompleted)
{
Thread.Sleep(200);
}
return(result);
}
/// <summary>Generic function for parsing simple transient function parameters.</summary>
/// <typeparam name="T"></typeparam>
/// <param name="mapper"></param>
/// <param name="paramTokens"></param>
/// <param name="minArgc"></param>
/// <returns></returns>
private T GetParameterTokens <T>(ParameterMapper <T> mapper, List <Token> paramTokens, int minArgc) where T : new()
{
mapper.Target = new T();
for (var i = 1;
i <= Math.Min(mapper.ByIndexCount, paramTokens.Count - 1);
i++) // start from 1 bc. first is method identifier
{
mapper.Set(i - 1, GetValue(paramTokens[i]));
}
if (paramTokens.Count < minArgc || paramTokens.Count > mapper.ByIndexCount + 1)
{
Context.Errors.Add(paramTokens[0].ToError(SpiceParserErrorCode.InvalidNumberOfArguments));
}
var t = mapper.Target;
mapper.Target = default(T); // free memory
return(t);
}
/// <summary>
/// Executes and returns an open IRecordSet, which encapsulates an OPEN DATAREADER. DISPOSE IN FINALLY CLAUSE.
/// </summary>
/// <param name="database"></param>
/// <param name="procedureName"></param>
/// <param name="parameterMapper"></param>
/// <returns></returns>
public static IRecordSet Execute(Database database, string procedureName, ParameterMapper parameterMapper)
{
SqlConnection connection = database.GetConnection();
SqlCommand command = CommandFactory.CreateParameterMappedCommand(connection, procedureName, parameterMapper);
try
{
command.Connection.Open();
IRecordSet record = new DataRecord(command.ExecuteReader(CommandBehavior.CloseConnection));
return record;
}
catch(Exception exc)
{
command.Connection.Close();
throw new Core.Data.Exceptions.DatabaseExecutionException(database, procedureName, command, exc);
}
}
public static IRecordSet Execute(Database database, string procedureName, ParameterMapper parameterMapper)
{
SqlConnection connection = database.GetConnection();
SqlCommand command = CommandFactory.CreateParameterMappedCommand(connection, database.InstanceName, procedureName, parameterMapper);
//if (log.IsDebugEnabled)
// log.MethodDebugFormat(LOG_PREFIX, "Database: {0}, Procedure: {1}, Parameters: {2}", database.InstanceName, procedureName, DebugUtil.GetParameterString(command));
try
{
command.Connection.Open();
IRecordSet record = new DataRecord(command.ExecuteReader(CommandBehavior.CloseConnection));
return(record);
}
catch (Exception ex)
{
command.Connection.Close();
throw new Exception();
}
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_logger = A.Fake <IOSPSuiteLogger>();
sut = new ExpressionContainerMapper(_parameterMapper, _logger);
_relativeExpressionParameter =
DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_moleculeExpressionContainer = new MoleculeExpressionContainer().WithName("EXP");
_moleculeExpressionContainer.Add(_relativeExpressionParameter);
_transporterRelativeExpressionParameter =
DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_transporterExpressionContainer = new TransporterExpressionContainer().WithName("TRANS");
_transporterExpressionContainer.TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular;
_bloodCellsExpressionContainer = new TransporterExpressionContainer().WithName(CoreConstants.Compartment.BLOOD_CELLS);
_bloodCellsExpressionContainer.TransportDirection = TransportDirectionId.BiDirectionalBloodCellsPlasma;
_transporterExpressionContainer.Add(_transporterRelativeExpressionParameter);
_individual = new Individual {
OriginData = new OriginData {
Species = new Species().WithName("Human")
}
};
_expressionContainerMapperContext = new ExpressionContainerMapperContext(new SnapshotContext())
{
};
_enzyme = new IndividualEnzyme {
_moleculeExpressionContainer
};
_transporter = new IndividualTransporter {
_transporterExpressionContainer, _bloodCellsExpressionContainer
};
return(_completed);
}
//public static bool ExecuteAndHydrateInstance<T>(T objectInstance,Database database, string procedureName, ParameterMapper parameterMapper, RecordMapper<T> recordMapper)
//{
// bool result = false;
// return result;
//}
public static bool ExecuteAndHydrateInstance <T>(T objectInstance, Database database,
string procedureName, ParameterMapper parameterMapper, RecordMapper <T> recordMapper)
{
bool result = false;
try
{
using (IRecordSet reader = Procdure.Execute(database, procedureName, parameterMapper))
{
if (reader.Read())
{
recordMapper(reader, objectInstance);
result = true;
}
}
}
catch (Exception ex) // Procedure class already wrapped all necessary data
{
throw ex;
}
return(result);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_representationInfoRepository = A.Fake <IRepresentationInfoRepository>();
_compoundProcessRepository = A.Fake <ICompoundProcessRepository>();
_cloner = A.Fake <ICloner>();
_speciesRepository = A.Fake <ISpeciesRepository>();
_compoundProcessTask = A.Fake <ICompoundProcessTask>();
_logger = A.Fake <IOSPSuiteLogger>();
sut = new CompoundProcessMapper(_parameterMapper, _representationInfoRepository, _compoundProcessRepository, _cloner, _speciesRepository, _compoundProcessTask, _logger);
_enzymaticProcess = new EnzymaticProcess
{
Name = "Enzymatic Process",
Description = "Process description",
InternalName = "A",
DataSource = "B",
MetaboliteName = "Meta"
};
//Same description as DB
A.CallTo(() => _representationInfoRepository.DescriptionFor(RepresentationObjectType.PROCESS, _enzymaticProcess.InternalName)).Returns(_enzymaticProcess.Description);
_enzymaticProcessWithSpecies = new EnzymaticProcessWithSpecies
{
Name = "Enzymatic process with species",
Description = "toto",
Species = new Species().WithName("Human"),
InternalName = "C",
DataSource = "D",
};
A.CallTo(() => _representationInfoRepository.DescriptionFor(RepresentationObjectType.PROCESS, _enzymaticProcessWithSpecies.InternalName)).Returns("Process description");
return(Task.FromResult(true));
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_transportContainerUpdater = A.Fake <ITransportContainerUpdater>();
_logger = A.Fake <ILogger>();
sut = new ExpressionContainerMapper(_parameterMapper, _transportContainerUpdater, _logger);
_relativeExpressionParameter = DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_moleculeExpressionContainer = new MoleculeExpressionContainer().WithName("EXP");
_moleculeExpressionContainer.Add(_relativeExpressionParameter);
_transporterRelativeExpressionParameter = DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_transporterExpressionContainer = new TransporterExpressionContainer().WithName("TRANS");
_transporterExpressionContainer.MembraneLocation = MembraneLocation.Apical;
_transporterExpressionContainer.Add(_transporterRelativeExpressionParameter);
_individual = new Individual {
OriginData = new Model.OriginData {
Species = new Species().WithName("Human")
}
};
_expressionContainerMapperContext = new ExpressionContainerMapperContext
{
SimulationSubject = _individual
};
_enzyme = new IndividualEnzyme {
_moleculeExpressionContainer
};
_transporter = new IndividualTransporter {
_transporterExpressionContainer
};
return(_completed);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_schemaItemFactory = A.Fake <ISchemaItemFactory>();
sut = new SchemaItemMapper(_parameterMapper, _schemaItemFactory);
_schemaItem = new SchemaItem
{
Name = "SchemaItem",
Description = "The schema item",
ApplicationType = ApplicationTypes.Intravenous,
FormulationKey = "F1",
TargetCompartment = "Cells",
TargetOrgan = "Liver"
};
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("Param1");
_schemaItem.Add(_parameter);
A.CallTo(() => _parameterMapper.MapToSnapshot(_parameter)).Returns(new Snapshots.Parameter().WithName(_parameter.Name));
return(Task.FromResult(true));
}
/// <summary>
/// Executes a single-result procedure and loads the results into a DataTable named after the procedure.
/// </summary>
/// <param name="database"></param>
/// <param name="procedureName"></param>
/// <param name="parameterMapper"></param>
/// <returns>A fully populated datatable</returns>
/// <remarks>Will throw an exception if one occurs, but will close database connection.</remarks>
public static DataTable Execute(Database database, string procedureName, ParameterMapper parameterMapper)
{
DataTable dt;
try
{
dt = new DataTable(procedureName);
using (IDataReader reader = Procedure.ExecuteReader(database, procedureName, parameterMapper))
{
dt.Load(reader, LoadOption.OverwriteChanges);
}
}
catch (Core.Data.Exceptions.DataException) // Procedure class already wrapped all necessary data
{
throw;
}
catch (Exception e)
{
throw new SafeProcedureException(database, procedureName, e);
}
return(dt);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_parameterAlternativeFactory = A.Fake <IParameterAlternativeFactory>();
_speciesRepository = A.Fake <ISpeciesRepository>();
_compoundAlternativeTask = A.Fake <ICompoundAlternativeTask>();
sut = new AlternativeMapper(_parameterMapper, _parameterAlternativeFactory, _compoundAlternativeTask, _speciesRepository);
_parameterGroup = new ParameterAlternativeGroup {
Name = "ParameterGroup"
};
_alternative = new ParameterAlternative
{
Name = "Alternative1",
IsDefault = true,
Description = "Hello"
};
_species = new Species {
Name = "Hello"
};
_alternativeWithSpecies = new ParameterAlternativeWithSpecies
{
Name = "Alternative2",
IsDefault = false,
Description = "Hello",
Species = _species
};
_parameterGroup.AddAlternative(_alternativeWithSpecies);
A.CallTo(() => _speciesRepository.All()).Returns(new[] { _species });
return(_completed);
}
/// <summary>
/// Executes a single-result procedure and fires a mapping delegate for each row that is returned and then fires a parameter mapping delegate for output params.
/// </summary>
/// <param name="database"></param>
/// <param name="procedureName"></param>
/// <param name="parameterMapper"></param>
/// <param name="recordMapper"></param>
/// <param name="outputMapper"></param>
public static void ExecuteAndMapRecords(Database database, string procedureName, ParameterMapper parameterMapper, RecordMapper recordMapper, OutputParameterMapper outputMapper)
{
try
{
using (SqlConnection connection = database.GetConnection())
{
SqlCommand command = CommandFactory.CreateParameterMappedCommand(connection, procedureName, parameterMapper);
connection.Open();
IRecordSet reader = new DataRecord(command.ExecuteReader(CommandBehavior.CloseConnection));
while (reader.Read())
{
recordMapper(reader);
}
connection.Close();
if (outputMapper != null)
{
outputMapper(new ParameterSet(command.Parameters));
}
}
}
catch (Exception e)
{
throw new SafeProcedureException(database, procedureName, e);
}
}
/// <summary>
/// Executes a single-result procedure and fires a mapping delegate for each row that is returned.
/// </summary>
/// <param name="database"></param>
/// <param name="procedureName"></param>
/// <param name="parameterMapper"></param>
/// <param name="recordMapper"></param>
public static void ExecuteAndMapRecords(Database database, string procedureName, ParameterMapper parameterMapper, RecordMapper recordMapper)
{
try
{
using (IRecordSet reader = Procedure.Execute(database, procedureName, parameterMapper))
{
while (reader.Read())
{
recordMapper(reader);
}
}
}
catch (Exception e)
{
throw new SafeProcedureException(database, procedureName, e);
}
}
