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Merge pull request #3420 from Open-Systems-Pharmacology/2278-create-expression-profile-from-r
Fixes #3421 Enable PK-Sim ExpressionProfile from MoBi.R
2 parents 4403830 + 3fad03d commit ab525b9

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3 files changed

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‎src/PKSim.Assets/PKSimConstants.cs‎

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Original file line numberDiff line numberDiff line change
@@ -868,6 +868,10 @@ public static string CouldNotFindMoleculeType(string moleculeType) =>
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public static string EffectiveMolWeightMustBeGreaterThan(double valueInDisplayUnit, string displayUnit) =>
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$"Effective mol weight must be greater than or equal to {valueInDisplayUnit} {displayUnit}";
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public static string InvalidProteinCategory(string category) => $"The category '{category}' is not a valid expression category";
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public static string CouldNotFindValidSpecies(string speciesName) => $"Could not find a valid species named '{speciesName}'";
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}
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public static class Information

‎src/PKSim.R/Exchange/BuildingBlockCreator.cs‎

Lines changed: 44 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -2,19 +2,25 @@
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using OSPSuite.Core.Snapshots;
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using OSPSuite.Core.Snapshots.Mappers;
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using OSPSuite.R.Domain;
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using PKSim.Assets;
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using PKSim.Core.Mappers;
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using PKSim.Core.Model;
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using PKSim.Core.Repositories;
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using PKSim.Core.Services;
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using PKSim.Core.Snapshots.Mappers;
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using System;
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using static PKSim.Assets.PKSimConstants.UI;
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namespace PKSim.R.Exchange;
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/// <summary>
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/// The class is intended to allow MoBi to dynamically load and call the method and receive a serialized individual building block
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/// We exchange data between PK-Sim and MoBi domains only through serializing and deserializing due to differences in the dimension systems.
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/// The systems are different in the sense that they each rely on dimensions being singular in the app, but by exchanging objects, that will not be the case.
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/// You will have two Mass dimension objects for example.
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/// The class is intended to allow MoBi to dynamically load and call the method and receive a serialized
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/// building blocks. We exchange data between PK-Sim and MoBi domains only through serializing and deserializing
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/// due to differences in the dimension systems. The systems are different in the sense that they each rely on
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/// dimensions being singular in the app, but by exchanging objects, that will not be the case.
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/// You will have two Mass dimension objects for example.
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/// </summary>
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public class BuildingBlockCreator
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public static class BuildingBlockCreator
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{
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public static string CreateIndividual(IndividualCharacteristics individualCharacteristics)
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{
@@ -26,4 +32,37 @@ public static string CreateIndividual(IndividualCharacteristics individualCharac
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return serializer.Serialize(mapper.MapFrom(buildingBlock));
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}
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public static string CreateExpressionProfile(string category, string moleculeName, string speciesName)
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{
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var (serializer, mapper) = Api.ResolveTasks<IPKMLPersistor, IExpressionProfileToExpressionProfileBuildingBlockMapper>();
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ExpressionProfile buildingBlock;
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if (string.Equals(category, TransportProtein))
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buildingBlock = createExpressionProfile<IndividualTransporter>(category, moleculeName, speciesName);
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else if (string.Equals(category, ProteinBindingPartner))
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buildingBlock = createExpressionProfile<IndividualOtherProtein>(category, moleculeName, speciesName);
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else if (string.Equals(category, MetabolizingEnzyme))
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buildingBlock = createExpressionProfile<IndividualEnzyme>(category, moleculeName, speciesName);
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else
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throw new ArgumentException(PKSimConstants.Error.InvalidProteinCategory(category));
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return serializer.Serialize(mapper.MapFrom(buildingBlock));
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}
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private static ExpressionProfile createExpressionProfile<T>(string category, string moleculeName, string speciesName) where T : IndividualMolecule
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{
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var (expressionProfileFactory, moleculeParameterTask, speciesRepository) = Api.ResolveTasks<IExpressionProfileFactory, IMoleculeParameterTask, ISpeciesRepository>();
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var species = speciesRepository.FindByName(speciesName);
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if (species == null)
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throw new ArgumentException(PKSimConstants.Error.CouldNotFindValidSpecies(speciesName));
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var expressionProfile = expressionProfileFactory.Create<T>(species, moleculeName);
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expressionProfile.Category = category;
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moleculeParameterTask.SetDefaultFor(expressionProfile);
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return expressionProfile;
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}
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}

‎tests/PKSim.R.Tests/BuildingBlockCreatorSpecs.cs‎

Lines changed: 101 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -1,46 +1,118 @@
1-
using OSPSuite.BDDHelper;
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using System;
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using OSPSuite.BDDHelper;
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using OSPSuite.BDDHelper.Extensions;
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using OSPSuite.Core.Snapshots;
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using OSPSuite.R.Domain;
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using PKSim.Assets;
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using PKSim.Core;
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using PKSim.R.Exchange;
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using static PKSim.Assets.PKSimConstants.UI;
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namespace PKSim.R
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namespace PKSim.R;
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internal class CreateExchangeIndividual : ContextForStaticIntegration
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{
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internal class CreateExchangeIndividual : ContextForStaticIntegration
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private IndividualCharacteristics _individualCharacteristics;
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private string _result;
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protected override void Context()
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{
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private IndividualCharacteristics _individualCharacteristics;
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private string _result;
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base.Context();
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_individualCharacteristics = new IndividualCharacteristics
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{
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Species = CoreConstants.Species.HUMAN,
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Population = CoreConstants.Population.ICRP,
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Age = new Parameter
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{
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Value = 30,
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Unit = "year(s)",
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},
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Weight = new Parameter
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{
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Value = 75,
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Unit = "kg",
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},
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Height = new Parameter
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{
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Value = 175,
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Unit = "cm",
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},
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Gender = CoreConstants.Gender.MALE
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};
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}
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protected override void Because()
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{
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_result = BuildingBlockCreator.CreateIndividual(_individualCharacteristics);
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}
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[Observation]
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public void an_exchangeable_string_is_created()
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{
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_result.ShouldNotBeNull();
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}
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}
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internal class CreateExchangeMetabolizingEnzyme : ContextForStaticIntegration
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{
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private string _result;
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protected override void Because()
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{
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_result = BuildingBlockCreator.CreateExpressionProfile(MetabolizingEnzyme, "CYP3A4", CoreConstants.Species.HUMAN);
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}
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15-
protected override void Context()
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[Observation]
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public void an_exchangeable_string_is_created()
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{
68+
_result.ShouldNotBeNull();
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}
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}
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internal class CreateExchangeExpressionProfileWithInvalidSpecies : ContextForStaticIntegration
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{
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[Observation]
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public void should_throw_an_argument_exception_with_species_not_found_message()
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{
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var message = string.Empty;
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The.Action(() =>
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{
17-
base.Context();
18-
_individualCharacteristics = new IndividualCharacteristics
80+
try
1981
{
20-
Species = CoreConstants.Species.HUMAN,
21-
Population = CoreConstants.Population.ICRP,
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Age = new Parameter
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{
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Value = 30,
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Unit = "year(s)",
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},
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Weight = new Parameter
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{
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Value = 75,
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Unit = "kg",
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},
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Height = new Parameter
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{
34-
Value = 175,
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Unit = "cm",
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},
37-
Gender = CoreConstants.Gender.MALE
38-
};
39-
}
82+
BuildingBlockCreator.CreateExpressionProfile(MetabolizingEnzyme, "CYP3A4", "InvalidSpecies");
83+
}
84+
catch (Exception e)
85+
{
86+
message = e.Message;
87+
throw;
88+
}
89+
}).ShouldThrowAn<ArgumentException>();
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message.ShouldBeEqualTo(PKSimConstants.Error.CouldNotFindValidSpecies("InvalidSpecies"));
91+
}
92+
}
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internal class CreateExchangeTransportProtein : ContextForStaticIntegration
95+
{
96+
private string _result;
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98+
protected override void Because()
99+
{
100+
_result = BuildingBlockCreator.CreateExpressionProfile(TransportProtein, "CYP3A4", CoreConstants.Species.HUMAN);
101+
}
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103+
[Observation]
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public void an_exchangeable_string_is_created()
105+
{
106+
_result.ShouldNotBeNull();
107+
}
108+
109+
internal class CreateExchangeProteinBindingPartner : ContextForStaticIntegration
110+
{
111+
private string _result;
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41113
protected override void Because()
42114
{
43-
_result = BuildingBlockCreator.CreateIndividual(_individualCharacteristics);
115+
_result = BuildingBlockCreator.CreateExpressionProfile(ProteinBindingPartner, "CYP3A4", CoreConstants.Species.HUMAN);
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}
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[Observation]

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