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Investigate differences batch #2002

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merged 2 commits into from
Dec 1, 2021
Merged

Investigate differences batch #2002

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972aa36
Remove unnecessary log
msevestre Dec 1, 2021
4042acb
Fixes ivnestigate differences in batch runs
msevestre Dec 1, 2021
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9 changes: 9 additions & 0 deletions src/PKSim.Core/Snapshots/Mappers/ExpressionProfileMapper.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -108,11 +108,20 @@ public override async Task<ModelExpressionProfile> MapToModel(SnapshotExpression

//We need to normalize relative expressions when loading from old format
if (isV9Format(snapshot))
{
//Global parameters were saved directly under the snapshot parameter
await updateGlobalMoleculeParameters(snapshot, molecule);
NormalizeRelativeExpressionCommand.NormalizeExpressions(individual, molecule);
}

return expressionProfile;
}

private Task updateGlobalMoleculeParameters(SnapshotExpressionProfile snapshot, IndividualMolecule molecule)
{
return _parameterMapper.MapParameters(snapshot.Parameters, molecule, molecule.Name);
}

private void updateMoleculePropertiesToMolecule(IndividualMolecule molecule, SnapshotExpressionProfile snapshot, ModelIndividual individual)
{
switch (molecule)
Expand Down
4 changes: 3 additions & 1 deletion src/PKSim.Core/Snapshots/Mappers/IndividualMapper.cs
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Expand Up @@ -87,9 +87,10 @@ private async Task convertMoleculesToExpressionProfiles(SnapshotIndividual indiv
var expressionProfiles = await _expressionProfileMapper.MapToModels(individualSnapshot.Molecules);
foreach (var expressionProfile in expressionProfiles)
{
var (molecule, individual) = expressionProfile;
project.AddBuildingBlock(expressionProfile);
//this needs to happen here since molecule parameters were defined in individual in v10
await updateIndividualParameters(individualSnapshot, expressionProfile.Individual);
await updateIndividualParameters(individualSnapshot, individual);
}

individualSnapshot.ExpressionProfiles = expressionProfiles.AllNames().ToArray();
Expand All @@ -102,5 +103,6 @@ private Task updateIndividualParameters(SnapshotIndividual snapshot, ModelIndivi
//We do not show warning for v10 format as we will FOR SURE have missing parameters
return _parameterMapper.MapLocalizedParameters(snapshot.Parameters, individual, showParameterNotFoundWarning: !isV10Format(snapshot));
}

}
}
4 changes: 3 additions & 1 deletion src/PKSim.Core/Snapshots/Mappers/ParameterMapper.cs
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Expand Up @@ -7,6 +7,7 @@
using OSPSuite.Core.Domain.Services;
using OSPSuite.Core.Domain.UnitSystem;
using OSPSuite.Core.Services;
using OSPSuite.Utility.Extensions;
using PKSim.Assets;
using SnapshotParameter = PKSim.Core.Snapshots.Parameter;
using SnapshotTableFormula = PKSim.Core.Snapshots.TableFormula;
Expand Down Expand Up @@ -136,7 +137,8 @@ private async Task<LocalizedParameter[]> orderByPath(Task<LocalizedParameter[]>

public virtual Task MapLocalizedParameters(IReadOnlyList<LocalizedParameter> localizedParameters, IContainer container, bool showParameterNotFoundWarning = true)
{
if (localizedParameters == null || !localizedParameters.Any())
//undefined or empty or actually not localized parameters (coming from conversions probably)
if (localizedParameters == null || !localizedParameters.Any() || localizedParameters.All(x=> x.Path.IsNullOrEmpty()))
return Task.FromResult(false);

var allParameters = _containerTask.CacheAllChildren<IParameter>(container);
Expand Down
190 changes: 190 additions & 0 deletions tests/PKSim.Tests/Data/ind_expression_v9.json
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@@ -0,0 +1,190 @@
{
"Version": 77,
"Individuals": [
{
"Name": "Ind",
"Seed": 17189110,
"OriginData": {
"CalculationMethods": [
"SurfaceAreaPlsInt_VAR1",
"Body surface area - Mosteller"
],
"Species": "Human",
"Population": "European_ICRP_2002",
"Gender": "MALE",
"Age": {
"Value": 30.0,
"Unit": "year(s)"
}
},
"Parameters": [
{
"Path": "Organism|Liver|EHC continuous fraction",
"Value": 1.0,
"ValueOrigin": {
"Source": "Unknown"
}
}
],
"Molecules": [
{
"Name": "CYP3A4",
"Type": "Enzyme",
"MembraneLocation": "Apical",
"TissueLocation": "Intracellular",
"IntracellularVascularEndoLocation": "Endosomal",
"Expression": [
{
"Name": "Brain",
"Value": 0.0041682898325
},
{
"Name": "Gonads",
"Value": 0.00078691079081
},
{
"Name": "Kidney",
"Value": 0.0053603428126
},
{
"Name": "Periportal",
"Value": 1.0
},
{
"Name": "Pericentral",
"Value": 1.0
},
{
"Name": "Lung",
"Value": 0.00042695753798
},
{
"Name": "SmallIntestine",
"Value": 0.0727697702
},
{
"Name": "Duodenum",
"Value": 0.0727697702
},
{
"Name": "UpperJejunum",
"Value": 0.0727697702
},
{
"Name": "LowerJejunum",
"Value": 0.0727697702
},
{
"Name": "UpperIleum",
"Value": 0.0727697702
},
{
"Name": "LowerIleum",
"Value": 0.0727697702
}
],
"Ontogeny": {
"Name": "CYP3A4"
},
"Parameters": [
{
"Name": "Reference concentration",
"Value": 4.32,
"Unit": "µmol/l"
},
{
"Name": "t1/2 (liver)",
"Value": 36.0,
"Unit": "h",
"ValueOrigin": {
"Source": "Unknown"
}
},
{
"Name": "t1/2 (intestine)",
"Value": 23.0,
"Unit": "h"
}
]
},
{
"Name": "CYP2C8",
"Type": "Enzyme",
"MembraneLocation": "Apical",
"TissueLocation": "Intracellular",
"IntracellularVascularEndoLocation": "Endosomal",
"Expression": [
{
"Name": "Brain",
"Value": 0.00041051218109
},
{
"Name": "Gonads",
"Value": 0.0138116248
},
{
"Name": "Kidney",
"Value": 0.0012660656052
},
{
"Name": "Periportal",
"Value": 1.0
},
{
"Name": "Pericentral",
"Value": 1.0
},
{
"Name": "Lung",
"Value": 0.00092269326683
},
{
"Name": "SmallIntestine",
"Value": 0.0031843468252
},
{
"Name": "Duodenum",
"Value": 0.0031843468252
},
{
"Name": "UpperJejunum",
"Value": 0.0031843468252
},
{
"Name": "LowerJejunum",
"Value": 0.0031843468252
},
{
"Name": "UpperIleum",
"Value": 0.0031843468252
},
{
"Name": "LowerIleum",
"Value": 0.0031843468252
}
],
"Ontogeny": {
"Name": "CYP2C8"
},
"Parameters": [
{
"Name": "Reference concentration",
"Value": 2.56,
"Unit": "µmol/l"
},
{
"Name": "t1/2 (liver)",
"Value": 23.000001425,
"Unit": "h"
},
{
"Name": "t1/2 (intestine)",
"Value": 23.0,
"Unit": "h"
}
]
}
]
}
]
}
46 changes: 46 additions & 0 deletions tests/PKSim.Tests/IntegrationTests/IndividualMapperSpecs.cs
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Expand Up @@ -92,4 +92,50 @@ public void should_have_added_the_newly_created_expression_profile_as_reference_
_individual.AllExpressionProfiles().ShouldContain(_expressionProfileEnzyme, _expressionProfileTransporter);
}
}

public class When_loading_a_snapshot_file_containing_expression_created_in_v9 : ContextWithLoadedSnapshot
{
private Individual _individual;
private ExpressionProfile _expressionProfileCYP3A4;
private ExpressionProfile _expressionProfileCYP2C8;

public override void GlobalContext()
{
base.GlobalContext();
LoadSnapshot("ind_expression_v9");
_individual = FindByName<Individual>("Ind");
_expressionProfileCYP3A4 = FindByName<ExpressionProfile>("CYP3A4|Human|Ind");
_expressionProfileCYP2C8 = FindByName<ExpressionProfile>("CYP2C8|Human|Ind");
}

[Observation]
public void should_have_created_an_expression_profile_based_on_the_value_defined_in_the_snapshot_file_for_the_enzyme_cyp3A4()
{
_expressionProfileCYP3A4.ShouldNotBeNull();
var (enzyme, individual) = _expressionProfileCYP3A4;
enzyme.Ontogeny.Name.ShouldBeEqualTo("CYP3A4");
enzyme.ReferenceConcentration.ValueInDisplayUnit.ShouldBeEqualTo(4.32);
var expressionInBone = individual.Organism.EntityAt<MoleculeExpressionContainer>("Brain", "Intracellular", enzyme.Name);
expressionInBone.RelativeExpressionParameter.Value.ShouldBeEqualTo(0.004168, 1e-2);
}

[Observation]
public void should_have_created_an_expression_profile_based_on_the_value_defined_in_the_snapshot_file_for_the_enzyme_cyp2C8()
{
_expressionProfileCYP2C8.ShouldNotBeNull();
var (enzyme, individual) = _expressionProfileCYP2C8;
enzyme.Ontogeny.Name.ShouldBeEqualTo("CYP2C8");
enzyme.ReferenceConcentration.ValueInDisplayUnit.ShouldBeEqualTo(2.56);
enzyme.HalfLifeIntestine.ValueInDisplayUnit.ShouldBeEqualTo(23);
var expressionInBone = individual.Organism.EntityAt<MoleculeExpressionContainer>("Kidney", "Intracellular", enzyme.Name);
expressionInBone.RelativeExpressionParameter.Value.ShouldBeEqualTo(0.0012661, 1e-2);
}

[Observation]
public void should_have_added_the_newly_created_expression_profile_as_reference_in_the_individual()
{
_individual.AllExpressionProfiles().ShouldContain(_expressionProfileCYP3A4, _expressionProfileCYP2C8);
}
}

}