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Merge pull request #3119 from Open-Systems-Pharmacology/3069-parameters-under-applications-are-not-found-when-importing-from-snapshot-created-with-v11-simulations-and-pis
Fixes #3069 Parameters under Applications are not found when importing from snapshot created with ≤ V11 (Simulations and PIs)
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+134
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‎src/PKSim.Core/Snapshots/Mappers/IdentificationParameterMapper.cs‎

Lines changed: 29 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,9 @@
66
using OSPSuite.Core.Extensions;
77
using OSPSuite.Core.Services;
88
using PKSim.Assets;
9-
using PKSim.Core.Model;
9+
using PKSim.Core.Extensions;
10+
using static OSPSuite.Core.Domain.Constants;
11+
using static PKSim.Core.CoreConstants.ContainerName;
1012
using ModelIdentificationParameter = OSPSuite.Core.Domain.ParameterIdentifications.IdentificationParameter;
1113
using SnapshotIdentificationParameter = PKSim.Core.Snapshots.IdentificationParameter;
1214

@@ -51,7 +53,7 @@ public override async Task<ModelIdentificationParameter> MapToModel(SnapshotIden
5153
if (snapshot.LinkedParameters == null || !snapshot.LinkedParameters.Any())
5254
return null;
5355

54-
var parameterSelections = snapshot.LinkedParameters.Select(x => parameterSelectionFrom(x, snapshotContext.Project));
56+
var parameterSelections = snapshot.LinkedParameters.Select(x => parameterSelectionFrom(x, snapshotContext));
5557

5658
var identificationParameter = _identificationParameterFactory.CreateFor(parameterSelections, snapshotContext.ParameterIdentification);
5759
if (identificationParameter == null)
@@ -73,22 +75,45 @@ public override async Task<ModelIdentificationParameter> MapToModel(SnapshotIden
7375
return identificationParameter;
7476
}
7577

76-
private ParameterSelection parameterSelectionFrom(string parameterFullPath, PKSimProject project)
78+
private ParameterSelection parameterSelectionFrom(string parameterFullPath, ParameterIdentificationContext parameterIdentificationContext)
7779
{
7880
var parameterPath = new ObjectPath(parameterFullPath.ToPathArray());
7981
if (parameterPath.Count == 0)
8082
return null;
8183

8284
var simulationName = parameterPath[0];
83-
var simulation = project.All<Model.Simulation>().FindByName(simulationName);
85+
var simulation = parameterIdentificationContext.Project.All<Model.Simulation>().FindByName(simulationName);
8486
if (simulation == null)
8587
{
8688
_logger.AddWarning(PKSimConstants.Error.CouldNotFindSimulation(simulationName));
8789
return null;
8890
}
8991

9092
parameterPath.RemoveAt(0);
93+
94+
if (parameterIdentificationContext.IsV11FormatOrEarlier)
95+
updatePathsForV12(parameterPath);
96+
9197
return new ParameterSelection(simulation, parameterPath);
9298
}
99+
100+
private static void updatePathsForV12(ObjectPath parameterPath)
101+
{
102+
parameterPath.Replace(Applications, EVENTS);
103+
104+
replaceRenalClearanceName(parameterPath, PKSimConstants.UI.GlomerularFiltration);
105+
replaceRenalClearanceName(parameterPath, PKSimConstants.UI.RenalClearance);
106+
}
107+
108+
// renal clearances container names have been modified to append the name of the compound
109+
private static void replaceRenalClearanceName(ObjectPath parameterPath, string processName)
110+
{
111+
var processContainerName = parameterPath.FirstOrDefault(x => x.StartsWith(processName));
112+
if (string.IsNullOrEmpty(processContainerName))
113+
return;
114+
115+
var compoundName = parameterPath.ElementAt(parameterPath.IndexOf(processContainerName) - 1);
116+
parameterPath.Replace(processContainerName, CompositeNameFor(processContainerName, compoundName));
117+
}
93118
}
94119
}

‎tests/PKSim.Tests/Core/IdentificationParameterMapperSpecs.cs‎

Lines changed: 105 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -4,10 +4,12 @@
44
using Microsoft.Extensions.Logging;
55
using OSPSuite.BDDHelper;
66
using OSPSuite.BDDHelper.Extensions;
7+
using OSPSuite.Core;
78
using OSPSuite.Core.Domain;
89
using OSPSuite.Core.Domain.ParameterIdentifications;
910
using OSPSuite.Core.Domain.Services.ParameterIdentifications;
1011
using OSPSuite.Core.Services;
12+
using OSPSuite.Utility.Extensions;
1113
using PKSim.Core.Model;
1214
using PKSim.Core.Snapshots.Mappers;
1315
using Parameter = PKSim.Core.Snapshots.Parameter;
@@ -19,26 +21,32 @@ public abstract class concern_for_IdentificationParameterMapper : ContextSpecifi
1921
protected ParameterMapper _parameterMapper;
2022
protected IdentificationParameter _identificationParameter;
2123
protected Snapshots.IdentificationParameter _snapshot;
22-
private Simulation _simulation;
24+
protected Simulation _simulation;
2325
private IParameter _parameter1;
2426
private IParameter _parameter2;
27+
private IParameter _parameter3;
2528
private IParameter _startValueParameter;
2629
protected Parameter _snapshotStartValueParameter;
2730
protected ParameterSelection _parameterSelection1;
2831
protected ParameterSelection _parameterSelection2;
32+
private ParameterSelection _parameterSelection3;
33+
private ParameterSelection _gfrSelection;
2934
protected IIdentificationParameterFactory _identificationParameterFactory;
3035
protected IOSPSuiteLogger _logger;
3136
protected ParameterIdentificationContext _parameterIdentificationContext;
3237
private ParameterIdentification _parameterIdentification;
3338
private PKSimProject _project;
3439
protected IIdentificationParameterTask _identificationParameterTask;
3540
private SnapshotContext _snapshotContext;
41+
private IParameter _gfrFraction;
42+
private IParameter _renalClearances;
43+
private ParameterSelection _renalSelection;
3644

3745
protected override Task Context()
3846
{
3947
_parameterMapper = A.Fake<ParameterMapper>();
40-
_identificationParameterFactory= A.Fake<IIdentificationParameterFactory>();
41-
_logger= A.Fake<IOSPSuiteLogger>();
48+
_identificationParameterFactory = A.Fake<IIdentificationParameterFactory>();
49+
_logger = A.Fake<IOSPSuiteLogger>();
4250
_identificationParameterTask = A.Fake<IIdentificationParameterTask>();
4351
sut = new IdentificationParameterMapper(_parameterMapper, _identificationParameterFactory, _identificationParameterTask, _logger);
4452

@@ -56,25 +64,55 @@ protected override Task Context()
5664
_identificationParameter.Name = "PARAM";
5765
_parameter1 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P1");
5866
_parameter2 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P2");
67+
_parameter3 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P3");
68+
_gfrFraction = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P4");
69+
_renalClearances = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P5");
5970
_simulation = A.Fake<Simulation>().WithName("S");
60-
_simulation.Model.Root = new Container {_parameter1, _parameter2};
71+
_simulation.Model.Root = new Container
72+
{
73+
_parameter1,
74+
_parameter2,
75+
new Container { _parameter3 }.WithName(CoreConstants.ContainerName.Applications),
76+
new Container
77+
{
78+
new Container
79+
{
80+
_gfrFraction
81+
}.WithName("Glomerular Filtration-GFR"),
82+
new Container
83+
{
84+
_renalClearances
85+
}.WithName("Renal Clearances-test")
86+
}.WithName("Alprazolam")
87+
};
6188

6289
_identificationParameter.Scaling = Scalings.Linear;
6390
_parameterSelection1 = new ParameterSelection(_simulation, _parameter1.Name);
6491
_parameterSelection2 = new ParameterSelection(_simulation, _parameter2.Name);
92+
_parameterSelection3 = new ParameterSelection(_simulation, new ObjectPath(CoreConstants.ContainerName.Applications, _parameter3.Name));
93+
_gfrSelection = new ParameterSelection(_simulation, new ObjectPath("Alprazolam", "Glomerular Filtration-GFR", _gfrFraction.Name));
94+
_renalSelection = new ParameterSelection(_simulation, new ObjectPath("Alprazolam", "Renal Clearances-test", _renalClearances.Name));
6595
_identificationParameter.AddLinkedParameter(_parameterSelection1);
6696
_identificationParameter.AddLinkedParameter(_parameterSelection2);
97+
_identificationParameter.AddLinkedParameter(_parameterSelection3);
98+
_identificationParameter.AddLinkedParameter(_gfrSelection);
99+
_identificationParameter.AddLinkedParameter(_renalSelection);
67100

68101
_snapshotStartValueParameter = new Parameter();
69102
A.CallTo(() => _parameterMapper.MapToSnapshot(_startValueParameter)).Returns(_snapshotStartValueParameter);
70103

71104
_project = new PKSimProject();
72105
_project.AddBuildingBlock(_simulation);
73-
_snapshotContext = new SnapshotContext(_project, ProjectVersions.Current);
106+
_snapshotContext = new SnapshotContext(_project, GetSnapshotContextVersion());
74107
_parameterIdentification = new ParameterIdentification();
75108
_parameterIdentificationContext = new ParameterIdentificationContext(_parameterIdentification, _snapshotContext);
76109
return _completed;
77110
}
111+
112+
protected virtual ProjectVersion GetSnapshotContextVersion()
113+
{
114+
return ProjectVersions.Current;
115+
}
78116
}
79117

80118
public class When_mapping_an_identification_parameter_to_snapshot : concern_for_IdentificationParameterMapper
@@ -167,4 +205,66 @@ public void should_log_a_warning()
167205
A.CallTo(() => _logger.AddToLog(A<string>._, LogLevel.Warning, A<string>._)).MustHaveHappened();
168206
}
169207
}
208+
209+
public class When_updating_a_v11_snapshot : concern_for_IdentificationParameterMapper
210+
{
211+
private IdentificationParameter _newParameterIdentification;
212+
213+
protected override async Task Context()
214+
{
215+
await base.Context();
216+
_snapshot = await sut.MapToSnapshot(_identificationParameter);
217+
A.CallTo(() => _identificationParameterFactory.CreateFor(A<IEnumerable<ParameterSelection>>._, _parameterIdentificationContext.ParameterIdentification)).ReturnsLazily(x => createNewIdentificationParameter(x.Arguments.Get<IEnumerable<ParameterSelection>>(0)));
218+
renameApplications(_simulation.Model);
219+
renameRenalClearances(_simulation.Model);
220+
}
221+
222+
protected override ProjectVersion GetSnapshotContextVersion()
223+
{
224+
return ProjectVersions.V11;
225+
}
226+
227+
private IdentificationParameter createNewIdentificationParameter(IEnumerable<ParameterSelection> parameterSelections)
228+
{
229+
var newIdentificationParameter = new IdentificationParameter();
230+
231+
parameterSelections.Each(newIdentificationParameter.AddLinkedParameter);
232+
return newIdentificationParameter;
233+
}
234+
235+
private void renameRenalClearances(IModel model)
236+
{
237+
model.Root.GetAllChildren<IContainer>().Each(container =>
238+
{
239+
if (container.Name.Equals("Glomerular Filtration-GFR"))
240+
container.Name = "Glomerular Filtration-GFR-Alprazolam";
241+
242+
if (container.Name.Equals("Renal Clearances-test"))
243+
container.Name = "Renal Clearances-test-Alprazolam";
244+
});
245+
}
246+
247+
private static void renameApplications(IModel model)
248+
{
249+
model.Root.GetAllChildren<IContainer>().Each(container =>
250+
{
251+
if (container.Name.Equals(CoreConstants.ContainerName.Applications))
252+
container.Name = "Events";
253+
});
254+
}
255+
256+
protected override async Task Because()
257+
{
258+
_newParameterIdentification = await sut.MapToModel(_snapshot, _parameterIdentificationContext);
259+
}
260+
261+
[Observation]
262+
public void should_change_the_parameter_selection_paths()
263+
{
264+
_newParameterIdentification.AllLinkedParameters.Count.ShouldBeEqualTo(5);
265+
_newParameterIdentification.AllLinkedParameters[2].PathArray.ShouldContain("Events");
266+
_newParameterIdentification.AllLinkedParameters[3].PathArray.ShouldContain("Glomerular Filtration-GFR-Alprazolam");
267+
_newParameterIdentification.AllLinkedParameters[4].PathArray.ShouldContain("Renal Clearances-test-Alprazolam");
268+
}
269+
}
170270
}

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