2525 creating individual from MoBi (PK-Sim code changes)

src/PKSim.Assets.Images/PKSim.Assets.Images.csproj

@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.111" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.111" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.114" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.114" />
   </ItemGroup>
 
   <ItemGroup>

src/PKSim.Assets/PKSim.Assets.csproj

@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.111" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.111" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.114" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.114" />
   </ItemGroup>
 
   <ItemGroup>

src/PKSim.BatchTool/BatchRegister.cs

@@ -19,7 +19,7 @@ public override void RegisterInContainer(IContainer container)
             scan.WithDefaultConvention();
          });
 
-         container.Register<IUserSettings, ICoreUserSettings, OSPSuite.Core.ICoreUserSettings, IPresentationUserSettings, BatchUserSettings>(LifeStyle.Singleton);
+         container.Register<IUserSettings, ICoreUserSettings, OSPSuite.Core.ICoreUserSettings, OSPSuite.Presentation.IPresentationUserSettings, BatchUserSettings>(LifeStyle.Singleton);
          container.Register<IDiagramModelToXmlMapper, CLIDiagramModelToXmlMapper>();
          container.Register<IDiagramModel, CLIDiagramModel>();
          container.Register<IJournalDiagramManagerFactory, CLIJournalDiagramManagerFactory>();

src/PKSim.BatchTool/PKSim.BatchTool.csproj

@@ -59,8 +59,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="12.0.111" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.111" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.114" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.114" />
     <PackageReference Include="OSPSuite.DevExpress" Version="21.2.3" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />

src/PKSim.CLI.Core/PKSim.CLI.Core.csproj

@@ -27,9 +27,9 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.111" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.114" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.111" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.114" />
   </ItemGroup>
 
   <ItemGroup>

src/PKSim.CLI/PKSim.CLI.csproj

@@ -61,9 +61,9 @@
   <ItemGroup>
     <PackageReference Include="CommandLineParser" Version="2.8.0" />
     <PackageReference Include="Microsoft.Extensions.Logging.Console" Version="3.1.0" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.111" />
-    <PackageReference Include="OSPSuite.Presentation" Version="12.0.111" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.111" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.114" />
+    <PackageReference Include="OSPSuite.Presentation" Version="12.0.114" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.114" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.54" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.53" GeneratePathProperty="true" />

src/PKSim.Core/Model/CompoundProcessParameterMapping.cs

@@ -21,13 +21,13 @@ public interface ICompoundProcessParameterMapping
       /// <summary>
       ///    Path to the mapped parameter (e.g. ORGANISM/Liver/Volume)
       /// </summary>
-      IObjectPath MappedParameterPath { get; set; }
+      ObjectPath MappedParameterPath { get; set; }
    }
 
    public class CompoundProcessParameterMapping : ICompoundProcessParameterMapping
    {
       public string ProcessName { get; set; }
       public string ParameterName { get; set; }
-      public IObjectPath MappedParameterPath { get; set; }
+      public ObjectPath MappedParameterPath { get; set; }
    }
 }

src/PKSim.Core/Model/FormulaFactory.cs

@@ -210,7 +210,7 @@ public IFormula DoseFromDosePerBodySurfaceAreaFor(IFormulaCache formulaCache)
          return RateFor(CoreConstants.CalculationMethod.APPLICATION_PARAMETER_HUMAN, CoreConstants.Rate.APPLICATION_DOSE_FROM_DOSE_PER_BODY_SURFACE_AREA, formulaCache);
       }
 
-      private IFormulaUsablePath pathInParentContainerFor(IParameter parameter, string alias)
+      private FormulaUsablePath pathInParentContainerFor(IParameter parameter, string alias)
       {
          return _objectPathFactory.CreateFormulaUsablePathFrom(ObjectPath.PARENT_CONTAINER, parameter.Name)
             .WithAlias(alias)
@@ -338,7 +338,7 @@ private IFormula createFormula(RateKey rateKey)
 
          foreach (var rateObjectPath in _rateObjectPathsRepository.ObjectPathsFor(rateKey))
          {
-            formula.AddObjectPath(rateObjectPath.Clone<IFormulaUsablePath>());
+            formula.AddObjectPath(rateObjectPath.Clone<FormulaUsablePath>());
          }
 
          addTimeReferenceIfNeeded(formula);
@@ -395,8 +395,8 @@ private IFormula createTableFormulaWithOffset(RateKey rateKey)
          if (tableObjectPath == null || offsetObjectPath == null)
             throw new ArgumentException(PKSimConstants.Error.TableFormulaWithOffsetMissingRefs(rateKey.ToString(), CoreConstants.Alias.TABLE, CoreConstants.Alias.OFFSET));
 
-         formula.AddTableObjectPath(tableObjectPath.Clone<IFormulaUsablePath>());
-         formula.AddOffsetObjectPath(offsetObjectPath.Clone<IFormulaUsablePath>());
+         formula.AddTableObjectPath(tableObjectPath.Clone<FormulaUsablePath>());
+         formula.AddOffsetObjectPath(offsetObjectPath.Clone<FormulaUsablePath>());
 
          //Table formula with offest has the same dimension as its referenced table object
          formula.Dimension = tableObjectPath.Dimension;

src/PKSim.Core/Model/MoleculeStartFormula.cs

@@ -10,7 +10,7 @@ public interface IMoleculeStartFormula
       /// <summary>
       ///    Database path to the molecule, e.g. "ORGANISM\Liver\Plasma\DRUG"
       /// </summary>
-      IObjectPath MoleculePath { get; }
+      ObjectPath MoleculePath { get; }
 
       /// <summary>
       ///    Calculation method and rate for given formula
@@ -20,13 +20,13 @@ public interface IMoleculeStartFormula
 
    public class MoleculeStartFormula : IMoleculeStartFormula
    {
-      public MoleculeStartFormula(IObjectPath moleculePath, string calculationMethod, string rate)
+      public MoleculeStartFormula(ObjectPath moleculePath, string calculationMethod, string rate)
       {
          MoleculePath = moleculePath;
          RateKey = new RateKey(calculationMethod, rate);
       }
 
-      public IObjectPath MoleculePath { get; private set; }
+      public ObjectPath MoleculePath { get; private set; }
       public RateKey RateKey { get; private set; }
    }
 }

src/PKSim.Core/Model/PKSimBuildingBlock.cs

@@ -125,6 +125,8 @@ public virtual ContainerMode Mode
       }
 
       public virtual IReadOnlyList<IEntity> Children => Root.Children;
+
+      public ObjectPath ParentPath { get; set; }
 
       public IEnumerator<IEntity> GetEnumerator()
       {

src/PKSim.Core/Model/RateObjectPaths.cs

@@ -7,29 +7,29 @@ public interface IRateObjectPaths
    {
       string Rate { get; }
       string CalculationMethod { get; }
-      IEnumerable<IFormulaUsablePath> ObjectPaths { get; }
-      void AddObjectPath(IFormulaUsablePath objectPath);
+      IEnumerable<FormulaUsablePath> ObjectPaths { get; }
+      void AddObjectPath(FormulaUsablePath objectPath);
    }
 
    public class RateObjectPaths : IRateObjectPaths
    {
-      private readonly IList<IFormulaUsablePath> _objectPaths;
+      private readonly IList<FormulaUsablePath> _objectPaths;
       public string Rate { get; private set; }
       public string CalculationMethod { get; private set; }
 
       public RateObjectPaths(string calculationMethod, string rate)
       {
          CalculationMethod = calculationMethod;
          Rate = rate;
-         _objectPaths = new List<IFormulaUsablePath>();
+         _objectPaths = new List<FormulaUsablePath>();
       }
 
-      public IEnumerable<IFormulaUsablePath> ObjectPaths
+      public IEnumerable<FormulaUsablePath> ObjectPaths
       {
          get { return _objectPaths; }
       }
 
-      public void AddObjectPath(IFormulaUsablePath objectPath)
+      public void AddObjectPath(FormulaUsablePath objectPath)
       {
          _objectPaths.Add(objectPath);
       }
@@ -40,12 +40,12 @@ public class NullObjectPaths : IRateObjectPaths
       public string Rate { get; private set; }
       public string CalculationMethod { get; private set; }
 
-      public IEnumerable<IFormulaUsablePath> ObjectPaths
+      public IEnumerable<FormulaUsablePath> ObjectPaths
       {
-         get { return new List<IFormulaUsablePath>(); }
+         get { return new List<FormulaUsablePath>(); }
       }
 
-      public void AddObjectPath(IFormulaUsablePath objectPath)
+      public void AddObjectPath(FormulaUsablePath objectPath)
       {
       }
    }

src/PKSim.Core/PKSim.Core.csproj

@@ -30,10 +30,10 @@
   <ItemGroup>
     <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="12.0.111" />
-    <PackageReference Include="OSPSuite.Assets" Version="12.0.111" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.111" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.111" />
+    <PackageReference Include="OSPSuite.Core" Version="12.0.114" />
+    <PackageReference Include="OSPSuite.Assets" Version="12.0.114" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="12.0.114" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="12.0.114" />
     <PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
   </ItemGroup>
 

src/PKSim.Core/PKSimStarterRegistrationConvention.cs

@@ -0,0 +1,51 @@
+using System;
+using OSPSuite.Utility.Container;
+using System.Collections.Generic;
+using System.Linq;
+using OSPSuite.Core;
+using OSPSuite.Core.Commands.Core;
+using OSPSuite.Utility;
+using OSPSuite.Utility.Extensions;
+
+namespace PKSim.Core
+{
+   /// <summary>
+   ///    Register components in the container that are relevant for the PKSimStarter
+   /// </summary>
+   public class PKSimStarterRegistrationConvention : PKSimRegistrationConvention
+   {
+      public override void Process(Type concreteType, IContainer container, LifeStyle lifeStyle)
+      {
+         if (!shouldRegisterType(concreteType))
+            return;
+
+         base.Process(concreteType, container, lifeStyle);
+      }
+
+      private bool shouldRegisterType(Type concreteType)
+      {
+         if (concreteType.FullName == null)
+            return false;
+
+         if (concreteType.FullName.Contains("ExpressionProfile"))
+            return true;
+
+         if (concreteType.FullName.Contains("Individual"))
+            return true;
+
+         if (concreteType.FullName.Contains("Parameter"))
+            return true;
+
+         if (concreteType.FullName.Contains("Mapper"))
+            return true;
+
+         if (concreteType.FullName.Contains("Factory"))
+            return true;
+
+         if (concreteType.FullName.Contains("Tooltip"))
+            return true;
+
+         return false;
+      }
+   }
+}

src/PKSim.Core/Repositories/ICompoundProcessParameterMappingRepository.cs

@@ -13,7 +13,7 @@ public interface ICompoundProcessParameterMappingRepository : IRepository<ICompo
       /// </summary>
       /// <param name="compoundProcessName">Internal name of the compound process</param>
       /// <param name="processParameterName">Name of parameter</param>
-      IObjectPath MappedParameterPathFor(string compoundProcessName, string processParameterName);
+      ObjectPath MappedParameterPathFor(string compoundProcessName, string processParameterName);
 
       /// <summary>
       ///    Returns true if a mapping is available for the give{Process, ParameterName} otherwise false

src/PKSim.Core/Repositories/IModelContainerMoleculeRepository.cs

@@ -31,13 +31,13 @@ public interface IModelContainerMoleculeRepository : IStartableRepository<string
       ///   - for moleculeName = DRUG return true
       ///   - for moleculeName != DRUG return false
       /// </summary>
-      bool IsPresent(string modelName, IObjectPath containerPath, string moleculeName);
+      bool IsPresent(string modelName, ObjectPath containerPath, string moleculeName);
 
       /// <summary>
       /// Checks if molecule is available in container (for given model).<para/>
       /// Default behaviour for the case no entry for {model, container, molecule} is found: return false
       /// </summary>
-      bool NegativeValuesAllowed(string modelName, IObjectPath containerPath, string moleculeName);
+      bool NegativeValuesAllowed(string modelName, ObjectPath containerPath, string moleculeName);
    }
 
 }

src/PKSim.Core/Repositories/IMoleculeStartFormulaRepository.cs

@@ -14,6 +14,6 @@ public interface IMoleculeStartFormulaRepository : IStartableRepository<IMolecul
       ///    <paramref name="moleculePath" /> must be a database path to the molecule (e.g. "ORGANISM\Liver\Plasma\DRUG")
       /// </summary>
       /// <returns>Rate key if found, null if not found</returns>
-      RateKey RateKeyFor(IObjectPath moleculePath, ModelProperties modelProperties);
+      RateKey RateKeyFor(ObjectPath moleculePath, ModelProperties modelProperties);
    }
 }

src/PKSim.Core/Repositories/IRateObjectPathsRepository.cs

@@ -7,12 +7,12 @@ namespace PKSim.Core.Repositories
 {
    public interface IRateObjectPathsRepository : IStartableRepository<IRateObjectPaths>
    {
-      IEnumerable<IFormulaUsablePath> ObjectPathsFor(string rate, string calculationMethod);
-      IEnumerable<IFormulaUsablePath> ObjectPathsFor(RateKey rateKey);
+      IEnumerable<FormulaUsablePath> ObjectPathsFor(string rate, string calculationMethod);
+      IEnumerable<FormulaUsablePath> ObjectPathsFor(RateKey rateKey);
 
       /// <summary>
       ///    returns the first path defined for the ratekey with the given alias. If not path is found, returns null
       /// </summary>
-      IFormulaUsablePath PathWithAlias(RateKey rateKey, string alias);
+      FormulaUsablePath PathWithAlias(RateKey rateKey, string alias);
    }
 }

src/PKSim.Core/Services/DataRepositoryFromResultsCreator.cs

@@ -87,11 +87,11 @@ private bool columnIsSelected(DataColumn column, OutputSelections outputSelectio
       /// <param name="simulation"></param>
       /// <param name="path"></param>
       /// <returns></returns>
-      private Tuple<IQuantity, IObjectPath> quantityAndPathFrom(Simulation simulation, IEnumerable<string> path)
+      private Tuple<IQuantity, ObjectPath> quantityAndPathFrom(Simulation simulation, IReadOnlyList<string> path)
       {
          var objectPath = _objectPathFactory.CreateObjectPathFrom(path).AndAddAtFront(simulation.Name);
          var quantity = objectPath.TryResolve<IQuantity>(simulation.Model.Root);
-         return new Tuple<IQuantity, IObjectPath>(quantity, objectPath);
+         return new Tuple<IQuantity, ObjectPath>(quantity, objectPath);
       }
 
       private DataRepository createDataRepositoryWithBaseGrid(Simulation simulation)

src/PKSim.Core/Services/DistributedParameterToTableParameterConverter.cs

@@ -226,7 +226,7 @@ private void createPlasmaProteinOntogenyTable(IBuildConfiguration buildConfigura
       private void createParameterValueVersionOntogenyTableParameter(
          IParameter ontogenyFactorParameter,
          IBuildConfiguration buildConfiguration,
-         IObjectPath ontogenyFactorPath,
+         ObjectPath ontogenyFactorPath,
          IndividualMolecule molecule)
       {
          var psv = buildConfiguration.ParameterStartValues;
@@ -345,7 +345,7 @@ PopulationSimulation populationSimulation
          }
       }
 
-      private void createPopulationOntogenyTableParameter(IParameter ontogenyFactorParameter, IObjectPath ontogenyFactorPath, IndividualMolecule molecule, PopulationSimulation populationSimulation)
+      private void createPopulationOntogenyTableParameter(IParameter ontogenyFactorParameter, ObjectPath ontogenyFactorPath, IndividualMolecule molecule, PopulationSimulation populationSimulation)
       {
          addAgingDataToPopulationSimulation(populationSimulation, ontogenyFactorPath.ToString(), ontogenyFactorParameter,
             p => createOntogenyTableFormulaFrom(p.Parameter, molecule.Ontogeny, p.OriginData, populationSimulation.RandomGenerator));

src/PKSim.Core/Services/InteractionKineticUpdaterSpecificationBase.cs

@@ -150,24 +150,24 @@ protected virtual IReadOnlyList<InteractionProcess> AllInteractionProcessesFor(s
          return _interactionTask.AllInteractionProcessesFor(moleculeName, _interactionType, simulation, compoundName);
       }
 
-      private IFormulaUsablePath kiPath(string kiParameter, Compound inhibitor, InteractionProcess process, string kiAlias)
+      private FormulaUsablePath kiPath(string kiParameter, Compound inhibitor, InteractionProcess process, string kiAlias)
       {
          return _objectPathFactory.CreateFormulaUsablePathFrom(inhibitor.Name, process.Name, kiParameter)
             .WithAlias(kiAlias)
             .WithDimension(_dimensionRepository.MolarConcentration);
       }
 
-      private IFormulaUsablePath inhibitorConcentrationPath(Compound inhibitor, string inhibitorAlias, IContainer processParameterContainer)
+      private FormulaUsablePath inhibitorConcentrationPath(Compound inhibitor, string inhibitorAlias, IContainer processParameterContainer)
       {
          return localInhibitorParameterPath(inhibitor, Constants.Parameters.CONCENTRATION, inhibitorAlias, processParameterContainer, _dimensionRepository.MolarConcentration);
       }
 
-      private IFormulaUsablePath kwaterPath(Compound inhibitor, string kwaterAlias, IContainer processParameterContainer)
+      private FormulaUsablePath kwaterPath(Compound inhibitor, string kwaterAlias, IContainer processParameterContainer)
       {
          return localInhibitorParameterPath(inhibitor, CoreConstants.Parameters.K_WATER, kwaterAlias, processParameterContainer, _dimensionRepository.NoDimension);
       }
 
-      private IFormulaUsablePath localInhibitorParameterPath(Compound inhibitor, string parameterName, string parameterAlias, IContainer processParameterContainer, IDimension dimension)
+      private FormulaUsablePath localInhibitorParameterPath(Compound inhibitor, string parameterName, string parameterAlias, IContainer processParameterContainer, IDimension dimension)
       {
          var objectPath = _objectPathFactory.CreateFormulaUsablePathFrom(inhibitor.Name, parameterName)
             .WithAlias(parameterAlias)