440 support mobi dimensions (#1397)

* Fixes update to new core * Fixes #440 support mobi dimensions * COnvert some reporting project to 7.4.0: * Update project to pass tests * Update project to pass tests * Fixes #1398 It should not be possible to use a TableFormulation without any point * Add missing converter 6.0.1 to 6.0.2: * Add missing converter 6.0.1 to 6.0.2: * Update to latest core to fix nuget issue
Open-Systems-Pharmacology · Jan 31, 2020 · 843ebe7 · 843ebe7
1 parent 8912b75
commit 843ebe7
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diff --git a/src/PKSim.Assets.Images/PKSim.Assets.Images.csproj b/src/PKSim.Assets.Images/PKSim.Assets.Images.csproj
@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="9.0.53" />
+    <PackageReference Include="OSPSuite.Assets" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="9.0.70" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.Assets/PKSim.Assets.csproj b/src/PKSim.Assets/PKSim.Assets.csproj
@@ -26,8 +26,8 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Assets" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="9.0.53" />
+    <PackageReference Include="OSPSuite.Assets" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="9.0.70" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.Assets/PKSimConstants.cs b/src/PKSim.Assets/PKSimConstants.cs
@@ -472,6 +472,8 @@ public static class Error
 
          public static string NotMappingDefinedForQualificationStep(string qualificationStepType) => $"No mapping defined for {ObjectTypes.QualificationStep.ToLower()} '{qualificationStepType}'";
 
+         public static string TableFormulationRequiresAtLeastOnePoint(string formulation) => $"Table formulation '{formulation}' requires at least one point to be used in a simulation.";
+
          public static string CouldNotFindSimulation(string simulationName) => CouldNotFind(OSPSuite.Assets.ObjectTypes.Simulation, simulationName);
 
          public static string SimulationResultsFileDoesNotHaveTheExpectedFormat

diff --git a/src/PKSim.BatchTool/PKSim.BatchTool.csproj b/src/PKSim.BatchTool/PKSim.BatchTool.csproj
@@ -63,10 +63,10 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="OSPSuite.Core" Version="9.0.53" />
+    <PackageReference Include="OSPSuite.Core" Version="9.0.70" />
     <PackageReference Include="OSPSuite.DevExpress" Version="19.2.4.1" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.44" GeneratePathProperty="true" />
-    <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.32" GeneratePathProperty="true" />
+    <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.33" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.7" GeneratePathProperty="true" />
     <PackageReference Include="System.Data.SQLite.Core" Version="1.0.112" GeneratePathProperty="true" />
   </ItemGroup>

diff --git a/src/PKSim.CLI.Core/MinimalImplementations/CLIEntityValidationTask.cs b/src/PKSim.CLI.Core/MinimalImplementations/CLIEntityValidationTask.cs
@@ -25,7 +25,7 @@ public bool Validate(IObjectBase objectToValidate)
          if (validationResult.ValidationState == ValidationState.Valid)
             return true;
 
-         var error = Error.EntityIsInvalid(this._executionContext.TypeFor<IObjectBase>(objectToValidate), objectToValidate.Name);
+         var error = Error.EntityIsInvalid(_executionContext.TypeFor(objectToValidate), objectToValidate.Name);
          _logger.AddError(error);
          return false;
       }

diff --git a/src/PKSim.CLI.Core/PKSim.CLI.Core.csproj b/src/PKSim.CLI.Core/PKSim.CLI.Core.csproj
@@ -28,7 +28,7 @@
 
   <ItemGroup>
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="9.0.53" />
+    <PackageReference Include="OSPSuite.Core" Version="9.0.70" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.CLI/PKSim.CLI.csproj b/src/PKSim.CLI/PKSim.CLI.csproj
@@ -60,13 +60,13 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="CommandLineParser" Version="2.6.0" />
+    <PackageReference Include="CommandLineParser" Version="2.7.82" />
     <PackageReference Include="Microsoft.Extensions.Logging.Console" Version="2.2.0" />
-    <PackageReference Include="OSPSuite.Core" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Presentation" Version="9.0.53" />
+    <PackageReference Include="OSPSuite.Core" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Presentation" Version="9.0.70" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
     <PackageReference Include="OSPSuite.FuncParser" Version="4.0.0.44" GeneratePathProperty="true" />
-    <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.32" GeneratePathProperty="true" />
+    <PackageReference Include="OSPSuite.SimModel" Version="4.0.0.33" GeneratePathProperty="true" />
     <PackageReference Include="OSPSuite.SimModelSolver_CVODES" Version="4.1.0.7" GeneratePathProperty="true" />
     <PackageReference Include="System.Data.SQLite.Core" Version="1.0.112" GeneratePathProperty="true" />
 

diff --git a/src/PKSim.Core/PKSim.Core.csproj b/src/PKSim.Core/PKSim.Core.csproj
@@ -30,11 +30,11 @@
   <ItemGroup>
     <PackageReference Include="Newtonsoft.Json" Version="12.0.3" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
-    <PackageReference Include="OSPSuite.Core" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Assets" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Assets.Images" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="9.0.53" />
-    <PackageReference Include="System.ComponentModel.Annotations" Version="4.6.0" />
+    <PackageReference Include="OSPSuite.Core" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Assets" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Assets.Images" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="9.0.70" />
+    <PackageReference Include="System.ComponentModel.Annotations" Version="4.7.0" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/src/PKSim.Core/ProjectVersions.cs b/src/PKSim.Core/ProjectVersions.cs
@@ -7,19 +7,7 @@ public static class ProjectVersions
    {
       private static readonly Cache<int, ProjectVersion> _knownVersions = new Cache<int, ProjectVersion>(x => x.Version, x => null);
 
-      public static readonly ProjectVersion V5_0_1 = addVersion(20, "5.0.1");
-      public static readonly ProjectVersion V5_1_3 = addVersion(21, "5.1.3");
-      public static readonly ProjectVersion V5_1_4 = addVersion(22, "5.1.4");
-      public static readonly ProjectVersion V5_1_5 = addVersion(51, "5.1.5");
-      public static readonly ProjectVersion V5_2_1 = addVersion(53, "5.2.1");
-      public static readonly ProjectVersion V5_2_2 = addVersion(55, "5.2.2");
-      public static readonly ProjectVersion V5_3_1 = addVersion(57, "5.3.1");
-      public static readonly ProjectVersion V5_3_2 = addVersion(58, "5.3.2");
-      public static readonly ProjectVersion V5_4_1 = addVersion(59, "5.4.1");
-      public static readonly ProjectVersion V5_5_1 = addVersion(60, "5.5.1");
-      public static readonly ProjectVersion V5_5_2 = addVersion(61, "5.5.2");
-      public static readonly ProjectVersion V5_6_1 = addVersion(62, "5.6.1");
-      public static readonly ProjectVersion V5_6_2 = addVersion(63, "5.6.2");
+      public const int UNSUPPORTED = 63;
       public static readonly ProjectVersion V6_0_1 = addVersion(64, "6.0.1");
       public static readonly ProjectVersion V6_0_2 = addVersion(65, "6.0.2");
       public static readonly ProjectVersion V6_1_2 = addVersion(66, "6.1.2");

diff --git a/src/PKSim.Core/Services/SimulationConfigurationValidator.cs b/src/PKSim.Core/Services/SimulationConfigurationValidator.cs
@@ -1,6 +1,7 @@
 using System.Collections.Generic;
 using System.Linq;
 using OSPSuite.Core.Domain;
+using OSPSuite.Core.Domain.Formulas;
 using OSPSuite.Utility.Extensions;
 using PKSim.Assets;
 using PKSim.Core.Mappers;
@@ -32,6 +33,7 @@ public void ValidateConfigurationFor(Simulation simulation)
          var compounds = simulation.Compounds;
          var simulationSubject = simulation.BuildingBlock<ISimulationSubject>();
          var protocols = simulation.Protocols;
+         var formulations = simulation.AllBuildingBlocks<Formulation>();
          var modelConfiguration = simulation.ModelConfiguration;
 
          //ForComp model can only be used with small molecules
@@ -64,6 +66,20 @@ public void ValidateConfigurationFor(Simulation simulation)
          });
 
          administeredCompoundWithSuperSaturationEnabled.Each(x => validateSupersaturationUsageFor(x.Compound, x.Protocol, x.FormulationMappings));
+
+         formulations.Where(x=>x.FormulationType==CoreConstants.Formulation.TABLE).Each(validateTableFormulation);
+      }
+
+      private void validateTableFormulation(Formulation tableFormulation)
+      {
+         var formulaParameter = tableFormulation.Parameter(CoreConstants.Parameters.FRACTION_DOSE);
+         var tableFormula = formulaParameter?.Formula as TableFormula;
+
+         //at least one point in this formulation
+         if(tableFormula!=null && tableFormula.AllPoints().Any()) 
+            return;
+
+         throw new InvalidSimulationConfigurationException(PKSimConstants.Error.TableFormulationRequiresAtLeastOnePoint(tableFormulation.Name));
       }
 
       private void validateSupersaturationUsageFor(Compound compound, Protocol protocol, IReadOnlyList<FormulationMapping> formulationMappings)

diff --git a/src/PKSim.Core/Services/SimulationModelCreator.cs b/src/PKSim.Core/Services/SimulationModelCreator.cs
@@ -69,7 +69,7 @@ public void CreateModelFor(Simulation simulation, bool shouldValidate = true, bo
       private void updateSimulationAfterModelCreation(Simulation simulation)
       {
          //last step. Once the model has been created, it is necessary to set the id of the simulation 
-         //in all paramater defined in the model
+         //in all parameter defined in the model
          _parameterIdUpdater.UpdateSimulationId(simulation);
 
          var allMoleculeAmounts = simulation.All<IMoleculeAmount>().ToList();

diff --git a/src/PKSim.Core/Services/SimulationPKParametersImportTask.cs b/src/PKSim.Core/Services/SimulationPKParametersImportTask.cs
@@ -9,7 +9,7 @@ namespace PKSim.Core.Services
 {
    public interface ISimulationPKParametersImportTask
    {
-      Task<SimulationPKParametersImport> ImportPKParameters(PopulationSimulation populationSimulation, string filefullPath, CancellationToken cancellationToken);
+      Task<SimulationPKParametersImport> ImportPKParameters(PopulationSimulation populationSimulation, string fileFullPath, CancellationToken cancellationToken);
    }
 
    public class SimulationPKParametersImportTask : ISimulationPKParametersImportTask
@@ -23,9 +23,9 @@ public SimulationPKParametersImportTask(ISimulationPKAnalysesImporter pkAnalyses
          _quantityRetriever = quantityRetriever;
       }
 
-      public async Task<SimulationPKParametersImport> ImportPKParameters(PopulationSimulation populationSimulation, string filefullPath, CancellationToken cancellationToken)
+      public async Task<SimulationPKParametersImport> ImportPKParameters(PopulationSimulation populationSimulation, string fileFullPath, CancellationToken cancellationToken)
       {
-         var importedPKAnalysis = await importPKAnalysesFromFile(filefullPath, cancellationToken);
+         var importedPKAnalysis = await importPKAnalysesFromFile(fileFullPath, cancellationToken);
          validateConsistencyWithSimulation(populationSimulation, importedPKAnalysis);
          addImportedPKToLogForSuccessfulImport(importedPKAnalysis);
          return importedPKAnalysis;
@@ -82,12 +82,12 @@ private void validateLength(PopulationSimulation populationSimulation, QuantityP
          importedPKParameter.AddError(PKSimConstants.Error.NotEnoughPKValuesForParameter(pkParameter.Name, pkParameter.QuantityPath, populationSimulation.NumberOfItems, pkParameter.Count));
       }
 
-      private Task<SimulationPKParametersImport> importPKAnalysesFromFile(string filefullPath, CancellationToken cancellationToken)
+      private Task<SimulationPKParametersImport> importPKAnalysesFromFile(string fileFullPath, CancellationToken cancellationToken)
       {
          return Task.Run(() =>
          {
-            var pKAnalysesFile = new PKAnalysesImportFile { FilePath = filefullPath };
-            var pkAnalyses = _pkAnalysesImporter.ImportPKParameters(filefullPath, pKAnalysesFile);
+            var pKAnalysesFile = new PKAnalysesImportFile { FilePath = fileFullPath };
+            var pkAnalyses = _pkAnalysesImporter.ImportPKParameters(fileFullPath, pKAnalysesFile);
             return new SimulationPKParametersImport(pkAnalyses, pKAnalysesFile);
          }, cancellationToken);
       }

diff --git a/src/PKSim.Infrastructure/InfrastructureRegister.cs b/src/PKSim.Infrastructure/InfrastructureRegister.cs
@@ -31,7 +31,6 @@
 using PKSim.Infrastructure.ORM.Mappers;
 using PKSim.Infrastructure.ORM.Repositories;
 using PKSim.Infrastructure.ProjectConverter;
-using PKSim.Infrastructure.ProjectConverter.v5_3;
 using PKSim.Infrastructure.ProjectConverter.v6_2;
 using PKSim.Infrastructure.Reporting.Markdown;
 using PKSim.Infrastructure.Reporting.Markdown.Builders;
@@ -307,13 +306,11 @@ private static void registerConverters(IContainer container)
             scan.IncludeNamespaceContainingType<IObjectConverter>();
             scan.ExcludeType<ProjectConverterLogger>();
             scan.ExcludeType<ObjectConverterFinder>();
-            scan.ExcludeType<Converter52To531>();
             scan.ExcludeType<Converter612To621>();
             scan.WithConvention<PKSimRegistrationConvention>();
          });
 
          //required as singleton because of element caching
-         container.Register<Converter52To531, IObjectConverter, Converter52To531>(LifeStyle.Singleton);
          container.Register<Converter612To621, IObjectConverter, Converter612To621>(LifeStyle.Singleton);
          container.Register<IObjectConverterFinder, ObjectConverterFinder>(LifeStyle.Singleton);
          container.Register<IProjectConverterLogger, ProjectConverterLogger>(LifeStyle.Singleton);

diff --git a/src/PKSim.Infrastructure/PKSim.Infrastructure.csproj b/src/PKSim.Infrastructure/PKSim.Infrastructure.csproj
@@ -38,15 +38,15 @@
     <PackageReference Include="LumenWorksCsvReader" Version="4.0.0" />
     <PackageReference Include="MarkdownLog.NS20" Version="0.10.1" />
     <PackageReference Include="Microsoft.Extensions.Logging" Version="2.2.0" />
-    <PackageReference Include="Newtonsoft.Json.Schema" Version="3.0.11" />
-    <PackageReference Include="OSPSuite.Core" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Infrastructure" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Infrastructure.Castle" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Infrastructure.Export" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="9.0.53" />
-    <PackageReference Include="OSPSuite.Presentation.Serialization" Version="9.0.53" />
+    <PackageReference Include="Newtonsoft.Json.Schema" Version="3.0.13" />
+    <PackageReference Include="OSPSuite.Core" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Infrastructure" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Infrastructure.Castle" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Infrastructure.Export" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Infrastructure.Import" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Infrastructure.Reporting" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Infrastructure.Serialization" Version="9.0.70" />
+    <PackageReference Include="OSPSuite.Presentation.Serialization" Version="9.0.70" />
     <PackageReference Include="OSPSuite.Utility" Version="4.0.0.4" />
   </ItemGroup>