601 fixing nightly build

src/MoBi.Engine/EngineRegister.cs

@@ -11,13 +11,13 @@ public override void RegisterInContainer(IContainer container)
          container.AddScanner(x =>
          {
             x.AssemblyContainingType<EngineRegister>();
+            x.WithConvention(new OSPSuiteRegistrationConvention(registerConcreteType: true));
             x.ExcludeType<UnitDefinitionImporter>();
             x.ExcludeType<FunctionDefinitionImporter>();
-            x.WithConvention(new OSPSuiteRegistrationConvention(registerConcreteType: true));
          });
 
-         //No idea why this is required explicitly. Maybe because the class only has yield operators?
          container.Register<SBMLImporterRepository, SBMLImporterRepository>();
+         container.Register<ASTHandler, ASTHandler>();
          container.Register<IUnitDefinitionImporter, UnitDefinitionImporter>(LifeStyle.Singleton);
          container.Register<IFunctionDefinitionImporter, FunctionDefinitionImporter>(LifeStyle.Singleton);
       }

src/MoBi.Engine/ISBMLInitializableImporter.cs

@@ -0,0 +1,7 @@
+namespace MoBi.Engine
+{
+   public interface ISBMLInitializableImporter
+   {
+      void Initialize();
+   }
+}

src/MoBi.Engine/Sbml/EventImporter.cs

@@ -42,11 +42,19 @@ protected override void Import(Model model)
       {
          _astHandler.NeedAbsolutePath = true;
          CreateEGBandEGBB();
-
-         for (long i = 0; i < model.getNumEvents(); i++)
+         var numEvents = model.getNumEvents();
+         if (numEvents == 0)
+         {
+            CreateEmptyEvent();
+         }
+         else
          {
-            CreateEvent(model.getEvent(i));
+            for (var i = 0; i < numEvents; i++)
+            {
+               CreateEvent(model.getEvent(i));
+            }
          }
+
          _astHandler.NeedAbsolutePath = false;
          AddToProject();
       }
@@ -90,6 +98,15 @@ internal void CreateEvent(Event sbmlEvent)
          EventGroupBuilder.Add(EventBuilder);
       }
 
+      private void CreateEmptyEvent()
+      {
+         EventGroupBuilder.Add(
+            new EventBuilder()
+               .WithId(SBMLConstants.SBML_EVENTBUILDER)
+               .WithName(SBMLConstants.SBML_DEFAULTEVENTNAME)
+         );
+      }
+
       /// <summary>
       ///    Creates warnings to inform the user, that "Delay" and "Priority" of events are not supported/considered.
       /// </summary>

src/MoBi.Engine/Sbml/FunctionDefinitionImporter.cs

@@ -11,7 +11,7 @@ public interface IFunctionDefinitionImporter : ISBMLImporter
       List<FunctionDefinition> FunctionDefinitions { get; }
    }
 
-   public class FunctionDefinitionImporter : SBMLImporter, IFunctionDefinitionImporter
+   public class FunctionDefinitionImporter : SBMLImporter, ISBMLInitializableImporter, IFunctionDefinitionImporter
    {
       private readonly List<FunctionDefinition> _functionDefinitions;
       public List<FunctionDefinition> FunctionDefinitions { get => _functionDefinitions; }
@@ -32,5 +32,10 @@ protected override void Import(Model model)
       public override void AddToProject()
       {
       }
+
+      public void Initialize()
+      {
+         _functionDefinitions.Clear();
+      }
    }
 }

src/MoBi.Engine/Sbml/SBMLConstants.cs

@@ -12,6 +12,7 @@ static class SBMLConstants
       public static string FORMULA = "Formula";
       public const string SBML_EVENT_ASSIGNMENT = "SBML Event Assignment ";
       public const string SBML_EVENTBUILDER = "EVENTBUILDER";
+      public const string SBML_DEFAULTEVENTNAME = "Default Event";
 
       //Building Block Names
       public const string SBML_REACTION_BB = "SBML Reactions";

src/MoBi.Engine/Sbml/SBMLImporterRepository.cs

@@ -4,49 +4,47 @@
 
 namespace MoBi.Engine.Sbml
 {
-   public class SBMLImporterRepository
-   {
-      private readonly IContainer _container;
+    public class SBMLImporterRepository
+    {
+        private readonly IContainer _container;
 
-      public SBMLImporterRepository(IContainer container)
-      {
-         _container = container;
-      }
+        public SBMLImporterRepository(IContainer container)
+        {
+            _container = container;
+        }
 
-      public IEnumerable<ISBMLImporter> All()
-      {
-         yield return _container.Resolve<IUnitDefinitionImporter>();
-         yield return _container.Resolve<CompartmentImporter>();
-         yield return _container.Resolve<SpeciesImporter>();
-         yield return _container.Resolve<ParameterImporter>();
-         yield return _container.Resolve<IFunctionDefinitionImporter>();
-         yield return _container.Resolve<ReactionImporter>();
-         yield return _container.Resolve<AssignmentImporter>();
-         yield return _container.Resolve<EventImporter>();
-      }
-
-      public IEnumerable<ISBMLImporter> AllFor(Model sbmlModel)
-      {
-         if (sbmlModel.getNumUnitDefinitions() != 0)
+        public IEnumerable<ISBMLImporter> All()
+        {
             yield return _container.Resolve<IUnitDefinitionImporter>();
-         yield return _container.Resolve<CompartmentImporter>();
-         if (sbmlModel.getNumSpecies() != 0)
+            yield return _container.Resolve<CompartmentImporter>();
             yield return _container.Resolve<SpeciesImporter>();
-         if (sbmlModel.getNumParameters() != 0)
             yield return _container.Resolve<ParameterImporter>();
-         if (sbmlModel.getNumFunctionDefinitions() != 0)
             yield return _container.Resolve<IFunctionDefinitionImporter>();
-         if (sbmlModel.getNumReactions() != 0)
             yield return _container.Resolve<ReactionImporter>();
-         yield return _container.Resolve<AssignmentImporter>();
-         if (sbmlModel.getNumEvents() != 0)
+            yield return _container.Resolve<AssignmentImporter>();
             yield return _container.Resolve<EventImporter>();
-      }
-
-      public IEnumerable<SBMLImporter> Assignment()
-      {
-         yield return _container.Resolve<RuleImporter>();
-         yield return _container.Resolve<InitialAssignmentImporter>();
-      }
-   }
+        }
+        public IEnumerable<ISBMLImporter> AllFor(Model sbmlModel)
+        {
+            if (sbmlModel.getNumUnitDefinitions() != 0)
+                yield return _container.Resolve<IUnitDefinitionImporter>();
+            yield return _container.Resolve<CompartmentImporter>();
+            if (sbmlModel.getNumSpecies() != 0)
+                yield return _container.Resolve<SpeciesImporter>();
+            if (sbmlModel.getNumParameters() != 0)
+                yield return _container.Resolve<ParameterImporter>();
+            if (sbmlModel.getNumFunctionDefinitions() != 0)
+                yield return _container.Resolve<IFunctionDefinitionImporter>();
+            if (sbmlModel.getNumReactions() != 0)
+                yield return _container.Resolve<ReactionImporter>();
+            yield return _container.Resolve<AssignmentImporter>();
+            if (sbmlModel.getNumEvents() != 0)
+                yield return _container.Resolve<EventImporter>();
+        }
+        public IEnumerable<SBMLImporter> Assignment()
+        {
+            yield return _container.Resolve<RuleImporter>();
+            yield return _container.Resolve<InitialAssignmentImporter>();
+        }
+    }
 }

src/MoBi.Engine/Sbml/SBMLTask.cs

@@ -49,6 +49,7 @@ public IMoBiCommand ImportModelFromSbml(string filename, IMoBiProject project)
          project.Name = getProjectName(model);
 
          reportConstraints(project, model);
+         _importerRepository.AllFor(model).OfType<ISBMLInitializableImporter>().Each(impoter => impoter.Initialize());
 
          foreach (var importer in _importerRepository.AllFor(model))
          {
@@ -105,14 +106,7 @@ public Model GetModel(string filename)
          {
             throw new MoBiException(SBMLConstants.ModelNotRead(sbmlDoc.getErrorLog().ToString()));
          }
-         try
-         {
-            convertSBML(sbmlDoc);
-         }
-         catch (Exception _)
-         {
-            throw new MoBiException(SBMLConstants.NoValidConversionToLevel3Version2);
-         }
+         convertSBML(sbmlDoc);
          var model = sbmlDoc.getModel();
          SaveSBMLInformation(model, sbmlDoc);
          return model;

src/MoBi.Engine/Sbml/UnitDefinitionImporter.cs

@@ -24,7 +24,7 @@ public interface IUnitDefinitionImporter : ISBMLImporter
       double[] ToMobiBaseUnit(string unit, IEnumerable<double> value);
    }
 
-   public class UnitDefinitionImporter : SBMLImporter, IUnitDefinitionImporter
+   public class UnitDefinitionImporter : SBMLImporter, ISBMLInitializableImporter, IUnitDefinitionImporter
    {
       private readonly IMoBiDimensionFactory _moBiDimensionFactory;
       private readonly IDictionary<int, Unit> _baseUnitsDictionary;
@@ -98,6 +98,7 @@ public IDimension ConvertUnit(UnitDefinition unitDefinition)
          if (dimension != Constants.Dimension.NO_DIMENSION)
          {
             _sbmlInformation.MobiDimension[sbmlUnit] = dimension;
+            _unitConvertionDictionary.Add(sbmlUnit, new UnitConvertionInfo() { Dimension = dimension, Unit = dimension.DefaultUnit, Rate = 1 });
             return dimension;
          }
 
@@ -114,6 +115,7 @@ public IDimension ConvertUnit(UnitDefinition unitDefinition)
                return unitDimension;
             }
          }
+         _unitConvertionDictionary.Add(sbmlUnit, new UnitConvertionInfo() { Dimension = dimension, Unit = dimension.DefaultUnit, Rate = 1 });
          return dimension;
       }
 
@@ -136,6 +138,11 @@ public double[] ToMobiBaseUnit(string unit, IEnumerable<double> value)
          var convertionData = _unitConvertionDictionary[unit];
          return convertionData.Dimension.UnitValuesToBaseUnitValues(convertionData.Unit, value.Select(v => v * convertionData.Rate));
       }
+
+      public void Initialize()
+      {
+         _unitConvertionDictionary.Clear();
+      }
    }
 
 }

tests/MoBi.Tests/Core/SBML/EventImporterSpecs.cs

@@ -24,6 +24,22 @@ protected override void Context()
       }
    }
 
+   public class DefaultEventImporterTests : ConcernForEventImporter
+   {
+      protected override void Because()
+      {
+         var sbmlModel = new Model(3, 1);
+
+         sut.DoImport(sbmlModel, new MoBiProject(), A.Fake<SBMLInformation>(), new MoBiMacroCommand());
+      }
+
+      [Observation]
+      public void LoadsDefaultIfNoEvent()
+      {
+         sut.EventGroupBuilder.Children.AllNames().ShouldNotBeEmpty();
+      }
+   }
+
    public class EventImporterTests : ConcernForEventImporter
    {
       protected override void Because()
@@ -74,7 +90,7 @@ public void EventCreationTest()
       public void TriggerCreationTest()
       {
          sut.EventGroupBuilder.Children.ExistsByName("e1").ShouldBeTrue();
-         var event1 = (EventBuilder) sut.EventGroupBuilder.Children.FindByName("e1");
+         var event1 = (EventBuilder)sut.EventGroupBuilder.Children.FindByName("e1");
          event1.Formula.ShouldNotBeNull();
       }
 

tests/MoBi.Tests/Core/SBML/Testfiles/UnitTestFile.xml

@@ -87,7 +87,7 @@
 <compartment metaid="default" id="default" size="1" units="volume"/>
 </listOfCompartments>
 <listOfSpecies>
-<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="5" substanceUnits="mole" hasOnlySubstanceUnits="true" charge="0">
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="5" substanceUnits="substance" hasOnlySubstanceUnits="true" charge="0">
 <annotation>
 <celldesigner:extension>
 <celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>

tests/MoBi.Tests/Core/SBML/UnitImporterSpecs.cs

@@ -15,7 +15,7 @@
 
 namespace MoBi.Core.SBML
 {
-   public abstract class UnitImporterSpecs : ContextForSBMLIntegration<UnitDefinitionImporter>
+   public abstract class UnitImporterSpecs : ContextForSBMLIntegration<IUnitDefinitionImporter>
    {
       private Model _sbmlModel;
 

tests/MoBi.Tests/MoBi.Tests.csproj

@@ -99,6 +99,9 @@
     <None Update="Core\SBML\Testfiles\Barros2021_RAJI.xml">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
+    <None Update="Core\SBML\Testfiles\UnitTestFile.xml">
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </None>
   </ItemGroup>