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601 fixing nightly build #606

Merged
merged 17 commits into from
Sep 15, 2021
Merged

601 fixing nightly build #606

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2cd3013
Tests
abdelr Aug 17, 2021
2dc17e0
fix
abdelr Aug 17, 2021
8982c99
Extending unitDefinitionImporter with the ability to translate SBML u…
abdelr Aug 31, 2021
b5518f3
Using unitDefinitionImporter successfully
abdelr Aug 31, 2021
a6ec4fb
Changing registration so importers can be injected
abdelr Sep 1, 2021
d75350c
Adding default event
abdelr Sep 2, 2021
9b51a93
Refactoring for code readability
abdelr Sep 2, 2021
2e0cb62
Do not mask all exceptions
abdelr Sep 9, 2021
54e37fa
Merge branch 'develop' into 598_create_default_building_blocks_on_sbm…
abdelr Sep 9, 2021
16d2ef5
Only ASTHandler as to be extra registered
abdelr Sep 14, 2021
460dc9d
using AllNames
abdelr Sep 14, 2021
e1eebcf
Merge branch '598_create_default_building_blocks_on_sbml_import' into…
abdelr Sep 14, 2021
7272bab
Singletons need to be initialized before each import process
abdelr Sep 14, 2021
970f2d0
Resolving UnitDefinitionImpoter by its interface
abdelr Sep 14, 2021
fe3c6bd
Create an entry in the unit conversion dictionary also for directly i…
abdelr Sep 14, 2021
77566b7
Merge branch 'develop' into 601_fixing_nightly_build
abdelr Sep 14, 2021
6b3a518
Using IStartable
abdelr Sep 15, 2021
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7 changes: 7 additions & 0 deletions src/MoBi.Engine/ISBMLInitializableImporter.cs
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
namespace MoBi.Engine
{
public interface ISBMLInitializableImporter
{
void Initialize();
}
}
7 changes: 6 additions & 1 deletion src/MoBi.Engine/Sbml/FunctionDefinitionImporter.cs
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Expand Up @@ -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; }
Expand All @@ -32,5 +32,10 @@ protected override void Import(Model model)
public override void AddToProject()
{
}

public void Initialize()
{
_functionDefinitions.Clear();
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is this class FunctionDefinitionImporter singleton? Why isn't it done in constructor?
We have a IStartable interface also... maybe that should be enough?

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It is a singleton yes. Then if you load a file and load a second file, it will remember all the units and functions defined so you need to clearly trigger "this is a new file" and reset to a clean state. This is why for example tests were failing.

}
}
}
1 change: 1 addition & 0 deletions src/MoBi.Engine/Sbml/SBMLTask.cs
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Expand Up @@ -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))
{
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9 changes: 8 additions & 1 deletion src/MoBi.Engine/Sbml/UnitDefinitionImporter.cs
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Expand Up @@ -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;
Expand Down Expand Up @@ -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;
}

Expand All @@ -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;
}

Expand All @@ -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()
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same question here

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Didn't know about IStartable... already committed.

{
_unitConvertionDictionary.Clear();
}
}

}
2 changes: 1 addition & 1 deletion tests/MoBi.Tests/Core/SBML/Testfiles/UnitTestFile.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion tests/MoBi.Tests/Core/SBML/UnitImporterSpecs.cs
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Expand Up @@ -15,7 +15,7 @@

namespace MoBi.Core.SBML
{
public abstract class UnitImporterSpecs : ContextForSBMLIntegration<UnitDefinitionImporter>
public abstract class UnitImporterSpecs : ContextForSBMLIntegration<IUnitDefinitionImporter>
{
private Model _sbmlModel;

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3 changes: 3 additions & 0 deletions tests/MoBi.Tests/MoBi.Tests.csproj
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Expand Up @@ -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>


Expand Down