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1429 metaData with empty values imported #1507

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merged 3 commits into from
Feb 22, 2022
Merged

1429 metaData with empty values imported #1507

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2d4162a
fix
georgeDaskalakis Feb 22, 2022
d7df912
refactoring integration tests
georgeDaskalakis Feb 22, 2022
49a6997
integration test added
georgeDaskalakis Feb 22, 2022
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4 changes: 3 additions & 1 deletion src/OSPSuite.Infrastructure.Import/Core/Mappers/DataSetToDataRepositoryMapper.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
using OSPSuite.Core.Domain.Services;
using OSPSuite.Core.Domain.UnitSystem;
using OSPSuite.Infrastructure.Import.Extensions;
using OSPSuite.Utility.Extensions;

namespace OSPSuite.Infrastructure.Import.Core.Mappers
{
Expand Down Expand Up @@ -39,7 +40,8 @@ public DataSetToDataRepositoryMappingResult ConvertImportDataSet(ImportedDataSet

foreach (var metaDataDescription in dataSet.MetaDataDescription)
{
dataRepository.ExtendedProperties.Add(new ExtendedProperty<string>() { Name = metaDataDescription.Name, Value = metaDataDescription.Value });
if (!metaDataDescription.Value.IsNullOrEmpty())
dataRepository.ExtendedProperties.Add(new ExtendedProperty<string>() { Name = metaDataDescription.Name, Value = metaDataDescription.Value });
}

var warningFlag = false;
Expand Down
Binary file modified tests/OSPSuite.Presentation.Tests/Data/IntegrationSample1.xlsx
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138 changes: 40 additions & 98 deletions tests/OSPSuite.Presentation.Tests/Services/DataImporterSpecs.cs
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Expand Up @@ -71,6 +71,28 @@ protected override void Context()
_metaDataCategories.First(md => md.Name == _dataImporterSettings.NameOfMetaDataHoldingMoleculeInformation).ListOfValues.Add("TestInputMolecule", "233");
}

protected List<DataFormatParameter> createTestParameters(string moleculeColumnName, UnitDescription timeUnitDescription, UnitDescription concentrationUnitDescription, IDimension _timeConcentrationDimension)
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ah ah yes!

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hehe not sure if you are agreeing on the refactoring or disagreeing somehow on the number of parameters of the function...

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I like this .. I was just waiting for the build to finish sorry. Merging

{
var parameterList = new List<DataFormatParameter>
{
new MappingDataFormatParameter("time [h]",
new Column() { Name = "Time", Dimension = _dimensionFactory.Dimension("Time"), Unit = timeUnitDescription }),
new MappingDataFormatParameter("conc [mg/l]",
new Column()
{
Name = "Concentration", Dimension = _timeConcentrationDimension, Unit = concentrationUnitDescription
}),
new MappingDataFormatParameter("SD [mg/l]",
new Column()
{
Name = "Error", ErrorStdDev = "Arithmetic Standard Deviation", Dimension = _massConcentrationDimension,
Unit = new UnitDescription("mg/l")
}),
new MetaDataFormatParameter("VenousBlood", "Organ", false),
new MetaDataFormatParameter(moleculeColumnName, "Molecule", false)
};
return parameterList;
}
protected string getFileFullName(string fileName) => Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "Data", fileName);

private IReadOnlyList<ColumnInfo> getDefaultColumnInfos()
Expand Down Expand Up @@ -145,24 +167,7 @@ public class When_importing_data_from_correct_configuration : concern_for_DataIm
{
protected override void Because()
{
var parameterList = new List<DataFormatParameter>
{
new MappingDataFormatParameter("time [h]",
new Column() {Name = "Time", Dimension = _dimensionFactory.Dimension("Time"), Unit = new UnitDescription("h")}),
new MappingDataFormatParameter("conc [mg/l]",
new Column()
{
Name = "Concentration", Dimension = _massConcentrationDimension, Unit = new UnitDescription("mg/l")
}),
new MappingDataFormatParameter("SD [mg/l]",
new Column()
{
Name = "Error", ErrorStdDev = "Arithmetic Standard Deviation", Dimension = _massConcentrationDimension,
Unit = new UnitDescription("mg/l")
}),
new MetaDataFormatParameter("VenousBlood", "Organ", false),
new MetaDataFormatParameter("TestInputMolecule", "Molecule", false)
};
var parameterList = createTestParameters("TestInputMolecule", new UnitDescription("h"), new UnitDescription("mg/l"), _massConcentrationDimension);
var parameterListMolecularWeight = new List<DataFormatParameter>(parameterList);
parameterListMolecularWeight.Add(new MetaDataFormatParameter("Molecular Weight", "Molecular Weight", true));
_importerConfiguration.CloneParametersFrom(parameterList);
Expand Down Expand Up @@ -281,24 +286,7 @@ public class When_importing_data_with_missing_columns : concern_for_DataImporter
{
protected override void Because()
{
var parameterList = new List<DataFormatParameter>
{
new MappingDataFormatParameter("time [h]",
new Column() {Name = "Time", Dimension = _dimensionFactory.Dimension("Time"), Unit = new UnitDescription("h")}),
new MappingDataFormatParameter("conc [mg/l]",
new Column()
{
Name = "Concentration", Dimension = _massConcentrationDimension, Unit = new UnitDescription("mg/l")
}),
new MappingDataFormatParameter("SD [mg/l]",
new Column()
{
Name = "Error", ErrorStdDev = "Arithmetic Standard Deviation", Dimension = _massConcentrationDimension,
Unit = new UnitDescription("mg/l")
}),
new MetaDataFormatParameter("VenousBlood", "Organ", false),
new MetaDataFormatParameter(null, "Molecule", false)
};
var parameterList = createTestParameters(null, new UnitDescription("h"), new UnitDescription("mg/l"), _massConcentrationDimension);
_importerConfiguration.CloneParametersFrom(parameterList);
}

Expand All @@ -323,24 +311,7 @@ public class When_importing_data_with_missing_unit_columns : concern_for_DataImp
{
protected override void Because()
{
var parameterList = new List<DataFormatParameter>
{
new MappingDataFormatParameter("time [h]",
new Column() {Name = "Time", Dimension = _dimensionFactory.Dimension("Time"), Unit = new UnitDescription("h", "timeUnitColumn")}),
new MappingDataFormatParameter("conc [mg/l]",
new Column()
{
Name = "Concentration", Dimension = _massConcentrationDimension, Unit = new UnitDescription("mg/l")
}),
new MappingDataFormatParameter("SD [mg/l]",
new Column()
{
Name = "Error", ErrorStdDev = "Arithmetic Standard Deviation", Dimension = _massConcentrationDimension,
Unit = new UnitDescription("mg/l")
}),
new MetaDataFormatParameter("VenousBlood", "Organ", false),
new MetaDataFormatParameter(null, "Molecule", false)
};
var parameterList = createTestParameters(null, new UnitDescription("h", "timeUnitColumn"), new UnitDescription("mg/l"), _massConcentrationDimension);
_importerConfiguration.CloneParametersFrom(parameterList);
}

Expand All @@ -353,33 +324,17 @@ public void should_set_unit_of_missing_column_to_undefined()
}
}

public class When_importing_data_from_incorrect_configuration : concern_for_DataImporter
public class When_importing_with_inconsistent_units_in_column : concern_for_DataImporter
{
protected override void Because()
{
var parameterList = new List<DataFormatParameter>
{
new MappingDataFormatParameter("time [h]",
new Column() {Name = "Time", Dimension = _dimensionFactory.Dimension("Time"), Unit = new UnitDescription("h")}),
new MappingDataFormatParameter("conc [mg/l]",
new Column()
{
Name = "Concentration", Dimension = _timeConcentrationDimension, Unit = new UnitDescription("s")
}),
new MappingDataFormatParameter("SD [mg/l]",
new Column()
{
Name = "Error", ErrorStdDev = "Arithmetic Standard Deviation", Dimension = _massConcentrationDimension,
Unit = new UnitDescription("mg/l")
}),
new MetaDataFormatParameter("VenousBlood", "Organ", false),
new MetaDataFormatParameter("TestInputMolecule", "Molecule", false)
};
var parameterList =
createTestParameters("TestInputMolecule", new UnitDescription("h"), new UnitDescription("s"), _timeConcentrationDimension);
_importerConfiguration.CloneParametersFrom(parameterList);
}

[Observation]
public void should_throw_exception_when_trying_to_import()
public void should_throw_exception()
{
The.Action(() =>
sut.ImportFromConfiguration(_importerConfiguration, _metaDataCategories, _columnInfos, _dataImporterSettings,
Expand All @@ -388,38 +343,25 @@ public void should_throw_exception_when_trying_to_import()
}
}

public class When_importing_with_inconsistent_units_in_column : concern_for_DataImporter
public class When_importing_empty_metadata_columns : concern_for_DataImporter
{
protected override void Because()
{
var parameterList = new List<DataFormatParameter>
{
new MappingDataFormatParameter("time [h]",
new Column() {Name = "Time", Dimension = _dimensionFactory.Dimension("Time"), Unit = new UnitDescription("h")}),
new MappingDataFormatParameter("conc [mg/l]",
new Column()
{
Name = "Concentration", Dimension = _timeConcentrationDimension, Unit = new UnitDescription("s")
}),
new MappingDataFormatParameter("SD [mg/l]",
new Column()
{
Name = "Error", ErrorStdDev = "Arithmetic Standard Deviation", Dimension = _massConcentrationDimension,
Unit = new UnitDescription("mg/l")
}),
new MetaDataFormatParameter("VenousBlood", "Organ", false),
new MetaDataFormatParameter("TestInputMolecule", "Molecule", false)
};
var parameterList = createTestParameters("TestInputMolecule", new UnitDescription("h"), new UnitDescription("mg/l"),
_massConcentrationDimension);
parameterList.Add(new MetaDataFormatParameter("Dose", "Dose", true));
_importerConfiguration.CloneParametersFrom(parameterList);
}

[Observation]
public void should_throw_exception()
public void should_not_import_empty_metadata()
{
The.Action(() =>
sut.ImportFromConfiguration(_importerConfiguration, _metaDataCategories, _columnInfos, _dataImporterSettings,
getFileFullName(
"IntegrationSample1.xlsx"))).ShouldThrowAn<OSPSuiteException>();
var result = sut.ImportFromConfiguration(_importerConfiguration, _metaDataCategories, _columnInfos, _dataImporterSettings,
getFileFullName(
"IntegrationSample1.xlsx"));
result.First().ExtendedProperties.Contains("Dose").ShouldBeFalse();


}
}
}