/// <summary>
/// Gets a dimension unit string in a data row. Indicate which row contains the unit
/// </summary>
/// <param name="rowIndex">The index of the row being converted</param>
/// <param name="unitColumn">The index of the column containing the unit</param>
/// <param name="dimensionColumn">The index of the column containing the dimension</param>
/// <param name="table">The table containing the row</param>
/// <returns>A dimension corresponding to the unit given</returns>
protected IDimension GetDimension(DataTable table, int rowIndex, int unitColumn, int dimensionColumn)
{
var row = table.Rows[rowIndex];
var unitName = row[unitColumn].ToString();
var dimension = _dimensionFactory.DimensionForUnit(unitName);
if (dimension == null)
{
throw new ImportQuantityDTOsFromDataTablesMapperException(row, rowIndex,
AppConstants.Exceptions.CouldNotFindDimensionFromUnits(unitName));
}
if (table.Columns.Count <= dimensionColumn)
{
return(dimension);
}
//now we may have a dimension specified
var dimensionName = row[dimensionColumn].ToString();
if (string.IsNullOrEmpty(dimensionName))
{
return(dimension);
}
if (!_dimensionFactory.Has(dimensionName))
{
throw new ImportQuantityDTOsFromDataTablesMapperException(row, rowIndex,
AppConstants.Exceptions.CouldNotFindDimension(dimensionName));
}
return(_dimensionFactory.Dimension(dimensionName));
}
protected void CreateDimensionFactory()
{
_concentrationDimension = new Dimension();
_concentrationDimension.AddUnit("mol", 1.0, 0);
_volumeDimension = new Dimension();
_volumeDimension.AddUnit("ml", 0.001, 0);
_timeDimension = new Dimension();
_timeDimension.AddUnit("s", 1 / 60.0, 0);
_dimensionFactory = A.Fake <IMoBiDimensionFactory>();
A.CallTo(() => _dimensionFactory.DimensionForUnit("mol")).Returns(_concentrationDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("ml")).Returns(_volumeDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("s")).Returns(_timeDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("r/h")).Returns(null);
A.CallTo(() => _dimensionFactory.DimensionForUnit("")).Throws <Exception>();
}
/// <summary>
/// Converts a SBML UnitDefinition into a MoBi Unit.
/// </summary>
public IDimension ConvertUnit(UnitDefinition unitDefinition)
{
var sbmlUnit = unitDefinition.getId();
var dimension = _moBiDimensionFactory.TryGetDimensionCaseInsensitive(sbmlUnit);
if (dimension != Constants.Dimension.NO_DIMENSION)
{
_sbmlInformation.MobiDimension[sbmlUnit] = dimension;
return(dimension);
}
var newFactor = 1.0;
var unitsList = new List <Unit>();
var brList = new List <BaseDimensionRepresentation>();
for (long i = 0; i < unitDefinition.getNumUnits(); i++)
{
var mobiUnit = SBMLBaseUnitToMoBi(unitDefinition.getUnit(i));
if (mobiUnit == null)
{
continue;
}
var unitDimension = _moBiDimensionFactory.DimensionForUnit(mobiUnit.Name);
var unitBr = unitDimension.BaseRepresentation;
unitBr = SetExponents(unitDefinition, unitBr, i);
brList.Add(unitBr);
if (Math.Abs(newFactor) < 0.0001)
{
newFactor = unitDefinition.getUnit(i).getMultiplier() * Math.Pow(10, unitDefinition.getUnit(i).getScale()) * Math.Pow(mobiUnit.Factor, unitDefinition.getUnit(i).getExponent());
}
else
{
newFactor = newFactor * unitDefinition.getUnit(i).getMultiplier() * Math.Pow(10, unitDefinition.getUnit(i).getScale()) * Math.Pow(mobiUnit.Factor, unitDefinition.getUnit(i).getExponent());
}
unitsList.Add(mobiUnit);
}
var baseDimensionRepresentation = CreateBaseDimRepresentationExponents(brList);
IDimension newDim = new Dimension(baseDimensionRepresentation, String.Format("SBML_{0}", unitDefinition.getId()), String.Format("SBML_{0}_BaseUnit", unitDefinition.getId()));
var newBaseUnit = newDim.BaseUnit;
newBaseUnit.Visible = false;
var newUnit = new Unit(unitDefinition.getId(), newFactor, 0);
newDim.AddUnit(newUnit);
newDim.DefaultUnit = newUnit;
_sbmlInformation.MobiDimension[sbmlUnit] = newDim;
if (_moBiDimensionFactory.Dimensions.All(dim => dim.Name != newDim.Name))
{
_moBiDimensionFactory.AddDimension(newDim);
}
return(newDim);
}
/// <summary>
/// Gets a dimension unit string in a data row. Indicate which row contains the unit
/// </summary>
/// <param name="rowIndex">The index of the row being converted</param>
/// <param name="columnIndex">The index of the column containing the unit</param>
/// <param name="table">The table containing the row</param>
/// <returns>A dimension corresponding to the unit given</returns>
protected IDimension GetDimension(DataTable table, int rowIndex, int columnIndex)
{
var row = table.Rows[rowIndex];
var dimension = _dimensionFactory.DimensionForUnit(row[columnIndex].ToString());
if (dimension == null)
{
throw new ImportQuantityDTOsFromDataTablesMapperException(row, rowIndex, AppConstants.Exceptions.CouldNotFindDimensionFromUnits(row[columnIndex].ToString()));
}
return(dimension);
}
protected void CreateDimensionFactory()
{
BaseDimensionRepresentation baseRepresentation = new BaseDimensionRepresentation();
_concentrationDimension = new Dimension(baseRepresentation, "Concentration", "mol");
_volumeDimension = new Dimension(baseRepresentation, "Volume", "l");
_volumeDimension.AddUnit("ml", 0.001, 0);
_timeDimension = new Dimension(baseRepresentation, "Time", "min");
_timeDimension.AddUnit("s", 1 / 60.0, 0);
_inversedTime = new Dimension(baseRepresentation, "Inversed time", "1/min");
_becquerel = new Dimension(baseRepresentation, "Becquerel", "1/min");
_dimensionFactory = A.Fake <IMoBiDimensionFactory>();
A.CallTo(() => _dimensionFactory.DimensionForUnit("mol")).Returns(_concentrationDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("ml")).Returns(_volumeDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("s")).Returns(_timeDimension);
A.CallTo(() => _dimensionFactory.DimensionForUnit("1/min")).Returns(_inversedTime);
A.CallTo(() => _dimensionFactory.Has(_inversedTime.Name)).Returns(true);
A.CallTo(() => _dimensionFactory.Has(_becquerel.Name)).Returns(true);
A.CallTo(() => _dimensionFactory.DimensionForUnit("r/h")).Returns(null);
A.CallTo(() => _dimensionFactory.DimensionForUnit("")).Throws <Exception>();
A.CallTo(() => _dimensionFactory.Dimension(_becquerel.Name)).Returns(_becquerel);
A.CallTo(() => _dimensionFactory.Dimension(_inversedTime.Name)).Returns(_inversedTime);
}