protected override void SetAddCommandDescription(TBuildingBlock newEntity, IMoBiProject parent, IMoBiCommand addCommand, MoBiMacroCommand macroCommand, IBuildingBlock buildingBlock)
{
addCommand.Description = AppConstants.Commands.AddToProjectDescription(addCommand.ObjectType, newEntity.Name);
macroCommand.Description = addCommand.Description;
}
public override IMoBiCommand GetRemoveCommand(TBuildingBlock objectToRemove, IMoBiProject parent,
IBuildingBlock buildingBlock)
{
return(new RemoveBuildingBlockCommand <TBuildingBlock>(objectToRemove));
}
public override IMoBiCommand GetAddCommand(TBuildingBlock itemToAdd, IMoBiProject parent,
IBuildingBlock buildingBlock)
{
return(new AddBuildingBlockCommand <TBuildingBlock>(itemToAdd));
}
private IParameter searchParamterInSpatialStructures(IObjectPath parameterPath, IParameterStartValuesBuildingBlock parent, IMoBiProject project)
{
IParameter parameter = searchParameterInContainers(parameterPath, project.SpatialStructureCollection.FirstOrDefault(ss => ss.Id.Equals(parent.SpatialStructureId)));
if (parameter == null)
{
foreach (var spatialStructure in project.SpatialStructureCollection)
{
parameter = searchParameterInContainers(parameterPath, spatialStructure);
if (parameter != null)
{
break;
}
}
}
return(parameter);
}
/// <summary>
/// Parses a SBML MathML expression into a MoBi Formula.
/// </summary>
/// <param name="rootNode"></param>
/// <param name="rootObjectId"> The id of the parent object of the rootNode to set the name of </param>
/// <param name="isRateRule"></param>
/// <param name="sbmlProject"></param>
/// <param name="sbmlInformation"></param>
public IFormula Parse(ASTNode rootNode, string rootObjectId, bool isRateRule, IMoBiProject sbmlProject,
SBMLInformation sbmlInformation)
{
try
{
_sbmlProject = sbmlProject;
_sbmlInformation = sbmlInformation;
_objectPaths.Clear();
_counter++;
var formulaString = Eval(rootNode);
if (string.IsNullOrEmpty(formulaString))
{
return(null);
}
var formula = _objectBaseFactory.Create <ExplicitFormula>()
.WithName(rootObjectId + _counter)
.WithFormulaString(formulaString);
if (isRateRule)
{
getObjectPathName(ObjectPath.PARENT_CONTAINER, rootObjectId);
}
foreach (var path in _objectPaths.Where(path => path != null))
{
formula.AddObjectPath(path);
}
if (string.IsNullOrEmpty(formula?.FormulaString))
{
createErrorMsg(rootNode);
return(null);
}
else
{
return(formula);
}
}
finally
{
_sbmlProject = null;
_sbmlInformation = null;
}
}
private IParameter searchParameterInMolecules(IParameterStartValue psv, IParameterStartValuesBuildingBlock parent, IMoBiProject project)
{
var parameterName = psv.Path.Last();
var tmpPath = psv.Path.Clone <IObjectPath>();
tmpPath.Remove(tmpPath.Last());
var moleculeName = tmpPath.Last();
var parameter = searchParameterInMoleculeBuildingBlock(project.MoleculeBlockCollection.FirstOrDefault(mb => mb.Id.Equals(parent.MoleculeBuildingBlockId)), moleculeName, parameterName);
foreach (var moleculeBuildingBlock in project.MoleculeBlockCollection)
{
parameter = searchParameterInMoleculeBuildingBlock(moleculeBuildingBlock, moleculeName, parameterName);
if (parameter != null)
{
break;
}
}
return(parameter);
}
private IParameter searchParamterInSpatialStructures(IParameterStartValue psv, IParameterStartValuesBuildingBlock parent, IMoBiProject project)
{
var parameterPath = psv.Path;
IParameter parameter = searchParamterInSpatialStructures(parameterPath, parent, project);
if (parameter == null)
{
parameterPath = psv.Path.Clone <IObjectPath>();
var parameterName = parameterPath.Last();
parameterPath.Remove(parameterName);
var tmp = parameterPath.Last();
parameterPath.Remove(tmp);
parameterPath.Add(Constants.MOLECULE_PROPERTIES);
parameterPath.Add(parameterName);
parameter = searchParamterInSpatialStructures(parameterPath, parent, project);
}
return(parameter);
}
private IParameter searchParameterInSimulations(IParameterStartValue psv, IParameterStartValuesBuildingBlock parent, IMoBiProject project)
{
IParameter parameter = null;
var simulations = project.Simulations.Where(sim => usesParameterStartValuesBB(sim, parent));
foreach (var simulation in simulations)
{
parameter = psv.Path.TryResolve <IParameter>(simulation.Model.Root);
if (parameter != null)
{
break;
}
}
return(parameter);
}
public IDimension GetDimensionFor(IParameterStartValue psv, IParameterStartValuesBuildingBlock parameterStartValuesBuildingBlock, IMoBiProject project)
{
if (project == null)
{
return(null);
}
var parameter =
searchParameterInSimulations(psv, parameterStartValuesBuildingBlock, project) ??
searchParamterInSpatialStructures(psv, parameterStartValuesBuildingBlock, project) ??
searchParameterInMolecules(psv, parameterStartValuesBuildingBlock, project);
return(parameter == null ? null : parameter.Dimension);
}
public override void GlobalContext()
{
base.GlobalContext();
_project = LoadProject("SimpleProject_341");
_simulation = _project.Simulations.First();
}
private void addToProject(IMoBiProject project)
{
project.AddBuildingBlock(_buildingBlock);
}
public override ISimulationSettings CreateNewEntity(IMoBiProject moleculeBuildingBlock)
{
return(_simulationSettingsFactory.CreateDefault());
}
public (int convertedToVersion, bool conversionHappened) ConvertXml(XElement element, IMoBiProject project)
{
return(_coreConverter.ConvertXml(element));
}
public (int convertedToVersion, bool conversionHappened) Convert(object objectToUpdate, IMoBiProject project)
{
return(_coreConverter.Convert(objectToUpdate));
}
