private async Task updateExpression(Molecule snapshot, ExpressionContainerMapperContext context)
{
await _expressionContainerMapper.MapToModels(snapshot.Expression, context);
//once expression have been set, we need to update normalized parameter
var normalizeExpressionCommand = new NormalizeRelativeExpressionCommand(context.Molecule, _executionContext);
normalizeExpressionCommand.Execute(_executionContext);
}
public override async Task <ModelExpressionProfile> MapToModel(SnapshotExpressionProfile snapshot, SnapshotContext snapshotContext)
{
var expressionProfile = _expressionProfileFactory.Create(snapshot.Type, snapshot.Species, snapshot.Molecule);
expressionProfile.Description = snapshot.Description;
expressionProfile.Category = snapshot.Category;
var(molecule, individual) = expressionProfile;
//Update molecule properties first
updateMoleculePropertiesToMolecule(molecule, snapshot, individual, snapshotContext);
//Then override all parameters that were set
await _parameterMapper.MapLocalizedParameters(snapshot.Parameters, individual, snapshotContext, !snapshotContext.IsV9FormatOrEarlier);
var snapshotWithSubjectContext = new SnapshotContextWithSubject(individual, snapshotContext);
var ontogeny = await _ontogenyMapper.MapToModel(snapshot.Ontogeny, snapshotWithSubjectContext);
_ontogenyTask.SetOntogenyForMolecule(molecule, ontogeny, individual);
var context = new ExpressionContainerMapperContext(snapshotContext)
{
Molecule = molecule,
ExpressionParameters = individual.AllExpressionParametersFor(molecule),
MoleculeExpressionContainers = individual.AllMoleculeContainersFor(molecule),
};
await _expressionContainerMapper.MapToModels(snapshot.Expression, context);
//We need to normalize relative expressions when loading from old format
if (snapshotContext.IsV9FormatOrEarlier)
{
//Make sure we load the default parameters from db just in case we were dealing with a standard molecule
_moleculeParameterTask.SetDefaultMoleculeParameters(molecule);
//Global parameters were saved directly under the snapshot parameter
await updateGlobalMoleculeParameters(snapshot, molecule, snapshotContext);
NormalizeRelativeExpressionCommand.NormalizeExpressions(individual, molecule);
}
return(expressionProfile);
}
private void convertMolecule(IndividualMolecule moleculeToConvert, Individual individual)
{
//Complete reorganization of molecules in the new version. We need to update value of relative expression.
//We know that localization was already updated during xml conversion
var factory = _individualMoleculeFactoryResolver.FactoryFor(moleculeToConvert);
//Remove from individual so that we can add it again.
individual.RemoveMolecule(moleculeToConvert);
//New molecules is added. We need to update all global parameters as well as relative expression parameters
var newMolecule = factory.AddMoleculeTo(individual, moleculeToConvert.Name);
if (newMolecule == null)
{
return;
}
newMolecule.Ontogeny = moleculeToConvert.Ontogeny;
var allExpressionParameters = individual.AllExpressionParametersFor(newMolecule);
moleculeToConvert.GetAllChildren <MoleculeExpressionContainer>().Each(x => { convertParameter(x.RelativeExpressionParameter, allExpressionParameters[x.Name]); });
moleculeToConvert.AllParameters().Each(p => convertParameter(p, newMolecule.Parameter(p.Name)));
//Perform normalization
NormalizeRelativeExpressionCommand.NormalizeExpressions(individual, newMolecule);
//Do reset default value that may be set to 0
allExpressionParameters.Each(x => x.DefaultValue = null);
//molecule specific conversion
convertIndividualProtein(moleculeToConvert, newMolecule, individual);
convertIndividualTransporter(moleculeToConvert, newMolecule, individual);
}
