private IEnumerable <string> predefinedValuesForCategory(Action <MetaDataCategory> action)
{
var category = new MetaDataCategory();
action(category);
return(category.ListOfValues.Values);
}
private void compoundNameCategory(MetaDataCategory nameCategory, Compound compound, bool canEditName)
{
if (nameCategory == null)
{
return;
}
nameCategory.IsListOfValuesFixed = !canEditName;
nameCategory.ListOfValues.Clear();
foreach (var existingCompound in _buildingBlockRepository.All <Compound>())
{
nameCategory.ListOfValues.Add(existingCompound.Name, existingCompound.MolWeight.ToString());
}
if (canEditName)
{
nameCategory.ListOfValues.Add(PKSimConstants.UI.Undefined, PKSimConstants.UI.Undefined);
}
if (compound != null)
{
nameCategory.DefaultValue = compound.Name;
nameCategory.SelectDefaultValue = true;
}
nameCategory.ShouldListOfValuesBeIncluded = true;
}
public IReadOnlyList <MetaDataCategory> DefaultMoBiMetaDataCategories()
{
var categories = new List <MetaDataCategory>();
var molWeightCategory = new MetaDataCategory
{
Name = "MolWeight",
DisplayName = "Molecular weight [Molecular weight]",
Description = "Molecular weight",
MetaDataType = typeof(double),
IsMandatory = false,
MinValue = 0,
MinValueAllowed = false
};
categories.Add(molWeightCategory);
var organCategory = createMetaDataCategory <string>(ObservedData.ORGAN, isMandatory: false, isListOfValuesFixed: true,
fixedValuesRetriever: addUndefinedValueTo);
categories.Add(organCategory);
var compartmentCategory = createMetaDataCategory <string>(ObservedData.COMPARTMENT, isMandatory: false, isListOfValuesFixed: true,
fixedValuesRetriever: addUndefinedValueTo);
categories.Add(compartmentCategory);
var moleculeCategory = createMetaDataCategory <string>(ObservedData.MOLECULE, isMandatory: false, isListOfValuesFixed: true,
fixedValuesRetriever: addUndefinedValueTo);
categories.Add(moleculeCategory);
return(categories);
}
private IEnumerable <string> predefinedValuesFor(Action <MetaDataCategory> predefinedValuesRetriever)
{
var category = new MetaDataCategory();
predefinedValuesRetriever(category);
return(category.ListOfValues.Values);
}
private void addPredefinedSpeciesValues(MetaDataCategory speciesCategory)
{
foreach (var species in _speciesRepository.All().OrderBy(x => x.Name))
{
addInfoToCategory(speciesCategory, species);
}
}
private MetaDataCategory compoundNameCategory(Compound compound, bool canEditName)
{
var nameCategory = new MetaDataCategory
{
Name = ObservedData.MOLECULE,
DisplayName = PKSimConstants.UI.Molecule,
Description = PKSimConstants.UI.MoleculeNameDescription,
MetaDataType = typeof(string),
IsListOfValuesFixed = !canEditName,
IsMandatory = true,
};
foreach (var existingCompound in _buildingBlockRepository.All <Compound>())
{
nameCategory.ListOfValues.Add(existingCompound.Name, existingCompound.Name);
}
if (canEditName)
{
nameCategory.ListOfValues.Add(PKSimConstants.UI.Undefined, PKSimConstants.UI.Undefined);
}
if (compound != null)
{
nameCategory.DefaultValue = compound.Name;
}
return(nameCategory);
}
private void addPredefinedMoleculeValues(MetaDataCategory moleculeCategory)
{
addUndefinedValueTo(moleculeCategory);
foreach (var existingCompound in _buildingBlockRepository.All <Compound>())
{
addInfoToCategory(moleculeCategory, existingCompound);
}
}
private void addPredefinedOrganValues(MetaDataCategory organCategory)
{
var defaultIndividual = _defaultIndividualRetriever.DefaultIndividual();
addUndefinedValueTo(organCategory);
foreach (var organ in defaultIndividual.Organism.OrgansByType(OrganType.PeripheralVenousBlood | OrganType.VascularSystem | OrganType.Tissue | OrganType.Lumen))
{
addInfoToCategory(organCategory, organ);
}
}
private void addPredefinedMoleculesForImporter(MetaDataCategory metaDataCategory)
{
if (metaDataCategory == null)
{
return;
}
metaDataCategory.ShouldListOfValuesBeIncluded = true;
allMolecules().OrderBy(molecule => molecule.Name).Each(molecule => addInfoToCategory(metaDataCategory, molecule));
}
private void addPredefinedGenderValues(MetaDataCategory genderMetaData)
{
addUndefinedValueTo(genderMetaData);
var defaultIndividual = _defaultIndividualRetriever.DefaultIndividual();
foreach (var gender in defaultIndividual.AvailableGenders())
{
addInfoToCategory(genderMetaData, gender);
}
}
private void addPredefinedCompartmentValues(MetaDataCategory metaDataCategory)
{
if (metaDataCategory == null)
{
return;
}
addUndefinedValueTo(metaDataCategory);
metaDataCategory.ShouldListOfValuesBeIncluded = true;
allCompartments().OrderBy(comp => comp.Name).Each(compartment => addInfoToCategory(metaDataCategory, compartment));
}
private void addInfoToCategory(MetaDataCategory metaDataCategory, IContainer container)
{
metaDataCategory.ListOfValues.Add(container.Name, container.Name);
var icon = ApplicationIcons.IconByName(container.Icon);
if (icon != ApplicationIcons.EmptyIcon)
{
metaDataCategory.ListOfImages.Add(container.Name, icon.IconName);
}
}
private void addPredefinedOrganValues(MetaDataCategory metaDataCategory)
{
if (metaDataCategory == null)
{
return;
}
addUndefinedValueTo(metaDataCategory);
metaDataCategory.ShouldListOfValuesBeIncluded = true;
allOrgans().OrderBy(org => org.Name).Each(organ => addInfoToCategory(metaDataCategory, organ));
}
private void addPredefinedOrganValues(MetaDataCategory organCategory)
{
var defaultIndividual = _defaultIndividualRetriever.DefaultIndividual();
var organism = defaultIndividual.Organism;
addUndefinedValueTo(organCategory);
addInfoToCategory(organCategory, organism.Organ(CoreConstants.Organ.PERIPHERAL_VENOUS_BLOOD));
foreach (var organ in organism.OrgansByType(OrganType.VascularSystem | OrganType.Tissue | OrganType.Lumen))
{
addInfoToCategory(organCategory, organ);
}
}
private void addPredefinedCompartmentValues(MetaDataCategory compCategory)
{
var defaultIndividual = _defaultIndividualRetriever.DefaultIndividual();
addUndefinedValueTo(compCategory);
foreach (var compartment in defaultIndividual.Organism.Organ(CoreConstants.Organ.Muscle).Compartments.Where(x => x.Visible))
{
addInfoToCategory(compCategory, compartment);
}
addInfoToCategory(compCategory, new Observer().WithName(CoreConstants.Observer.TISSUE));
addInfoToCategory(compCategory, new Observer().WithName(CoreConstants.Observer.INTERSTITIAL_UNBOUND));
addInfoToCategory(compCategory, new Observer().WithName(CoreConstants.Observer.INTRACELLULAR_UNBOUND));
addInfoToCategory(compCategory, new Observer().WithName(CoreConstants.Compartment.URINE));
addInfoToCategory(compCategory, new Observer().WithName(CoreConstants.Compartment.FECES));
}
private void speciesNameCategory(MetaDataCategory nameCategory)
{
if (nameCategory == null)
{
return;
}
nameCategory.ListOfValues.Clear();
foreach (var species in _speciesRepository.All().OrderBy(x => x.Name))
{
nameCategory.ListOfValues.Add(species.Name, species.Name);
}
nameCategory.ShouldListOfValuesBeIncluded = true;
}
private static MetaDataCategory createMetaDataCategory <T>(string descriptiveName, bool isMandatory = false, bool isListOfValuesFixed = false, Action <MetaDataCategory> fixedValuesRetriever = null)
{
var category = new MetaDataCategory
{
Name = descriptiveName,
DisplayName = descriptiveName,
Description = descriptiveName,
MetaDataType = typeof(T),
IsMandatory = isMandatory,
IsListOfValuesFixed = isListOfValuesFixed
};
fixedValuesRetriever?.Invoke(category);
return(category);
}
private void genderNameCategory(MetaDataCategory nameCategory)
{
if (nameCategory == null)
{
return;
}
nameCategory.ListOfValues.Clear();
var defaultIndividual = _defaultIndividualRetriever.DefaultIndividual();
foreach (var gender in defaultIndividual.AvailableGenders)
{
nameCategory.ListOfValues.Add(gender.Name, gender.Name);
}
nameCategory.ShouldListOfValuesBeIncluded = true;
}
private void addInfoToCategory(MetaDataCategory metaDataCategory, IObjectBase objectBase)
{
var info = _representationInfoRepository.InfoFor(objectBase);
if (info == null)
{
metaDataCategory.ListOfValues.Add(objectBase.Name, objectBase.Name);
return;
}
//only add with display name as information will be used in data repository as is
metaDataCategory.ListOfValues.Add(info.DisplayName, info.DisplayName);
var icon = ApplicationIcons.IconByName(info.IconName);
if (icon != ApplicationIcons.EmptyIcon)
{
metaDataCategory.ListOfImages.Add(info.DisplayName, icon);
}
}
private void organNameCategory(MetaDataCategory nameCategory)
{
if (nameCategory == null)
{
return;
}
nameCategory.ListOfValues.Clear();
var defaultIndividual = _defaultIndividualRetriever.DefaultIndividual();
var organism = defaultIndividual.Organism;
addInfoToCategory(nameCategory, organism.Organ(CoreConstants.Organ.PERIPHERAL_VENOUS_BLOOD));
foreach (var organ in organism.OrgansByType(OrganType.VascularSystem | OrganType.Tissue | OrganType.Lumen))
{
nameCategory.ListOfValues.Add(organ.Name, organ.Name);
}
nameCategory.ShouldListOfValuesBeIncluded = true;
}
private bool columnNameHasManualInput(ColumnMappingDTO model, MetaDataCategory metaDataCategory)
{
if (model.Source == null)
{
return(false);
}
var source = model.Source as MetaDataFormatParameter;
if (source.ColumnName == null)
{
return(false);
}
if (source.IsColumn)
{
return(false);
}
return(!metaDataCategory.ListOfValues.Keys.Union(availableColumns()).Contains(model.ExcelColumn));
}
private void compartmentNameCategory(MetaDataCategory nameCategory)
{
if (nameCategory == null)
{
return;
}
nameCategory.ListOfValues.Clear();
var defaultIndividual = _defaultIndividualRetriever.DefaultIndividual();
foreach (var compartment in defaultIndividual.Organism.Organ(CoreConstants.Organ.MUSCLE).Compartments.Where(x => x.Visible))
{
nameCategory.ListOfValues.Add(compartment.Name, compartment.Name);
}
nameCategory.ListOfValues.Add(CoreConstants.Observer.TISSUE, CoreConstants.Observer.TISSUE);
nameCategory.ListOfValues.Add(CoreConstants.Observer.INTERSTITIAL_UNBOUND, CoreConstants.Observer.INTERSTITIAL_UNBOUND);
nameCategory.ListOfValues.Add(CoreConstants.Observer.INTRACELLULAR_UNBOUND, CoreConstants.Observer.INTRACELLULAR_UNBOUND);
nameCategory.ListOfValues.Add(CoreConstants.Observer.WHOLE_BLOOD, CoreConstants.Observer.WHOLE_BLOOD);
nameCategory.ListOfValues.Add(CoreConstants.Compartment.URINE, CoreConstants.Compartment.URINE);
nameCategory.ListOfValues.Add(CoreConstants.Compartment.FECES, CoreConstants.Compartment.FECES);
nameCategory.ShouldListOfValuesBeIncluded = true;
}
private void addUndefinedValueTo(MetaDataCategory metaDataCategory)
{
metaDataCategory.ListOfValues.Add("Undefined", "Undefined");
}
private static StringBuilder formatPatternItem(StringBuilder sb, MetaDataCategory x, string token)
{
return(sb.Append(string.Format(token, x.Name)));
}
private static void addUndefinedValueTo(MetaDataCategory metaDataCategory)
{
metaDataCategory.ListOfValues.Add(PKSimConstants.UI.Undefined, PKSimConstants.UI.Undefined);
}
