protected override Task Context()
{
_containerTask = A.Fake <IContainerTask>();
_progressManager = A.Fake <IProgressManager>();
_individualCacheImporter = A.Fake <IIndividualPropertiesCacheImporter>();
_cloner = A.Fake <ICloner>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_advancedParameterFactory = A.Fake <IAdvancedParameterFactory>();
_createdPopulation = A.Fake <ImportPopulation>();
_individual = new Individual();
_cloneIndividual = new Individual();
A.CallTo(() => _cloner.Clone(_individual)).Returns(_cloneIndividual);
A.CallTo(() => _objectBaseFactory.Create <ImportPopulation>()).Returns(_createdPopulation);
A.CallTo(() => _createdPopulation.IndividualPropertiesCache).Returns(A.Fake <IndividualPropertiesCache>());
sut = new ImportPopulationFactory(_objectBaseFactory, _progressManager, _individualCacheImporter, _cloner, _containerTask, _advancedParameterFactory);
A.CallTo(() => _containerTask.CacheAllChildren <IParameter>(_cloneIndividual)).Returns(_allParameters);
A.CallTo(() => _containerTask.CacheAllChildrenSatisfying(_cloneIndividual, A <Func <IParameter, bool> > ._)).Returns(_allCreateIndividualParameters);
_popFile1 = A.Fake <IndividualPropertiesCache>();
_popFile2 = A.Fake <IndividualPropertiesCache>();
A.CallTo(() => _individualCacheImporter.ImportFrom(_file1, _allParameters, A <IImportLogger> ._)).Returns(_popFile1);
A.CallTo(() => _individualCacheImporter.ImportFrom(_file2, _allParameters, A <IImportLogger> ._)).Returns(_popFile2);
return(_completed);
}
protected override void Context()
{
base.Context();
_individualPropertiesCache = A.Fake <IndividualPropertiesCache>();
_patchCache = new PathCacheForSpecs <IParameter>();
var individualParameter = A.Fake <IParameter>();
A.CallTo(() => individualParameter.IsChangedByCreateIndividual).Returns(true);
_patchCache.Add("Path1", individualParameter);
var advancedParameter = A.Fake <IParameter>();
A.CallTo(() => advancedParameter.IsChangedByCreateIndividual).Returns(false);
advancedParameter.CanBeVariedInPopulation = true;
_patchCache.Add("PathAdvanced", advancedParameter);
A.CallTo(() => _individualPropertiesCache.AllParameterPaths()).Returns(new[] { "Path1", "Path2", "PathAdvanced" });
A.CallTo(() => _individualPropertiesCache.ParameterValuesFor("Path1")).Returns(_value1);
A.CallTo(() => _individualPropertiesCache.ParameterValuesFor("Path2")).Returns(_value2);
A.CallTo(() => _individualPropertiesCache.ParameterValuesFor("PathAdvanced")).Returns(_value3);
_populationSimulation = A.Fake <PopulationSimulation>();
_parameterValueCache = A.Fake <ParameterValuesCache>();
A.CallTo(() => _populationSimulation.ParameterValuesCache).Returns(_parameterValueCache);
_mobiPopulation = A.Fake <MoBiPopulation>();
A.CallTo(_simulationFactory).WithReturnType <PopulationSimulation>().Returns(_populationSimulation);
A.CallTo(() => _objectBaseFactory.Create <MoBiPopulation>()).Returns(_mobiPopulation);
A.CallTo(() => _individualPropertiesCacheImporter.ImportFrom(_populationFile, A <IImportLogger> ._)).Returns(_individualPropertiesCache);
A.CallTo(() => _parameterRetriever.ParametersFrom(_populationSimulation)).Returns(_patchCache);
_advancedParameterContainer = new AdvancedParameter();
A.CallTo(() => _advancedParameterFactory.Create(advancedParameter, DistributionTypes.Unknown)).Returns(_advancedParameterContainer);
}
private IndividualPropertiesCache createIndividualPropertiesFromCSV(CsvReader csv, string[] headers)
{
var individualPropertiesCache = new IndividualPropertiesCache();
//first create a cache of all possible values
var covariateCache = new Cache <string, List <string> >();
var parameterValues = new Cache <string, List <double> >();
int fieldCount = csv.FieldCount;
int indexIndividualId = 0;
for (int i = 0; i < headers.Length; i++)
{
var header = headers[i];
if (string.Equals(header, Constants.Population.INDIVIDUAL_ID_COLUMN))
{
indexIndividualId = i;
continue;
}
if (entryRepresentsParameter(header))
{
parameterValues[header] = new List <double>();
}
else
{
covariateCache[header] = new List <string>();
}
}
while (csv.ReadNextRecord())
{
for (int i = 0; i < fieldCount; i++)
{
if (i == indexIndividualId)
{
continue;
}
var header = headers[i];
if (parameterValues.Contains(header))
{
parameterValues[header].Add(csv.DoubleAt(i));
}
else
{
covariateCache[header].Add(csv[i]);
}
}
}
//now fill the property cache
addCovariates(individualPropertiesCache, covariateCache);
foreach (var parameterValue in parameterValues.KeyValues)
{
individualPropertiesCache.SetValues(parameterValue.Key, parameterValue.Value);
}
return(individualPropertiesCache);
}
private void ensureCovariatesAreDefined(IndividualPropertiesCache individualPropertiesCache)
{
//this should ensure that the covariates were defined for the population. If not, the file does not have the accurate structure
if (!individualPropertiesCache.AllCovariates.Any())
{
throw new PKSimException(PKSimConstants.Error.GenderAndOrPopulationMissingFromFile);
}
}
private void addCovariates(IndividualPropertiesCache individualPropertiesCache, string parameterPath, IEnumerable <double> values)
{
if (string.Equals(parameterPath, CoreConstants.Parameters.RACE_INDEX))
{
individualPropertiesCache.AddPopulations(values.Select(index => _populationRepository.FindByIndex((int)index)).ToList());
}
else if (string.Equals(parameterPath, CoreConstants.Parameters.GENDER))
{
individualPropertiesCache.AddGenders(values.Select(index => _genderRepository.FindByIndex((int)index)).ToList());
}
}
protected override void Context()
{
base.Context();
_individualPropertiesCache = new IndividualPropertiesCache();
_parameterValues = new ParameterValues("A|Path|With|Unit [l]");
_individualPropertiesCache.Add(_parameterValues);
A.CallTo(() => _individualCacheImporter.ImportFrom(_file1, A <IImportLogger> ._)).Returns(_individualPropertiesCache);
var pathCache = A.Fake <PathCache <IParameter> >();
A.CallTo(() => pathCache.Contains("A|Path|With|Unit")).Returns(true);
A.CallTo(() => _containerTask.CacheAllChildren <IParameter>(_cloneIndividual)).Returns(pathCache);
}
private void addCovariates(IndividualPropertiesCache individualPropertiesCache, Cache <string, List <string> > covariateCache)
{
foreach (var covariate in covariateCache.KeyValues)
{
if (covariate.Key.IsOneOf(CoreConstants.Parameters.RACE_INDEX, CoreConstants.Parameters.GENDER))
{
addCovariates(individualPropertiesCache, covariate.Key, covariate.Value.Select(x => double.Parse(x, NumberFormatInfo.InvariantInfo)));
}
else
{
individualPropertiesCache.AddConvariate(covariate.Key, covariate.Value);
}
}
}
private void removeUnits(IndividualPropertiesCache individualValues, ParameterValues parameterValue, PathCache <IParameter> allParameters)
{
var parameterPath = parameterValue.ParameterPath;
if (allParameters.Contains(parameterPath))
{
return;
}
var pathWithUnitsRemoved = importedPathWithUnitsRemoved(parameterPath);
if (allParameters.Contains(pathWithUnitsRemoved))
{
individualValues.RenamePath(parameterPath, pathWithUnitsRemoved);
parameterValue.ParameterPath = pathWithUnitsRemoved;
}
}
protected override void Context()
{
base.Context();
_originalValueCache = A.Fake <ParameterValuesCache>();
_parameterCache = A.Fake <PathCache <IParameter> >();
_cov1 = new IndividualCovariates();
_cov2 = new IndividualCovariates();
_cov3 = new IndividualCovariates();
_cov4 = new IndividualCovariates();
_cacheToMerge = A.Fake <ParameterValuesCache>();
_originalCovariates = new List <IndividualCovariates> {
_cov1, _cov2
};
_covariatesToMerge = new List <IndividualCovariates> {
_cov3, _cov4
};
sut = new IndividualPropertiesCache(_originalValueCache, _originalCovariates);
_individualPropertiesCacheToMerge = new IndividualPropertiesCache(_cacheToMerge, _covariatesToMerge);
}
private void loadOldCSVFormat(IndividualPropertiesCache individualPropertiesCache, CsvReader csv)
{
int fieldCount = csv.FieldCount;
while (csv.ReadNextRecord())
{
var parameterPath = csv[PARAMETER_PATH];
var values = getValuesFrom(csv, fieldCount);
if (entryRepresentsParameter(parameterPath))
{
ensureCovariatesAreDefined(individualPropertiesCache);
individualPropertiesCache.SetValues(parameterPath, values);
}
else
{
addCovariates(individualPropertiesCache, parameterPath, values);
}
}
}
protected override void Context()
{
_containerTask = A.Fake <IContainerTask>();
_progressManager = A.Fake <IProgressManager>();
_individualCacheImporter = A.Fake <IIndividualPropertiesCacheImporter>();
_cloner = A.Fake <ICloner>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_advancedParameterFactory = A.Fake <IAdvancedParameterFactory>();
_createdPopulation = A.Fake <ImportPopulation>();
_individual = new Individual();
_cloneIndividual = new Individual();
A.CallTo(() => _cloner.Clone(_individual)).Returns(_cloneIndividual);
A.CallTo(() => _objectBaseFactory.Create <ImportPopulation>()).Returns(_createdPopulation);
A.CallTo(() => _createdPopulation.IndividualPropertiesCache).Returns(A.Fake <IndividualPropertiesCache>());
sut = new ImportPopulationFactory(_objectBaseFactory, _progressManager, _individualCacheImporter, _cloner, _containerTask, _advancedParameterFactory);
_popFile1 = A.Fake <IndividualPropertiesCache>();
_popFile2 = A.Fake <IndividualPropertiesCache>();
A.CallTo(() => _individualCacheImporter.ImportFrom(_file1, A <IImportLogger> ._)).Returns(_popFile1);
A.CallTo(() => _individualCacheImporter.ImportFrom(_file2, A <IImportLogger> ._)).Returns(_popFile2);
}
private IndividualPropertiesCache individualPropertiesCacheFrom(string fileFullPath, IImportLogger logger, char delimiter)
{
var individualPropertiesCache = new IndividualPropertiesCache();
using (var reader = new CsvReaderDisposer(fileFullPath, delimiter))
{
var csv = reader.Csv;
var headers = csv.GetFieldHeaders();
if (headers.Contains(Constants.Population.INDIVIDUAL_ID_COLUMN))
{
loadNewCSVFormat(individualPropertiesCache, csv, headers);
}
else
{
loadOldCSVFormat(individualPropertiesCache, csv);
logger.AddWarning(PKSimConstants.Warning.PopulationFileIsUsingOldFormatAndWontBeSupportedInTheNextVersion);
}
}
return(individualPropertiesCache);
}
protected override void Because()
{
_results = sut.ImportFrom(DomainHelperForSpecs.PopulationFilePathFor("corrupt1"), _logger);
}
protected override void Because()
{
_results = sut.ImportFrom(DomainHelperForSpecs.PopulationFilePathFor("pop_10_semi_colon"), _logger);
}
protected override void Because()
{
_results = sut.ImportFrom(_fileName, _logger);
}
protected override void Because()
{
_results = sut.ImportFrom(DomainHelperForSpecs.PopulationFilePathFor("new_format_with_comment"), _logger);
}
private IndividualPropertiesCache withPathsContainingUnitsUpdated(IndividualPropertiesCache individualPropertiesCache, PathCache <IParameter> allParameters)
{
individualPropertiesCache.AllParameterValues.ToList().Each(parameterValue => { removeUnits(individualPropertiesCache, parameterValue, allParameters); });
return(individualPropertiesCache);
}
protected override void Because()
{
_results = sut.ImportFrom(DomainHelperForSpecs.PopulationFilePathFor("pop_10_old_format"), _allParameters, _logger);
}
protected override void Because()
{
_results = sut.ImportFrom(DomainHelperForSpecs.PopulationFilePathFor("path_with_units"), _allParameters, _logger);
}
