public DataExportObject GetQueryResult(Guid combinedQueryId)
{
var combinedQuery = _combinedQueryRepository.Get(combinedQueryId);
var queryResult = new DataExportObject();
var projectId = combinedQuery.ProjectId;
//TODO: the list of included proerties should reflect the selected subject properties
//IE if StudyArm is selected as a field, then include it, if CollectionStudyDay is included, then include it ...etc
//INSTEAD OF INCLUDING ALL PROPERTIES WHICH WOOULD MAKE THE QUERY REALLY SLOW
queryResult.Subjects = _subjectRepository.FindAll(
s => s.Study.ProjectId == projectId,
new List <string>()
{
"StudyArm", "Study", "SubjectCharacteristics.CharacteristicFeature"
}).ToList();
//QUERY FOR CLINICAL OBSERVATIONS
_getObservations(combinedQuery, ref queryResult);
//QUERY FOR SUBJECT CHARACTERISITIC (e.g. AGE)
foreach (var subjCharQuery in combinedQuery.SubjectCharacteristics)
{
var characteristics = _subjectCharacteristicRepository.FindAll(
sc =>
sc.Subject.Study.ProjectId == projectId &&
subjCharQuery.QueryWhereValue == sc.CharacteristicFeatureId.ToString(),
new List <string>()
{
"Subject"
}).ToList();
//APPLY FILTERING IF FILTER PRESENT
if (characteristics.Any() && subjCharQuery.IsFiltered)
{
characteristics = (subjCharQuery.DataType == "string")
? characteristics.FindAll(sc => subjCharQuery.FilterExactValues.Contains(sc.VerbatimValue))
: characteristics.FindAll(sc =>
int.Parse(sc.VerbatimValue) >= subjCharQuery.FilterRangeFrom &&
int.Parse(sc.VerbatimValue) <= subjCharQuery.FilterRangeTo);
}
//ADD TO EXPORT DATA
queryResult.SubjChars.AddRange(characteristics);
}
//IF A REQUESTED OBSERVATION HAS LONGITUDINAL DATA, AUTOMATICALLY ADD A TIMING COLUMN (ASSUMING VISIT AS DEFAULT FOR NOW) SHOULD BE LATER DECIDED BASED ON O3
if (queryResult.HasLongitudinalData)
{
combinedQuery.DesignElements.Add(new Query()
{
QueryFor = nameof(Visit)
});
}
foreach (var deQuery in combinedQuery.DesignElements)
{
switch (deQuery.QueryFor)
{
case nameof(HumanSubject.StudyArm):
if (deQuery.IsFiltered)
{
queryResult.Arms = _armRepository.FindAll(
a => a.Studies.Select(s => s.Study).All(s => s.ProjectId == projectId) &&
deQuery.FilterExactValues.Contains(a.Name)).ToList();
}
else
{
queryResult.Arms = _armRepository.FindAll(
a => a.Studies.Select(s => s.Study.ProjectId).Contains(projectId)).ToList();
}
break;
case nameof(HumanSubject.Study):
if (deQuery.IsFiltered)
{
queryResult.Studies = _studyRepository.FindAll(
s => s.ProjectId == projectId &&
deQuery.FilterExactValues.Contains(s.Name),
new List <string>()
{
"Subjects"
}).ToList();
}
else
{
queryResult.Studies = _studyRepository.FindAll(s => s.ProjectId == projectId).ToList();
}
break;
case nameof(Visit):
var visits = _visitRepository.FindAll(
v => v.Study.ProjectId == projectId
//apply filter if present
).ToList();
queryResult.Visits = visits;
break;
}
}
//FOR NOW SHOULD NOT BE ALLOWED UNLESS WE DECIDED TO PROPAGATE ALL ASSAY SPECIFIC FILTERS TO ALL ASSAYS IN THE COMBINED QUERY
//if (combinedQuery.AssayPanels.Any() && combinedQuery.AssayPanels.Count > 1)
// return null;
var apQuery = combinedQuery.AssayPanels.FirstOrDefault();
if (apQuery != null)
{
//TODO:BRING BACK COLLECTIONSTUDYDAY
var assaySamples =
_biosampleRepository.FindAll(s => s.AssayId == apQuery.AssayId,
new List <string>()
{
"Subject", "SampleCharacteristics.CharacteristicFeature", "CollectionStudyDay"
}).ToList();
queryResult.Samples = assaySamples;
//HOW DO I FILTER THE SAMPLES BY THE QUERED PROPERTIES?
//HOW DO I filter samples by collectionStudyDay?
//TODO: TEMP SOLUTION FOR COLLECTION STUDY DAY
//foreach (var sampleQuery in apQuery.SampleQueries.Where(sq=>sq.QueryFor != nameof(Biosample.SampleCharacteristics)))
//{
// assaySamples.FindAll(b =>
// int.Parse(b.GetType().GetProperty("CollectionStudyDay").GetValue(b).properyObj?.GetType().GetProperty(query.QuerySelectProperty)?.GetValue(properyObj)?.ToString().ToString()) >= sampleQuery.FilterRangeFrom &&
// int.Parse(b.GetType().GetProperty("CollectionStudyDay").GetValue(b).ToString()) <= sampleQuery.FilterRangeTo
// );
//}
if (apQuery.SampleQueries.Exists(sq => sq.QueryFor == nameof(Biosample.CollectionStudyDay)))
{
var dayQuery = apQuery.SampleQueries.Find(sq => sq.QueryFor == nameof(Biosample.CollectionStudyDay));
if (dayQuery.IsFiltered)
{
queryResult.Samples = assaySamples.FindAll(
s =>
s.CollectionStudyDay?.Number != null &&
dayQuery.FilterExactValues.Contains(s.CollectionStudyDay?.Number.Value.ToString()));
}
}
//QUERY AND FILTER SAMPLE CHARACTERISTICS
foreach (var sampleQuery in apQuery.SampleQueries.Where(sq => sq.QueryFor == nameof(Biosample.SampleCharacteristics)))
{
var characteristics = _sampleCharacteristicRepository.FindAll(
sc =>
sc.Sample.Study.ProjectId == projectId &&
sampleQuery.QueryWhereValue == sc.CharacteristicFeatureId.ToString(),
new List <string>()
{
"Sample"
}).ToList();
//APPLY FILTERING IF FILTER PRESENT
if (characteristics.Any() && sampleQuery.IsFiltered)
{
characteristics = (sampleQuery.DataType == "string")
? characteristics.FindAll(sc => sampleQuery.FilterExactValues.Contains(sc.VerbatimValue))
: characteristics.FindAll(sc =>
int.Parse(sc.VerbatimValue) >= sampleQuery.FilterRangeFrom &&
int.Parse(sc.VerbatimValue) <= sampleQuery.FilterRangeTo);
}
//ADD TO EXPORT DATA
queryResult.SampleCharacteristics.AddRange(characteristics);
}
}
queryResult.FilterAndJoin();
return(queryResult);
}
