public async Task <bool> LoadBioSamples(Dataset dataset, int fileId, bool reload)
{
var descriptor = SdtmSampleDescriptor.GetSdtmSampleDescriptor(dataset);
List <SdtmRow> sampleData = await _sdtmRepository.FindAllAsync(
dm => dm.DatasetId.Equals(dataset.Id) && dm.DatafileId.Equals(fileId));
if (sampleData.Count == 0)
{
return(false);
}
var projectId = sampleData.First().ProjectId;
var projectAccession = sampleData.First().ProjectAccession;
var assayId = sampleData.First().ActivityId;
var datasetId = sampleData.First().DatasetId;
var datafileId = sampleData.First().DatafileId;
if (projectId == 0 || assayId == 0)
{
return(false);
}
var assay = _assayRepository.Get(assayId);
if (reload)
{
_bioSampleRepository.DeleteMany(o => o.DatasetId == datasetId && o.DataFileId == datafileId);
_dataContext.Save().Equals("CREATED");
}
var studyMap = new Dictionary <string, int>();
//RETRIEVE PREVIOUSLY LOADED CHARACTERISTIC FEATURES FOR THIS ASSAY THAT MIGHT HAVE BEEN LOADED BEFORE FOR OTHER STUDIES
var featureList = _characteristicObjRepository.FindAll(s => s.ProjectId == projectId && s.ActivityId == assayId).ToList();
_featureMap = featureList.ToDictionary(co => co.ShortName);
var subjects = _subjectRepository.FindAll(s => s.Study.ProjectId == projectId).ToList();
var sampleDayMap = new Dictionary <string, int>();
foreach (var sdtmRow in sampleData)
{
//RETRIEVE STUDYID FROM DB AND STORE IN MAP LOCALLY TO AVOID MAKING TOO MANY DB CALLS
int studyid;
if (!studyMap.TryGetValue(sdtmRow.StudyId, out studyid))
{
var study = _studyRepository.FindSingle(s => s.Name == sdtmRow.StudyId && s.ProjectId == projectId);
studyMap.Add(sdtmRow.StudyId, study.Id);
studyid = study.Id;
}
/**
* ADDING BIOSAMPLE
*/
var bioSample = new Biosample()
{
BiosampleStudyId = sdtmRow.SampleId,
AssayId = sdtmRow.ActivityId,
SubjectId = subjects.Find(s => s.UniqueSubjectId == sdtmRow.USubjId)?.Id,
StudyId = studyid,
CollectionStudyDay = sdtmRow.CollectionStudyDay,
DatasetId = sdtmRow.DatasetId,
DataFileId = sdtmRow.DatafileId,
IsBaseline = sdtmRow.Qualifiers != null && descriptor.IsBaseLineVariable != null && (sdtmRow.Qualifiers.ContainsKey(descriptor.IsBaseLineVariable?.Name) && sdtmRow.Qualifiers[descriptor.IsBaseLineVariable?.Name] == "Y")
};
//CHECK IF ASSAY HAS TEMOPORALDATA
if (bioSample.CollectionStudyDay?.Number != null && !assay.HasTemporalData)
{
if (sampleDayMap.ContainsKey(bioSample.SubjectId) &&
sampleDayMap[bioSample.SubjectId] != bioSample.CollectionStudyDay.Number.Value &&
!assay.HasTemporalData)
{
assay.HasTemporalData = true;
}
else
{
if (!sampleDayMap.ContainsKey(bioSample.SubjectId))
{
sampleDayMap.Add(bioSample.SubjectId, bioSample.CollectionStudyDay.Number.Value);
}
}
}
//ADD CHARACTERISTIC FEATURE IN BSTEST
string charValue;
var characValueVariable = descriptor.GetValueVariable(sdtmRow);
if (characValueVariable != null && sdtmRow.ResultQualifiers.TryGetValue(characValueVariable.Name, out charValue))
{
var charFeature = getCharacteristicFeature(sdtmRow.Topic, sdtmRow.TopicSynonym, characValueVariable.DataType);
charFeature.ActivityId = assayId;
charFeature.ProjectId = projectId;
bioSample.SampleCharacteristics.Add(new SampleCharacteristic()
{
CharacteristicFeature = charFeature,
VerbatimName = sdtmRow.TopicSynonym,
VerbatimValue = charValue,
DatafileId = datafileId,
DatasetId = datasetId
});
}
//ADDING SPECIMEN TYPE TO CHARACTERISTICS
string st;
if (descriptor.SpecimenTypeVariable != null && sdtmRow.Qualifiers.TryGetValue(descriptor.SpecimenTypeVariable.Name, out st))
{
var feature = getCharacteristicFeature(descriptor.SpecimenTypeVariable.Name, descriptor.SpecimenTypeVariable.Label,
descriptor.SpecimenTypeVariable.DataType);
feature.ActivityId = assayId;
feature.ProjectId = projectId;
bioSample.SampleCharacteristics.Add(new SampleCharacteristic()
{
CharacteristicFeature = feature,
VerbatimName = descriptor.SpecimenTypeVariable?.Name,
VerbatimValue = st,
DatafileId = datafileId,
DatasetId = datasetId
});
}
//ADD ANATOMIC REGION TO CHARACTERISTICS
if (descriptor.AnatomicRegionVariable != null && sdtmRow.QualifierQualifiers.TryGetValue(descriptor.AnatomicRegionVariable.Name, out st))
{
var feature = getCharacteristicFeature(descriptor.AnatomicRegionVariable.Name, descriptor.AnatomicRegionVariable.Label,
descriptor.AnatomicRegionVariable.DataType);
feature.ActivityId = assayId;
feature.ProjectId = projectId;
bioSample.SampleCharacteristics.Add(new SampleCharacteristic()
{
CharacteristicFeature = feature,
VerbatimName = descriptor.AnatomicRegionVariable.Name,
VerbatimValue = st,
DatafileId = datafileId,
DatasetId = datasetId
});
}
_bioSampleRepository.Insert(bioSample);
_assayRepository.Update(assay);
}
return(_dataContext.Save().Equals("CREATED"));
}
public bool LoadBioSamples(List <SdtmRow> sampleData, int datasetId)
{
var dataset = _datasetRepository.FindSingle(d => d.Id.Equals(datasetId), new List <string>()
{
"Variables.VariableDefinition"
});
var studyMap = new Dictionary <string, int>();
var scoList = _characteristicObjRepository.FindAll(s => s.ProjectId.Equals(dataset.Activity.ProjectId)).ToList();
var scos = scoList.ToDictionary(co => co.ShortName);
foreach (SdtmRow sdtmEntity in sampleData)
{
Study study;
int studyid;
if (!studyMap.TryGetValue(sdtmEntity.StudyId, out studyid))
{
study = _studyRepository.FindSingle(s => s.Name.Equals(sdtmEntity.StudyId));
studyMap.Add(sdtmEntity.StudyId, study.Id);
studyid = study.Id;
}
/**
* ADDING BIOSAMPLE
*/
var bioSample = new Biosample()
{
BiosampleStudyId = sdtmEntity.SampleId,
AssayId = sdtmEntity.ActivityId,
SubjectId = sdtmEntity.USubjId,
StudyId = studyid,
//Visit = sdtmEntity.Visit,
//CollectionStudyDay = sdtmEntity.CollectionStudyDay,
DatasetId = sdtmEntity.DatasetId,
IsBaseline = sdtmEntity.BaseLineFlag
};
/**
* ADDING SAMPLE CHARACTERISTICS
*/
foreach (var resqualifier in sdtmEntity.ResultQualifiers)
{
var dsVar = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name.Equals(resqualifier.Key));
if (dsVar != null)
{
CharacteristicFeature sco;
scos.TryGetValue(sdtmEntity.Topic, out sco);
if (sco == null)
{
/**
* CREATING NEW CHARACTERISTIC OBJECT
*/
sco = new CharacteristicFeature()
{
ShortName = sdtmEntity.Topic, //characteristicVar.VariableDefinition.Name,
FullName = sdtmEntity.TopicSynonym, //characteristicVar.VariableDefinition.Label,
Domain = "BS",
ProjectId = dataset.Activity.ProjectId,
//DataType = dsVar.VariableDefinition.DataType
};
scos.Add(sdtmEntity.Topic, sco);
}
bioSample.SampleCharacteristics.Add(new SampleCharacteristic()
{
// DatasetVariable = dsVar,
CharacteristicFeature = sco,
VerbatimName = sdtmEntity.TopicSynonym,
VerbatimValue = resqualifier.Value,
//DatasetDomainCode = sdtmEntity.DomainCode
});
}
}
foreach (var qualifier in sdtmEntity.Qualifiers)
{
var dsVar = dataset.Variables.SingleOrDefault(v => v.VariableDefinition.Name.Equals(qualifier.Key));
if (dsVar != null)
{
CharacteristicFeature sco;
scos.TryGetValue(qualifier.Key, out sco);
if (sco == null)
{
/**
* CREATING NEW CHARACTERISTIC OBJECT
*/
sco = new CharacteristicFeature()
{
ShortName = dsVar.VariableDefinition.Name,
FullName = dsVar.VariableDefinition.Label,
Domain = "BS",
ProjectId = dataset.Activity.ProjectId,
//DataType = dsVar.VariableDefinition.DataType
};
scos.Add(dsVar.VariableDefinition.Name, sco);
}
bioSample.SampleCharacteristics.Add(new SampleCharacteristic()
{
VerbatimName = qualifier.Key,
VerbatimValue = qualifier.Value,
//DatasetDomainCode = sdtmEntity.DomainCode,
//DatasetVariable =dsVar,
CharacteristicFeature = sco,
});
}
}
_bioSampleRepository.Insert(bioSample);
}
return(_dataContext.Save().Equals("CREATED"));
}
