private CharacteristicFeature getCharacteristicFeature(string sname, string fname, string dataType)
{
// FETCH PREVIOUSLY LOADED CHARACTERISTIC FEATURE
CharacteristicFeature feature;
_featureMap.TryGetValue(sname, out feature);
if (feature == null)
{
/**
* CREATING NEW CHARACTERISTIC OBJECT
*/
feature = new CharacteristicFeature()
{
ShortName = sname,
FullName = fname,
Domain = "BS",
DataType = dataType
};
_featureMap.Add(sname, feature);
}
return(feature);
}
public async Task <bool> LoadSubjects(Dataset dataset, int fileId, bool reload)
{
var descriptor = SdtmSubjectDescriptor.GetSdtmSubjectDescriptor(dataset);
List <SdtmRow> sdtmData = await _sdtmRepository.FindAllAsync(
dm => dm.DatasetId.Equals(dataset.Id) && dm.DatafileId.Equals(fileId));
if (sdtmData.Count == 0)
{
return(false);
}
var projectId = sdtmData.First().ProjectId;
var projectAccession = sdtmData.First().ProjectAccession;
var activityId = sdtmData.First().ActivityId;
var datafileId = sdtmData.First().DatafileId;
if (reload)
{
_subjectRepository.DeleteMany(o => o.DatasetId == dataset.Id && o.DatafileId == datafileId);
_dataContext.Save().Equals("CREATED");
}
//Project related subject characteristics
var scoList = _characteristicObjRepository.FindAll(s => s.ProjectId == projectId).ToList();
var scos = scoList.ToDictionary(co => co.ShortName);
//Project related studies
var studies = _studtRepository.FindAll(s => s.ProjectId == projectId, new List <string> {
"Arms.Arm"
}).ToList();
var studyMap = studies.ToDictionary(study => study.Name);
//Project related arms
var arms = studies.SelectMany(s => s.Arms.Select(a => a.Arm)).Distinct();
var armMap = arms.ToDictionary(arm => arm.Name);
//Previously loaded subjects for this project that might be update by this load
//TODO: should I add datafileId to subject as well? to be able to delete subjects for this datafile
var subjects = _subjectRepository.FindAll(s => s.Study.ProjectId == projectId).ToList();
foreach (var sdtmSubject in sdtmData)
{
Study study;
if (!studyMap.TryGetValue(sdtmSubject.StudyId, out study))
{
study = new Study()
{
Name = sdtmSubject.StudyId,
Accession = "S-" + projectAccession.Substring(2) + "-" + (studies.Count() + 1).ToString("00"),
ProjectId = projectId
}; studyMap.Add(study.Name, study);
}
Arm arm;
if (!armMap.TryGetValue(sdtmSubject.QualifierSynonyms[descriptor.ArmVariable.Name], out arm))
{
arm = new Arm()
{
Id = "P-" + projectId + "-ARM-" + sdtmSubject.Qualifiers[descriptor.ArmCodeVariable.Name],
Code = sdtmSubject.Qualifiers[descriptor.ArmCodeVariable.Name],
Name = sdtmSubject.QualifierSynonyms[descriptor.ArmVariable.Name]
};
armMap.Add(arm.Name, arm);
}
if (!arm.Studies.Exists(s => s.Study.Name == study.Name))
{
arm.Studies.Add(new StudyArm()
{
Arm = arm, Study = study
});
}
var subjNewFlag = false;
/**
* ADDING SUBJECTS
*/
var subject = subjects.Find(s => s.UniqueSubjectId == sdtmSubject.USubjId);
if (subject == null)
{
subject = new HumanSubject
{
Id = "P-" + projectId + "-" + sdtmSubject.USubjId,
UniqueSubjectId = sdtmSubject.USubjId,
SubjectStudyId = sdtmSubject.SubjectId,
Arm = sdtmSubject.QualifierSynonyms[descriptor.ArmVariable.Name], //Will put in characteristics for now
ArmCode = sdtmSubject.Qualifiers[descriptor.ArmCodeVariable.Name],
DatasetId = sdtmSubject.DatasetId,
DatafileId = sdtmSubject.DatafileId,
Study = study,
StudyArm = arm
};
subjNewFlag = true;
}
else
{
subjNewFlag = false;
subject.DatasetId = dataset.Id;
subject.DatafileId = sdtmSubject.DatafileId;
subject.Arm = sdtmSubject.QualifierSynonyms[descriptor.ArmVariable.Name];
subject.ArmCode = sdtmSubject.Qualifiers[descriptor.ArmCodeVariable.Name];
subject.Study = study;
subject.StudyArm = arm;
}
//SET/UPDATE SUBJECT CHARACTERISTICS
if (descriptor.RefStartDate != null && sdtmSubject.Qualifiers.ContainsKey(descriptor?.RefStartDate?.Name))
{
DateTime startDate;
if (DateTime.TryParse(sdtmSubject.Qualifiers[descriptor.RefStartDate?.Name], out startDate))
{
subject.SubjectStartDate = startDate;
}
}
if (descriptor.RefEndDate != null && sdtmSubject.Qualifiers.ContainsKey(descriptor?.RefEndDate?.Name))
{
DateTime endDate;
if (DateTime.TryParse(sdtmSubject.Qualifiers[descriptor.RefEndDate.Name], out endDate))
{
subject.SubjectEndDate = endDate;
}
}
//THIS METHOD WILL DELETE ALL SUBJECT CHARACTERISTICS PREVIOUSLY LOADED
//FOR THIS SUBJECT FOR THE SAME DATAFILE
//((List<SubjectCharacteristic>)subject.SubjectCharacteristics)
// .RemoveAll(sc=>sc.DatafileId == datafileId && sc.DatasetId == datasetId);
//_subjectRepository.Update(subject);
//_dataContext.Save();
/**
* ADDING SUBJECT CHARACTERISTICS
*/
foreach (var qualifier in sdtmSubject.Qualifiers)
{
//THIS CHECKS THAT ONLY COLUMNS IN DATA THAT ARE PRESENT IN THE TEMPLATE ARE PARSED
var dsVar = descriptor.QualifierVariables.SingleOrDefault(v => v.Name.Equals(qualifier.Key));
if (descriptor.CharacteristicProperties.Exists(c => c.Name == qualifier.Key) ||
descriptor.TimingVariableDefinitions.Exists(c => c.Name == qualifier.Key))
{
CharacteristicFeature sco;
scos.TryGetValue(qualifier.Key, out sco);
if (sco == null)
{
/**
* CREATING NEW CHARACTERISTIC OBJECT
*/
sco = new CharacteristicFeature()
{
ShortName = dsVar.Name,
FullName = dsVar.Label,
Domain = "DM",
ProjectId = projectId,
DataType = dsVar.DataType,
ActivityId = activityId
};
scos.Add(dsVar.Name, sco);
}
/**
* ADDING SUBJECT CHARACTERISTIC
*/
subject.SubjectCharacteristics.Add(new SubjectCharacteristic()
{
CharacteristicFeature = sco,
VerbatimValue = qualifier.Value,
VerbatimName = sco.ShortName,
Subject = subject,
DatasetId = dataset.Id,
DatafileId = datafileId
});
}
}
if (subjNewFlag)
{
_subjectRepository.Insert(subject);
}
else
{
_subjectRepository.Update(subject);
}
}
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"));
}
