private UserDataset CreateOrFindAssayPanelDataset(AssayPanelQuery assayPanelQuery, Guid combinedQueryId, string userId, int projectId)
{
var assayPanelDataset = _userDatasetRepository.FindSingle(
d => d.ProjectId == projectId &&
d.QueryId == combinedQueryId &&
d.Type == "ASSAY" &&
d.OwnerId == userId);
//TODO:should add AssayId???
if (assayPanelDataset != null)
{
return(assayPanelDataset);
}
assayPanelDataset = new UserDataset
{
Id = Guid.NewGuid(),
OwnerId = userId,
ProjectId = projectId,
Type = "ASSAY",
Name = assayPanelQuery.AssayName + " Data Matrix",
QueryId = combinedQueryId,
FileStatus = 0
};
var exportData = _queryService.GetQueryResult(combinedQueryId);
assayPanelDataset.SubjectCount = exportData.Subjects.Count;
assayPanelDataset.SampleCount = exportData.Samples.Count;
_userDatasetRepository.Insert(assayPanelDataset);
_dataContext.Save();
return(assayPanelDataset);
}
private ExportFileDefinition GetSampleFileDefinition(CombinedQuery query)
{
AssayPanelQuery assayPanelQuery = query.AssayPanels.Single();
// This is for the subject to sample mapping
var assaySampleDataset = new ExportFileDefinition
{
ProjectId = query.ProjectId,
ContentType = "BIOSAMPLES",
Name = assayPanelQuery.AssayName + " Samples",
QueryId = query.Id
};
//CREATE DATAFIELDS
// 1. ADD SubjectId Field
assaySampleDataset.Fields.Add(CreateSubjectIdField());
// 2.ADD sample Id Field
assaySampleDataset.Fields.Add(CreateSampleIdField());
// 3. ADD Study Id
assaySampleDataset.Fields.Add(CreateStudyIdField());
// 4. ADD Sample characteristics
assaySampleDataset.Fields.AddRange(assayPanelQuery.SampleQueries.Select(qObj => new DatasetField()
{
QueryObjectType = nameof(SampleCharacteristic),
QueryObject = qObj,
ColumnHeader = qObj.QueryObjectName
}));
return(assaySampleDataset);
}
private UserDataset CreateOrFindAssaySampleDataset(AssayPanelQuery assayPanelQuery, Guid combinedQueryId, string userId, int projectId)
{
var assaySampleDataset = _userDatasetRepository.FindSingle(
d => d.ProjectId == projectId &&
d.QueryId == combinedQueryId &&
d.Type == "BIOSAMPLES" &&
d.OwnerId == userId);
//TODO:should add AssayId???
if (assaySampleDataset != null)
{
return(assaySampleDataset);
}
// This is for the subject to sample mapping
assaySampleDataset = new UserDataset
{
Id = Guid.NewGuid(),
OwnerId = userId,
ProjectId = projectId,
Type = "BIOSAMPLES",
Name = assayPanelQuery.AssayName + " Samples",
QueryId = combinedQueryId,
FileStatus = 0
};
//CREATE DATAFIELDS
// 1. ADD SubjectId Field
assaySampleDataset.Fields.Add(CreateSubjectIdField());
// 2.ADD sample Id Field
assaySampleDataset.Fields.Add(CreateSampleIdField());
// 3. ADD Study Id
assaySampleDataset.Fields.Add(CreateStudyIdField());
// 4. ADD Sample characteristics
assaySampleDataset.Fields.AddRange(assayPanelQuery.SampleQueries.Select(qObj => new DatasetField()
{
QueryObjectType = nameof(SampleCharacteristic),
QueryObject = qObj,
ColumnHeader = qObj.QueryObjectName
}));
var exportData = _queryService.GetQueryResult(combinedQueryId);
assaySampleDataset.SubjectCount = exportData.Subjects.Count;
assaySampleDataset.SampleCount = exportData.Samples.Count;
_userDatasetRepository.Insert(assaySampleDataset);
_dataContext.Save();
return(assaySampleDataset);
}
private ExportFileDefinition GetAssayDataFileDefinition(CombinedQuery query)
{
AssayPanelQuery assayPanelQuery = query.AssayPanels.Single();
var assayPanelDataset = new ExportFileDefinition
{
ProjectId = query.ProjectId,
ContentType = "ASSAY",
Name = assayPanelQuery.AssayName + " Data File",
QueryId = query.Id
};
return(assayPanelDataset);
}
private static AssayPanelDTO GetDTOforAssayPanelQuery(AssayPanelQuery apQuery)
{
var apDTO = new AssayPanelDTO()
{
AssayId = apQuery.AssayId,
AssayName = apQuery.AssayName
};
foreach (var sampleQuery in apQuery.SampleQueries)
{
apDTO.SampleQuery.Add(GetDTOforQuery(sampleQuery));
}
return(apDTO);
}
public CombinedQuery CreateSingleAssayCombinedQuery(CombinedQuery cQuery, AssayPanelQuery apQuery)
{
var singleAssayCombinedQuery = new CombinedQuery
{
ProjectId = cQuery.ProjectId,
ClinicalObservations = cQuery.ClinicalObservations,
DesignElements = cQuery.DesignElements,
GroupedObservations = cQuery.GroupedObservations,
SubjectCharacteristics = cQuery.SubjectCharacteristics,
UserId = cQuery.UserId,
Id = Guid.NewGuid()
};
singleAssayCombinedQuery.AssayPanels.Add(apQuery);
_combinedQueryRepository.Insert(singleAssayCombinedQuery);
return(singleAssayCombinedQuery);
}
public CombinedQuery SaveQuery(CombinedQueryDTO cdto, string userId, int projectId)
{
CombinedQuery cQuery = new CombinedQuery();
cQuery.Name = cdto.Name;
cQuery.UserId = Guid.Parse(userId);
cQuery.ProjectId = projectId;
cQuery.Id = Guid.NewGuid();
cQuery.IsSavedByUser = cdto.IsSavedByUser;
var requests = cdto.ObsRequests.Union(cdto.SubjCharRequests);
foreach (var request in requests)
{
if (!request.IsMultipleObservations)
{
var query = GetQueryFromQueryDTO(request);
if (request.IsSubjectCharacteristics)
{
cQuery.SubjectCharacteristics.Add(query);
}
if (request.IsClinicalObservations)
{
cQuery.ClinicalObservations.Add((ObservationQuery)query);
}
if (request.IsDesignElement)
{
cQuery.DesignElements.Add(query);
}
}
else
{
var goq = new GroupedObservationsQuery()
{
//Name = request.Name,
GroupedObsName = request.O3,
PropertyName = request.QO2,
PropertyLabel = request.QO2_label,
PropertyId = request.QO2id,
Group = request.Group,
GroupedObservations = new List <ObservationQuery>(),
DataType = request.DataType,
FilterExactValues = request.FilterExactValues,
FilterRangeFrom = request.FilterRangeFrom,
FilterRangeTo = request.FilterRangeTo,
IsFiltered = request.IsFiltered,
ProjectId = request.ProjectId
};
goq.GroupedObservations.AddRange(request.GroupedObservations.Select(obsReq => new ObservationQuery()
{
TermId = obsReq.O3id,
TermName = obsReq.O3,
PropertyId = obsReq.QO2id,
PropertyName = obsReq.QO2,
Group = obsReq.Group,
IsOntologyEntry = obsReq.IsOntologyEntry,
TermCategory = obsReq.OntologyEntryCategoryName,
DataType = obsReq.DataType,
ProjectId = obsReq.ProjectId
}));
cQuery.GroupedObservations.Add(goq);
}
}
var assaypanels = cdto.AssayPanelRequests.Values.Where(ap => ap.IsRequested);
foreach (var assayRequest in assaypanels)
{
var assayPanelQuery = new AssayPanelQuery();
assayPanelQuery.AssayId = assayRequest.AssayId;
assayPanelQuery.AssayName = assayRequest.AssayName;
foreach (var sampleQuery in assayRequest.SampleQuery)
{
var query = GetQueryFromQueryDTO(sampleQuery);
assayPanelQuery.SampleQueries.Add(query);
}
cQuery.AssayPanels.Add(assayPanelQuery);
}
return(_combinedQueryRepository.Insert(cQuery));
}
