public static UserDatasetDTO WriteDTO(UserDataset dataset)
{
return(new UserDatasetDTO()
{
Id = dataset.Id.ToString(),
Description = dataset.Description,
LastModified = dataset.LastModified,
Name = dataset.Name,
OwnerId = dataset.OwnerId,
ProjectId = dataset.ProjectId,
Type = dataset.Type,
SubjectCount = dataset.SubjectCount,
SampleCount = dataset.SampleCount,
FileStatus = dataset.FileStatus,
Filters = dataset.Filters.Select(f => new DataFilterDTO()
{
}).ToList(),
//Fields = dataset.Fields.Select(f => new DataFieldDTO()
//{
// Entity = f.Entity,
// EntityId = f.EntityId,
// Property = f.Property,
// PropertyId = f.PropertyId,
// DataType = f.DataType,
// IsFiltered = f.IsFiltered,
// FieldName = f.FieldName
//}).ToList()
});
}
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 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);
}
public void UpdateUserDataset(UserDataset dataset, string userId)
{
//check that the owner of this dataset is the caller
//var dataset = ReadDTO(dto);
var datasetToUpdate = _userDatasetRepository.FindSingle(d => d.Id == dataset.Id);
//datasetToUpdate = ReadDTO(dto, datasetToUpdate);
datasetToUpdate.IsSaved = true;
datasetToUpdate.LastModified = DateTime.Today.ToString("f");
datasetToUpdate.Description = dataset.Description;
datasetToUpdate.Name = dataset.Name;
_userDatasetRepository.Update(datasetToUpdate);
}
public IActionResult UpdateUserDataset(Guid datasetId, [FromBody] UserDataset dataset)
{
try
{
if (!User.Identity.IsAuthenticated)
{
return(null);
}
var userId = User.FindFirst(ClaimTypes.UserData).Value;
_userDataService.UpdateUserDataset(dataset, userId);
return(new AcceptedResult());
}
catch (Exception e)
{
return(new BadRequestObjectResult(e.Message));
}
}
private UserDataset ReadDTO(UserDatasetDTO dto, UserDataset copyInto = null)
{
UserDataset ds;
ds = copyInto ?? new UserDataset();
ds.Name = dto.Name;
ds.Description = dto.Description;
ds.Tags = dto.Tags;
//ds.OwnerId = dto.OwnerId;
//ds.ProjectId = dto.ProjectId;
ds.Type = dto.Type;
ds.LastModified = DateTime.Now.ToString("d");// ToShortDateString();
ds.Filters = new List <DataFilter>();
//ds.Fields = new List<DataField>();
foreach (var filterDto in dto.Filters)
{
if (filterDto.IsNumeric)
{
var filter = new DataFilterRange();
filter.DataField = getDataField(filterDto.Field);
filter.Lowerbound = filterDto.From;
filter.Upperbound = filterDto.To;
ds.Filters.Add(filter);
}
else
{
var filter = new DataFilterExact();
filter.DataField = getDataField(filterDto.Field);
filter.Values = filterDto.FilterValues;
ds.Filters.Add(filter);
}
}
foreach (var fieldDto in dto.Fields)
{
// ds.Fields.Add(getDataField(fieldDto));
}
return(ds);
}
public SecurityToken CreateToken(UserDataset user)
{
var claims = new[]
{
new Claim(JwtRegisteredClaimNames.Sub, user.UserId.ToString()),
new Claim(JwtRegisteredClaimNames.Email, user.Email),
new Claim(ClaimTypes.Role, "user"),
new Claim(JwtRegisteredClaimNames.Jti, Guid.NewGuid().ToString()),
};
var key = new SymmetricSecurityKey(Encoding.ASCII.GetBytes(_appSettings.JwtSecret));
var jwtDescriptor = new SecurityTokenDescriptor()
{
Subject = new ClaimsIdentity(claims),
SigningCredentials = new SigningCredentials(key, SecurityAlgorithms.HmacSha512Signature),
Audience = _appSettings.Audience,
Issuer = _appSettings.Issuer,
Expires = DateTime.Now.AddDays(1),
};
var toke = new JwtSecurityTokenHandler().CreateToken(jwtDescriptor);
Console.WriteLine(toke);
return(toke);
}
private UserDataset CreateOrFindSubjectClinicalDataset(CombinedQuery query, string userId)
{
var phenoDataset = _userDatasetRepository.FindSingle(
d => d.ProjectId == query.ProjectId &&
d.QueryId == query.Id &&
d.Type == "PHENO" &&
d.OwnerId == userId);
if (phenoDataset != null)
{
return(phenoDataset);
}
phenoDataset = new UserDataset
{
Id = Guid.NewGuid(),
OwnerId = userId,
ProjectId = query.ProjectId,
Type = "PHENO",
Name = "Subjects",
QueryId = query.Id,
FileStatus = 0,
};
//ADD SUBJECTID & STUDYID DATAFIELD
phenoDataset.Fields.Add(CreateSubjectIdField());
phenoDataset.Fields.Add(CreateStudyIdField());
//ADD DESIGN ELEMENT FIELDS (STUDY, VISIT, ARM...etc)
phenoDataset.Fields.AddRange(query.DesignElements.Select(qObj => new DatasetField()
{
QueryObject = qObj,
QueryObjectType = qObj.QueryFor,
ColumnHeader = qObj.QueryObjectName
}));
//ADD SUBJECT CHARACTERISTICS (AGE, RACE, SEX ...etc)
phenoDataset.Fields.AddRange(query.SubjectCharacteristics.Select(qObj => new DatasetField()
{
QueryObject = qObj,
QueryObjectType = nameof(SubjectCharacteristic),
ColumnHeader = qObj.QueryObjectName//.ObservationName
}));
//ADD CLINICAL OBSERVATIONS
foreach (var co in query.ClinicalObservations)
{
phenoDataset.Fields.Add(new DatasetField()
{
QueryObject = co,
QueryObjectType = nameof(SdtmRow),
ColumnHeader = co.ObservationName
});
if (co.HasLongitudinalData)
{
phenoDataset.Fields.Add(new DatasetField()
{
QueryObject = new Query()
{
QueryFor = nameof(Visit), QueryFrom = nameof(SdtmRow), QuerySelectProperty = "Name"
},
QueryObjectType = nameof(Visit),
ColumnHeader = "visit"
});
}
if (co.HasTPT)
{
phenoDataset.Fields.Add(new DatasetField()
{
QueryObject = new Query()
{
QueryFor = nameof(SdtmRow.CollectionStudyTimePoint), QueryFrom = nameof(SdtmRow), QuerySelectProperty = "Name"
},
QueryObjectType = nameof(RelativeTimePoint),
ColumnHeader = "timepoint"
});
}
}
//phenoDataset.Fields.AddRange(query.ClinicalObservations.Select(qObj => new DatasetField()
//{
// QueryObject = qObj,
// QueryObjectType = nameof(SdtmRow),
// ColumnHeader = qObj.ObservationName
//}));
//ADD GROUPED CLINICAL OBSERVATIONS
phenoDataset.Fields.AddRange(query.GroupedObservations.Select(gObs => new DatasetField()
{
QueryObject = gObs,
QueryObjectType = nameof(SdtmRow),
ColumnHeader = gObs.ObservationName
}));
var exportData = _queryService.GetQueryResult(query.Id);
phenoDataset.SubjectCount = exportData.Subjects.Count;
_userDatasetRepository.Insert(phenoDataset);
_dataContext.Save();
return(phenoDataset);
}
