/// <summary>
/// Retrieves datasetDTO for selected activity including a union of VarDefs and TemplateVariables from the relevant Domain
/// //TODO: This method should change once users are allowed to add their own Variables
/// In this case VarDEFs should take precedence and the issue of adding CVterms to VarDEFs shuold be settled
/// </summary>
/// <param name="datasetId"></param>
/// <returns></returns>
public DatasetDTO GetActivityDatasetDTO(int datasetId)
{
DatasetDTO dto = new DatasetDTO();
Dataset ds = _datasetRepository.FindSingle(
d => d.Id.Equals(datasetId),
new List <string>()
{
"Variables.VariableDefinition",
"Template.Fields.ControlledVocabulary.Xref.DB",
"Activity"
});
dto.Id = ds.Id; //Set DatasetDTO id to Dataset.Id (int)
dto.Class = ds.Template.Class;
dto.Description = ds.Template.Description;
dto.Name = ds.Template.Domain;
dto.DomainId = ds.Template.Id;
dto.Structure = ds.Template.Structure;
dto.Code = ds.Template.Code;
dto.ProjectId = ds.Activity.ProjectId;
//ds.Domain.Variables.Where(v=> !v.IsGeneric).
foreach (DatasetTemplateField vt in ds.Template.Fields.OrderBy(v => v.Order))
//foreach (var vt in ds.Variables)
{
DatasetVariableDTO dv = new DatasetVariableDTO();
dv.Name = vt.Name;
dv.Description = vt.Description;
dv.Label = vt.Label;
dv.Accession = vt.Id;
dv.DataType = vt.DataType;
dv.IsCurated = true;
dv.RoleId = vt.RoleId;
if (vt.ControlledVocabulary != null)
{
dv.DictionaryName = vt.ControlledVocabulary.Name;
dv.DictionaryDefinition = vt.ControlledVocabulary.Definition;
dv.DictionaryXrefURL = vt.ControlledVocabulary.Xref.DB.UrlPrefix +
vt.ControlledVocabulary.Xref.Accession;
}
var vr = ds.Variables.SingleOrDefault(v => v.VariableDefinition.Name.Equals(vt.Name));
if (vr != null)
{
dv.IsRequired = vr.IsRequired;
dv.KeySequence = vr.KeySequence;
dv.OrderNumber = vr.OrderNumber;
dv.Id = vr.VariableDefinitionId;
dv.isSelected = true;
}
dto.Variables.Add(dv);
}
foreach (VariableReference vr in ds.Variables)
{
if (!dto.Variables.Exists(v => v.Accession.Equals(vr.VariableDefinition.Accession)))
{
DatasetVariableDTO dv = new DatasetVariableDTO();
dv.Name = vr.VariableDefinition.Name;
dv.Description = vr.VariableDefinition.Description;
dv.Label = vr.VariableDefinition.Label;
dv.Accession = vr.VariableDefinition.Accession;
dv.DataType = vr.VariableDefinition.DataType;
dv.IsCurated = vr.VariableDefinition.IsCurated;
dv.IsComputed = vr.VariableDefinition.IsComputed ?? false;
dv.RoleId = vr.VariableDefinition.RoleId;
dv.IsRequired = vr.IsRequired;
dv.KeySequence = vr.KeySequence;
dv.OrderNumber = vr.OrderNumber;
dv.Id = vr.VariableDefinitionId;
dv.isSelected = true;
dto.Variables.Add(dv);
}
}
return(dto);
}
private DatasetDTO GetDatasetDTO(DatasetTemplate datasetTemplate)
{
var dto = new DatasetDTO
{
Class = datasetTemplate.Class,
Description = datasetTemplate.Description,
Name = datasetTemplate.Domain,
DomainId = datasetTemplate.Id,
Structure = datasetTemplate.Structure,
Code = datasetTemplate.Code,
HasHeader = datasetTemplate.Fields.Any(f => f.Section == "HEADER")
};
foreach (var vt in datasetTemplate.Fields.OrderBy(c => c.Order))
{
var dv = new DatasetVariableDTO
{
Name = vt.Name,
Description = vt.Description,
Label = vt.Label,
Accession = vt.Id,
RoleId = vt.RoleId,
DataType = vt.DataType,
UsageId = vt.UsageId,
IsRequired = false,
KeySequence = null,
OrderNumber = null,
IsCurated = true,
IsComputed = false,
varType = "STANDARD",
IsGeneric = vt.IsGeneric,
AllowedQualifiers = vt.QualifiersDictionary?.Terms?.Select(t => t.Name).ToList(),
DictionaryName = vt.ControlledVocabulary?.Name,
DictionaryXrefURL = vt.ControlledVocabulary?.Xref.DB.UrlPrefix + vt.ControlledVocabulary?.Xref.Accession
};
if (dv.UsageId.Equals("CL-Compliance-T-1") || dv.UsageId.Equals("CL-Compliance-T-2"))
{
dv.isSelected = true;
if (dv.UsageId.Equals("CL-Compliance-T-1"))
{
dv.IsRequired = true;
}
}
if (vt.Section == "HEADER")
{
dto.HeaderFields.Add(dv);
}
if (vt.IsGeneric)
{
dto.GenericFields.Add(dv);
}
else if (vt.Section == "COLUMN")
{
dto.Variables.Add(dv);
}
}
return(dto);
}
