public AssayDTO AddAssay(AssayDTO assayDto)
{
var assay = new Assay();
//var project = _projectRepository.FindSingle(d => d.Accession
// .Equals(assayDto.ProjectAcc));
assay.Name = assayDto.Name;
assay.ProjectId = assayDto.ProjectId;
assay.TechnologyPlatformId = assayDto.Platform;
assay.TechnologyTypeId = assayDto.Technology;
//assay.DesignType = getCVterm(assayDto.AssayDesignType);
assay.MeasurementTypeId = assayDto.Type;
if (assayDto.SamplesDataset != null)
{
assayDto.SamplesDataset.ProjectId = assayDto.ProjectId;
}
if (assayDto.FeaturesDataset != null)
{
assayDto.FeaturesDataset.ProjectId = assayDto.ProjectId;
}
if (assayDto.ObservationsDataset != null)
{
assayDto.ObservationsDataset.ProjectId = assayDto.ProjectId;
}
var BSdataset = _datasetService.CreateDataset(assayDto.SamplesDataset);
if (BSdataset != null)
{
assay.Datasets.Add(BSdataset);
}
var FEdataset = _datasetService.CreateDataset(assayDto.FeaturesDataset);
if (FEdataset != null)
{
assay.Datasets.Add(FEdataset);
}
var OBdataset = _datasetService.CreateDataset(assayDto.ObservationsDataset);
if (OBdataset != null)
{
assay.Datasets.Add(OBdataset);
}
assay = _assayRepository.Insert(assay);
if (_dataContext.Save().Equals("CREATED"))
{
assayDto.Id = assay.Id;
return(assayDto);
}
return(null);
}
public IActionResult UpdateAssay(int assayId, [FromBody] AssayDTO assayDTO)
{
try
{
_assayService.UpdateAssay(assayDTO, assayId);
return(new AcceptedAtRouteResult("GetAssayById", new { assayId = assayDTO.Id }, assayDTO));
}
catch (Exception e)
{
return(new BadRequestObjectResult(e.Message));
}
}
public IActionResult AddAssay([FromBody] AssayDTO assayDTO)
{
if (!ModelState.IsValid)
{
return(BadRequest());
}
var addedAssay = _assayService.AddAssay(assayDTO);
if (addedAssay != null)
{
return(new CreatedAtRouteResult("GetAssayById", new { assayId = addedAssay.Id }, addedAssay));
}
return(new StatusCodeResult(StatusCodes.Status409Conflict));
}
/**
* Assay Methods
* */
public AssayDTO GetAssay(int assayId)
{
var assay = _assayRepository.FindSingle(
d => d.Id.Equals(assayId),
new List <string>()
{
"Datasets.Template",
"TechnologyType",
"TechnologyPlatform",
"MeasurementType",
"DesignType"
}
);
var assayDTO = new AssayDTO();
assayDTO.Name = assay.Name;
assayDTO.Id = assay.Id;
assayDTO.ProjectId = assay.ProjectId;
assayDTO.Type = assay.MeasurementType?.Id;
assayDTO.Technology = assay.TechnologyType?.Id;
assayDTO.Platform = assay.TechnologyPlatform?.Id;
assayDTO.Design = assay.DesignType?.Id;
foreach (var dst in assay.Datasets.Select(ds => _datasetService.GetActivityDatasetDTO(ds.Id)))
{
//TODO: convert to enums or CVterms
if (dst.Class == "Assay Samples")
{
assayDTO.SamplesDataset = dst;
}
if (dst.Class == "Assay Observations")
{
assayDTO.ObservationsDataset = dst;
}
if (dst.Class == "Assay Features")
{
assayDTO.FeaturesDataset = dst;
}
}
return(assayDTO);
}
public string UpdateAssay(AssayDTO assayDTO, int assayId)
{
Assay assayToUpdate = _assayRepository.Get(assayId);
assayToUpdate.Name = assayDTO.Name;
assayToUpdate.TechnologyPlatformId = assayDTO.Platform;
assayToUpdate.TechnologyTypeId = assayDTO.Technology;
//assay.DesignType = getCVterm(assayDto.AssayDesignType);
assayToUpdate.MeasurementTypeId = assayDTO.Type;
assayDTO.Datasets.Clear();
assayDTO.Datasets.Add(assayDTO.FeaturesDataset);
assayDTO.Datasets.Add(assayDTO.SamplesDataset);
assayDTO.Datasets.Add(assayDTO.ObservationsDataset);
foreach (var datasetDto in assayDTO.Datasets)
{
if (datasetDto == null)
{
continue;
}
datasetDto.ProjectId = assayDTO.ProjectId;
if (datasetDto.IsNew)
{
var dataset = _datasetService.CreateDataset(datasetDto);
assayToUpdate.Datasets.Add(dataset);
_assayRepository.Update(assayToUpdate);
}
else
{
_datasetService.UpdateDataset(datasetDto);
}
}
return(_dataContext.Save());
}
