public void AdvanceAllBarcodes(IRepositoryFactory repositoryFactory, UserJob userJob, Stage stage)
{
var barcodes = userJob.UserJobPlates.SelectMany(a => a.Barcodes).Where(a => a.Stage == stage && !a.Done);
if (barcodes.Any())
{
foreach(var bc in barcodes)
{
AdvanceStage(repositoryFactory, bc, userJob);
}
}
}
public void AdvanceStage(IRepositoryFactory repositoryFactory, Barcode barcode, UserJob userJob)
{
// barcode is complete and cannot be advanced
if (barcode.Stage.IsComplete) return;
var jobType = userJob.JobType;
var stage = barcode.Stage;
var plate = barcode.UserJobPlate;
// by default only insert one new barcode
var subPlates = 1;
// jobs with large plate, gets broken down to 4 barcodes
if (_largeplateJobs.Contains(jobType.Id) && userJob.PlateType == PlateTypes.ThreeEightyFour && stage.Order == 2)
{
subPlates = 4;
}
Primer primer1 = barcode.Primer;
Primer primer2 = null;
var directional = false;
// if it's directional, you need a forward and back for each sub plate to generate
if (_directionalJobs.Contains(jobType.Id))
{
// bacterial clone, 2nd stage, take the direction
if (jobType.Id == (int)JobTypeIds.BacterialClone && stage.Order == 3 && userJob.UserJobBacterialClone.SequenceDirection == SequenceDirection.Backward)
{
directional = true;
primer1 = userJob.UserJobBacterialClone.Primer1;
primer2 = userJob.UserJobBacterialClone.Primer2;
}
// frankly, I think this was old code that isn't used any more
// pcr and purified dna take the direction at 1st stage
if ((jobType.Id == (int)JobTypeIds.PCRProduct || jobType.Id == (int)JobTypeIds.PurifiedDna) && stage.Order == 2 && userJob.UserJobDna.SequenceDirection == SequenceDirection.Backward)
{
directional = true;
primer1 = userJob.UserJobDna.Primer1;
primer2 = userJob.UserJobDna.Primer2;
}
}
// load the next stage
var nextStage = jobType.Stages.First(a => a.Order == stage.Order + 1);
for (var i = 0; i < subPlates; i++)
{
// write the first plate
var newBarcode1 = new Barcode() { SourceBarcode = barcode, Stage = nextStage, Primer = primer1, SubPlateId = i + 1};
plate.AddBarcode(newBarcode1);
if (directional)
{
var newBarcode2 = new Barcode() { SourceBarcode = barcode, Stage = nextStage, Primer = primer2, SubPlateId = i + 1 };
plate.AddBarcode(newBarcode2);
}
}
barcode.Done = true;
repositoryFactory.UserJobPlateRepository.EnsurePersistent(plate);
userJob.LastUpdate = DateTime.Now;
repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
}
private bool SaveUserRunSubmission(SequencingPostModel postModel)
{
ValidateUserRunSubmission(postModel);
if (ModelState.IsValid)
{
var userJob = new UserJob();
var userJobUserRun = new UserJobUserRun();
AutoMapper.Mapper.Map(postModel, userJob);
AutoMapper.Mapper.Map(postModel, userJobUserRun);
userJob.UserJobUserRun = userJobUserRun;
userJob.User = GetCurrentUser(true);
userJob.RechargeAccount = postModel.RechargeAccount;
AddPlates(postModel.PlateNames, userJob, userJob.JobType);
_repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
return true;
}
return false;
}
private bool SaveSublibrarySubmission(SequencingPostModel postModel)
{
ValidateSublibrarySubmission(postModel);
if (ModelState.IsValid)
{
var userJob = new UserJob();
var userJobSublibrary = new UserJobSublibrary();
AutoMapper.Mapper.Map(postModel, userJob);
AutoMapper.Mapper.Map(postModel, userJobSublibrary);
userJob.UserJobSublibrary = userJobSublibrary;
userJob.User = GetCurrentUser(true);
userJob.RechargeAccount = postModel.RechargeAccount;
AddPlates(new List<string>() {userJob.Name}, userJob, userJob.JobType);
_repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
return true;
}
return false;
}
private bool SaveBacterialClone(SequencingPostModel postModel)
{
ValidateBacterialClone(postModel);
if (ModelState.IsValid)
{
var userJob = new UserJob();
var userJobBacterialClone = new UserJobBacterialClone();
AutoMapper.Mapper.Map(postModel, userJob);
AutoMapper.Mapper.Map(postModel, userJobBacterialClone);
userJob.UserJobBacterialClone = userJobBacterialClone;
userJob.User = GetCurrentUser(true);
userJob.RechargeAccount = postModel.RechargeAccount;
AddPlates(postModel.PlateNames, userJob, userJob.JobType);
if (postModel.Strain != null && postModel.Strain.IsOther())
{
var strain = new Strain() { Name = postModel.NewStrain, Bacteria = postModel.Bacteria, Supplied = false };
userJob.UserJobBacterialClone.Strain = strain;
}
_repositoryFactory.UserJobRepository.EnsurePersistent(userJob);
return true;
}
return false;
}
/// <summary>
/// Adds the plates necessary for the original submission
/// </summary>
/// <param name="plateNames"></param>
/// <param name="userJob"></param>
private void AddPlates(List<string> plateNames, UserJob userJob, JobType jobType)
{
// figure out the stage
Stage stage = null;
switch(jobType.Id)
{
case (int)JobTypeIds.BacterialClone:
stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.BcWebSubmittedPlates);
break;
case (int)JobTypeIds.PCRProduct:
stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.PcrWebSubmittedPlates);
break;
case (int)JobTypeIds.UserRunSequencing:
stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.UrsWebSubmittedPlates);
break;
case (int)JobTypeIds.PurifiedDna:
stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.PdWebSubmittedPlates);
break;
case (int)JobTypeIds.Sublibrary:
stage = _repositoryFactory.StageRepository.GetNullableById(StageIds.SlWebSubmittedPlates);
break;
}
if (stage == null)
{
throw new ArgumentException("JobType");
}
foreach(var name in plateNames)
{
var plate = new UserJobPlate() {Name = name};
var barcode = new Barcode() {Stage = stage};
plate.AddBarcode(barcode);
userJob.AddUserJobPlates(plate);
}
}
