public async Task <IEnumerable <SynthesisActivityItemViewModel> > GetCurrentSynthesisActivities()
{
GeneSynthesisProcess currentGeneSynthesisProcess = await GetCurrentGeneSynthesisProcess();
if (currentGeneSynthesisProcess?.GeneSynthesisActivities != null && currentGeneSynthesisProcess.GeneSynthesisActivities.Any())
{
IList <SynthesisActivityItemViewModel> currentSynthesisActivities = new List <SynthesisActivityItemViewModel>();
foreach (GeneSynthesisActivity geneSynthesisActivity in currentGeneSynthesisProcess.GeneSynthesisActivities)
{
SynthesisActivityItemViewModel synthesisActivityItemViewModel = new SynthesisActivityItemViewModel();
synthesisActivityItemViewModel.Id = geneSynthesisActivity.Id;
synthesisActivityItemViewModel.ChannelNumber = geneSynthesisActivity.ChannelNumber;
synthesisActivityItemViewModel.DNASequence = geneSynthesisActivity.DNASequence;
synthesisActivityItemViewModel.TotalTime = geneSynthesisActivity.TotalTime;
synthesisActivityItemViewModel.SynthesisCycle = new SynthesisCycleItemViewModel()
{
Id = geneSynthesisActivity.SynthesisCycle.Id,
Name = geneSynthesisActivity.SynthesisCycle.Name
};
currentSynthesisActivities.Add(synthesisActivityItemViewModel);
}
return(currentSynthesisActivities);
}
return(Enumerable.Empty <SynthesisActivityItemViewModel>());
}
public async Task UpdateSynthesisProcess(GeneSynthesisProcessViewModel viewModel)
{
GeneSynthesisProcess entity = await GetCurrentGeneSynthesisProcess();
entity.DenaturationTempGeneAssembly = viewModel.DenaturationTempGeneAssembly;
entity.DenaturationTimeGeneAssembly = viewModel.DenaturationTimeGeneAssembly;
entity.AnnealingTempGeneAssembly = viewModel.AnnealingTempGeneAssembly;
entity.AnnealingTimeGeneAssembly = viewModel.AnnealingTimeGeneAssembly;
entity.ElongationTempGeneAssembly = viewModel.ElongationTempGeneAssembly;
entity.ElongationTimeGeneAssembly = viewModel.ElongationTimeGeneAssembly;
entity.DenaturationTempGeneAmplification = viewModel.DenaturationTempGeneAmplification;
entity.DenaturationTimeGeneAmplification = viewModel.DenaturationTimeGeneAmplification;
entity.AnnealingTempGeneAmplification = viewModel.AnnealingTempGeneAmplification;
entity.AnnealingTimeGeneAmplification = viewModel.AnnealingTimeGeneAmplification;
entity.ElongationTempGeneAmplification = viewModel.ElongationTempGeneAmplification;
entity.ElongationTimeGeneAmplification = viewModel.ElongationTimeGeneAmplification;
entity.NumberOfGeneAssemblyCycles = viewModel.NumberOfGeneAssemblyCycles;
entity.NumberOfGeneAmplificationCycles = viewModel.NumberOfGeneAmplificationCycles;
CalcGeneSynthesisProcessTotalTime(entity);
unitOfWork.Commit();
}
public GeneSynthesisProcess CreateGeneSynthesisProcess()
{
var geneSynthesisProcess = new GeneSynthesisProcess();
geneSynthesisProcess.Gene = CreateGene();
return(GetOrCreate(() => geneSynthesisProcess));
}
public async Task DeleteSynthesisProcess(string id)
{
GeneSynthesisProcess currentGeneSynthesisProcess = await GetCurrentGeneSynthesisProcess();
currentGeneSynthesisProcess.Deleted = true;
unitOfWork.Commit();
}
private async Task ChangeSynthesisProcessStatus(SynthesisProcessStatus newStatus)
{
GeneSynthesisProcess currentGeneSynthesisProcess = await GetCurrentGeneSynthesisProcess();
currentGeneSynthesisProcess.Status = newStatus;
unitOfWork.InsertOrUpdate(currentGeneSynthesisProcess);
unitOfWork.Commit();
}
public async Task <GeneSynthesisProcessViewModel> GetCurrentSynthesisProcess()
{
GeneSynthesisProcessViewModel geneSynthesisProcessViewModel;
GeneSynthesisProcess currentGeneSynthesisProcess = await GetCurrentGeneSynthesisProcess();
if (currentGeneSynthesisProcess != null)
{
geneSynthesisProcessViewModel = new GeneSynthesisProcessViewModel()
{
Id = currentGeneSynthesisProcess.Id,
GeneId = currentGeneSynthesisProcess.GeneId,
Status = currentGeneSynthesisProcess.Status,
TotalTime = currentGeneSynthesisProcess.TotalTime,
SelectedGeneId = currentGeneSynthesisProcess.GeneId,
DenaturationTempGeneAssembly = currentGeneSynthesisProcess.DenaturationTempGeneAssembly,
DenaturationTimeGeneAssembly = currentGeneSynthesisProcess.DenaturationTimeGeneAssembly,
AnnealingTempGeneAssembly = currentGeneSynthesisProcess.AnnealingTempGeneAssembly,
AnnealingTimeGeneAssembly = currentGeneSynthesisProcess.AnnealingTimeGeneAssembly,
ElongationTempGeneAssembly = currentGeneSynthesisProcess.ElongationTempGeneAssembly,
ElongationTimeGeneAssembly = currentGeneSynthesisProcess.ElongationTimeGeneAssembly,
DenaturationTempGeneAmplification = currentGeneSynthesisProcess.DenaturationTempGeneAmplification,
DenaturationTimeGeneAmplification = currentGeneSynthesisProcess.DenaturationTimeGeneAmplification,
AnnealingTempGeneAmplification = currentGeneSynthesisProcess.AnnealingTempGeneAmplification,
AnnealingTimeGeneAmplification = currentGeneSynthesisProcess.AnnealingTimeGeneAmplification,
ElongationTempGeneAmplification = currentGeneSynthesisProcess.ElongationTempGeneAmplification,
ElongationTimeGeneAmplification = currentGeneSynthesisProcess.ElongationTimeGeneAmplification,
NumberOfGeneAssemblyCycles = currentGeneSynthesisProcess.NumberOfGeneAssemblyCycles,
NumberOfGeneAmplificationCycles = currentGeneSynthesisProcess.NumberOfGeneAmplificationCycles,
};
}
else
{
geneSynthesisProcessViewModel = new GeneSynthesisProcessViewModel()
{
Status = SynthesisProcessStatus.NotStarted,
SelectedGeneId = "",
};
}
User currentUser = GetCurrentUser();
IEnumerable <Gene> allGenes = await unitOfWork.GetAll <Gene>()
.Where(x => x.UserId == currentUser.Id)
.ToListAsync();
geneSynthesisProcessViewModel.AllGenes = allGenes.Select(x => new ListItem()
{
Id = x.Id, Text = x.Name
});
return(geneSynthesisProcessViewModel);
}
private async Task <GeneSynthesisProcess> GetCurrentGeneSynthesisProcess()
{
var currentPrincipal = identityStorage.GetPrincipal();
GeneSynthesisProcess geneSynthesisProcess = await unitOfWork.GetAll <GeneSynthesisProcess>()
.Include(x => x.Gene.User)
.Include(x => x.GeneSynthesisActivities.Select(y => y.SynthesisCycle.CycleSteps))
.Where(x => !x.Deleted && x.Gene.UserId == currentPrincipal.UserId && (x.Status == SynthesisProcessStatus.NotStarted ||
x.Status == SynthesisProcessStatus.InProgress || x.Status == SynthesisProcessStatus.Suspended))
.FirstOrDefaultAsync();
return(geneSynthesisProcess);
}
private void CalcGeneSynthesisProcessTotalTime(GeneSynthesisProcess geneSynthesisProcess)
{
int totalTimeActivities = geneSynthesisProcess.GeneSynthesisActivities.Sum(x => x.TotalTime);
int totalTimeGeneAssembly =
(geneSynthesisProcess.DenaturationTimeGeneAssembly + geneSynthesisProcess.AnnealingTimeGeneAssembly + geneSynthesisProcess.ElongationTimeGeneAssembly) *
geneSynthesisProcess.NumberOfGeneAssemblyCycles;
int totalTimeGeneAmplification =
(geneSynthesisProcess.DenaturationTimeGeneAmplification + geneSynthesisProcess.AnnealingTimeGeneAmplification + geneSynthesisProcess.ElongationTimeGeneAmplification) *
geneSynthesisProcess.NumberOfGeneAmplificationCycles;
geneSynthesisProcess.TotalTime = totalTimeActivities + totalTimeGeneAssembly + totalTimeGeneAmplification;
}
public async Task CreateGeneSynthesisProcess(string geneId)
{
Gene gene = await unitOfWork.GetAll <Gene>().Include(x => x.GeneFragments).SingleAsync(x => x.Id == geneId);
await AssertGeneFragmentsCorrespondsToConfiguredChannels(gene.GeneFragments);
GeneSynthesisProcess currentGeneSynthesisProcess = await GetCurrentGeneSynthesisProcess();
if (currentGeneSynthesisProcess != null)
{
currentGeneSynthesisProcess.Deleted = true;
}
GeneSynthesisProcess newGeneSynthesisProcess = new GeneSynthesisProcess
{
Status = SynthesisProcessStatus.NotStarted,
Gene = gene,
};
unitOfWork.InsertOrUpdate(newGeneSynthesisProcess);
unitOfWork.Commit();
// create synthesis activities from gene fragments
SynthesisCycle defaultSynthesisCycle = await unitOfWork.GetAll <SynthesisCycle>()
.Include(x => x.CycleSteps)
.SingleAsync(x => x.UserId == null);
IList <GeneSynthesisActivity> geneSynthesisActivities = new List <GeneSynthesisActivity>();
foreach (GeneFragment geneFragment in gene.GeneFragments)
{
GeneSynthesisActivity newSynthesisActivity =
await CreateSynthesisActivity(geneFragment.OligoSequence, newGeneSynthesisProcess, defaultSynthesisCycle);
geneSynthesisActivities.Add(newSynthesisActivity);
}
await AssignChannelNumbers(geneSynthesisActivities);
await unitOfWork.InsertAll(geneSynthesisActivities);
newGeneSynthesisProcess.TotalTime = geneSynthesisActivities.Sum(x => x.TotalTime);
unitOfWork.Commit();
}
private async Task <GeneSynthesisActivity> CreateSynthesisActivity(
string dnaSequence, GeneSynthesisProcess currentGeneSynthesisProcess, SynthesisCycle defaultSynthesisCycle)
{
GeneSynthesisActivity geneSynthesisActivity = new GeneSynthesisActivity();
geneSynthesisActivity.GeneSynthesisProcessId = currentGeneSynthesisProcess.Id;
geneSynthesisActivity.GeneSynthesisProcess = currentGeneSynthesisProcess;
geneSynthesisActivity.SynthesisCycleId = defaultSynthesisCycle.Id;
geneSynthesisActivity.SynthesisCycle = defaultSynthesisCycle;
geneSynthesisActivity.DNASequence = !string.IsNullOrWhiteSpace(dnaSequence) ? dnaSequence.ToUpper() : "A";
CalcGeneSynthesisActivityTotalTime(geneSynthesisActivity);
return(geneSynthesisActivity);
}
public async Task CreateOrUpdateSynthesisActivity(SynthesisActivityItemViewModel item)
{
GeneSynthesisActivity entity;
GeneSynthesisProcess currentGeneSynthesisProcess = await GetCurrentGeneSynthesisProcess();
if (string.IsNullOrWhiteSpace(item.Id))
{
entity = new GeneSynthesisActivity();
entity.GeneSynthesisProcess = currentGeneSynthesisProcess;
}
else
{
entity = await unitOfWork.GetAll <GeneSynthesisActivity>()
.Include(x => x.SynthesisCycle)
.Include(x => x.GeneSynthesisProcess)
.SingleAsync(x => x.Id == item.Id);
}
entity.DNASequence = !string.IsNullOrWhiteSpace(item.DNASequence) ? item.DNASequence.ToUpper() : "A";
if (item.SynthesisCycle != null && !string.IsNullOrWhiteSpace(item.SynthesisCycle.Id))
{
entity.SynthesisCycle = unitOfWork.GetById <SynthesisCycle>(item.SynthesisCycle.Id);
}
else
{
SynthesisCycle defaultSynthesisCycle = await unitOfWork.GetAll <SynthesisCycle>()
.SingleAsync(x => x.UserId == null);
entity.SynthesisCycle = defaultSynthesisCycle;
}
await AssignToChannel(entity, currentGeneSynthesisProcess.GeneSynthesisActivities);
CalcGeneSynthesisActivityTotalTime(entity);
unitOfWork.InsertOrUpdate(entity);
unitOfWork.Commit();
currentGeneSynthesisProcess = await GetCurrentGeneSynthesisProcess();
CalcGeneSynthesisProcessTotalTime(currentGeneSynthesisProcess);
unitOfWork.Commit();
}
private async Task StartGeneSynthesisProcess()
{
ICloudTable <GeneSynthesisProcess> geneSynthesisProcessTable = null;
GeneSynthesisProcess currentGeneSynthesisProcess = null;
try
{
await AwaitPreviousSynthesisProcess();
LogAction("Syncing gene synthesis process...");
var currentUserId = GetCurrentUserId();
await CloudService.SyncOfflineCacheAsync();
LogAction("Sync completed.");
geneSynthesisProcessTable = await CloudService.GetTableAsync <GeneSynthesisProcess>();
var allGeneSynthesisProcesses = await geneSynthesisProcessTable.ReadAllItemsAsync();
currentGeneSynthesisProcess = allGeneSynthesisProcesses.Where(x => x.Gene.UserId == currentUserId)
.OrderByDescending(x => x.CreatedAt)
.FirstOrDefault();
if (currentGeneSynthesisProcess == null)
{
LogAction("Gene synthesis process not found.");
}
var hardwareFunctionTable = await CloudService.GetTableAsync <HardwareFunction>();
var allHardwareFunctions = await hardwareFunctionTable.ReadAllItemsAsync();
IEnumerable <HardwareFunction> bAndTetToColFunctions = allHardwareFunctions.Where(
x => x.FunctionType == HardwareFunctionType.AAndTetToCol ||
x.FunctionType == HardwareFunctionType.CAndTetToCol ||
x.FunctionType == HardwareFunctionType.TAndTetToCol ||
x.FunctionType == HardwareFunctionType.GAndTetToCol);
HardwareFunction closeAllValvesFunction =
allHardwareFunctions.Single(x => x.FunctionType == HardwareFunctionType.CloseAllValves);
SynthesisProcessTotalTime = currentGeneSynthesisProcess.TotalTime;
MessagingCenter.Send <LogsViewModel>(this, "SynthesisProcessStarted");
int geneSynthesisProcessRemainingTime = currentGeneSynthesisProcess.TotalTime;
LogAction($"Starting a new gene synthesis process. Total Time: {geneSynthesisProcessRemainingTime} s");
foreach (GeneSynthesisActivity geneSynthesisActivity in currentGeneSynthesisProcess.GeneSynthesisActivities.OrderBy(x => x.ChannelNumber))
{
int oligoSynthesisActivityTotalTime = geneSynthesisActivity.TotalTime;
await Task.Run(async() =>
{
await oligoSynthesizerRestService.StartSynthesis(geneSynthesisActivity, bAndTetToColFunctions,
closeAllValvesFunction, oligoSynthesisActivityTotalTime);
});
geneSynthesisProcessRemainingTime -= oligoSynthesisActivityTotalTime;
LogAction($"Total remaining time: {geneSynthesisProcessRemainingTime} s");
}
//currentOligoSynthesisProcess.Status = SynthesisProcessStatus.Completed;
//await oligoSynthesisProcessTable.UpdateItemAsync(currentOligoSynthesisProcess);
}
catch (Exception ex)
{
//currentOligoSynthesisProcess.Status = SynthesisProcessStatus.Failed;
//await oligoSynthesisProcessTable.UpdateItemAsync(currentOligoSynthesisProcess);
LogAction($"Gene synthesis process failed: {ex.Message}");
}
finally
{
await CloudService.SyncOfflineCacheAsync();
}
}
